diff --git a/CHANGELOG b/CHANGELOG
index aec8ac1362e2dbbf2f1e4d06a6ec6422e921b3d3..20e7a36a38c83e77511d058c8e9f459732964672 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -5,7 +5,36 @@
Changelog
================================================================================
-Release 1.1
+Release 1.2.0
+--------------------------------------------------------------------------------
+
+* Graph optimizer has been separated from the sidechain module and can now be
+ used for arbitrary optimization problems. Available optimization algorithms
+ are TreePack, AStar and MonteCarlo.
+* Make it possible to distinguish between the scores of a loop towards a constant
+ environment (external scores) and the scores within the loop itself
+ (internal scores).
+* Most scores based on pairwise interactions are now pairwise decomposable.
+* Disconnected loops at several locations can be scored at once.
+* Avoid the usage of the DSSP executable and use the OpenStructure internal
+ secondary structure assignment instead.
+* Allow to decide whether the CB atom belongs to the actual rotamer or to the
+ constant frame in sidechain optimization. This can be useful in design
+ questions, where the identity of a rotamer is not given and you want to
+ allow glycine or alanine.
+* The naming of the entries in the StructureDB is not strictly limited to
+ 4 letter codes anymore, arbitrary strings can be used instead.
+* Adding coordinates to the StructureDB does not require external tools anymore
+ (msms, dssp etc.), internal implementations are used instead.
+* The data that is stored in a StructureDB can be controlled at initialization,
+ everything except the sequence and the actual coordinates is optional.
+* Entries in the StructureDB can be removed again.
+* Allow to search positions of arbitrary copies in DynamicSpatialOrganizer
+ by providing RT operators.
+* Several minor bug fixes, improvements, and speed-ups
+
+
+Release 1.1.0
--------------------------------------------------------------------------------
* Updated dependencies: need Eigen 3.3.0 and OST 1.7
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 7dd378fb162fe14960ac583ef3d2c8c792996f36..f8f1e39cc62f23c259804f99dcfe3d8e91afaa36 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -16,7 +16,7 @@ include(PROMOD3)
# versioning info
set(PROMOD3_VERSION_MAJOR 1)
-set(PROMOD3_VERSION_MINOR 1)
+set(PROMOD3_VERSION_MINOR 2)
set(PROMOD3_VERSION_PATCH 0)
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_MAJOR}.${PROMOD3_VERSION_MINOR})
set(PROMOD3_VERSION_STRING ${PROMOD3_VERSION_STRING}.${PROMOD3_VERSION_PATCH})
@@ -84,9 +84,9 @@ if(NOT DISABLE_DOCUMENTATION)
find_package(Sphinx ${PYTHON_VERSION} REQUIRED)
set(PYTHON_DOC_URL "https://docs.python.org/${PYTHON_VERSION}")
# set this to the URL corresponding to the version of OST you are using
- set(OST_DOC_URL "http://www.openstructure.org/docs/dev")
+ set(OST_DOC_URL "https://www.openstructure.org/docs/dev")
endif()
-find_package(OPENSTRUCTURE 1.7 REQUIRED
+find_package(OPENSTRUCTURE 1.8 REQUIRED
COMPONENTS io mol seq seq_alg mol_alg conop img mol_mm)
if(CMAKE_COMPILER_IS_GNUCXX)
@@ -126,8 +126,8 @@ set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES
add_subdirectory(config)
add_subdirectory(core)
add_subdirectory(loop)
-add_subdirectory(sidechain)
add_subdirectory(scoring)
+add_subdirectory(sidechain)
add_subdirectory(modelling)
add_subdirectory(scripts)
add_subdirectory(actions)
diff --git a/actions/pm-build-model b/actions/pm-build-model
index c1d4541eed7bda1aee0fdb1ca0677455e78836c1..1dcd882c96ebdf1a5a71af4a4d4126771d8237f0 100755
--- a/actions/pm-build-model
+++ b/actions/pm-build-model
@@ -13,7 +13,6 @@ Please see the ProMod3 documentation for details on more advanced usage.
import os
import ost
from ost import io, settings
-from ost.bindings import dssp
from promod3 import modelling
from promod3.core import pm3argparse, helper
@@ -38,19 +37,12 @@ if len(opts.alignments) == 1:
elif len(opts.alignments) > 1:
ost.LogInfo("Build " + str(len(opts.alignments)) + " models with the "+
"following alignments:")
-dssp_usable = True
+
for aln in opts.alignments:
ost.LogInfo(aln.ToString(80))
- if dssp_usable:
- for i in range(1, aln.GetCount()):
- try:
- dssp.AssignDSSP(aln.GetSequence(i).GetAttachedView())
- except settings.FileNotFound:
- dssp_usable = False
- break
-if not dssp_usable:
- ost.LogInfo("dssp binary is missing. You can get better modelling results "+
- "if you install dssp.")
+ for i in range(1, aln.GetCount()):
+ ost.mol.alg.AssignSecStruct(aln.GetSequence(i).GetAttachedView())
+
# model it
try:
diff --git a/core/doc/CMakeLists.txt b/core/doc/CMakeLists.txt
index 5da8abe07b778967a28892705eb3e06caa6b7a55..dbef6e9d851f876a6f64690fcb1f08d58156ad45 100644
--- a/core/doc/CMakeLists.txt
+++ b/core/doc/CMakeLists.txt
@@ -5,6 +5,7 @@ helper.rst
geometry.rst
runtime_profiling.rst
setcompoundschemlib.rst
+graph_minimizer.rst
)
add_doc_source(NAME core RST ${CORE_RST})
diff --git a/core/doc/graph_minimizer.rst b/core/doc/graph_minimizer.rst
new file mode 100644
index 0000000000000000000000000000000000000000..a1ddb9639f2816086ee62f64861e5e2e5b9dacb2
--- /dev/null
+++ b/core/doc/graph_minimizer.rst
@@ -0,0 +1,235 @@
+Graph Minimizer
+================================================================================
+
+.. currentmodule:: promod3.core
+
+The graph minimizer solves an energy minimization problem where we have n
+nodes :math:`N_i`, with each node having several possible solutions.
+Every solution has a self energy :math:`E_{self}` and pairwise energies in between nodes
+are possible. The goal is to select exactly one solution per node to obtain
+a set :math:`X=[x_1, x_2, ..., x_n]` that minimizes:
+
+.. math::
+ F(X)=\displaystyle\sum_iE_{self}(N_i[x_i]) +\displaystyle \sum_i \displaystyle \sum_{j>i}E_{pair}(N_i[x_i], N_j[x_j])
+
+
+
+.. class:: GraphMinimizer
+
+ .. method:: AddNode(self_energies)
+
+ Adds a node to the graph.
+
+ :param self_energies: Directly controls the number of possible solutions in that
+ node and assigns the corresponding self energies
+ :type self_energies: :class:`list` of :class:`float`
+
+ :returns: The idx of the added node
+ :rtype: :class:`int`
+
+
+ .. method:: AddEdge(node_idx_one, node_idx_two, pairwise_energies)
+
+ Adds an edge between the specified nodes.
+
+ :param node_idx_one: Index of the first node
+ :param node_idx_two: Index of the second node
+ :param pairwise_energies: The pairwise energies that contribute to the
+ overall energy function. There must be a list for
+ every possible solution in node one. All of those
+ lists must have exactly the length of possible
+ solutions in node two.
+
+ :type node_idx_one: :class:`int`
+ :type node_idx_two: :class:`int`
+ :type pairwise_energies: :class:`list` of :class:`list` of :class:`float`
+
+ :returns: The idx of the added edge
+ :rtype: :class:`int`
+ :raises: :exc:`~exceptions.RuntimeError` if *node_idx_one* or *node_idx_two*
+ specify non existent nodes or when *pairwise_energies* is
+ inconsistent with the number of solutions in the specified nodes.
+
+
+ .. method:: ApplyDEE(node_idx, [e_cut=0.0])
+
+ Applies dead end elimination on one particular node and potentially
+ deactivates certain solutions. The goldstein criterion is described in
+ [goldstein1994]_.
+
+ :param node_idx: Node to apply dead end elimination
+ :param e_cut: If set to
+ 0.0, the default goldstein criterion is applied =>
+ a solution is removed if it's dominated by all other
+ solutions in the same node. If you increase this value,
+ a solution must be dominated by at least this **e_cut**.
+
+ :type node_idx: :class:`int`
+ :type e_cut: :class:`float`
+
+ :returns: :class:`bool` whether any solution has been deactivated.
+
+
+ .. method:: ApplyEdgeDecomposition(edge_idx, epsilon)
+
+ Applies edge decomposition on one particular edge and potentially
+ deactivates it. The exact decomposition procedure is described in
+ [krivov2009]_.
+
+ :param edge_idx: Edge to decompose.
+ :param epsilon: The energy threshold to perform edge decomposition.
+
+ :type edge_idx: :class:`int`
+ :type epsilon: :class:`float`
+
+
+ :returns: :class:`bool` whether the edge has been decomposed and
+ deactivated
+
+
+
+ .. method:: Prune(epsilon, [e_cut=0.0, consider_all_nodes=False])
+
+ Performs edge decomposition followed by dead end elimination in an
+ iterative manner until no changes can be observed anymore given
+ **epsilon**.
+
+ :param epsilon: The energy threshold to perform edge decomposition.
+ :param e_cut: Parameter to control dead end elimination.
+ :param consider_all_nodes: Flag, wether the dead end elimination should be
+ applied to all nodes, or only those who are
+ connected with an edge removed by edge
+ decomposition. This is useful if already a Prune
+ operation has been performed => only those nodes
+ connected to a removed edge have the chance for
+ successful dead end elimination.
+
+ :type epsilon: :class:`float`
+ :type e_cut: :class:`float`
+ :type consider_all_nodes: :class:`bool`
+
+
+ .. method:: Reset()
+
+ Resets the graph by undoing any pruning operation (DEE and edge decomposition)
+
+
+ .. method:: TreeSolve([max_complexity=inf, initial_epsilon=0.02])
+
+ The method solves a graph using a minimal width tree decomposition
+ approach in an iterative manner. In every iteration, the algorithm performs
+ a pruning step (DEE / Edge Decomposition) and subsequently tries to solve
+ each connected component in the graph separately.
+ If the number of possible enumerations in the tree constructetd from a
+ particular connected component is is larger **max_complexity**,
+ this component is solved in a later iteration. The algorithm iterates until
+ all connected components are solved and steadily increases the epsilon value
+ resulting in a more and more agressive edge decomposition.
+ Algorithm further descsribed in [krivov2009]_.
+
+ :param max_complexity: Max number of possible permutations, that have to
+ be enumerated in the resulting tree after tree
+ decomposition.
+
+ :param initial_epsilon: The initial energy threshold to perform edge
+ decomposition.
+
+ :type max_complexity: :class:`int`
+ :type initial_epsilon: :class:`float`
+
+ :returns: A tuple with the first element being a list of indices
+ representing the single solutions minimizing
+ the overall energy function.
+ The second element is the according energy value.
+
+
+ .. method:: AStarSolve(e_thresh, [max_n=100, max_visited_nodes=100000000])
+
+ The method solves a graph using the A\* algorithm. Besides creating the
+ minimal energy solution, the function produces a maximum of **max_n**
+ solutions sorted by energy. It aborts as soon as it sees the first solution
+ with an energy difference of **e_thresh** to the optimal solution or hits
+ **max_n**. If you're only interested in the optimal solution you should use
+ the TreeSolve function since it's much faster and uses less memory.
+ There is no automatic pruning of the graph using DEE or edge decomposition,
+ so you have to do it by yourself, otherwise you'll have a looooooong
+ runtime or even hit the **max_visited_nodes** parameter that caps the memory
+ usage.
+ To have a valid solution you have to take care that you set the **e_cut**
+ parameter in the pruning function to **e_tresh**.
+ Algorithm is described in [leach1998]_.
+
+ :param e_thresh: Maximal energy difference of a solution to the
+ optimal solution to be considered.
+
+ :param max_n: The maximum number of solutions that will be generated.
+
+ :param max_visited_nodes: Caps the memory usage of the algorithm. Besides
+ The memory used for pairwise energies and self
+ energies, the algorithm uses about
+ **max_visited_nodes** * 20 bytes.
+
+
+ :type e_thresh: :class:`float`
+ :type max_n: :class:`int`
+ :type max_visited_nodes: :class:`int`
+
+ :returns: A tuple with the first element being a list of
+ solutions. The second element is a list
+ of energies for the according solutions.
+
+
+ .. method:: MCSolve([n=100, mc_steps=100000, start_temperature=1000.0, \\
+ change_frequency=1000, cooling_factor=0.9, seed=0])
+
+ Does a total of **n** Monte Carlo runs to find low energy solutions
+ of the graph. Each run starts with a random
+ configuration. At each of the **mc_steps** steps, a random node and
+ a random solution at that location is selected and an energy difference
+ of that random selection relative to the current configuration is
+ estimated. If the difference in energy is negative, the step is
+ accepted. If not, the step is accepted with a probability given by
+ the temperature dependent Metropolis criterion
+ :math:`exp^{\left(\frac{-e_{diff}}{T}\right)}`.
+ The temperature for every run starts with **start_temperature**
+ and is multiplied every **change_frequency** steps with **cooling_factor**
+ to achieve a simulated annealing effect.
+ There is no automatic pruning of the graph using DEE or edge decomposition,
+ you have to do that by yourself.
+
+ :param n: Number of Monte Carlo runs
+ :param mc_steps: Number of Monte Carlo steps per run
+ :param start_temperature: Start temperature for the temperature dependent
+ Metropolis criterion
+ :param change_frequency: Number of steps the temperature stays the same
+ :param cooling_factor: Factor to multiply temperature each
+ **change_frequency** steps
+ :param seed: Seed for random number generator
+
+ :type n: :class:`int`
+ :type mc_steps: :class:`int`
+ :type start_temperature: :class:`float`
+ :type change_frequency: :class:`int`
+ :type cooling_factor: :class:`float`
+ :type seed: :class:`float`
+
+ :returns: A tuple with the first element being a list of
+ solutions. The second element is a list
+ of energies for the according solutions.
+
+ .. method:: NaiveSolve()
+
+ Don't even think of using this... This function only exists for debug
+ purposes and does the full enumeration of the solution space.
+ It might become faster with the appropriate
+ `techniques <https://www.youtube.com/watch?v=fQGbXmkSArs>`_.
+
+ :returns: A tuple with the first element being a list of indices
+ representing the single solutions minimizing
+ the overall energy function.
+ The second element is the according energy value.
+
+
+.. [goldstein1994] Goldstein RF (1994). Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys J.
+
+.. [leach1998] Leach AR, Lemon AP (1998). Explring the conformational space of prootein side chains using dead-end elimination and the A* algorithm. Proteins.
diff --git a/core/doc/index.rst b/core/doc/index.rst
index 17f9534aea783a5b313ec58c5ba52b4b9d199fcc..2af5fca9cace92deef375d4857a1c9b55f9ec0d5 100644
--- a/core/doc/index.rst
+++ b/core/doc/index.rst
@@ -16,3 +16,4 @@ Contents:
helper
geometry
runtime_profiling
+ graph_minimizer
diff --git a/core/pymod/CMakeLists.txt b/core/pymod/CMakeLists.txt
index fb24a4d09633f2657e20aa8538a90c31b85d8509..563feb76131b0461e24434761c9071ced9a47a56 100644
--- a/core/pymod/CMakeLists.txt
+++ b/core/pymod/CMakeLists.txt
@@ -2,6 +2,7 @@
set(CORE_CPP
export_geom.cc
export_runtime_profiling.cc
+ export_graph_minimizer.cc
wrap_core.cc
)
diff --git a/core/pymod/export_graph_minimizer.cc b/core/pymod/export_graph_minimizer.cc
new file mode 100644
index 0000000000000000000000000000000000000000..bd301c84f7a3289d6ee1f3f9e91f8975be0718f7
--- /dev/null
+++ b/core/pymod/export_graph_minimizer.cc
@@ -0,0 +1,158 @@
+#include <boost/python.hpp>
+#include <boost/python/register_ptr_to_python.hpp>
+#include <promod3/core/graph_minimizer.hh>
+#include <promod3/core/eigen_types.hh>
+#include <promod3/core/export_helper.hh>
+#include <promod3/core/message.hh>
+
+using namespace boost::python;
+
+namespace {
+
+
+int WrapAddNode(promod3::core::GraphMinimizerPtr graph,
+ const boost::python::list& self_energies) {
+
+ std::vector<Real> v_self_energies;
+ promod3::core::ConvertListToVector(self_energies, v_self_energies);
+ return graph->AddNode(v_self_energies);
+}
+
+
+int WrapAddEdge(promod3::core::GraphMinimizerPtr graph,
+ int node_idx_one, int node_idx_two,
+ const boost::python::list& pairwise_energies) {
+
+ int num_rows = boost::python::len(pairwise_energies);
+
+ if(num_rows == 0) {
+ throw promod3::Error("Pairwise energies must not be empty!");
+ }
+
+ int num_cols = len(extract<list>(pairwise_energies[0]));
+
+ promod3::core::EMatXX emat = promod3::core::EMatXX::Zero(num_rows, num_cols);
+
+ for(int i = 0; i < num_rows; ++i) {
+ list current_list = extract<list>(pairwise_energies[i]);
+ if(len(current_list) != num_cols) {
+ throw promod3::Error("All lists must have exactly the same length!");
+ }
+ for(int j = 0; j < num_cols; ++j) {
+ emat(i,j) = extract<Real>(current_list[j]);
+ }
+ }
+
+ return graph->AddEdge(node_idx_one, node_idx_two, emat);
+}
+
+
+boost::python::tuple WrapTreeSolve(promod3::core::GraphMinimizerPtr graph,
+ uint64_t max_complexity,
+ Real initial_epsilon) {
+
+ std::pair<std::vector<int>, Real>
+ full_solution = graph->TreeSolve(max_complexity, initial_epsilon);
+ std::vector<int> solution = full_solution.first;
+ Real energy = full_solution.second;
+ boost::python::list return_list;
+ promod3::core::AppendVectorToList(solution, return_list);
+ return boost::python::make_tuple(return_list, energy);
+}
+
+
+boost::python::tuple WrapAStarSolve(promod3::core::GraphMinimizerPtr graph,
+ Real e_thresh, uint max_n,
+ uint max_visited_nodes) {
+
+ std::pair<std::vector<std::vector<int> >, std::vector<Real> >
+ full_solution = graph->AStarSolve(e_thresh, max_n, max_visited_nodes);
+
+ std::vector<std::vector<int> > solutions = full_solution.first;
+ std::vector<Real> energies = full_solution.second;
+
+ boost::python::list solution_list;
+ boost::python::list energy_list;
+
+ for(uint i = 0; i < solutions.size(); ++i){
+ boost::python::list actual_solution;
+ promod3::core::AppendVectorToList(solutions[i], actual_solution);
+ solution_list.append(actual_solution);
+ }
+ promod3::core::AppendVectorToList(energies, energy_list);
+
+ return boost::python::make_tuple(solution_list, energy_list);
+}
+
+
+boost::python::tuple WrapMCSolve(promod3::core::GraphMinimizerPtr graph, int n,
+ int mc_steps, Real start_temperature,
+ int change_frequency, Real cooling_factor,
+ int seed) {
+
+ std::pair<std::vector<std::vector<int> >, std::vector<Real> >
+ full_solution = graph->MCSolve(n, mc_steps, start_temperature,
+ change_frequency, cooling_factor, seed);
+
+ std::vector<std::vector<int> > solutions = full_solution.first;
+ std::vector<Real> energies = full_solution.second;
+
+ boost::python::list solution_list;
+ boost::python::list energy_list;
+
+ for(uint i = 0; i < solutions.size(); ++i){
+ boost::python::list actual_solution;
+ promod3::core::AppendVectorToList(solutions[i], actual_solution);
+ solution_list.append(actual_solution);
+ }
+ promod3::core::AppendVectorToList(energies, energy_list);
+
+ return boost::python::make_tuple(solution_list, energy_list);
+}
+
+
+boost::python::tuple WrapNaiveSolve(promod3::core::GraphMinimizerPtr graph) {
+
+ std::pair<std::vector<int>, Real>
+ full_solution = graph->NaiveSolve();
+ std::vector<int> solution = full_solution.first;
+ Real energy = full_solution.second;
+ boost::python::list return_list;
+ promod3::core::AppendVectorToList(solution, return_list);
+ return boost::python::make_tuple(return_list, energy);
+}
+
+}
+
+
+void export_graph_minimizer()
+{
+
+ class_<promod3::core::GraphMinimizer,
+ boost::noncopyable>("GraphMinimizer", init<>())
+
+ .def("AddNode", &WrapAddNode, (arg("self_energies")))
+ .def("AddEdge", &WrapAddEdge, (arg("node_idx_one"), arg("node_idx_two"),
+ arg("pairwise_energies")))
+ .def("ApplyDEE", &promod3::core::GraphMinimizer::ApplyDEE,
+ (arg("node_idx"), arg("e_thresh")=0.0))
+ .def("ApplyEdgeDecomposition",
+ &promod3::core::GraphMinimizer::ApplyEdgeDecomposition,
+ (arg("edge_idx"), arg("e_thresh")=0.02))
+ .def("Prune", &promod3::core::GraphMinimizer::Prune,
+ (arg("epsilon")=0.0, arg("e_cut")=0.0, arg("consider_all_nodes")=false))
+ .def("Reset", &promod3::core::GraphMinimizer::Reset)
+ .def("TreeSolve", &WrapTreeSolve,
+ (arg("max_complexity")=std::numeric_limits<uint64_t>::max(),
+ arg("initial_epsilon")=0.02))
+ .def("AStarSolve", &WrapAStarSolve,
+ (arg("e_thresh")=1.0, arg("max_n")=100,
+ arg("max_visited_nodes")=100000000))
+ .def("MCSolve", &WrapMCSolve,
+ (arg("n")=100, arg("mc_steps")=100000, arg("start_temperature")=1000.0,
+ arg("change_frequency")=1000, arg("cooling_factor")=0.9, arg("seed")=0))
+ .def("NaiveSolve", &WrapNaiveSolve)
+ ;
+
+ register_ptr_to_python<promod3::core::GraphMinimizerPtr>();
+}
diff --git a/core/pymod/wrap_core.cc b/core/pymod/wrap_core.cc
index 989fe8ed9c941f8db39e0317dfa60314b2fd181f..ae1381eb24b990738ffa5c5751665f231856ff2f 100644
--- a/core/pymod/wrap_core.cc
+++ b/core/pymod/wrap_core.cc
@@ -2,9 +2,11 @@
void export_geom();
void export_runtime_profiling();
+void export_graph_minimizer();
BOOST_PYTHON_MODULE(_core)
{
export_geom();
export_runtime_profiling();
+ export_graph_minimizer();
}
diff --git a/core/src/CMakeLists.txt b/core/src/CMakeLists.txt
index 83d41512144c95e10ab60c3a81160d1ac9a96bf4..a8419fd0b01c29ee9544e3c34cf5d0a2ce5c4c4e 100644
--- a/core/src/CMakeLists.txt
+++ b/core/src/CMakeLists.txt
@@ -15,6 +15,8 @@ set(CORE_HEADERS
graph.hh
tree.hh
tetrahedral_polytope.hh
+ graph_minimizer.hh
+ eigen_types.hh
)
set(CORE_SOURCES
@@ -25,6 +27,7 @@ set(CORE_SOURCES
graph.cc
tree.cc
tetrahedral_polytope.cc
+ graph_minimizer.cc
)
module(NAME core HEADERS ${CORE_HEADERS} SOURCES ${CORE_SOURCES}
diff --git a/core/src/dynamic_spatial_organizer.hh b/core/src/dynamic_spatial_organizer.hh
index 242de5cf2f592cb8ad2cf0f165028b794e01091f..455389667c1fd725595dad3276d308a4c7a55ffb 100644
--- a/core/src/dynamic_spatial_organizer.hh
+++ b/core/src/dynamic_spatial_organizer.hh
@@ -20,7 +20,7 @@ class SpatialOrganizerCell{
public:
SpatialOrganizerCell(): num_items_(0),
- capacity_(32){
+ capacity_(32) {
x_ = new Real[capacity_];
y_ = new Real[capacity_];
z_ = new Real[capacity_];
@@ -28,7 +28,7 @@ public:
distance_buffer_ = new Real[capacity_];
}
- ~SpatialOrganizerCell(){
+ ~SpatialOrganizerCell() {
delete [] x_;
delete [] y_;
delete [] z_;
@@ -36,14 +36,14 @@ public:
delete [] distance_buffer_;
}
- void AddItem(ITEM* item, Real x, Real y, Real z){
+ void AddItem(ITEM* item, Real x, Real y, Real z) {
int idx = this->GetIdx(item);
- if(idx != -1){
+ if(idx != -1) {
throw promod3::Error("Item is already in spatial organizer cell!");
}
- if(num_items_ == capacity_){
+ if(num_items_ == capacity_) {
capacity_ *= 2;
Real* new_x = new Real[capacity_];
@@ -77,19 +77,19 @@ public:
++num_items_;
}
- void RemoveItem(ITEM* item){
+ void RemoveItem(ITEM* item) {
- if(num_items_ == 0){
+ if(num_items_ == 0) {
throw promod3::Error("Cannot remove item from empty spatial organizer cell!");
}
int idx = this->GetIdx(item);
- if(idx == -1){
+ if(idx == -1) {
throw promod3::Error("Cannot Remove inexistent item from spatial organizer cell!");
}
- if(idx < (num_items_-1)){
+ if(idx < (num_items_-1)) {
int num_bytes = (num_items_-(idx+1))*sizeof(Real);
memmove(&x_[idx],&x_[idx+1],num_bytes);
memmove(&y_[idx],&y_[idx+1],num_bytes);
@@ -99,9 +99,9 @@ public:
--num_items_;
}
- void ResetPos(ITEM* item, Real x, Real y, Real z){
+ void ResetPos(ITEM* item, Real x, Real y, Real z) {
int idx = this->GetIdx(item);
- if(idx == -1){
+ if(idx == -1) {
throw promod3::Error("Cannot reset pos of inexistent item from spatial organizer cell!");
}
x_[idx] = x;
@@ -115,15 +115,15 @@ public:
Real dx, dy, dz;
Real squared_cutoff = dist*dist;
- for(int i = 0; i < num_items_; ++i){
+ for(int i = 0; i < num_items_; ++i) {
dx = x_[i] - x;
dy = y_[i] - y;
dz = z_[i] - z;
distance_buffer_[i] = dx*dx + dy*dy + dz*dz;
}
- for(int i = 0; i < num_items_; ++i){
- if(distance_buffer_[i] <= squared_cutoff){
+ for(int i = 0; i < num_items_; ++i) {
+ if(distance_buffer_[i] <= squared_cutoff) {
result_vec.push_back(std::make_pair(pointers_[i],std::sqrt(distance_buffer_[i])));
}
}
@@ -132,8 +132,8 @@ public:
private:
- int GetIdx(ITEM* ptr){
- for(int i = 0; i < num_items_; ++i){
+ int GetIdx(ITEM* ptr) {
+ for(int i = 0; i < num_items_; ++i) {
if(pointers_[i] == ptr) return i;
}
return -1;
@@ -202,14 +202,21 @@ private:
public:
- DynamicSpatialOrganizer(Real delta): delta_(delta) {
- if(delta==0.0) {
- throw "delta cannot be zero";
+ DynamicSpatialOrganizer(Real delta,
+ const std::vector<geom::Mat4>& transformations =
+ std::vector<geom::Mat4>()): delta_(delta) {
+ if(delta <= 0.0) {
+ throw "delta must be positive!";
+ }
+
+ for(uint i = 0; i < transformations.size(); ++i) {
+ geom::Mat4 inv_t = geom::Invert(transformations[i]);
+ inverted_transformations_.push_back(inv_t);
}
}
- ~DynamicSpatialOrganizer(){
- for(typename ItemMap::iterator i = map_.begin(); i != map_.end(); ++i){
+ ~DynamicSpatialOrganizer() {
+ for(typename ItemMap::iterator i = map_.begin(); i != map_.end(); ++i) {
delete i->second;
}
}
@@ -219,7 +226,7 @@ public:
Index indx=gen_index(pos);
typename ItemMap::iterator it = map_.find(indx);
- if(it == map_.end()){
+ if(it == map_.end()) {
map_[indx] = new SpatialOrganizerCell<ITEM>;
it = map_.find(indx);
}
@@ -230,7 +237,7 @@ public:
void Remove(ITEM* item, const geom::Vec3& pos) {
Index indx=gen_index(pos);
typename ItemMap::iterator i = map_.find(indx);
- if(i != map_.end()){
+ if(i != map_.end()) {
i->second->RemoveItem(item);
}
else{
@@ -238,14 +245,14 @@ public:
}
}
- void Reset(ITEM* item, const geom::Vec3& actual_pos, const geom::Vec3& new_pos){
+ void Reset(ITEM* item, const geom::Vec3& actual_pos, const geom::Vec3& new_pos) {
Index actual_indx=gen_index(actual_pos);
Index new_indx=gen_index(new_pos);
- if(actual_indx != new_indx){
+ if(actual_indx != new_indx) {
typename ItemMap::iterator i = map_.find(actual_indx);
- if(i != map_.end()){
+ if(i != map_.end()) {
typename ItemMap::iterator j = map_.find(new_indx);
- if(j == map_.end()){
+ if(j == map_.end()) {
map_[new_indx] = new SpatialOrganizerCell<ITEM>;
j = map_.find(new_indx);
}
@@ -257,7 +264,7 @@ public:
}
else{
typename ItemMap::iterator i = map_.find(actual_indx);
- if(i != map_.end()){
+ if(i != map_.end()) {
i->second->ResetPos(item,new_pos[0],new_pos[1],new_pos[2]);
}
else{
@@ -266,11 +273,17 @@ public:
}
}
- WithinResult FindWithin(const geom::Vec3& pos, Real dist) const{
+ WithinResult FindWithin(const geom::Vec3& pos, Real dist,
+ bool clear_buffer = true) const{
+
Index imin = gen_index(pos-geom::Vec3(dist,dist,dist));
Index imax = gen_index(pos+geom::Vec3(dist,dist,dist));
- result_buffer_.clear();
+ if(clear_buffer) {
+ result_buffer_.clear();
+ }
+
+ int first_buffer_position = result_buffer_.size();
for(int wc=imin.w;wc<=imax.w;++wc) {
for(int vc=imin.v;vc<=imax.v;++vc) {
@@ -285,18 +298,43 @@ public:
WithinResult result;
- if(!result_buffer_.empty()){
- result = std::make_pair(&result_buffer_[0],result_buffer_.size());
+ if(!result_buffer_.empty()) {
+ result = std::make_pair(&result_buffer_[first_buffer_position],
+ result_buffer_.size() - first_buffer_position);
}
else{
- result = std::make_pair(static_cast<std::pair<ITEM*,Real>* >(NULL),0);
+ result = std::make_pair(static_cast<std::pair<ITEM*,Real>* >(NULL), 0);
}
return result;
}
+ std::vector<WithinResult> FindWithinFull(const geom::Vec3& pos,
+ Real dist) {
+
+ int n = inverted_transformations_.size();
+ std::vector<WithinResult> return_vec(n + 1);
+
+ // do first the FindWithin on the actual non transformed positions
+ return_vec[0] = this->FindWithin(pos, dist, true);
+
+ for(int i = 0; i < n; ++i) {
+ // instead of transforming all positions in the organizer, we apply
+ // the corresponding inverted transform to the query position
+ // Thanks David Sehnal for the trick!!!
+ const geom::Mat4& t = inverted_transformations_[i];
+ Real a = t(0,0)*pos[0] + t(0,1)*pos[1] + t(0,2)*pos[2] + t(0,3);
+ Real b = t(1,0)*pos[0] + t(1,1)*pos[1] + t(1,2)*pos[2] + t(1,3);
+ Real c = t(2,0)*pos[0] + t(2,1)*pos[1] + t(2,2)*pos[2] + t(2,3);
+ geom::Vec3 transformed_pos(a, b, c);
+ return_vec[i + 1] = this->FindWithin(transformed_pos, dist, false);
+ }
- void Clear(){
- for(typename ItemMap::iterator i = map_.begin(); i != map_.end(); ++i){
+ return return_vec;
+ }
+
+
+ void Clear() {
+ for(typename ItemMap::iterator i = map_.begin(); i != map_.end(); ++i) {
delete i->second;
}
map_.clear();
@@ -304,9 +342,10 @@ public:
private:
+ Real delta_;
+ std::vector<geom::Mat4> inverted_transformations_;
ItemMap map_;
mutable WithinList result_buffer_;
- Real delta_;
Index gen_index(const geom::Vec3& pos) const {
Index nrvo(static_cast<int>(round(pos[0]/delta_)),
diff --git a/core/src/eigen_types.hh b/core/src/eigen_types.hh
new file mode 100644
index 0000000000000000000000000000000000000000..8eff20ee824802fee2c78246bcc9126a5fc48c47
--- /dev/null
+++ b/core/src/eigen_types.hh
@@ -0,0 +1,37 @@
+#ifndef PROMOD3_EIGEN_TYPES_HH
+#define PROMOD3_EIGEN_TYPES_HH
+
+#include <ost/base.hh>
+
+#include <Eigen/Dense>
+#include <Eigen/StdVector>
+
+namespace promod3 { namespace core {
+
+ // some quadratic matrices
+ typedef Eigen::Matrix<Real,3,3> EMat3;
+ typedef Eigen::Matrix<Real,4,4> EMat4;
+ typedef Eigen::Matrix<double,8,8> EMat8;
+ typedef Eigen::Matrix<double,16,16> EMat16;
+
+ typedef Eigen::Matrix<Real,3,1> EVec3;
+ typedef Eigen::Matrix<Real,4,1> EVec4;
+
+ typedef Eigen::Matrix<Real,1,3> ERVec3;
+ typedef Eigen::Matrix<Real,1,4> ERVec4;
+
+
+ // some special matrices used at various locations
+ typedef Eigen::Matrix<Real,Eigen::Dynamic,3> EMatX3;
+ typedef Eigen::Matrix<Real, Eigen::Dynamic, Eigen::Dynamic> EMatXX;
+ typedef Eigen::Matrix<double,16,3> EMat16_3;
+
+
+ // If you want to use stl containers of fixed sized Eigentype (e.g. EMatX3)
+ // you must use a custom allocator provided by Eigen to ensure proper memory
+ // alignment (more on that in the Eigen documentation)
+ typedef std::vector<EMatX3,Eigen::aligned_allocator<EMatX3> > EMatX3List;
+
+}} // ns
+
+#endif
diff --git a/core/src/graph_minimizer.cc b/core/src/graph_minimizer.cc
new file mode 100644
index 0000000000000000000000000000000000000000..e524efc2fb53447967c9c37b2f9fc985072b1b00
--- /dev/null
+++ b/core/src/graph_minimizer.cc
@@ -0,0 +1,1848 @@
+#include <algorithm>
+#include <queue>
+#include <limits>
+#include <map>
+
+#include <promod3/core/graph_minimizer.hh>
+#include <promod3/core/tree.hh>
+#include <promod3/core/runtime_profiling.hh>
+#include <promod3/core/enumerator.hh>
+#include <promod3/core/message.hh>
+
+#include <boost/random/mersenne_twister.hpp>
+#include <boost/random/uniform_01.hpp>
+
+
+namespace{
+
+////////////////////////////////////////////////////////////////
+//FUNCTIONS AND DATA STRUCTURES FOR THE TREE SOLVING ALGORITHM//
+////////////////////////////////////////////////////////////////
+
+typedef promod3::core::TreeBag<int> TBag;
+
+// calculates a linear idx for a certain combination in the lset
+struct LSetIdxCalculator{
+
+ LSetIdxCalculator() { }
+
+ LSetIdxCalculator(const std::vector<unsigned short>& num_candidates) {
+ lset_size = num_candidates.size();
+ for(int i = 0; i < lset_size; ++i) {
+ int temp = 1;
+ for(int j = i + 1; j < lset_size; ++j) {
+ temp *= num_candidates[j];
+ }
+ idx_helper.push_back(temp);
+ }
+ idx_helper.push_back(1);
+ }
+
+ inline int GetLIdx(const std::vector<unsigned short>& indices) const {
+ int idx = 0;
+ for(int i = 0; i < lset_size; ++i) {
+ idx += idx_helper[i] * indices[i];
+ }
+ return idx;
+ }
+
+ inline int GetIdxHelper(int idx) {
+ return idx_helper[idx];
+ }
+
+ std::vector<int> idx_helper;
+ int lset_size;
+};
+
+
+struct BagData{
+
+ // members of the bag that are also present in parent bag
+ std::vector<int> lset;
+ // members of the bag that are not present in parent bag
+ std::vector<int> rset;
+
+ // number of solutions for every entry in lset/rset
+ uint num_l_combinations;
+ uint num_r_combinations;
+ std::vector<unsigned short> num_l_solutions;
+ std::vector<unsigned short> num_r_solutions;
+
+ // optimal solution in r set given a certain combination in l
+ // the index for a certain combination in l can be estimated with
+ // l_set_idx_calculator
+ // assuming an l_idx of x, the according optimal rset data starts
+ // at x * rset.size()
+ std::vector<unsigned short> optimal_rset_combination;
+
+ // the according score
+ std::vector<Real> optimal_r_score;
+
+ // calculates an index in optimal_r_combination/optimal_r_score
+ // given a certain combination in l
+ LSetIdxCalculator lset_idx_calculator;
+
+ // the bag data indices for the children attached to this bag
+ std::vector<int> children_indices;
+ int num_children;
+
+ // super complicated mapping structure of getting stuff out from the children
+ // the idea is, that we can calculate the lset idx in several steps in the
+ // enumeration procedure...
+
+ // for every child we have a vector of with indices describing the
+ // elements in the current lset being part of the childrens lset
+ std::vector<std::vector<int> > lset_child_l_indices;
+ // the number it has to be multiplied to construct the index for
+ // that particular child lset
+ std::vector<std::vector<int> > lset_child_l_index_helpers;
+ // store the size of the stuff above for every child
+ std::vector<int> num_lset_child_l;
+
+ // equivalent for the current rset
+ std::vector<std::vector<int> > rset_child_l_indices;
+ std::vector<std::vector<int> > rset_child_l_index_helpers;
+ std::vector<int> num_rset_child_l;
+
+ // this data structure will be altered during the calculation and is a
+ // placeholder to query optimal solutions for certain lsets of the children
+ std::vector<std::vector<int> > children_l_combinations;
+
+ // self energies of the rset
+ std::vector<std::vector<Real> > r_self_energies;
+
+ // stuff for lr and rl pairwise energies
+ std::vector<promod3::core::EMatXX> lr_energies;
+ std::vector<int> lr_index_in_I;
+ std::vector<int> lr_index_in_R;
+
+ // stuff for rr pairwise energies
+ std::vector<promod3::core::EMatXX> rr_energies;
+ std::vector<int> rr_index_in_R_one;
+ std::vector<int> rr_index_in_R_two;
+};
+
+
+// Fills only the bare minimum of data into the BagData vector and already
+// estimates the complexity of the tree solving procedure. All other data
+// gets filled in the FillBagData function
+uint64_t FillRawBagData(const std::vector<TBag*>& traversal,
+ const std::vector<int>& num_active_solutions,
+ std::vector<BagData>& bag_data) {
+
+ uint64_t complexity = 0;
+
+ bag_data.clear();
+ bag_data.resize(traversal.size());
+
+ for(uint bag_idx = 0; bag_idx < traversal.size(); ++bag_idx) {
+
+ TBag* bag = traversal[bag_idx];
+ TBag* parent = traversal[bag_idx]->GetParent();
+
+ // assign rset and lset
+ if(parent == NULL) {
+ // it's the root, lets shuffle all to rset
+ bag_data[bag_idx].rset.assign(bag->members_begin(),
+ bag->members_end());
+ }
+ else{
+ for(TBag::const_member_iterator it = bag->members_begin();
+ it != bag->members_end(); ++it) {
+ if(parent->HasMember(*it)) bag_data[bag_idx].lset.push_back(*it);
+ else bag_data[bag_idx].rset.push_back(*it);
+ }
+ }
+
+ // figure out how many solutions there are
+ bag_data[bag_idx].num_l_combinations = 1;
+ bag_data[bag_idx].num_r_combinations = 1;
+
+ for(std::vector<int>::iterator i = bag_data[bag_idx].lset.begin();
+ i != bag_data[bag_idx].lset.end(); ++i) {
+ bag_data[bag_idx].num_l_solutions.push_back(num_active_solutions[*i]);
+ bag_data[bag_idx].num_l_combinations *= num_active_solutions[*i];
+ }
+
+ for(std::vector<int>::iterator i = bag_data[bag_idx].rset.begin();
+ i != bag_data[bag_idx].rset.end(); ++i) {
+ bag_data[bag_idx].num_r_solutions.push_back(num_active_solutions[*i]);
+ bag_data[bag_idx].num_r_combinations *= num_active_solutions[*i];
+ }
+
+ complexity += (bag_data[bag_idx].num_l_combinations *
+ bag_data[bag_idx].num_r_combinations);
+ }
+
+ return complexity;
+}
+
+
+void FillBagData(const std::vector<TBag*>& traversal,
+ const std::vector<promod3::core::GMNode*>& nodes,
+ const std::vector<promod3::core::GMEdge*>& edges,
+ const std::vector<std::pair<int, int> >& edge_indices,
+ std::vector<BagData>& bag_data) {
+
+ for(uint bag_idx = 0; bag_idx < traversal.size(); ++bag_idx) {
+
+ TBag* bag = traversal[bag_idx];
+ BagData& current_data = bag_data[bag_idx];
+ int current_data_lsize = current_data.lset.size();
+ int current_data_rsize = current_data.rset.size();
+
+ // allocate required space for optimal r combination for every possible lset
+ current_data.optimal_rset_combination.resize(current_data_rsize *
+ current_data.num_l_combinations);
+
+ current_data.optimal_r_score.resize(current_data.num_l_combinations);
+
+ // generate a new lset idxgenerator...
+ current_data.lset_idx_calculator =
+ LSetIdxCalculator(current_data.num_l_solutions);
+
+ // get all the children stuff right
+ for(TBag::const_child_iterator it = bag->children_begin();
+ it != bag->children_end(); ++it) {
+ current_data.children_indices.push_back((*it)->GetIdx());
+ }
+ current_data.num_children = current_data.children_indices.size();
+
+ // handle current lset
+ current_data.lset_child_l_indices.resize(current_data.num_children);
+ current_data.lset_child_l_index_helpers.resize(current_data.num_children);
+ for(int i = 0; i < current_data_lsize; ++i) {
+ int val = current_data.lset[i];
+ // go through all children
+ for(int j = 0; j < current_data.num_children; ++j) {
+ int ch_idx = current_data.children_indices[j];
+ // we can be sure of the children lsets being set due to the postorder
+ // traversal of the tree
+ const std::vector<int>& child_lset = bag_data[ch_idx].lset;
+ std::vector<int>::const_iterator it = std::find(child_lset.begin(),
+ child_lset.end(),
+ val);
+ if(it != child_lset.end()) {
+ // its in the childs lset!
+ int idx_in_child_l = it - child_lset.begin();
+ current_data.lset_child_l_indices[j].push_back(i);
+ int helper =
+ bag_data[ch_idx].lset_idx_calculator.GetIdxHelper(idx_in_child_l);
+ current_data.lset_child_l_index_helpers[j].push_back(helper);
+ }
+ }
+ }
+ for(int i = 0; i < current_data.num_children; ++i) {
+ int size = current_data.lset_child_l_indices[i].size();
+ current_data.num_lset_child_l.push_back(size);
+ }
+
+ // do the same for the rset
+ current_data.rset_child_l_indices.resize(current_data.num_children);
+ current_data.rset_child_l_index_helpers.resize(current_data.num_children);
+ for(int i = 0; i < current_data_rsize; ++i) {
+ int val = current_data.rset[i];
+ // go through all children
+ for(int j = 0; j < current_data.num_children; ++j) {
+ int ch_idx = current_data.children_indices[j];
+ // we can be sure of the children lsets being set due to the postorder
+ // traversal of the tree
+ const std::vector<int>& child_lset = bag_data[ch_idx].lset;
+ std::vector<int>::const_iterator it = std::find(child_lset.begin(),
+ child_lset.end(),
+ val);
+ if(it != child_lset.end()) {
+ // its in the childs lset!
+ int idx_in_child_l = it - child_lset.begin();
+ current_data.rset_child_l_indices[j].push_back(i);
+ int helper =
+ bag_data[ch_idx].lset_idx_calculator.GetIdxHelper(idx_in_child_l);
+ current_data.rset_child_l_index_helpers[j].push_back(helper);
+ }
+ }
+ }
+ for(int i = 0; i < current_data.num_children; ++i) {
+ int size = current_data.rset_child_l_indices[i].size();
+ current_data.num_rset_child_l.push_back(size);
+ }
+
+ // prepare the lset combinations
+ for(std::vector<int>::iterator i = current_data.children_indices.begin();
+ i != current_data.children_indices.end(); ++i) {
+ int size = bag_data[*i].lset.size();
+ current_data.children_l_combinations.push_back(std::vector<int>(size,0));
+ }
+
+ // fill the rset self energies
+ current_data.r_self_energies.resize(current_data_rsize);
+ for(int i = 0; i < current_data_rsize; ++i) {
+ promod3::core::GMNode* n = nodes[current_data.rset[i]];
+ n->FillActiveSelfEnergies(current_data.r_self_energies[i]);
+ }
+
+ // Search for all pairs in lset / rset, that have an edge
+
+ std::vector<promod3::core::GMEdge*> lr_edges;
+
+ for(int i = 0; i < current_data_lsize; ++i) {
+ for(int j = 0; j < current_data_rsize; ++j) {
+
+ std::pair<int,int> idx_pair = std::make_pair(current_data.lset[i],
+ current_data.rset[j]);
+ std::vector<std::pair<int,int> >::const_iterator idx_it =
+ std::find(edge_indices.begin(), edge_indices.end(), idx_pair);
+
+ if(idx_it != edge_indices.end()) {
+ int edge_idx = idx_it - edge_indices.begin();
+ lr_edges.push_back(edges[edge_idx]);
+ current_data.lr_index_in_I.push_back(i);
+ current_data.lr_index_in_R.push_back(j);
+ continue;
+ }
+ idx_pair = std::make_pair(current_data.rset[j], current_data.lset[i]);
+ idx_it = std::find(edge_indices.begin(), edge_indices.end(), idx_pair);
+ if(idx_it != edge_indices.end()) {
+ int edge_idx = idx_it - edge_indices.begin();
+ lr_edges.push_back(edges[edge_idx]);
+ current_data.lr_index_in_I.push_back(i);
+ current_data.lr_index_in_R.push_back(j);
+ }
+ }
+ }
+
+ // fill the active energies and make sure, that the energy matrices are
+ // organized with the lset elements being the rows and rset elements
+ // being the cols (potentially transpose)
+ current_data.lr_energies.resize(lr_edges.size());
+ for(uint i = 0; i < lr_edges.size(); ++i) {
+ lr_edges[i]->FillActiveEnergies(current_data.lr_energies[i]);
+ if(current_data.lset[current_data.lr_index_in_I[i]] >
+ current_data.rset[current_data.lr_index_in_R[i]]) {
+ current_data.lr_energies[i].transposeInPlace();
+ }
+ }
+
+ // Search for all pairs in rset, that have an edge
+
+ std::vector<promod3::core::GMEdge*> rr_edges;
+
+ for(int i = 0; i < current_data_rsize; ++i) {
+ for(int j = i + 1; j < current_data_rsize; ++j) {
+
+ std::pair<int,int> idx_pair = std::make_pair(current_data.rset[i],
+ current_data.rset[j]);
+ std::vector<std::pair<int,int> >::const_iterator idx_it =
+ std::find(edge_indices.begin(), edge_indices.end(), idx_pair);
+
+ if(idx_it != edge_indices.end()) {
+ int edge_idx = idx_it - edge_indices.begin();
+ rr_edges.push_back(edges[edge_idx]);
+ current_data.rr_index_in_R_one.push_back(i);
+ current_data.rr_index_in_R_two.push_back(j);
+ continue;
+ }
+
+ idx_pair = std::make_pair(current_data.rset[j], current_data.rset[i]);
+ idx_it = std::find(edge_indices.begin(), edge_indices.end(), idx_pair);
+ if(idx_it != edge_indices.end()) {
+ int edge_idx = idx_it - edge_indices.begin();
+ rr_edges.push_back(edges[edge_idx]);
+ current_data.rr_index_in_R_one.push_back(i);
+ current_data.rr_index_in_R_two.push_back(j);
+ }
+ }
+ }
+
+ // fill the active energies and make sure, that the energy matrices are
+ // organized with the rset element with the lower overall index defining
+ // the rows and the other the cols
+ current_data.rr_energies.resize(rr_edges.size());
+ for(uint i = 0; i < rr_edges.size(); ++i) {
+ rr_edges[i]->FillActiveEnergies(current_data.rr_energies[i]);
+ if(current_data.rset[current_data.rr_index_in_R_one[i]] >
+ current_data.rset[current_data.rr_index_in_R_two[i]]) {
+ current_data.rr_energies[i].transposeInPlace();
+ }
+ }
+ }
+}
+
+
+void EnumerateBagData(std::vector<BagData>& bag_data) {
+
+ for(uint bag_idx = 0; bag_idx < bag_data.size(); ++bag_idx) {
+
+ // data of the current bag
+ BagData& data = bag_data[bag_idx];
+ int rset_size = data.rset.size();
+ int num_lr_energies = data.lr_energies.size();
+ int num_rr_energies = data.rr_energies.size();
+
+ // the lset of this bag we have to enumerate
+ promod3::core::Enumerator<unsigned short>
+ l_set_enumerator(data.num_l_solutions);
+ std::vector<unsigned short>& current_l_enum =
+ l_set_enumerator.CurrentEnum();
+
+ int num_children = data.children_indices.size();
+ std::vector<int> partial_l_indices(num_children, 0);
+
+ do {
+
+ partial_l_indices.assign(num_children, 0);
+ for(int j = 0; j < num_children; ++j) {
+ for(int k = 0; k < data.num_lset_child_l[j]; ++k) {
+ partial_l_indices[j] +=
+ (current_l_enum[data.lset_child_l_indices[j][k]] *
+ data.lset_child_l_index_helpers[j][k]);
+ }
+ }
+
+ promod3::core::Enumerator<unsigned short>
+ r_set_enumerator(data.num_r_solutions);
+ std::vector<unsigned short>& current_r_enum =
+ r_set_enumerator.CurrentEnum();
+
+ Real score;
+ Real best_score = std::numeric_limits<Real>::max();
+ std::vector<unsigned short> best_rset = current_r_enum;
+
+ // let's find the optimal r combination given the current l combination...
+ do {
+
+ score = 0.0;
+
+ // sum up the r self energies
+ for(int i = 0; i < rset_size; ++i) {
+ score += data.r_self_energies[i][current_r_enum[i]];
+ }
+
+ // sum up the lr pairwise energies
+ for(int i = 0; i < num_lr_energies; ++i) {
+ score += data.lr_energies[i](current_l_enum[data.lr_index_in_I[i]],
+ current_r_enum[data.lr_index_in_R[i]]);
+ }
+
+ // sum up the rr pairwise energies
+ for(int i = 0; i < num_rr_energies; ++i) {
+ score += data.rr_energies[i](current_r_enum[data.rr_index_in_R_one[i]],
+ current_r_enum[data.rr_index_in_R_two[i]]);
+ }
+
+ for(int i = 0; i < num_children; ++i) {
+ int l_idx = partial_l_indices[i];
+ for(int j = 0; j < data.num_rset_child_l[i]; ++j) {
+ l_idx += (current_r_enum[data.rset_child_l_indices[i][j]] *
+ data.rset_child_l_index_helpers[i][j]);
+ }
+ score += bag_data[data.children_indices[i]].optimal_r_score[l_idx];
+ }
+
+ if(score < best_score) {
+ best_score = score;
+ best_rset = current_r_enum;
+ }
+
+ } while(r_set_enumerator.Next());
+
+ int l_idx = data.lset_idx_calculator.GetLIdx(current_l_enum);
+ memcpy(&data.optimal_rset_combination[l_idx*rset_size],
+ &best_rset[0], rset_size * sizeof(unsigned short));
+ data.optimal_r_score[l_idx] = best_score;
+
+ } while(l_set_enumerator.Next());
+ }
+}
+
+
+void CollectSolutionFromBagData(const std::vector<BagData>& bag_data,
+ int bag_idx, std::vector<int>& solution) {
+
+ const BagData& bag = bag_data[bag_idx];
+
+ // collect the lset values from the solution
+ std::vector<unsigned short> l_solution(bag.lset.size(), 0);
+ for(uint i = 0; i < l_solution.size(); ++i) {
+ l_solution[i] = solution[bag.lset[i]];
+ }
+
+ // get the index of the ideal r_combination given that l solution
+ int r_idx = bag.lset_idx_calculator.GetLIdx(l_solution);
+ // and fill the according values into the solution
+ int rset_size = bag.rset.size();
+ int data_start_idx = r_idx * rset_size;
+ for(int i = 0; i < rset_size; ++i) {
+ solution[bag.rset[i]] = bag.optimal_rset_combination[data_start_idx+i];
+ }
+
+ // recursively call this function for all the children
+ for(std::vector<int>::const_iterator i = bag.children_indices.begin();
+ i != bag.children_indices.end(); ++i) {
+ CollectSolutionFromBagData(bag_data, *i, solution);
+ }
+}
+
+
+/////////////////////////////////////////////////////////////////
+//FUNCTIONS AND DATA STRUCTURES FOR THE ASTAR SOLVING ALGORITHM//
+/////////////////////////////////////////////////////////////////
+
+struct AStarNode{
+
+ AStarNode(uint idx, uint p_idx, unsigned short s_idx,
+ unsigned short t_d, Real gs, Real hs): node_idx(idx),
+ parent_idx(p_idx),
+ solution_idx(s_idx),
+ tree_depth(t_d),
+ gstar(gs),
+ hstar(hs) { }
+
+ uint node_idx;
+ uint parent_idx;
+ unsigned short solution_idx;
+ unsigned short tree_depth;
+ Real gstar;
+ Real hstar;
+};
+
+
+struct CompareAStarNodes{
+ bool operator() (AStarNode* a, AStarNode* b) {
+ return (a->gstar + a->hstar) > (b->gstar + b->hstar);
+ }
+};
+
+
+void ReconstructSearchTreePath(const std::vector<AStarNode>& node_array,
+ uint start_idx,
+ std::vector<int>& path) {
+
+ path.resize(node_array[start_idx].tree_depth);
+ uint current_node_idx = start_idx;
+
+ while(current_node_idx != 0) {
+ path[node_array[current_node_idx].tree_depth-1] =
+ node_array[current_node_idx].solution_idx;
+ current_node_idx = node_array[current_node_idx].parent_idx;
+ }
+}
+
+
+/////////////////////////////////////////////////////////////////
+//FUNCTIONS AND DATA STRUCTURES FOR THE MC SOLVING ALGORITHM//
+/////////////////////////////////////////////////////////////////
+
+Real GetSolutionEnergy(int node_idx, int solution_idx,
+ const std::vector<int>& current_solution,
+ const std::vector<std::vector<Real> >& self_energies,
+ const std::vector<promod3::core::EMatXX>& pairwise_energies,
+ const std::vector<std::vector<std::pair<int,int> > >&
+ pairwise_energy_mapper) {
+
+ Real e = self_energies[node_idx][solution_idx];
+
+ const std::vector<std::pair<int, int> >& e_mapper =
+ pairwise_energy_mapper[node_idx];
+ int num_pairwise_energies = e_mapper.size();
+
+ for(int i = 0; i < num_pairwise_energies; ++i) {
+
+ int other_node_idx = e_mapper[i].first;
+ int emat_idx = e_mapper[i].second;
+
+ if(other_node_idx > node_idx) {
+ e += pairwise_energies[emat_idx](solution_idx,
+ current_solution[other_node_idx]);
+ }
+ else {
+ e += pairwise_energies[emat_idx](current_solution[other_node_idx],
+ solution_idx);
+ }
+ }
+
+ return e;
+}
+
+
+Real GetGlobalEnergy(const std::vector<int>& solution,
+ const std::vector<std::vector<Real> >& self_energies,
+ const std::vector<promod3::core::EMatXX>& pairwise_energies,
+ const std::vector<std::vector<std::pair<int, int> > >&
+ pairwise_energy_mapper) {
+
+ Real e = 0.0;
+
+ // sum up self energies
+ int num_nodes = solution.size();
+ for(int i = 0; i < num_nodes; ++i) {
+ e += self_energies[i][solution[i]];
+ }
+
+ // sum up pairwise energies
+ for(int i = 0; i < num_nodes; ++i) {
+ const std::vector<std::pair<int, int> >& e_mapper =
+ pairwise_energy_mapper[i];
+ int num_pairwise_energies = e_mapper.size();
+ for(int j = 0; j < num_pairwise_energies; ++j) {
+ int other_node_idx = e_mapper[j].first;
+ if(other_node_idx > i) {
+ int emat_idx = e_mapper[j].second;
+ e += pairwise_energies[emat_idx](solution[i], solution[other_node_idx]);
+ }
+ }
+ }
+
+ return e;
+}
+
+
+struct SolutionSelector {
+
+ SolutionSelector(std::vector<int> num_solutions, int random_seed):
+ n(num_solutions.size()),
+ n_solutions(num_solutions),
+ rng(random_seed),
+ zeroone(rng) { }
+
+ int SelectNode() {
+ return static_cast<int>(zeroone() * n);
+ }
+
+ int SelectSolution(int node_idx) {
+ return static_cast<int>(zeroone() * n_solutions[node_idx]);
+ }
+
+ void InitSolutionSelection(std::vector<int>& current_solution) {
+ current_solution.resize(n);
+ for(int i = 0; i < n; ++i) {
+ current_solution[i] = this->SelectSolution(i);
+ }
+ }
+
+ Real GetRandomNumber() {
+ return zeroone();
+ }
+
+ int n;
+ std::vector<int> n_solutions;
+ boost::mt19937 rng;
+ boost::uniform_01<boost::mt19937&> zeroone;
+};
+
+} // anon ns
+
+namespace promod3{ namespace core{
+
+GMEdge::GMEdge(uint index,
+ GMNode* node_a,
+ GMNode* node_b,
+ const EMatXX& emat): index_(index),
+ active_(true) {
+
+ if(node_a->GetNumSolutions() != static_cast<uint>(emat.rows())) {
+ throw promod3::Error("Number of solutions in node_a must be number "
+ "of rows in emat!");
+ }
+
+ if(node_b->GetNumSolutions() != static_cast<uint>(emat.cols())) {
+ throw promod3::Error("Number of solutions in node_b must be number "
+ "of cols in emat!");
+ }
+
+ if(node_a->GetIndex() == node_b->GetIndex()) {
+ throw promod3::Error("Cant Initialize GMEdge with the same GMNode Twice!");
+ }
+
+ // node_1 is by definition the one with the lower index
+ if(node_a->GetIndex() < node_b->GetIndex()) {
+ node1_ = node_a;
+ node2_ = node_b;
+ emat_ = emat;
+ }
+ else {
+ node1_ = node_b;
+ node2_ = node_a;
+ emat_ = emat.transpose();
+ }
+}
+
+
+void GMEdge::Reset() {
+ active_ = true;
+}
+
+
+bool GMEdge::Decompose(Real thresh) {
+
+ if(!active_) return false;
+
+ Real summed_e = 0.0;
+ uint m = node1_->GetNumActiveSolutions();
+ uint n = node2_->GetNumActiveSolutions();
+
+ for(GMNode::iterator i = node1_->active_solutions_begin();
+ i != node1_->active_solutions_end(); ++i) {
+ for(GMNode::iterator j = node2_->active_solutions_begin();
+ j != node2_->active_solutions_end(); ++j) {
+ summed_e += emat_(*i, *j);
+ }
+ }
+
+ Real avg_value = summed_e/(2*n*m);
+
+ std::vector<Real> ak(m);
+ std::vector<Real> bl(n);
+
+ uint m_counter = 0;
+ for(GMNode::iterator i = node1_->active_solutions_begin();
+ i != node1_->active_solutions_end(); ++i) {
+ summed_e = 0.0;
+ for(GMNode::iterator j = node2_->active_solutions_begin();
+ j != node2_->active_solutions_end(); ++j) {
+ summed_e += emat_(*i, *j);
+ }
+ ak[m_counter] = summed_e/n - avg_value;
+ ++m_counter;
+ }
+
+ uint n_counter = 0;
+ for(GMNode::iterator i = node2_->active_solutions_begin();
+ i != node2_->active_solutions_end(); ++i) {
+ summed_e = 0.0;
+ for(GMNode::iterator j = node1_->active_solutions_begin();
+ j != node1_->active_solutions_end(); ++j) {
+ summed_e += emat_(*j, *i);
+ }
+ bl[n_counter] = summed_e/m - avg_value;
+
+ // we directly check, whether any of the energy approximations
+ // related to *i is above the thresh and don't evaluate the rest
+ // if not necessary
+ m_counter = 0;
+ for(GMNode::iterator j = node1_->active_solutions_begin();
+ j != node1_->active_solutions_end(); ++j) {
+ if(std::abs(emat_(*j, *i) - ak[m_counter] - bl[n_counter]) > thresh) {
+ return false;
+ }
+ ++m_counter;
+ }
+ ++n_counter;
+ }
+
+ // it ran through! This edge can be decomposed!
+
+ int counter = 0;
+ for(GMNode::iterator j = node1_->active_solutions_begin();
+ j != node1_->active_solutions_end(); ++j, ++counter) {
+ node1_->AddValue(*j, ak[counter]);
+ }
+
+ counter = 0;
+ for(GMNode::iterator j = node2_->active_solutions_begin();
+ j != node2_->active_solutions_end(); ++j, ++counter) {
+ node2_->AddValue(*j, bl[counter]);
+ }
+
+ this->Deactivate();
+ node1_->RemoveFromActiveEdges(this);
+ node2_->RemoveFromActiveEdges(this);
+
+ return true;
+}
+
+
+Real GMEdge::EMinDiff(const GMNode* node_ptr, uint idx1, uint idx2) const {
+
+ Real min_e = std::numeric_limits<Real>::max();
+
+ if(node_ptr == node1_) {
+ for(GMNode::const_iterator i = node2_->active_solutions_begin();
+ i != node2_->active_solutions_end(); ++i) {
+ min_e = std::min(min_e, emat_(idx1, *i) - emat_(idx2, *i));
+ }
+ return min_e;
+ }
+ else if(node_ptr == node2_) {
+ for(GMNode::const_iterator i = node1_->active_solutions_begin();
+ i != node1_->active_solutions_end(); ++i) {
+ min_e = std::min(min_e, emat_(*i, idx1) - emat_(*i, idx2));
+ }
+ return min_e;
+ }
+
+ throw promod3::Error("Cannot evaluate Node which is unconnected to the edge "
+ "of interest!");
+}
+
+
+void GMEdge::FillActiveEnergies(EMatXX& emat) const {
+
+ int idx1 = 0;
+ int idx2 = 0;
+ emat = EMatXX::Zero(node1_->GetNumActiveSolutions(),
+ node2_->GetNumActiveSolutions());
+
+ for(GMNode::const_iterator i = node1_->active_solutions_begin();
+ i != node1_->active_solutions_end(); ++i, ++idx1) {
+ idx2 = 0;
+ for(GMNode::const_iterator j = node2_->active_solutions_begin();
+ j != node2_->active_solutions_end(); ++j, ++idx2) {
+ emat(idx1, idx2) = emat_(*i, *j);
+ }
+ }
+}
+
+
+GMNode* GMEdge::GetOtherNode(GMNode* node) {
+ if(node == node1_) return node2_;
+ if(node == node2_) return node1_;
+ throw promod3::Error("Node does not belong to edge!");
+}
+
+
+GMNode::GMNode(uint index,
+ const std::vector<Real>& self_energies):
+ index_(index),
+ active_(true),
+ self_energies_(self_energies),
+ original_self_energies_(self_energies) {
+
+ for(uint i = 0; i < self_energies_.size(); ++i) {
+ active_solutions_.push_back(i);
+ }
+
+ this->FillSortedActiveSolutions();
+}
+
+
+void GMNode::Reset() {
+
+ active_ = true;
+ self_energies_ = original_self_energies_;
+
+ // clear everything
+ active_solutions_.clear();
+ active_edges_.clear();
+
+ // and refill
+ for(uint i = 0; i < self_energies_.size(); ++i) {
+ active_solutions_.push_back(i);
+ }
+ this->FillSortedActiveSolutions();
+
+
+ for(uint i = 0; i < edges_.size(); ++i) {
+ active_edges_.push_back(i);
+ }
+
+ for(std::vector<GMEdge*>::iterator i = edges_.begin();
+ i != edges_.end(); ++i) {
+ (*i)->Reset();
+ }
+}
+
+
+void GMNode::Deactivate(int index) {
+
+ if(!active_) {
+ return;
+ }
+
+ active_ = false;
+
+ // if the given index is -1 (default), we simply search for the
+ // the solution with the lowest self energy as the last active solution,
+ // a.k.a. the solution for this node.
+ // In all other cases we take the solution at given index.
+ if(index == -1) {
+ // lets first figure out which is the lowest energy
+ // solution and set it to the only active one
+ Real e_min = std::numeric_limits<Real>::max();
+ index = 0;
+ for(uint i = 0; i < active_solutions_.size(); ++i) {
+ if(self_energies_[active_solutions_[i]] < e_min) {
+ e_min = self_energies_[active_solutions_[i]];
+ index = active_solutions_[i];
+ }
+ }
+ }
+
+ active_solutions_.resize(1);
+ active_solutions_[0] = index;
+
+ sorted_active_solutions_.resize(1);
+ sorted_active_solutions_[0] = index;
+
+ // deactivate all edges connected to this node
+ for(iterator i = this->active_edges_begin();
+ i != this->active_edges_end(); ++i) {
+ GMNode* other = edges_[*i]->GetOtherNode(this);
+ other->RemoveFromActiveEdges(edges_[*i]);
+ edges_[*i]->Deactivate();
+ }
+ active_edges_.clear();
+}
+
+
+void GMNode::AddEdge(GMEdge* edge) {
+ active_edges_.push_back(edges_.size());
+ edges_.push_back(edge);
+}
+
+
+void GMNode::AddValue(uint node_idx, Real val) {
+ self_energies_[node_idx] += val;
+}
+
+
+void GMNode::RemoveFromActiveEdges(GMEdge* edge) {
+
+ for(uint i = 0; i < edges_.size(); ++i) {
+ if(edge == edges_[i]) {
+ iterator it = std::find(active_edges_.begin(), active_edges_.end(), i);
+ if(it != active_edges_.end()) active_edges_.erase(it);
+ }
+ }
+}
+
+
+bool GMNode::DEE(Real e_cut) {
+
+ if(active_solutions_.size() <= 1) return false;
+
+ bool something_happened = false;
+ Real sum;
+ int solution_to_eliminate = sorted_active_solutions_.size()-1;
+
+ while(solution_to_eliminate >= 0) {
+
+ for(int i = 0; i < static_cast<int>(sorted_active_solutions_.size()); ++i) {
+
+ if(i == solution_to_eliminate) continue;
+
+ sum =
+ self_energies_[sorted_active_solutions_[solution_to_eliminate]] -
+ self_energies_[sorted_active_solutions_[i]];
+
+ for(iterator j = this->active_edges_.begin();
+ j != this->active_edges_.end(); ++j) {
+ sum +=
+ edges_[*j]->EMinDiff(this,
+ sorted_active_solutions_[solution_to_eliminate],
+ sorted_active_solutions_[i]);
+ }
+
+ if(sum >= e_cut) {
+
+ something_happened = true;
+ std::vector<uint>::iterator it =
+ std::find(active_solutions_.begin(), active_solutions_.end(),
+ sorted_active_solutions_[solution_to_eliminate]);
+ active_solutions_.erase(it);
+ sorted_active_solutions_.erase(sorted_active_solutions_.begin() +
+ solution_to_eliminate);
+ break;
+ }
+ }
+ --solution_to_eliminate;
+ }
+
+ return something_happened;
+}
+
+
+void GMNode::FillActiveSelfEnergies(std::vector<Real>& self_energies) const {
+
+ self_energies.resize(active_solutions_.size());
+
+ for(uint i = 0; i < active_solutions_.size(); ++i) {
+ self_energies[i] = self_energies_[active_solutions_[i]];
+ }
+}
+
+
+void GMNode::FillSortedActiveSolutions() {
+
+ if(active_solutions_.size() != self_energies_.size()) {
+ throw promod3::Error("Can only sort active solutions when ALL solutions "
+ "are active!");
+ }
+
+ std::vector<std::pair<Real, uint> > temp;
+ for(uint i = 0; i < self_energies_.size(); ++i) {
+ temp.push_back(std::make_pair(self_energies_[i], i));
+ }
+ std::sort(temp.begin(), temp.end());
+
+ sorted_active_solutions_.clear();
+ for(uint i = 0; i < temp.size(); ++i) {
+ sorted_active_solutions_.push_back(temp[i].second);
+ }
+}
+
+
+GraphMinimizer::~GraphMinimizer() {
+
+ for(uint i = 0; i < nodes_.size(); ++i) {
+ delete nodes_[i];
+ }
+
+ for(uint i = 0; i < edges_.size(); ++i) {
+ delete edges_[i];
+ }
+}
+
+
+int GraphMinimizer::AddNode(const std::vector<Real>& self_energies) {
+
+ int node_idx = nodes_.size();
+ nodes_.push_back(new GMNode(node_idx, self_energies));
+ return node_idx;
+}
+
+
+int GraphMinimizer::AddEdge(uint node_idx_one, uint node_idx_two,
+ const EMatXX& emat) {
+
+ if(node_idx_one >= nodes_.size() || node_idx_two >= nodes_.size()) {
+ throw promod3::Error("Invalid node idx provided!");
+ }
+
+ int edge_idx = edges_.size();
+ // check for valid energy matrix happens in GMEdge constructor
+ edges_.push_back(new GMEdge(edge_idx, nodes_[node_idx_one],
+ nodes_[node_idx_two], emat));
+
+ // the edge also has to be added to the nodes
+ nodes_[node_idx_one]->AddEdge(edges_.back());
+ nodes_[node_idx_two]->AddEdge(edges_.back());
+
+ return edge_idx;
+}
+
+
+bool GraphMinimizer::ApplyDEE(uint idx, Real e_thresh) {
+
+ if(idx >= nodes_.size()) {
+ throw promod3::Error("Invalid Index observed when applying DEE!");
+ }
+
+ return nodes_[idx]->DEE(e_thresh);
+}
+
+
+bool GraphMinimizer::ApplyEdgeDecomposition(uint idx, Real e_thresh) {
+
+ if(idx >= edges_.size()) {
+ throw promod3::Error("Invalid Index observed when applying Edge "
+ "Decomposition!");
+ }
+
+ return edges_[idx]->Decompose(e_thresh);
+}
+
+
+void GraphMinimizer::Prune(Real epsilon, Real e_cut, bool consider_all_nodes) {
+
+ // nodes/edges, where something happened
+ std::vector<bool> hot_edges(edges_.size(),true);
+ std::vector<bool> hot_nodes;
+ if(consider_all_nodes)hot_nodes.resize(nodes_.size(),true);
+ else hot_nodes.resize(nodes_.size(),false);
+
+ bool something_happened = true;
+ while(something_happened) {
+ something_happened = false;
+ // let's first do edge decomposition
+ for(uint i = 0; i < hot_edges.size(); ++i) {
+ if(!hot_edges[i]) continue;
+ if(this->ApplyEdgeDecomposition(i, epsilon)) {
+ // let's set the status hot to the nodes connected by the
+ // edge
+ hot_nodes[edges_[i]->GetNode1()->GetIndex()] = true;
+ hot_nodes[edges_[i]->GetNode2()->GetIndex()] = true;
+ something_happened = true;
+ }
+ // either nothing happened, or successfully decomposed...
+ // edge is not hot anymore
+ hot_edges[i] = false;
+ }
+ // let's do DEE
+ for(uint i = 0; i < hot_nodes.size(); ++i) {
+ if(!hot_nodes[i]) continue;
+ if(this->ApplyDEE(i, e_cut)) {
+ // let's set the status hot to the edges, as well as other
+ // nodes connected to that node
+ for(GMNode::iterator j = nodes_[i]->active_edges_begin();
+ j != nodes_[i]->active_edges_end(); ++j) {
+ GMEdge* current_edge = nodes_[i]->GetEdge(*j);
+ hot_edges[current_edge->GetIndex()] = true;
+ // one of the following connected node is the checked node
+ // itself... will be set to false again...
+ hot_nodes[current_edge->GetNode1()->GetIndex()] = true;
+ hot_nodes[current_edge->GetNode2()->GetIndex()] = true;
+ }
+ something_happened = true;
+ }
+ // either nothing happened, or successful DEE...
+ // node is not hot anymore
+ hot_nodes[i] = false;
+ }
+ }
+}
+
+
+void GraphMinimizer::Reset() {
+
+ for(std::vector<GMNode*>::iterator i = nodes_.begin();
+ i != nodes_.end(); ++i) {
+ (*i)->Reset();
+ }
+ for(std::vector<GMEdge*>::iterator i = edges_.begin();
+ i != edges_.end(); ++i) {
+ (*i)->Reset();
+ }
+}
+
+
+promod3::core::Graph GraphMinimizer::ToRawGraph() const {
+
+ promod3::core::Graph raw_graph(nodes_.size());
+ std::map<GMNode*, int> ptr_mapper;
+ for(uint i = 0; i < nodes_.size(); ++i) {
+ ptr_mapper[nodes_[i]] = i;
+ }
+ for(std::vector<GMEdge*>::const_iterator i = edges_.begin();
+ i != edges_.end(); ++i) {
+ if((*i)->IsActive()) {
+ int idx_one = ptr_mapper[(*i)->GetNode1()];
+ int idx_two = ptr_mapper[(*i)->GetNode2()];
+ raw_graph.Connect(idx_one,idx_two);
+ }
+ }
+ return raw_graph;
+}
+
+
+bool GraphMinimizer::HasActiveNodes() const {
+
+ for(uint i = 0; i < nodes_.size(); ++i) {
+ if(nodes_[i]->IsActive()) {
+ return true;
+ }
+ }
+
+ return false;
+}
+
+
+std::pair<std::vector<int>, Real>
+GraphMinimizer::TreeSolve(uint64_t max_complexity, Real initial_epsilon) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "GraphMinimizer::TreeSolve", 2);
+
+ // all nodes must be active in the beginning
+ for(std::vector<GMNode*>::iterator i = nodes_.begin();
+ i != nodes_.end(); ++i) {
+ if(!(*i)->IsActive()) {
+ String err = "All nodes of graph must be active for TreeSolving.";
+ err += " Either construct a new graph or reset the current one!";
+ throw promod3::Error(err);
+ }
+ }
+
+ std::vector<int> overall_solution(nodes_.size(), 0);
+ Real overall_energy = 0.0;
+
+ // handle the case where graph is empty
+ if(nodes_.empty()) {
+ return std::make_pair(overall_solution, overall_energy);
+ }
+
+ // handle the case where graph only contains one item
+ if(nodes_.size() == 1) {
+ nodes_[0]->Deactivate();
+ overall_solution[0] = nodes_[0]->GetOverallIndex(0);
+ overall_energy += nodes_[0]->GetSelfEnergy(overall_solution[0]);
+ return std::make_pair(overall_solution, overall_energy);
+ }
+
+ bool first_iteration = true;
+
+ while(this->HasActiveNodes()) {
+
+ this->Prune(initial_epsilon, 0.0, first_iteration);
+
+ // build raw graph and extract connected components
+ promod3::core::Graph raw_graph = this->ToRawGraph();
+
+ // generate the connected components
+ std::vector<std::vector<int> > connected_components;
+ raw_graph.ConnectedComponents(connected_components);
+
+ // solve the connected components seperately if the according
+ // complexity is feasible
+
+ for(uint component_idx = 0; component_idx < connected_components.size();
+ ++component_idx) {
+
+ const std::vector<int>& component = connected_components[component_idx];
+
+ if(component.size() == 1) {
+ if(nodes_[component[0]]->IsActive()) {
+ // note, that lowest energy solution will be the only active one upon
+ // calling Deactivate
+ nodes_[component[0]]->Deactivate();
+ int overall_idx = nodes_[component[0]]->GetOverallIndex(0);
+ overall_solution[component[0]] = overall_idx;
+ overall_energy += nodes_[component[0]]->GetSelfEnergy(overall_idx);
+ }
+ continue;
+ }
+
+ // create initial data required to solve the enumeration problem
+ std::vector<int> num_active_solutions(component.size());
+ for(uint i = 0; i < component.size(); ++i) {
+ // Check, whether any of the nodes has too many solutions
+ // (due to memory reasons we use unsigned shorts as solution
+ // identifier in the tree solving algorithms)
+ if(nodes_[component[i]]->GetNumActiveSolutions() >
+ std::numeric_limits<unsigned short>::max()) {
+ std::stringstream ss;
+ ss << "Due to technical reasons the maximum number of solutions per ";
+ ss << "position is limited to ";
+ ss << std::numeric_limits<unsigned short>::max();
+ ss << ". Observed a location with ";
+ ss << nodes_[component[i]]->GetNumActiveSolutions();
+ ss << " solutions. Either use less solutions or perform more pruning";
+ ss << " operations before using the TreeSolve algorithm.";
+ throw promod3::Error(ss.str());
+ }
+ num_active_solutions[i] = nodes_[component[i]]->GetNumActiveSolutions();
+ }
+
+ promod3::core::Graph component_graph = raw_graph.SubGraph(component);
+
+ TBag* component_tree =
+ promod3::core::GenerateMinimalWidthTree(component_graph);
+
+ // generate post order traversal of previously constructed tree
+ std::vector<TBag*> traversal =
+ promod3::core::PostOrderTraversal(component_tree);
+
+ // this only fills some initial data, that is required to estimate
+ // the complexity to solve this component
+ std::vector<BagData> bag_data;
+ uint64_t component_complexity = FillRawBagData(traversal,
+ num_active_solutions,
+ bag_data);
+
+ // check whether complexity of current connected component is solvable...
+ // if not, we simply perform another iteration of pruning.
+ if(component_complexity > max_complexity) {
+ if(initial_epsilon <= 0.0) {
+ std::stringstream ss;
+ ss << "One of the connected components in the GraphMinimizer ";
+ ss << "reaches a complexity of "<< component_complexity;
+ ss << ", which is above the max_complexity of "<<max_complexity;
+ ss << ". The idea is to prune more and more aggressively by ";
+ ss << "multiplying the initial_epsilon value by a factor of 2. ";
+ ss << "Your initial_epsilon is "<<initial_epsilon;
+ ss << ", the complexity of this connected ";
+ ss << "component will therefore never fall below max_complexity. ";
+ ss << "To successfully solve the Graph you either have to ";
+ ss << "give initial_epsilon a value above 0.0 or increase ";
+ ss << "max_complexity";
+ throw promod3::Error(ss.str());
+ }
+ continue;
+ }
+
+ // The complexity is low enough... let's fill remaining data and
+ // solve it! GOGOGO!
+
+ std::vector<GMNode*> component_nodes;
+ std::vector<GMEdge*> component_edges;
+ std::vector<std::pair<int, int> > component_edge_indices;
+
+ for(uint i = 0; i < component.size(); ++i) {
+ component_nodes.push_back(nodes_[component[i]]);
+ }
+
+ for(uint i = 0; i < edges_.size(); ++i) {
+
+ GMEdge* edge = edges_[i];
+
+ // is the edge active?
+ if(!edge->IsActive()) continue;
+
+ // does it affect the current component?
+ int a = edge->GetNode1()->GetIndex();
+ int b = edge->GetNode2()->GetIndex();
+
+ std::vector<int>::const_iterator a_it = std::find(component.begin(),
+ component.end(), a);
+ if(a_it == component.end()) continue; // it's not part of the component
+
+ std::vector<int>::const_iterator b_it = std::find(component.begin(),
+ component.end(), b);
+ if(b_it == component.end()) continue; // it's not part of the component
+
+ int a_in_component = a_it - component.begin();
+ int b_in_component = b_it - component.begin();
+
+ component_edges.push_back(edge);
+ component_edge_indices.push_back(std::make_pair(a_in_component,
+ b_in_component));
+ }
+
+ // let's fill in remaining data (energies and stuff)
+ FillBagData(traversal, component_nodes, component_edges,
+ component_edge_indices, bag_data);
+
+ // let's do the whole enumeration game
+ EnumerateBagData(bag_data);
+
+ // let's get the solution out
+ std::vector<int> component_solution(component.size(), 0);
+ CollectSolutionFromBagData(bag_data, bag_data.size() - 1,
+ component_solution);
+
+ overall_energy += bag_data.back().optimal_r_score[0];
+
+ // alter the graph accordingly
+ for(uint i = 0; i < component.size(); ++i) {
+ uint overall_idx =
+ nodes_[component[i]]->GetOverallIndex(component_solution[i]);
+ nodes_[component[i]]->Deactivate(overall_idx);
+ overall_solution[component[i]] = overall_idx;
+ }
+ }
+
+ first_iteration = false;
+ initial_epsilon *= 2;
+ }
+
+ return std::make_pair(overall_solution, overall_energy);
+}
+
+
+std::pair<std::vector<std::vector<int> >, std::vector<Real> >
+GraphMinimizer::AStarSolve(Real e_thresh, uint max_n, uint max_visited_nodes) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "GraphMinimizer::AStarSolve", 2);
+
+ // all nodes must be active in the beginning
+ for(std::vector<GMNode*>::iterator i = nodes_.begin();
+ i != nodes_.end(); ++i) {
+ if(!(*i)->IsActive()) {
+ String err = "All nodes of graph must be active for AStarSolving.";
+ err += " Either construct a new graph or reset the current one!";
+ throw promod3::Error(err);
+ }
+ }
+
+ // e_thresh and max_n must be positive
+ if(e_thresh < 0.0) throw promod3::Error("e_thresh must be positive!");
+ if(max_n <= 0) throw promod3::Error("max_n must be positive!");
+
+ std::vector<std::vector<int> > solutions;
+ std::vector<Real> solution_energies;
+ int num_graph_nodes = nodes_.size();
+ int num_graph_edges = edges_.size();
+
+ // handle the case where graph is empty
+ if(num_graph_nodes == 0) {
+ return std::make_pair(solutions, solution_energies);
+ }
+
+ // handle the case where graph only contains one item
+ if(num_graph_nodes == 1) {
+
+ uint num_active_solutions = nodes_[0]->GetNumActiveSolutions();
+ if(num_active_solutions == 0) {
+ return std::make_pair(solutions, solution_energies);
+ }
+
+ std::vector<std::pair<Real, int> > sorted_solutions;
+ sorted_solutions.reserve(num_active_solutions);
+ std::vector<Real> active_energies;
+ nodes_[0]->FillActiveSelfEnergies(active_energies);
+ for(uint i = 0; i < num_active_solutions; ++i) {
+ sorted_solutions.push_back(std::make_pair(active_energies[i], i));
+ }
+ std::sort(sorted_solutions.begin(), sorted_solutions.end());
+ Real emin = sorted_solutions[0].first;
+ for(uint i = 0; i < std::min(max_n, num_active_solutions); ++i) {
+ if((sorted_solutions[i].first - emin) > e_thresh ||
+ solutions.size() >= max_n) {
+ break;
+ }
+ int overall_idx = nodes_[0]->GetOverallIndex(sorted_solutions[i].second);
+ solutions.push_back(std::vector<int>(1, overall_idx));
+ solution_energies.push_back(sorted_solutions[i].first);
+ }
+ return std::make_pair(solutions, solution_energies);
+ }
+
+ // extract the energies of the active solutions
+ std::vector<int> num_active_solutions(nodes_.size());
+ std::vector<std::vector<Real> > self_energies(nodes_.size());
+
+ for(int i = 0; i < num_graph_nodes; ++i) {
+ num_active_solutions[i] = nodes_[i]->GetNumActiveSolutions();
+ }
+
+ for(int i = 0; i < num_graph_nodes; ++i) {
+ nodes_[i]->FillActiveSelfEnergies(self_energies[i]);
+ }
+
+ // pairwise energies are stored a bit more complicated...
+ // One vector per node.
+ // Every element in that vector contains the index to another node with LOWER
+ // idx and the corresponding energy matrix
+ std::vector<std::vector<std::pair<int, EMatXX> > >
+ pairwise_energies(num_graph_nodes);
+ std::vector<int> num_pairwise_energies(num_graph_nodes);
+
+ // to avoid too many reallocations and copying of the eigen matrices, we
+ // build up a temporary data structure first
+ std::vector<std::vector<std::pair<int, GMEdge*> > > temp(num_graph_nodes);
+
+ for(int i = 0; i < num_graph_edges; ++i) {
+ if(edges_[i]->IsActive()) {
+ GMEdge* edge = edges_[i];
+ int a = edge->GetNode1()->GetIndex();
+ int b = edge->GetNode2()->GetIndex();
+
+ // b is larger...
+ temp[b].push_back(std::make_pair(a, edge));
+ }
+ }
+
+ for(int i = 0; i < num_graph_nodes; ++i) {
+ int n = temp[i].size();
+ num_pairwise_energies[i] = n;
+ pairwise_energies[i].resize(n);
+ for(int j = 0; j < n; ++j) {
+ pairwise_energies[i][j].first = temp[i][j].first;
+ temp[i][j].second->FillActiveEnergies(pairwise_energies[i][j].second);
+ }
+ }
+
+ // following data structure is a precalculation to increase the speed
+ // of hstar calculation...
+
+ // for every every position there is a vector for every solution at
+ // that position. Every element in that vector contains the minimal
+ // energy towards every position that comes before, zero if no
+ // interaction is observed
+ std::vector<std::vector<std::vector<Real> > >
+ min_pairwise_e_before(num_graph_nodes, std::vector<std::vector<Real> >());
+
+ for(int i = 0; i < num_graph_nodes; ++i) {
+ min_pairwise_e_before[i].resize(num_active_solutions[i]);
+ for(int j = 0; j < num_active_solutions[i]; ++j) {
+ min_pairwise_e_before[i][j].assign(i,0.0);
+ for(int k = 0; k < num_pairwise_energies[i]; ++k) {
+
+ int other_node = pairwise_energies[i][k].first;
+ const EMatXX& emat = pairwise_energies[i][k].second;
+
+ Real e_min = std::numeric_limits<Real>::max();
+ for(int l = 0; l < num_active_solutions[other_node]; ++l) {
+ e_min = std::min(e_min, emat(l, j));
+ }
+
+ min_pairwise_e_before[i][j][other_node] = e_min;
+ }
+ }
+ }
+
+ // Data structures to hold the visited nodes and sort them in a priority queue
+ std::priority_queue<AStarNode*,std::vector<AStarNode*>,CompareAStarNodes>
+ node_queue;
+ std::vector<AStarNode> node_array;
+ // we already have to reserve node_array, since we deal with pointers
+ // to it and reallocations are a bit bad in these cases...
+ node_array.reserve(max_visited_nodes);
+
+ // we first add the root node with g* = 0.0 and h* = max_real
+ node_array.push_back(AStarNode(0, 0, 0, 0, 0.0,
+ std::numeric_limits<Real>::max()));
+
+ node_queue.push(&node_array[0]);
+ Real min_energy = std::numeric_limits<Real>::max();
+
+ while(!node_queue.empty()) {
+
+ AStarNode* current_node = node_queue.top();
+ node_queue.pop();
+
+ std::vector<int> path;
+ ReconstructSearchTreePath(node_array, current_node->node_idx, path);
+
+ if(current_node->tree_depth >= num_graph_nodes) {
+ // it is a solution!!!!!
+ Real fstar = current_node->gstar; //note, that hstar must be zero...
+ if(solutions.empty()) {
+ // it's the first solution and therefore the GMEC
+ // (Global Minimum Energy Conformation Fuck Yeah...)
+ min_energy = fstar;
+ }
+ else{
+ // there is at least one solution around! let's check whether
+ // the current solution is within e_thresh
+ if(fstar - min_energy > e_thresh) break;
+ }
+
+ // let's add it
+ solutions.push_back(path);
+ solution_energies.push_back(fstar);
+
+ // check whether we have enough solutions
+ if(solutions.size() >= max_n) break;
+
+ continue;
+ }
+
+ // current node has to be expanded
+ // => new node for every single solution in node
+
+ // we first check whether we become bigger than max_visited_nodes
+ if(node_array.size() + num_active_solutions[current_node->tree_depth] >
+ max_visited_nodes) {
+ throw promod3::Error("Reached max_visited_nodes => increase this"
+ "parameter or reduce the problem size!");
+ }
+
+ // following variables will be the same for all expaned nodes
+ int pos_in_graph = current_node->tree_depth;
+ uint parent_idx = current_node->node_idx;
+ unsigned short tree_depth = current_node->tree_depth + 1;
+
+ // We already add an element to the path for the node to be expaned.
+ // This saves an if in the hstar calculation
+ path.push_back(0);
+
+ for(int solution_idx = 0; solution_idx < num_active_solutions[pos_in_graph];
+ ++solution_idx) {
+
+ // set the hacky last element of the path
+ path.back() = solution_idx;
+
+ // variable specific for expanded node
+ uint node_idx = node_array.size();
+ Real gstar = current_node->gstar;
+ Real hstar = 0.0;
+
+ // we still need to adapt the energy values (gstar and hstar)
+
+ // in case of gstar we have to add the self energy of the current
+ // solution and the pairwise energy towards all previous solutions in
+ // the path towards this node
+
+ // let's add the self energy
+ gstar += self_energies[pos_in_graph][solution_idx];
+
+ // let's add all pairwise energies towards the already set solutions
+ for(int i = 0; i < num_pairwise_energies[pos_in_graph]; ++i) {
+ int other_node = pairwise_energies[pos_in_graph][i].first;
+ const EMatXX& emat = pairwise_energies[pos_in_graph][i].second;
+ gstar += emat(path[other_node], solution_idx);
+ }
+
+ // in case of hstar we have to add the minimal pairwise energy towards
+ // all nodes still to be determined
+ int last_path_idx = path.size()-1;
+ for(int non_set_pos_idx = pos_in_graph + 1;
+ non_set_pos_idx < num_graph_nodes; ++non_set_pos_idx) {
+
+ Real min_e = std::numeric_limits<Real>::max();
+
+ // iterate over all possible solutions at position non_set_pos_idx
+ for(int i = 0; i < num_active_solutions[non_set_pos_idx]; ++i) {
+
+ // start with its self energy
+ Real actual_e = self_energies[non_set_pos_idx][i];
+
+ // add all pairwise energies towards solutions that have already been
+ // set in this path, the according minimal energy that could be
+ // achieved respectively
+ for(int j = 0; j < num_pairwise_energies[non_set_pos_idx]; ++j) {
+ int other_node = pairwise_energies[non_set_pos_idx][j].first;
+ if(other_node <= last_path_idx) {
+ // add the energy to the already determined energy from the path
+ const EMatXX& emat = pairwise_energies[non_set_pos_idx][j].second;
+ actual_e += emat(path[other_node], i);
+ }
+ else{
+ // add the minimal possible energy...
+ actual_e += min_pairwise_e_before[non_set_pos_idx][i][other_node];
+ }
+ }
+ min_e = std::min(min_e, actual_e);
+ }
+ hstar += min_e;
+ }
+
+ node_array.push_back(AStarNode(node_idx, parent_idx,
+ solution_idx, tree_depth, gstar,
+ hstar));
+
+ // it's all done, we finally have to insert it into the priority queue
+ node_queue.push(&node_array[node_idx]);
+ }
+ }
+
+ // the solutions are relative to the active solutions, we still have to
+ // translate them into overall indices
+ for(uint i = 0; i < solutions.size(); ++i) {
+ for(uint j = 0; j < solutions[i].size(); ++j) {
+ solutions[i][j] = nodes_[j]->GetOverallIndex(solutions[i][j]);
+ }
+ }
+
+ return std::make_pair(solutions, solution_energies);
+}
+
+
+std::pair<std::vector<std::vector<int> >, std::vector<Real> >
+GraphMinimizer::MCSolve(int n, int mc_steps, Real start_temperature,
+ int change_frequency, Real cooling_factor, int seed) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "GraphMinimizer::MCSolve", 2);
+
+ // all nodes must be active in the beginning
+ for(std::vector<GMNode*>::iterator i = nodes_.begin();
+ i != nodes_.end(); ++i) {
+ if(!(*i)->IsActive()) {
+ String err = "All nodes of graph must be active for MCSolving.";
+ err += " Either construct a new graph or reset the current one!";
+ throw promod3::Error(err);
+ }
+ }
+
+ std::vector<std::vector<int> > solutions;
+ std::vector<Real> solution_energies;
+ int num_graph_nodes = nodes_.size();
+ int num_graph_edges = edges_.size();
+
+ // handle the case where graph is empty
+ if(num_graph_nodes == 0) {
+ throw promod3::Error("Cannot run MCSolve on an empty Graph!");
+ }
+
+ // extract the number of active solutions and the self energies
+ // of all the nodes
+ std::vector<int> num_active_solutions(num_graph_nodes);
+ std::vector<std::vector<Real> > self_energies(num_graph_nodes);
+ for(int i = 0; i < num_graph_nodes; ++i) {
+ nodes_[i]->FillActiveSelfEnergies(self_energies[i]);
+ num_active_solutions[i] = self_energies[i].size();
+ }
+
+ // a vector for every node... every vector contains pairs describing the
+ // interactions towards other nodes.
+ // first pair element: idx to OTHER node
+ // second pair element: idx to energy mat
+ std::vector<std::vector<std::pair<int, int> > > pairwise_energy_mapper;
+ pairwise_energy_mapper.resize(num_graph_nodes);
+ std::vector<GMEdge*> active_edges;
+
+ // buildup the pairwise_energy_mapper
+ for(int i = 0; i < num_graph_edges; ++i) {
+ GMEdge* edge = edges_[i];
+ if(edge->IsActive()) {
+ int n1_idx = edge->GetNode1()->GetIndex();
+ int n2_idx = edge->GetNode2()->GetIndex();
+ int edge_idx = active_edges.size();
+ pairwise_energy_mapper[n1_idx].push_back(std::make_pair(n2_idx, edge_idx));
+ pairwise_energy_mapper[n2_idx].push_back(std::make_pair(n1_idx, edge_idx));
+ active_edges.push_back(edge);
+ }
+ }
+
+ // fill the actual energies
+ int num_active_edges = active_edges.size();
+ std::vector<EMatXX> pairwise_energies(num_active_edges);
+ for(int i = 0; i < num_active_edges; ++i) {
+ active_edges[i]->FillActiveEnergies(pairwise_energies[i]);
+ }
+
+ // temporary object to perform a sorting by energy in the end
+ std::vector<std::pair<Real, int> > sorting_vector;
+
+ // let the sampling begin!
+ SolutionSelector solution_selector(num_active_solutions, seed);
+
+ for(int trajectory_idx = 0; trajectory_idx < n; ++trajectory_idx) {
+
+ std::vector<int> current_solution;
+ solution_selector.InitSolutionSelection(current_solution);
+ Real temperature = start_temperature / cooling_factor;
+
+ for(int current_step = 0; current_step < mc_steps; ++current_step) {
+
+ if (current_step % change_frequency == 0) {
+ temperature *= cooling_factor;
+ }
+
+ int node_idx = solution_selector.SelectNode();
+ int solution_idx = current_solution[node_idx];
+ int proposed_solution_idx = solution_selector.SelectSolution(node_idx);
+
+ Real e_current = GetSolutionEnergy(node_idx, solution_idx,
+ current_solution, self_energies,
+ pairwise_energies,
+ pairwise_energy_mapper);
+
+ Real e_new = GetSolutionEnergy(node_idx, proposed_solution_idx,
+ current_solution, self_energies,
+ pairwise_energies, pairwise_energy_mapper);
+
+ Real e_diff = e_new - e_current;
+
+ if (e_diff < Real(0.0)) {
+ current_solution[node_idx] = proposed_solution_idx;
+ }
+ else {
+ Real acceptance_probability = std::exp(-e_diff/temperature);
+ if (solution_selector.GetRandomNumber() < acceptance_probability) {
+ current_solution[node_idx] = proposed_solution_idx;
+ }
+ }
+ }
+
+ // the trajectory solution!!!
+ Real e = GetGlobalEnergy(current_solution, self_energies, pairwise_energies,
+ pairwise_energy_mapper);
+ solution_energies.push_back(e);
+ solutions.push_back(current_solution);
+ sorting_vector.push_back(std::make_pair(e, trajectory_idx));
+ }
+
+ // the solutions are relative to the active solutions, we still have to
+ // translate them into overall indices
+ for(int i = 0; i < n; ++i) {
+ for(int j = 0; j < num_graph_nodes; ++j) {
+ solutions[i][j] = nodes_[j]->GetOverallIndex(solutions[i][j]);
+ }
+ }
+
+ // perform a final sorting by energy
+ std::sort(sorting_vector.begin(), sorting_vector.end());
+ std::vector<std::vector<int> > sorted_solutions(n);
+ std::vector<Real> sorted_solution_energies(n);
+ for(int i = 0; i < n; ++i) {
+ sorted_solutions[i] = solutions[sorting_vector[i].second];
+ sorted_solution_energies[i] = solution_energies[sorting_vector[i].second];
+ }
+
+ return std::make_pair(sorted_solutions, sorted_solution_energies);
+}
+
+
+std::pair<std::vector<int>, Real> GraphMinimizer::NaiveSolve() {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "GraphMinimizer::NaiveSolve", 2);
+
+ // all nodes must be active in the beginning
+ for(std::vector<GMNode*>::iterator i = nodes_.begin();
+ i != nodes_.end(); ++i) {
+ if(!(*i)->IsActive()) {
+ String err = "All nodes of graph must be active for NaiveSolving.";
+ err += " Either construct a new graph or reset the current one!";
+ throw promod3::Error(err);
+ }
+ }
+
+ int num_graph_nodes = nodes_.size();
+ int num_graph_edges = edges_.size();
+
+ // handle the case where graph is empty
+ if(num_graph_nodes == 0) {
+ throw promod3::Error("Cannot run NaiveSolve on an empty Graph!");
+ }
+
+ // extract the number of active solutions and the self energies
+ // of all the nodes
+ std::vector<unsigned short> num_active_solutions(num_graph_nodes);
+ std::vector<std::vector<Real> > self_energies(num_graph_nodes);
+ for(int i = 0; i < num_graph_nodes; ++i) {
+ nodes_[i]->FillActiveSelfEnergies(self_energies[i]);
+ int active_solutions = self_energies[i].size();
+ if(active_solutions > std::numeric_limits<unsigned short>::max()) {
+ std::stringstream ss;
+ ss << "Due to technical reasons there must be no nodes with more than ";
+ ss << active_solutions << " possible solutions in NaiveSolve!";
+ throw promod3::Error(ss.str());
+ }
+ num_active_solutions[i] = active_solutions;
+ }
+
+ std::vector<EMatXX> pairwise_energies;
+ std::vector<GMEdge*> active_edges;
+ std::vector<std::pair<int,int> > pairwise_energy_indices;
+
+ for(int i = 0; i < num_graph_edges; ++i) {
+ GMEdge* edge = edges_[i];
+ if(edge->IsActive()) {
+ int n1_idx = edge->GetNode1()->GetIndex();
+ int n2_idx = edge->GetNode2()->GetIndex();
+ pairwise_energy_indices.push_back(std::make_pair(n1_idx, n2_idx));
+ active_edges.push_back(edge);
+ }
+ }
+
+ int num_pairwise_energies = active_edges.size();
+ pairwise_energies.resize(num_pairwise_energies);
+ for(int i = 0; i < num_pairwise_energies; ++i) {
+ active_edges[i]->FillActiveEnergies(pairwise_energies[i]);
+ }
+
+ // This is the most stupid piece of code I ever wrote... SLOOOOOOOW
+ promod3::core::Enumerator<unsigned short> enumerator(num_active_solutions);
+ std::vector<unsigned short>& current_solution = enumerator.CurrentEnum();
+
+ Real best_energy = std::numeric_limits<Real>::max();
+ std::vector<unsigned short> best_solution = current_solution;
+
+ do {
+
+ Real current_energy = 0.0;
+
+ // sum up the internal energies
+ for(int i = 0; i < num_graph_nodes; ++i) {
+ current_energy += self_energies[i][current_solution[i]];
+ }
+
+ for(int i = 0; i < num_pairwise_energies; ++i) {
+ int n1_idx = pairwise_energy_indices[i].first;
+ int n2_idx = pairwise_energy_indices[i].second;
+ current_energy += pairwise_energies[i](current_solution[n1_idx],
+ current_solution[n2_idx]);
+ }
+
+ if(current_energy < best_energy) {
+ best_energy = current_energy;
+ best_solution = current_solution;
+ }
+
+ } while(enumerator.Next());
+
+ // the solution is relative to the active solution, we still have to
+ // translate them into overall indices
+ std::vector<int> final_solution(num_graph_nodes);
+ for(int i = 0; i < num_graph_nodes; ++i) {
+ final_solution[i] = nodes_[i]->GetOverallIndex(best_solution[i]);
+ }
+
+ return std::make_pair(final_solution, best_energy);
+}
+
+}} // ns
diff --git a/core/src/graph_minimizer.hh b/core/src/graph_minimizer.hh
new file mode 100644
index 0000000000000000000000000000000000000000..410cc21d0eb4664f1b6c8ef70e4b7caf6ec6535b
--- /dev/null
+++ b/core/src/graph_minimizer.hh
@@ -0,0 +1,178 @@
+#ifndef PROMOD3_GRAPH_MINIMIZER_HH
+#define PROMOD3_GRAPH_MINIMIZER_HH
+
+#include <vector>
+#include <limits.h>
+
+#include <boost/shared_ptr.hpp>
+
+#include <ost/base.hh>
+#include <ost/stdint.hh>
+
+#include <promod3/core/eigen_types.hh>
+#include <promod3/core/graph.hh>
+
+
+namespace promod3 { namespace core {
+
+class GMEdge;
+class GMNode;
+class GraphMinimizer;
+
+typedef boost::shared_ptr<GraphMinimizer> GraphMinimizerPtr;
+
+class GMEdge {
+
+public:
+ GMEdge(uint index, GMNode* node_a, GMNode* node_b, const EMatXX& emat);
+
+ void Reset();
+
+ void Deactivate() {active_ = false; };
+
+ bool IsActive() const { return active_; }
+
+ uint GetIndex() const { return index_; }
+
+ bool Decompose(Real thresh);
+
+ Real GetPairwiseEnergy(uint i, uint j) const { return emat_(i, j); }
+
+ GMNode* GetNode1() const { return node1_; }
+
+ GMNode* GetNode2() const { return node2_; }
+
+ GMNode* GetOtherNode(GMNode* node);
+
+ // resolves the expression min_x(EPair(idx1,x)-EPair(idx2,x))
+ // in the DEE formalism, where x only considers the active
+ // solutions from the OTHER node than node_ptr
+ Real EMinDiff(const GMNode* node_ptr, uint idx1, uint idx2) const;
+
+ void FillActiveEnergies(EMatXX& emat) const;
+
+private:
+ uint index_;
+ bool active_;
+ GMNode* node1_;
+ GMNode* node2_;
+ EMatXX emat_;
+};
+
+class GMNode {
+
+public:
+ GMNode(uint index, const std::vector<Real>& self_energies);
+
+ void Reset();
+
+ void Deactivate(int index = -1);
+
+ bool IsActive() const { return active_; }
+
+ uint GetIndex() const { return index_; }
+
+ void AddEdge(GMEdge* edge);
+
+ GMEdge* GetEdge(uint idx) const { return edges_.at(idx); }
+
+ void RemoveFromActiveEdges(GMEdge* edge);
+
+ void AddValue(uint node_idx, Real val);
+
+ bool DEE(Real e_cut = 0.0);
+
+ uint GetOverallIndex(uint active_index) const {
+ return active_solutions_.at(active_index); }
+
+ size_t GetNumActiveSolutions() const { return active_solutions_.size(); }
+
+ size_t GetNumActiveEdges() const { return active_edges_.size(); }
+
+ size_t GetNumSolutions() const { return self_energies_.size(); }
+
+ size_t GetNumEdges() const { return edges_.size(); }
+
+ Real GetSelfEnergy(uint index) const { return self_energies_[index]; }
+
+ void FillActiveSelfEnergies(std::vector<Real>& self_energies) const;
+
+ typedef std::vector<uint>::const_iterator const_iterator;
+ typedef std::vector<uint>::iterator iterator;
+
+ iterator active_solutions_begin() { return active_solutions_.begin(); }
+ iterator active_solutions_end() { return active_solutions_.end(); }
+ iterator active_edges_begin() { return active_edges_.begin(); }
+ iterator active_edges_end() { return active_edges_.end(); }
+
+ const_iterator active_solutions_begin() const {
+ return active_solutions_.begin(); }
+ const_iterator active_solutions_end() const {
+ return active_solutions_.end(); }
+ const_iterator active_edges_begin() const { return active_edges_.begin(); }
+ const_iterator active_edges_end() const { return active_edges_.end(); }
+
+private:
+
+ void FillSortedActiveSolutions();
+
+ uint index_;
+ bool active_;
+ std::vector<Real> self_energies_;
+ std::vector<Real> original_self_energies_;
+ std::vector<uint> active_solutions_;
+ std::vector<uint> sorted_active_solutions_;
+ std::vector<uint> active_edges_;
+ std::vector<GMEdge*> edges_;
+};
+
+
+class GraphMinimizer {
+
+public:
+
+ GraphMinimizer() { }
+
+ virtual ~GraphMinimizer();
+
+ int AddNode(const std::vector<Real>& self_energies);
+
+ int AddEdge(uint node_idx_one, uint node_idx_two, const EMatXX& emat);
+
+ bool ApplyDEE(uint node_idx, Real e_thresh = 0.0);
+
+ bool ApplyEdgeDecomposition(uint edge_idx, Real e_tresh);
+
+ void Prune(Real epsilon, Real e_cut = 0.0, bool consider_all_nodes = true);
+
+ void Reset();
+
+ promod3::core::Graph ToRawGraph() const;
+
+ bool HasActiveNodes() const;
+
+ std::pair<std::vector<int>, Real>
+ TreeSolve(uint64_t max_complexity = std::numeric_limits<uint64_t>::max(),
+ Real intial_epsilon = 0.02);
+
+ std::pair<std::vector<std::vector<int> >, std::vector<Real> >
+ AStarSolve(Real e_thresh, uint max_n = 100,
+ uint max_visited_nodes = 100000000);
+
+ std::pair<std::vector<std::vector<int> >, std::vector<Real> >
+ MCSolve(int n = 10, int mc_steps = 1000, Real start_temperature = 100.0,
+ int change_frequency = 100, Real cooling_factor = 0.9,
+ int seed = 0);
+
+ // Don't complain when it takes ages...
+ std::pair<std::vector<int>, Real> NaiveSolve();
+
+private:
+
+ std::vector<GMNode*> nodes_;
+ std::vector<GMEdge*> edges_;
+};
+
+}} // ns
+
+#endif
diff --git a/core/src/superpose.cc b/core/src/superpose.cc
index 597fa69c5b814409e923ce3a60b7e1f8bfd0cd2c..717b9de6b7fb06794fa42412ce072d3d69c93a9a 100644
--- a/core/src/superpose.cc
+++ b/core/src/superpose.cc
@@ -1,4 +1,6 @@
#include <promod3/core/superpose.hh>
+#include <Eigen/SVD>
+#include <Eigen/Geometry>
#include <map>
namespace{
diff --git a/core/src/superpose.hh b/core/src/superpose.hh
index 8e9839c9575695d1fdc8520250cba9f9b02223e1..8a3fdcec3b0c4d4e8e3ce13c7bdce1ef286304d1 100644
--- a/core/src/superpose.hh
+++ b/core/src/superpose.hh
@@ -4,26 +4,14 @@
#include <ost/geom/vecmat3_op.hh>
#include <ost/geom/mat4.hh>
#include <ost/tri_matrix.hh>
-#include <promod3/core/message.hh>
-#include <Eigen/SVD>
-#include <Eigen/Geometry>
-#include <Eigen/StdVector>
+#include <promod3/core/eigen_types.hh>
+#include <promod3/core/message.hh>
#include <vector>
namespace promod3 { namespace core {
-typedef Eigen::Matrix<Real,3,3> EMat3;
-typedef Eigen::Matrix<Real,3,1> EVec3;
-typedef Eigen::Matrix<Real,1,3> ERVec3;
-typedef Eigen::Matrix<Real,Eigen::Dynamic,3> EMatX3;
-
-// If you want to use stl containers of fixed sized Eigentype (e.g. EMatX3)
-// you must use a custom allocator provided by Eigen to ensure proper memory
-// alignment (more on that in the Eigen documentation)
-typedef std::vector<EMatX3,Eigen::aligned_allocator<EMatX3> > EMatX3List;
-
// Following functions are intended to be used by other code. Fill the eigen
// matrices by themselves to avoid shouffling around too much data.
// NOTE: the EMatX3 objects get altered inside some of these functions!
diff --git a/core/src/tetrahedral_polytope.cc b/core/src/tetrahedral_polytope.cc
index 041c8104e9a32999a293b104ae675f54076699d3..576ab1fd82093f5c4c0c8cc6a18f8c987577796d 100644
--- a/core/src/tetrahedral_polytope.cc
+++ b/core/src/tetrahedral_polytope.cc
@@ -129,6 +129,10 @@ void TetrahedralPolytopeTree::ResetTree(const std::vector<Real>& x,
indices[i] = i;
}
+ if(num_leaf_nodes_ == 0) {
+ return; // tree is empty... we don't even have to call Generate
+ }
+
root_node_ = this->Generate(x, y, z, indices);
}
diff --git a/core/src/tetrahedral_polytope.hh b/core/src/tetrahedral_polytope.hh
index 705640dbb1ff8ad69584bec32a7073e81d8b0da6..3a2863b2854aaca9f2eee184c5fa9a8260d3125e 100644
--- a/core/src/tetrahedral_polytope.hh
+++ b/core/src/tetrahedral_polytope.hh
@@ -95,11 +95,19 @@ public:
const std::vector<Real>& radii);
bool Overlap(const TetrahedralPolytope& other) const{
- return nodes_[root_node_].Overlap(other);
+ if(num_leaf_nodes_ == 0) {
+ return false;
+ } else {
+ return nodes_[root_node_].Overlap(other);
+ }
}
bool Overlap(const TetrahedralPolytopeTree& other) const{
- return nodes_[root_node_].Overlap(other.nodes_[other.root_node_]);
+ if(num_leaf_nodes_ == 0 || other.num_leaf_nodes_ == 0) {
+ return false;
+ } else {
+ return nodes_[root_node_].Overlap(other.nodes_[other.root_node_]);
+ }
}
void OverlappingPolytopes(const TetrahedralPolytopeTree& other,
@@ -108,6 +116,10 @@ public:
ScopedTimerPtr prof = StaticRuntimeProfiler::StartScoped(
"TetrahedralPolytopeTree::OverlappingPolytopes", 2);
+ if(num_leaf_nodes_ == 0 || other.num_leaf_nodes_ == 0) {
+ return; // no overlaps...
+ }
+
TraverseTree(other, root_node_, other.root_node_, overlap);
}
diff --git a/core/tests/CMakeLists.txt b/core/tests/CMakeLists.txt
index 0794903226604ba639ff96afb174875e2f233045..b7eebec0e86b04939ab02ac83281e74ac17ab1ef 100644
--- a/core/tests/CMakeLists.txt
+++ b/core/tests/CMakeLists.txt
@@ -4,6 +4,7 @@ set(CORE_UNIT_TESTS
test_pm3argparse.py
test_check_io.cc
test_portable_binary.cc
+ test_graph_minimizer.cc
tests.cc
)
diff --git a/core/tests/test_graph_minimizer.cc b/core/tests/test_graph_minimizer.cc
new file mode 100644
index 0000000000000000000000000000000000000000..7a52ae53b6e1cc49eab7cab236c3a9b304c9b589
--- /dev/null
+++ b/core/tests/test_graph_minimizer.cc
@@ -0,0 +1,105 @@
+#include <promod3/core/eigen_types.hh>
+#include <promod3/core/graph_minimizer.hh>
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+
+#include <ost/base.hh>
+#include <vector>
+#include <stdlib.h>
+
+BOOST_AUTO_TEST_SUITE( core );
+
+using namespace promod3::core;
+
+
+GraphMinimizerPtr GenerateTestGraph() {
+
+ // setup a simple graph that can naively be enumerated
+
+ std::srand(0);
+ GraphMinimizerPtr graph(new GraphMinimizer);
+ std::vector<int> num_solutions;
+
+ num_solutions.push_back(3);
+ num_solutions.push_back(5);
+ num_solutions.push_back(2);
+ num_solutions.push_back(8);
+ num_solutions.push_back(3);
+ num_solutions.push_back(5);
+
+ std::vector<std::pair<int, int> > edges;
+ edges.push_back(std::make_pair(0,1));
+ edges.push_back(std::make_pair(0,3));
+ edges.push_back(std::make_pair(0,4));
+ edges.push_back(std::make_pair(0,5));
+ edges.push_back(std::make_pair(1,2));
+ edges.push_back(std::make_pair(2,3));
+ edges.push_back(std::make_pair(2,4));
+ edges.push_back(std::make_pair(3,1));
+ edges.push_back(std::make_pair(4,5));
+ edges.push_back(std::make_pair(5,1));
+
+
+ for(uint i = 0; i < num_solutions.size(); ++i) {
+
+ std::vector<Real> self_energies;
+ for(int j = 0; j < num_solutions[i]; ++j) {
+ self_energies.push_back(static_cast<Real>(std::rand()) / RAND_MAX);
+ }
+
+ graph->AddNode(self_energies);
+ }
+
+ for(uint i = 0; i < edges.size(); ++i) {
+ EMatXX emat = EMatXX::Random(num_solutions[edges[i].first],
+ num_solutions[edges[i].second]);
+ graph->AddEdge(edges[i].first, edges[i].second, emat);
+ }
+
+ return graph;
+}
+
+
+BOOST_AUTO_TEST_CASE(test_graph_minimizer) {
+
+ // simple test to at least run all solving algorithms once
+
+ GraphMinimizerPtr graph = GenerateTestGraph();
+
+ std::pair<std::vector<int>, Real> naive_solution = graph->NaiveSolve();
+ graph->Reset();
+
+ std::pair<std::vector<int>, Real> tree_solution = graph->TreeSolve();
+ graph->Reset();
+
+ std::pair<std::vector<std::vector<int> >, std::vector<Real> > astar_solution =
+ graph->AStarSolve(10.0);
+ graph->Reset();
+
+ std::pair<std::vector<std::vector<int> >, std::vector<Real> > mc_solution =
+ graph->MCSolve();
+
+ // the solutions and coresponding energies in naive, tree and astar must be
+ // the same
+
+ BOOST_CHECK(naive_solution.first == tree_solution.first);
+ BOOST_CHECK(naive_solution.first == astar_solution.first[0]);
+
+ BOOST_CHECK_CLOSE(naive_solution.second, tree_solution.second, Real(1e-3));
+ BOOST_CHECK_CLOSE(naive_solution.second, astar_solution.second[0], Real(1e-3));
+
+ // check, whether the energies in the astar solution are sorted
+
+ for(uint i = 1; i < astar_solution.second.size(); ++i) {
+ BOOST_CHECK(astar_solution.second[i] >= astar_solution.second[i-1]);
+ }
+
+ // check, whether the energies in the mc solution are sorted
+
+ for(uint i = 1; i < mc_solution.second.size(); ++i) {
+ BOOST_CHECK(mc_solution.second[i] >= mc_solution.second[i-1]);
+ }
+}
+
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/doc/buildsystem.rst b/doc/buildsystem.rst
index 4bb192686d60b60c60d52e9c0e8fb56b3334a91e..a601d619b695a46a2f15352e312e4bdaf91ab90f 100644
--- a/doc/buildsystem.rst
+++ b/doc/buildsystem.rst
@@ -143,11 +143,11 @@ safely delete the whole source folder.
.. |qmean| replace:: QMEAN
.. |eigen3| replace:: Eigen 3
.. |openmm| replace:: OpenMM
-.. _qmean: http://swissmodel.expasy.org/qmean/cgi/index.cgi?
-.. _ost_l: http://www.OpenStructure.org
+.. _qmean: https://swissmodel.expasy.org/qmean/
+.. _ost_l: https://www.OpenStructure.org
.. _cmake: https://cmake.org/
.. _python: https://www.python.org/
-.. _boost: http://www.boost.org/
+.. _boost: https://www.boost.org/
.. _eigen3: http://eigen.tuxfamily.org/index.php?title=Main_Page
.. _openmm: http://openmm.org
diff --git a/doc/conf.py.in b/doc/conf.py.in
index 3453b6e9740f3b71777b6143d5e918808fd030a3..1219c73e05d9a4047ac23d72dcc449f8581265eb 100644
--- a/doc/conf.py.in
+++ b/doc/conf.py.in
@@ -59,7 +59,7 @@ master_doc = 'index'
# General information about the project.
project = u'ProMod3'
-copyright = u'2017, ProMod3 authors'# pylint: disable=redefined-builtin
+copyright = u'2018, ProMod3 authors'# pylint: disable=redefined-builtin
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
@@ -288,7 +288,7 @@ rst_epilog = """
.. |boost| replace:: Boost
.. |git| replace:: Git
.. |C++| replace:: C++
-.. _ost_s: http://www.OpenStructure.org
+.. _ost_s: https://www.OpenStructure.org
.. _nameattr: @PYTHON_DOC_URL@/library/__main__.html
.. _mainattr: @PYTHON_DOC_URL@/library/__main__.html
.. _descattr: @PYTHON_DOC_URL@/library/argparse.html#description
diff --git a/doc/contributing.rst b/doc/contributing.rst
index 832af70cc2e46a71d3850967a075a8f423ece6d8..ae3c842c641522624e55d208c51e6a146773a033 100644
--- a/doc/contributing.rst
+++ b/doc/contributing.rst
@@ -201,7 +201,7 @@ sporting a single monolithic :file:`test_sidechain_reconstruction.py`.
|python| code is evaluated using its own :py_docs:`unit testing framework
<library/unittest.html>` with a little help from |ost_s|_ (|C++| uses the
|boost| `Test Library
-<http://www.boost.org/doc/libs/1_47_0/libs/test/doc/html/index.html>`_). The
+<https://www.boost.org/doc/libs/1_53_0/libs/test/doc/html/index.html>`_). The
basic scheme is to import your module, subclass :class:`unittest.TestCase` and
make the whole file runnable as script using the most common |nameattr|_
attribute. As an example we test the
@@ -477,7 +477,7 @@ repository comes with a top-level :file:`doc` directory.
While you should not spend to much time thinking about how to format
documentation, here is a helpful list of standard formatters:
-http://sphinx-doc.org/markup/inline.html
+http://sphinx-doc.org/en/stable/markup/inline.html
If you write new functionality for |project|, or fix bugs, feel free to extend
the :file:`CHANGELOG` file. It will be automatically pulled into the
diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index d3d433139b3918ebe25756b2ec513617ee1d0c4c..6964cf96734a79a1c9de4932da5588a9924935da 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Overview: module code — ProMod3 1.1.0 documentation</title>
+ <title>Overview: module code — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,13 +23,15 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -37,22 +39,26 @@
<div class="body" role="main">
<h1>All modules for which code is available</h1>
-<ul><li><a href="AllAtomEnv.html">AllAtomEnv</a></li>
+<ul><li><a href="AllAtomClashScorer.html">AllAtomClashScorer</a></li>
+<li><a href="AllAtomEnv.html">AllAtomEnv</a></li>
<li><a href="AllAtomInteractionScorer.html">AllAtomInteractionScorer</a></li>
<li><a href="AllAtomOverallScorer.html">AllAtomOverallScorer</a></li>
<li><a href="AllAtomPackingScorer.html">AllAtomPackingScorer</a></li>
<li><a href="AllAtomPositions.html">AllAtomPositions</a></li>
<li><a href="AllAtomRelaxer.html">AllAtomRelaxer</a></li>
+<li><a href="AllAtomScorer.html">AllAtomScorer</a></li>
<li><a href="AminoAcidLookup.html">AminoAcidLookup</a></li>
<li><a href="BBDepRotamerLib.html">BBDepRotamerLib</a></li>
<li><a href="BackboneList.html">BackboneList</a></li>
<li><a href="BackboneOverallScorer.html">BackboneOverallScorer</a></li>
<li><a href="BackboneRelaxer.html">BackboneRelaxer</a></li>
<li><a href="BackboneScoreEnv.html">BackboneScoreEnv</a></li>
+<li><a href="BackboneScorer.html">BackboneScorer</a></li>
<li><a href="CBPackingScorer.html">CBPackingScorer</a></li>
<li><a href="CBetaScorer.html">CBetaScorer</a></li>
<li><a href="CCD.html">CCD</a></li>
<li><a href="CCDCloser.html">CCDCloser</a></li>
+<li><a href="ClashScorer.html">ClashScorer</a></li>
<li><a href="DirtyCCDCloser.html">DirtyCCDCloser</a></li>
<li><a href="DiscoContainer.html">DiscoContainer</a></li>
<li><a href="ExponentialCooler.html">ExponentialCooler</a></li>
@@ -66,13 +72,14 @@
<li><a href="FrameResidue.html">FrameResidue</a></li>
<li><a href="FullGapExtender.html">FullGapExtender</a></li>
<li><a href="GapExtender.html">GapExtender</a></li>
+<li><a href="GraphMinimizer.html">GraphMinimizer</a></li>
<li><a href="HBondScorer.html">HBondScorer</a></li>
<li><a href="KIC.html">KIC</a></li>
<li><a href="KICCloser.html">KICCloser</a></li>
-<li><a href="LinearScorer.html">LinearScorer</a></li>
<li><a href="LoopCandidates.html">LoopCandidates</a></li>
<li><a href="MmSystemCreator.html">MmSystemCreator</a></li>
<li><a href="ModellingHandle.html">ModellingHandle</a></li>
+<li><a href="PairwiseScorer.html">PairwiseScorer</a></li>
<li><a href="Particle.html">Particle</a></li>
<li><a href="PhiPsiSampler.html">PhiPsiSampler</a></li>
<li><a href="PsipredPrediction.html">PsipredPrediction</a></li>
@@ -132,9 +139,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -142,11 +146,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/_modules/promod3.html b/doc/html/_modules/promod3.html
index 26f55e3abbf5e32a066e3b2d6749959bc84d1c91..140c70b9d3e7b6edc1001cd57344d3a21c5babd7 100644
--- a/doc/html/_modules/promod3.html
+++ b/doc/html/_modules/promod3.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3 — ProMod3 1.1.0 documentation</title>
+ <title>promod3 — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,14 +23,16 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="Module code" href="index.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -38,22 +40,22 @@
<div class="body" role="main">
<h1>Source code for promod3</h1><div class="highlight"><pre>
-<span class="c"># enable access to loop and modelling via "import promod3"</span>
+<span></span><span class="c1"># enable access to loop and modelling via "import promod3"</span>
<span class="kn">import</span> <span class="nn">promod3.core</span>
<span class="kn">import</span> <span class="nn">promod3.sidechain</span>
<span class="kn">import</span> <span class="nn">promod3.loop</span>
<span class="kn">import</span> <span class="nn">promod3.scoring</span>
<span class="kn">import</span> <span class="nn">promod3.modelling</span>
-<span class="c"># load compounds library</span>
-<span class="c"># That way we do not need to call our scripts with the OST starter and are more</span>
-<span class="c"># flexible.</span>
+<span class="c1"># load compounds library</span>
+<span class="c1"># That way we do not need to call our scripts with the OST starter and are more</span>
+<span class="c1"># flexible.</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">ost</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">conop</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<div class="viewcode-block" id="SetCompoundsChemlib"><a class="viewcode-back" href="../core/setcompoundschemlib.html#promod3.SetCompoundsChemlib">[docs]</a><span class="k">def</span> <span class="nf">SetCompoundsChemlib</span><span class="p">(</span><span class="n">path_to_chemlib</span><span class="o">=</span><span class="s">"/users/staff/bioz/taurielg/GT/Code/ost/build/stage/share/openstructure/compounds.chemlib"</span><span class="p">):</span>
+<div class="viewcode-block" id="SetCompoundsChemlib"><a class="viewcode-back" href="../core/setcompoundschemlib.html#promod3.SetCompoundsChemlib">[docs]</a><span class="k">def</span> <span class="nf">SetCompoundsChemlib</span><span class="p">(</span><span class="n">path_to_chemlib</span><span class="o">=</span><span class="s2">"/home/taurielg/GT/Code/ost/build/stage/share/openstructure/compounds.chemlib"</span><span class="p">):</span>
<span class="sd">"""SetCompoundsChemlib(path_to_chemlib)</span>
<span class="sd"> Load a compounds library. Does not return anything, the library is just</span>
<span class="sd"> enabled globally.</span>
@@ -62,58 +64,58 @@
<span class="sd"> :type path_to_chemlib: :class:`str`</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">path_to_chemlib</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">path_to_chemlib</span><span class="p">):</span>
- <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">"Invalid path to chemlib '"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">path_to_chemlib</span><span class="p">)</span>
- <span class="o">+</span> <span class="s">"' specified!</span><span class="se">\n</span><span class="s">A compounds library must either be "</span>
- <span class="o">+</span> <span class="s">"set at compile-time ('compounds.chemlib' file in "</span>
- <span class="o">+</span> <span class="s">"$OST_ROOT/share or below) or set in OST with "</span>
- <span class="o">+</span> <span class="s">"ost.conop.SetDefaultLib before importing any "</span>
- <span class="o">+</span> <span class="s">"promod3 module!"</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"Invalid path to chemlib '"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">path_to_chemlib</span><span class="p">)</span>
+ <span class="o">+</span> <span class="s2">"' specified!</span><span class="se">\n</span><span class="s2">A compounds library must either be "</span>
+ <span class="o">+</span> <span class="s2">"set at compile-time ('compounds.chemlib' file in "</span>
+ <span class="o">+</span> <span class="s2">"$OST_ROOT/share or below) or set in OST with "</span>
+ <span class="o">+</span> <span class="s2">"ost.conop.SetDefaultLib before importing any "</span>
+ <span class="o">+</span> <span class="s2">"promod3 module!"</span><span class="p">)</span>
<span class="n">compound_lib_path</span> <span class="o">=</span> <span class="n">path_to_chemlib</span>
<span class="n">compound_lib</span> <span class="o">=</span> <span class="n">conop</span><span class="o">.</span><span class="n">CompoundLib</span><span class="o">.</span><span class="n">Load</span><span class="p">(</span><span class="n">compound_lib_path</span><span class="p">)</span>
<span class="n">conop</span><span class="o">.</span><span class="n">SetDefaultLib</span><span class="p">(</span><span class="n">compound_lib</span><span class="p">)</span>
- <span class="n">io</span><span class="o">.</span><span class="n">profiles</span><span class="p">[</span><span class="s">'DEFAULT'</span><span class="p">]</span><span class="o">.</span><span class="n">processor</span> <span class="o">=</span> <span class="n">conop</span><span class="o">.</span><span class="n">RuleBasedProcessor</span><span class="p">(</span><span class="n">compound_lib</span><span class="p">)</span>
-</div>
+ <span class="n">io</span><span class="o">.</span><span class="n">profiles</span><span class="p">[</span><span class="s1">'DEFAULT'</span><span class="p">]</span><span class="o">.</span><span class="n">processor</span> <span class="o">=</span> <span class="n">conop</span><span class="o">.</span><span class="n">RuleBasedProcessor</span><span class="p">(</span><span class="n">compound_lib</span><span class="p">)</span></div>
+
<span class="k">def</span> <span class="nf">GetProMod3SharedDataPath</span><span class="p">():</span>
<span class="sd">"""Get path to the shared data folder. Used for binaries.</span>
<span class="sd"> Returns None if not set.</span>
<span class="sd"> """</span>
- <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s">"PROMOD3_SHARED_DATA_PATH"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s2">"PROMOD3_SHARED_DATA_PATH"</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">SetProMod3SharedDataPath</span><span class="p">(</span><span class="n">path</span><span class="p">):</span>
<span class="sd">"""Set path to the shared data folder. Used for binaries."""</span>
- <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s">"PROMOD3_SHARED_DATA_PATH"</span><span class="p">]</span> <span class="o">=</span> <span class="n">path</span>
+ <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s2">"PROMOD3_SHARED_DATA_PATH"</span><span class="p">]</span> <span class="o">=</span> <span class="n">path</span>
-<span class="c"># check if we already have an OST PrefixPath</span>
+<span class="c1"># check if we already have an OST PrefixPath</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">ost</span><span class="o">.</span><span class="n">GetSharedDataPath</span><span class="p">()</span>
<span class="k">except</span> <span class="ne">RuntimeError</span><span class="p">,</span> <span class="n">rt_err</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">SetPrefixPath</span><span class="p">(</span><span class="s">"/users/staff/bioz/taurielg/GT/Code/ost/build/stage"</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">SetPrefixPath</span><span class="p">(</span><span class="s2">"/home/taurielg/GT/Code/ost/build/stage"</span><span class="p">)</span>
<span class="k">except</span><span class="p">:</span>
<span class="k">raise</span>
-<span class="c"># check if we do have a compounds library</span>
+<span class="c1"># check if we do have a compounds library</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">conop</span><span class="o">.</span><span class="n">GetDefaultLib</span><span class="p">():</span>
<span class="n">SetCompoundsChemlib</span><span class="p">()</span>
-<span class="c"># ensure that PROMOD3_SHARED_DATA_PATH env. var. set and override if needed</span>
+<span class="c1"># ensure that PROMOD3_SHARED_DATA_PATH env. var. set and override if needed</span>
<span class="k">if</span> <span class="n">GetProMod3SharedDataPath</span><span class="p">()</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
- <span class="c"># module_path = PROMOD3_ROOT/lib64/python2.7/site-packages/promod3</span>
+ <span class="c1"># module_path = PROMOD3_ROOT/lib64/python2.7/site-packages/promod3</span>
<span class="n">module_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">__file__</span><span class="p">))</span>
- <span class="c"># get PROMOD3_ROOT</span>
+ <span class="c1"># get PROMOD3_ROOT</span>
<span class="n">promod3_lib</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">module_path</span><span class="p">)))</span>
<span class="n">promod3_root</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">promod3_lib</span><span class="p">)</span>
- <span class="n">SetProMod3SharedDataPath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">promod3_root</span><span class="p">,</span> <span class="s">"share"</span><span class="p">,</span> <span class="s">"promod3"</span><span class="p">))</span>
+ <span class="n">SetProMod3SharedDataPath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">promod3_root</span><span class="p">,</span> <span class="s2">"share"</span><span class="p">,</span> <span class="s2">"promod3"</span><span class="p">))</span>
-<span class="c"># set version</span>
-<span class="n">__version__</span> <span class="o">=</span> <span class="s">"1.1.0"</span>
-<span class="n">__version_extended__</span> <span class="o">=</span> <span class="s">"1.1.0 (release-1.1|ed199a7)"</span>
+<span class="c1"># set version</span>
+<span class="n">__version__</span> <span class="o">=</span> <span class="s2">"1.2.0"</span>
+<span class="n">__version_extended__</span> <span class="o">=</span> <span class="s2">"1.2.0 (release-1.2.0|d086aed)"</span>
-<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s">'SetCompoundsChemlib'</span><span class="p">,</span> <span class="s">'GetProMod3SharedDataPath'</span><span class="p">,</span>
- <span class="s">'SetProMod3SharedDataPath'</span><span class="p">)</span>
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s1">'SetCompoundsChemlib'</span><span class="p">,</span> <span class="s1">'GetProMod3SharedDataPath'</span><span class="p">,</span>
+ <span class="s1">'SetProMod3SharedDataPath'</span><span class="p">)</span>
-<span class="c"># LocalWords: OST os ost conop io SetCompoundsChemlib CHEMLIB param chemlib</span>
-<span class="c"># LocalWords: str SetDefaultLib RuleBasedProcessor PrefixPath RuntimeError</span>
-<span class="c"># LocalWords: GetSharedDataPath SetPrefixPath GetDefaultLib</span>
+<span class="c1"># LocalWords: OST os ost conop io SetCompoundsChemlib CHEMLIB param chemlib</span>
+<span class="c1"># LocalWords: str SetDefaultLib RuleBasedProcessor PrefixPath RuntimeError</span>
+<span class="c1"># LocalWords: GetSharedDataPath SetPrefixPath GetDefaultLib</span>
</pre></div>
</div>
@@ -137,9 +139,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -147,11 +146,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/_modules/promod3/core/helper.html b/doc/html/_modules/promod3/core/helper.html
index cf69dc55340fc739cdb0373cb30c01f8600762f0..2266f1a35bc7f1a3cb8be03cbadf869949896d0b 100644
--- a/doc/html/_modules/promod3/core/helper.html
+++ b/doc/html/_modules/promod3/core/helper.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.core.helper — ProMod3 1.1.0 documentation</title>
+ <title>promod3.core.helper — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,14 +23,16 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../../../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
+ <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -38,7 +40,7 @@
<div class="body" role="main">
<h1>Source code for promod3.core.helper</h1><div class="highlight"><pre>
-<span class="sd">"""</span>
+<span></span><span class="sd">"""</span>
<span class="sd">Uncategorised functions which may come handy at several places.</span>
<span class="sd">"""</span>
@@ -61,8 +63,8 @@
<span class="sd"> :returns: No return value, exits script with value ``exit_status``.</span>
<span class="sd"> '''</span>
<span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
- <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">exit_status</span><span class="p">)</span>
-</div>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">exit_status</span><span class="p">)</span></div>
+
<div class="viewcode-block" id="FileExists"><a class="viewcode-back" href="../../../core/helper.html#promod3.core.helper.FileExists">[docs]</a><span class="k">def</span> <span class="nf">FileExists</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Checks if a file exists, terminates if not. The error message displayed is</span>
@@ -83,9 +85,9 @@
<span class="sd"> is missing.</span>
<span class="sd"> '''</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
- <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file does not exist: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">filename</span><span class="p">),</span>
- <span class="n">exit_status</span><span class="p">)</span>
-</div>
+ <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s1">'</span><span class="si">%s</span><span class="s1"> file does not exist: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">filename</span><span class="p">),</span>
+ <span class="n">exit_status</span><span class="p">)</span></div>
+
<div class="viewcode-block" id="FileGzip"><a class="viewcode-back" href="../../../core/helper.html#promod3.core.helper.FileGzip">[docs]</a><span class="k">def</span> <span class="nf">FileGzip</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">allowed</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> See if a file is gzipped or not. This is basically done by checking for a</span>
@@ -113,14 +115,14 @@
<span class="sd"> '''</span>
<span class="n">_</span><span class="p">,</span> <span class="n">fileext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
<span class="n">is_gz</span> <span class="o">=</span> <span class="bp">False</span>
- <span class="k">if</span> <span class="n">fileext</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">'.gz'</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">fileext</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">'.gz'</span><span class="p">:</span>
<span class="n">is_gz</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">allowed</span><span class="p">:</span>
- <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file in Gzip not supported: </span><span class="si">%s</span><span class="s">. '</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
+ <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s1">'</span><span class="si">%s</span><span class="s1"> file in Gzip not supported: </span><span class="si">%s</span><span class="s1">. '</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
<span class="n">filename</span><span class="p">),</span>
<span class="n">exit_status</span><span class="p">)</span>
- <span class="k">return</span> <span class="n">is_gz</span>
-</div>
+ <span class="k">return</span> <span class="n">is_gz</span></div>
+
<div class="viewcode-block" id="FileExtension"><a class="viewcode-back" href="../../../core/helper.html#promod3.core.helper.FileExtension">[docs]</a><span class="k">def</span> <span class="nf">FileExtension</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">extensions</span><span class="p">,</span> <span class="n">gzip</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Checks a file to carry a known extension given by a list of strings. Since</span>
@@ -158,22 +160,22 @@
<span class="sd"> '''</span>
<span class="n">pfilename</span><span class="p">,</span> <span class="n">fileext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
<span class="n">is_gz</span> <span class="o">=</span> <span class="bp">False</span>
- <span class="k">if</span> <span class="n">fileext</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">'.gz'</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">fileext</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">'.gz'</span><span class="p">:</span>
<span class="n">is_gz</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">pfilename</span><span class="p">,</span> <span class="n">fileext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">pfilename</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">gzip</span><span class="p">:</span>
- <span class="n">extension_string</span> <span class="o">=</span> <span class="s">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
- <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. '</span> <span class="o">%</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
+ <span class="n">extension_string</span> <span class="o">=</span> <span class="s1">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
+ <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s1">'</span><span class="si">%s</span><span class="s1"> file extension not supported: </span><span class="si">%s</span><span class="s1">. '</span> <span class="o">%</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
<span class="n">filename</span><span class="p">)</span><span class="o">+</span>
- <span class="s">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
+ <span class="s1">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
<span class="n">exit_status</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">fileext</span> <span class="o">==</span> <span class="s">''</span><span class="p">:</span>
- <span class="n">extension_string</span> <span class="o">=</span> <span class="s">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">fileext</span> <span class="o">==</span> <span class="s1">''</span><span class="p">:</span>
+ <span class="n">extension_string</span> <span class="o">=</span> <span class="s1">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
<span class="k">if</span> <span class="n">gzip</span><span class="p">:</span>
- <span class="n">extension_string</span> <span class="o">+=</span> <span class="s">', '</span> <span class="o">+</span> <span class="s">'.gz, '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s">'.gz'</span>
- <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. '</span> <span class="o">%</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
+ <span class="n">extension_string</span> <span class="o">+=</span> <span class="s1">', '</span> <span class="o">+</span> <span class="s1">'.gz, '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s1">'.gz'</span>
+ <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s1">'</span><span class="si">%s</span><span class="s1"> file extension not supported: </span><span class="si">%s</span><span class="s1">. '</span> <span class="o">%</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
<span class="n">filename</span><span class="p">)</span><span class="o">+</span>
- <span class="s">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
+ <span class="s1">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
<span class="n">exit_status</span><span class="p">)</span>
<span class="n">fileext</span> <span class="o">=</span> <span class="n">fileext</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
<span class="k">for</span> <span class="n">ext</span> <span class="ow">in</span> <span class="n">extensions</span><span class="p">:</span>
@@ -182,21 +184,21 @@
<span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">pfilename</span><span class="p">),</span> <span class="n">fileext</span><span class="p">,</span> <span class="n">is_gz</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">pfilename</span><span class="p">),</span> <span class="n">fileext</span>
- <span class="n">extension_string</span> <span class="o">=</span> <span class="s">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
+ <span class="n">extension_string</span> <span class="o">=</span> <span class="s1">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
<span class="k">if</span> <span class="n">gzip</span><span class="p">:</span>
- <span class="n">extension_string</span> <span class="o">+=</span> <span class="s">', '</span> <span class="o">+</span> <span class="s">'.gz, '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s">'.gz'</span>
- <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. '</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
+ <span class="n">extension_string</span> <span class="o">+=</span> <span class="s1">', '</span> <span class="o">+</span> <span class="s1">'.gz, '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s1">'.gz'</span>
+ <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s1">'</span><span class="si">%s</span><span class="s1"> file extension not supported: </span><span class="si">%s</span><span class="s1">. '</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
<span class="n">filename</span><span class="p">)</span><span class="o">+</span>
- <span class="s">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
- <span class="n">exit_status</span><span class="p">)</span>
-</div>
+ <span class="s1">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s1">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
+ <span class="n">exit_status</span><span class="p">)</span></div>
+
<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span>
- <span class="s">'MsgErrorAndExit'</span><span class="p">,</span>
- <span class="s">'FileExists'</span><span class="p">,</span>
- <span class="s">'FileExtension'</span><span class="p">,</span>
+ <span class="s1">'MsgErrorAndExit'</span><span class="p">,</span>
+ <span class="s1">'FileExists'</span><span class="p">,</span>
+ <span class="s1">'FileExtension'</span><span class="p">,</span>
<span class="p">)</span>
-<span class="c"># LocalWords: gzipped gz param str gzip bool</span>
+<span class="c1"># LocalWords: gzipped gz param str gzip bool</span>
</pre></div>
</div>
@@ -222,9 +224,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -232,11 +231,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/_modules/promod3/core/pm3argparse.html b/doc/html/_modules/promod3/core/pm3argparse.html
index a7e1be3fbe452bb61a94591e499bba82eefce2f9..e10fff03f913d8b7779021287b59d397b5f58634 100644
--- a/doc/html/_modules/promod3/core/pm3argparse.html
+++ b/doc/html/_modules/promod3/core/pm3argparse.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.core.pm3argparse — ProMod3 1.1.0 documentation</title>
+ <title>promod3.core.pm3argparse — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,14 +23,16 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../../../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
+ <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -38,7 +40,7 @@
<div class="body" role="main">
<h1>Source code for promod3.core.pm3argparse</h1><div class="highlight"><pre>
-<span class="sd">"""</span>
+<span></span><span class="sd">"""</span>
<span class="sd">Extensions for the argparse module.</span>
<span class="sd">"""</span>
@@ -47,9 +49,9 @@
<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">gzip</span>
<span class="kn">import</span> <span class="nn">tempfile</span>
-<span class="c">#try:</span>
-<span class="c"># import ujson as json</span>
-<span class="c">#except ImportError:</span>
+<span class="c1">#try:</span>
+<span class="c1"># import ujson as json</span>
+<span class="c1">#except ImportError:</span>
<span class="kn">import</span> <span class="nn">json</span>
<span class="kn">import</span> <span class="nn">ost</span>
@@ -66,9 +68,9 @@
<span class="n">unzip_str</span> <span class="o">=</span> <span class="n">zip_fh</span><span class="o">.</span><span class="n">read</span><span class="p">()</span>
<span class="n">zip_fh</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
<span class="k">except</span> <span class="ne">IOError</span><span class="p">,</span> <span class="n">ioe</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">msg_prefix</span> <span class="o">+</span> <span class="s">" gzip file '"</span> <span class="o">+</span> <span class="n">filename</span> <span class="o">+</span>
- <span class="s">"' cannot be opened: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">ioe</span><span class="p">),</span> <span class="mi">14</span><span class="p">)</span>
- <span class="n">unzip_file</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">NamedTemporaryFile</span><span class="p">(</span><span class="n">mode</span><span class="o">=</span><span class="s">'w'</span><span class="p">,</span> <span class="n">suffix</span><span class="o">=</span><span class="n">suffix</span><span class="p">)</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">msg_prefix</span> <span class="o">+</span> <span class="s2">" gzip file '"</span> <span class="o">+</span> <span class="n">filename</span> <span class="o">+</span>
+ <span class="s2">"' cannot be opened: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">ioe</span><span class="p">),</span> <span class="mi">14</span><span class="p">)</span>
+ <span class="n">unzip_file</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">NamedTemporaryFile</span><span class="p">(</span><span class="n">mode</span><span class="o">=</span><span class="s1">'w'</span><span class="p">,</span> <span class="n">suffix</span><span class="o">=</span><span class="n">suffix</span><span class="p">)</span>
<span class="n">unzip_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">unzip_str</span><span class="p">)</span>
<span class="n">unzip_file</span><span class="o">.</span><span class="n">flush</span><span class="p">()</span>
<span class="k">return</span> <span class="n">unzip_file</span>
@@ -77,22 +79,22 @@
<span class="sd">'''Check a key/value in a sequence exists and is of certain type.</span>
<span class="sd"> '''</span>
<span class="k">if</span> <span class="n">key_name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">json_aln</span><span class="p">[</span><span class="n">seqtype</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"JSON 'alignmentlist' '</span><span class="si">%s</span><span class="s">' "</span> <span class="o">%</span> <span class="n">seqtype</span><span class="o">+</span>
- <span class="s">"from '</span><span class="si">%s</span><span class="s">' is "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
- <span class="s">"missing the '</span><span class="si">%s</span><span class="s">' key"</span> <span class="o">%</span> <span class="n">key_name</span><span class="p">,</span> <span class="mi">27</span><span class="p">)</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"JSON 'alignmentlist' '</span><span class="si">%s</span><span class="s2">' "</span> <span class="o">%</span> <span class="n">seqtype</span><span class="o">+</span>
+ <span class="s2">"from '</span><span class="si">%s</span><span class="s2">' is "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
+ <span class="s2">"missing the '</span><span class="si">%s</span><span class="s2">' key"</span> <span class="o">%</span> <span class="n">key_name</span><span class="p">,</span> <span class="mi">27</span><span class="p">)</span>
<span class="n">altype</span> <span class="o">=</span> <span class="nb">type</span><span class="p">(</span><span class="n">json_aln</span><span class="p">[</span><span class="n">seqtype</span><span class="p">][</span><span class="n">key_name</span><span class="p">])</span>
<span class="k">if</span> <span class="n">val_type</span> <span class="ow">is</span> <span class="nb">str</span> <span class="ow">or</span> <span class="n">val_type</span> <span class="ow">is</span> <span class="nb">unicode</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">altype</span> <span class="ow">is</span> <span class="nb">unicode</span> <span class="ow">or</span> <span class="n">altype</span> <span class="ow">is</span> <span class="nb">str</span><span class="p">):</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"JSON 'alignmentlist' '</span><span class="si">%s</span><span class="s">' "</span> <span class="o">%</span> <span class="n">seqtype</span><span class="o">+</span>
- <span class="s">"'</span><span class="si">%s</span><span class="s">' from"</span> <span class="o">%</span> <span class="n">key_name</span><span class="o">+</span>
- <span class="s">"'</span><span class="si">%s</span><span class="s">' is not a "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
- <span class="s">"</span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">val_type</span><span class="p">),</span> <span class="mi">28</span><span class="p">)</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"JSON 'alignmentlist' '</span><span class="si">%s</span><span class="s2">' "</span> <span class="o">%</span> <span class="n">seqtype</span><span class="o">+</span>
+ <span class="s2">"'</span><span class="si">%s</span><span class="s2">' from"</span> <span class="o">%</span> <span class="n">key_name</span><span class="o">+</span>
+ <span class="s2">"'</span><span class="si">%s</span><span class="s2">' is not a "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
+ <span class="s2">"</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">val_type</span><span class="p">),</span> <span class="mi">28</span><span class="p">)</span>
<span class="k">elif</span> <span class="ow">not</span> <span class="n">altype</span> <span class="ow">is</span> <span class="n">val_type</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"JSON 'alignmentlist' '</span><span class="si">%s</span><span class="s">' "</span> <span class="o">%</span> <span class="n">seqtype</span><span class="o">+</span>
- <span class="s">"'</span><span class="si">%s</span><span class="s">' from"</span> <span class="o">%</span> <span class="n">key_name</span><span class="o">+</span>
- <span class="s">"'</span><span class="si">%s</span><span class="s">' is not a "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
- <span class="s">"</span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">val_type</span><span class="p">),</span> <span class="mi">28</span><span class="p">)</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"JSON 'alignmentlist' '</span><span class="si">%s</span><span class="s2">' "</span> <span class="o">%</span> <span class="n">seqtype</span><span class="o">+</span>
+ <span class="s2">"'</span><span class="si">%s</span><span class="s2">' from"</span> <span class="o">%</span> <span class="n">key_name</span><span class="o">+</span>
+ <span class="s2">"'</span><span class="si">%s</span><span class="s2">' is not a "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
+ <span class="s2">"</span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">val_type</span><span class="p">),</span> <span class="mi">28</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_GetAlnFromJSON</span><span class="p">(</span><span class="n">json_object</span><span class="p">,</span> <span class="n">json_source</span><span class="p">):</span>
<span class="sd">"""Create alignments from a JSON object.</span>
@@ -100,49 +102,49 @@
<span class="sd"> Iterate the alignments in a JSON object and deliver OST alignments via the</span>
<span class="sd"> yield operator.</span>
<span class="sd"> """</span>
- <span class="c"># alignments are stored via the 'alignmentlist' key</span>
- <span class="k">if</span> <span class="s">'alignmentlist'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">json_object</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"JSON object from '</span><span class="si">%s</span><span class="s">' does not "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
- <span class="s">"provide an 'alignmentlist' key."</span><span class="p">,</span> <span class="mi">21</span><span class="p">)</span>
- <span class="c"># alignments come as lists, to enable hetero oligos</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="nb">type</span><span class="p">(</span><span class="n">json_object</span><span class="p">[</span><span class="s">'alignmentlist'</span><span class="p">])</span> <span class="ow">is</span> <span class="nb">list</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"JSON object from '</span><span class="si">%s</span><span class="s">' does not"</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
- <span class="s">"provide a list behind 'alignmentlist'."</span><span class="p">,</span> <span class="mi">24</span><span class="p">)</span>
- <span class="c"># take the alignments apart, each alignment is a dictionary</span>
- <span class="k">for</span> <span class="n">json_aln</span> <span class="ow">in</span> <span class="n">json_object</span><span class="p">[</span><span class="s">'alignmentlist'</span><span class="p">]:</span>
- <span class="c"># json_aln needs to be a dictionary</span>
+ <span class="c1"># alignments are stored via the 'alignmentlist' key</span>
+ <span class="k">if</span> <span class="s1">'alignmentlist'</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">json_object</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"JSON object from '</span><span class="si">%s</span><span class="s2">' does not "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
+ <span class="s2">"provide an 'alignmentlist' key."</span><span class="p">,</span> <span class="mi">21</span><span class="p">)</span>
+ <span class="c1"># alignments come as lists, to enable hetero oligos</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="nb">type</span><span class="p">(</span><span class="n">json_object</span><span class="p">[</span><span class="s1">'alignmentlist'</span><span class="p">])</span> <span class="ow">is</span> <span class="nb">list</span><span class="p">:</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"JSON object from '</span><span class="si">%s</span><span class="s2">' does not"</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
+ <span class="s2">"provide a list behind 'alignmentlist'."</span><span class="p">,</span> <span class="mi">24</span><span class="p">)</span>
+ <span class="c1"># take the alignments apart, each alignment is a dictionary</span>
+ <span class="k">for</span> <span class="n">json_aln</span> <span class="ow">in</span> <span class="n">json_object</span><span class="p">[</span><span class="s1">'alignmentlist'</span><span class="p">]:</span>
+ <span class="c1"># json_aln needs to be a dictionary</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">type</span><span class="p">(</span><span class="n">json_aln</span><span class="p">)</span> <span class="ow">is</span> <span class="nb">dict</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"JSON 'alignmentlist' member from "</span><span class="o">+</span>
- <span class="s">"'</span><span class="si">%s</span><span class="s">' is not a ' "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
- <span class="s">" dictionary: </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">json_aln</span><span class="p">,</span> <span class="mi">25</span><span class="p">)</span>
- <span class="c"># an alignment has a 'target' and a 'template' dictionary</span>
- <span class="c"># each of them has a 'name' and a 'seqres' pair</span>
- <span class="k">for</span> <span class="n">flav</span> <span class="ow">in</span> <span class="p">[</span><span class="s">'target'</span><span class="p">,</span> <span class="s">'template'</span><span class="p">]:</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"JSON 'alignmentlist' member from "</span><span class="o">+</span>
+ <span class="s2">"'</span><span class="si">%s</span><span class="s2">' is not a ' "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
+ <span class="s2">" dictionary: </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="n">json_aln</span><span class="p">,</span> <span class="mi">25</span><span class="p">)</span>
+ <span class="c1"># an alignment has a 'target' and a 'template' dictionary</span>
+ <span class="c1"># each of them has a 'name' and a 'seqres' pair</span>
+ <span class="k">for</span> <span class="n">flav</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'target'</span><span class="p">,</span> <span class="s1">'template'</span><span class="p">]:</span>
<span class="k">if</span> <span class="n">flav</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">json_aln</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"JSON 'alignmentlist' from "</span><span class="o">+</span>
- <span class="s">"'</span><span class="si">%s</span><span class="s">' does not "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
- <span class="s">"provide a '</span><span class="si">%s</span><span class="s">' key."</span> <span class="o">%</span> <span class="n">flav</span><span class="p">,</span> <span class="mi">22</span><span class="p">)</span>
- <span class="c"># check sequence to be dictionary</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"JSON 'alignmentlist' from "</span><span class="o">+</span>
+ <span class="s2">"'</span><span class="si">%s</span><span class="s2">' does not "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
+ <span class="s2">"provide a '</span><span class="si">%s</span><span class="s2">' key."</span> <span class="o">%</span> <span class="n">flav</span><span class="p">,</span> <span class="mi">22</span><span class="p">)</span>
+ <span class="c1"># check sequence to be dictionary</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">type</span><span class="p">(</span><span class="n">json_aln</span><span class="p">[</span><span class="n">flav</span><span class="p">])</span> <span class="ow">is</span> <span class="nb">dict</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"JSON 'alignmentlist' '</span><span class="si">%s</span><span class="s">' from"</span> <span class="o">%</span> <span class="n">flav</span><span class="o">+</span>
- <span class="s">"'</span><span class="si">%s</span><span class="s">' is not a "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
- <span class="s">"dictionary: </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">json_aln</span><span class="p">[</span><span class="n">flav</span><span class="p">],</span> <span class="mi">26</span><span class="p">)</span>
- <span class="c"># check for keys needed by both sequences:</span>
- <span class="k">for</span> <span class="n">aln_key</span> <span class="ow">in</span> <span class="p">[</span><span class="s">'name'</span><span class="p">,</span> <span class="s">'seqres'</span><span class="p">]:</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"JSON 'alignmentlist' '</span><span class="si">%s</span><span class="s2">' from"</span> <span class="o">%</span> <span class="n">flav</span><span class="o">+</span>
+ <span class="s2">"'</span><span class="si">%s</span><span class="s2">' is not a "</span> <span class="o">%</span> <span class="n">json_source</span><span class="o">+</span>
+ <span class="s2">"dictionary: </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="n">json_aln</span><span class="p">[</span><span class="n">flav</span><span class="p">],</span> <span class="mi">26</span><span class="p">)</span>
+ <span class="c1"># check for keys needed by both sequences:</span>
+ <span class="k">for</span> <span class="n">aln_key</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'name'</span><span class="p">,</span> <span class="s1">'seqres'</span><span class="p">]:</span>
<span class="n">_CheckJSONAlnSeqKeyType</span><span class="p">(</span><span class="n">aln_key</span><span class="p">,</span> <span class="nb">str</span><span class="p">,</span> <span class="n">json_aln</span><span class="p">,</span> <span class="n">flav</span><span class="p">,</span>
<span class="n">json_source</span><span class="p">)</span>
- <span class="n">_CheckJSONAlnSeqKeyType</span><span class="p">(</span><span class="s">'offset'</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="n">json_aln</span><span class="p">,</span> <span class="s">'template'</span><span class="p">,</span>
+ <span class="n">_CheckJSONAlnSeqKeyType</span><span class="p">(</span><span class="s1">'offset'</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="n">json_aln</span><span class="p">,</span> <span class="s1">'template'</span><span class="p">,</span>
<span class="n">json_source</span><span class="p">)</span>
- <span class="c"># create and yield alignment</span>
- <span class="n">trg_name</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">json_aln</span><span class="p">[</span><span class="s">'target'</span><span class="p">][</span><span class="s">'name'</span><span class="p">])</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
- <span class="n">trg_seq</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">json_aln</span><span class="p">[</span><span class="s">'target'</span><span class="p">][</span><span class="s">'seqres'</span><span class="p">])</span>
- <span class="n">tpl_name</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">json_aln</span><span class="p">[</span><span class="s">'template'</span><span class="p">][</span><span class="s">'name'</span><span class="p">])</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
- <span class="n">tpl_seq</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">json_aln</span><span class="p">[</span><span class="s">'template'</span><span class="p">][</span><span class="s">'seqres'</span><span class="p">])</span>
+ <span class="c1"># create and yield alignment</span>
+ <span class="n">trg_name</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">json_aln</span><span class="p">[</span><span class="s1">'target'</span><span class="p">][</span><span class="s1">'name'</span><span class="p">])</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+ <span class="n">trg_seq</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">json_aln</span><span class="p">[</span><span class="s1">'target'</span><span class="p">][</span><span class="s1">'seqres'</span><span class="p">])</span>
+ <span class="n">tpl_name</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">json_aln</span><span class="p">[</span><span class="s1">'template'</span><span class="p">][</span><span class="s1">'name'</span><span class="p">])</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+ <span class="n">tpl_seq</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">json_aln</span><span class="p">[</span><span class="s1">'template'</span><span class="p">][</span><span class="s1">'seqres'</span><span class="p">])</span>
<span class="n">new_aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="n">trg_name</span><span class="p">,</span> <span class="n">trg_seq</span><span class="p">),</span>
<span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="n">tpl_name</span><span class="p">,</span> <span class="n">tpl_seq</span><span class="p">))</span>
- <span class="n">new_aln</span><span class="o">.</span><span class="n">SetSequenceRole</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="s">'TARGET'</span><span class="p">)</span>
- <span class="n">new_aln</span><span class="o">.</span><span class="n">SetSequenceRole</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="s">'TEMPLATE'</span><span class="p">)</span>
- <span class="n">new_aln</span><span class="o">.</span><span class="n">SetSequenceOffset</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">json_aln</span><span class="p">[</span><span class="s">'template'</span><span class="p">][</span><span class="s">'offset'</span><span class="p">])</span>
+ <span class="n">new_aln</span><span class="o">.</span><span class="n">SetSequenceRole</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="s1">'TARGET'</span><span class="p">)</span>
+ <span class="n">new_aln</span><span class="o">.</span><span class="n">SetSequenceRole</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="s1">'TEMPLATE'</span><span class="p">)</span>
+ <span class="n">new_aln</span><span class="o">.</span><span class="n">SetSequenceOffset</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">json_aln</span><span class="p">[</span><span class="s1">'template'</span><span class="p">][</span><span class="s1">'offset'</span><span class="p">])</span>
<span class="k">yield</span> <span class="n">new_aln</span>
<span class="k">def</span> <span class="nf">_GetJSONOBject</span><span class="p">(</span><span class="n">json_input</span><span class="p">):</span>
@@ -158,28 +160,28 @@
<span class="sd"> As returnvalue we only use JSON objects.</span>
<span class="sd"> """</span>
- <span class="k">if</span> <span class="n">json_input</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s">'{'</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s">"JSON Alignment"</span><span class="p">,</span> <span class="mi">12</span><span class="p">,</span> <span class="n">json_input</span><span class="p">)</span>
- <span class="n">is_gz</span> <span class="o">=</span> <span class="n">helper</span><span class="o">.</span><span class="n">FileGzip</span><span class="p">(</span><span class="s">"JSON alignment"</span><span class="p">,</span> <span class="mi">13</span><span class="p">,</span> <span class="n">json_input</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">json_input</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">!=</span> <span class="s1">'{'</span><span class="p">:</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s2">"JSON Alignment"</span><span class="p">,</span> <span class="mi">12</span><span class="p">,</span> <span class="n">json_input</span><span class="p">)</span>
+ <span class="n">is_gz</span> <span class="o">=</span> <span class="n">helper</span><span class="o">.</span><span class="n">FileGzip</span><span class="p">(</span><span class="s2">"JSON alignment"</span><span class="p">,</span> <span class="mi">13</span><span class="p">,</span> <span class="n">json_input</span><span class="p">)</span>
<span class="n">readfile</span> <span class="o">=</span> <span class="n">json_input</span>
<span class="k">if</span> <span class="n">is_gz</span><span class="p">:</span>
- <span class="n">unzip_file</span> <span class="o">=</span> <span class="n">_TmpForGZip</span><span class="p">(</span><span class="n">json_input</span><span class="p">,</span> <span class="s">'.json'</span><span class="p">,</span> <span class="s">"JSON alignment"</span><span class="p">)</span>
+ <span class="n">unzip_file</span> <span class="o">=</span> <span class="n">_TmpForGZip</span><span class="p">(</span><span class="n">json_input</span><span class="p">,</span> <span class="s1">'.json'</span><span class="p">,</span> <span class="s2">"JSON alignment"</span><span class="p">)</span>
<span class="n">readfile</span> <span class="o">=</span> <span class="n">unzip_file</span><span class="o">.</span><span class="n">name</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">jfh</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">readfile</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">IOError</span><span class="p">,</span> <span class="n">ioe</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"'--json' file '</span><span class="si">%s</span><span class="s">' "</span> <span class="o">%</span> <span class="n">json_input</span><span class="o">+</span>
- <span class="s">"can not be processed: </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">ioe</span><span class="o">.</span><span class="n">strerror</span><span class="p">,</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"'--json' file '</span><span class="si">%s</span><span class="s2">' "</span> <span class="o">%</span> <span class="n">json_input</span><span class="o">+</span>
+ <span class="s2">"can not be processed: </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="n">ioe</span><span class="o">.</span><span class="n">strerror</span><span class="p">,</span>
<span class="mi">19</span><span class="p">)</span>
<span class="k">except</span><span class="p">:</span>
<span class="k">raise</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">json_object</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">load</span><span class="p">(</span><span class="n">jfh</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">vae</span><span class="p">:</span>
- <span class="k">if</span> <span class="n">vae</span><span class="o">.</span><span class="n">message</span> <span class="o">==</span> <span class="s">'No JSON object could be decoded'</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"'--json' file '</span><span class="si">%s</span><span class="s">' could "</span> <span class="o">%</span> <span class="n">json_input</span><span class="o">+</span>
- <span class="s">"not be processed into a JSON object, "</span><span class="o">+</span>
- <span class="s">"probably it's empty."</span><span class="p">,</span> <span class="mi">20</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">vae</span><span class="o">.</span><span class="n">message</span> <span class="o">==</span> <span class="s1">'No JSON object could be decoded'</span><span class="p">:</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"'--json' file '</span><span class="si">%s</span><span class="s2">' could "</span> <span class="o">%</span> <span class="n">json_input</span><span class="o">+</span>
+ <span class="s2">"not be processed into a JSON object, "</span><span class="o">+</span>
+ <span class="s2">"probably it's empty."</span><span class="p">,</span> <span class="mi">20</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">raise</span>
<span class="k">except</span><span class="p">:</span>
@@ -189,121 +191,121 @@
<span class="k">try</span><span class="p">:</span>
<span class="n">json_object</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">json_input</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">ValueError</span><span class="p">,</span> <span class="n">vae</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"'--json' string '</span><span class="si">%s</span><span class="s">' "</span> <span class="o">%</span> <span class="n">json_input</span><span class="o">+</span>\
- <span class="s">"could not be decoded: </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="n">vae</span><span class="o">.</span><span class="n">message</span><span class="p">,</span> <span class="mi">23</span><span class="p">)</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"'--json' string '</span><span class="si">%s</span><span class="s2">' "</span> <span class="o">%</span> <span class="n">json_input</span><span class="o">+</span>\
+ <span class="s2">"could not be decoded: </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="n">vae</span><span class="o">.</span><span class="n">message</span><span class="p">,</span> <span class="mi">23</span><span class="p">)</span>
<span class="k">return</span> <span class="n">json_object</span>
<span class="k">def</span> <span class="nf">_FetchAlnFromFile</span><span class="p">(</span><span class="n">seqfile</span><span class="p">,</span> <span class="n">allow_multitemplate</span><span class="p">,</span> <span class="n">format</span><span class="p">):</span>
<span class="sd">"""Read alignment from seqfile and return it."""</span>
- <span class="n">argstr</span> <span class="o">=</span> <span class="s">"'--"</span> <span class="o">+</span> <span class="n">format</span> <span class="o">+</span> <span class="s">" "</span> <span class="o">+</span> <span class="n">seqfile</span> <span class="o">+</span> <span class="s">"'"</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s">"Alignment"</span><span class="p">,</span> <span class="mi">12</span><span class="p">,</span> <span class="n">seqfile</span><span class="p">)</span>
- <span class="c"># checking if alignment file has 'gz' extension</span>
- <span class="n">is_gz</span> <span class="o">=</span> <span class="n">helper</span><span class="o">.</span><span class="n">FileGzip</span><span class="p">(</span><span class="s">"Alignment"</span><span class="p">,</span> <span class="mi">13</span><span class="p">,</span> <span class="n">seqfile</span><span class="p">)</span>
- <span class="c"># loading the alignment, switch for gzip</span>
+ <span class="n">argstr</span> <span class="o">=</span> <span class="s2">"'--"</span> <span class="o">+</span> <span class="n">format</span> <span class="o">+</span> <span class="s2">" "</span> <span class="o">+</span> <span class="n">seqfile</span> <span class="o">+</span> <span class="s2">"'"</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s2">"Alignment"</span><span class="p">,</span> <span class="mi">12</span><span class="p">,</span> <span class="n">seqfile</span><span class="p">)</span>
+ <span class="c1"># checking if alignment file has 'gz' extension</span>
+ <span class="n">is_gz</span> <span class="o">=</span> <span class="n">helper</span><span class="o">.</span><span class="n">FileGzip</span><span class="p">(</span><span class="s2">"Alignment"</span><span class="p">,</span> <span class="mi">13</span><span class="p">,</span> <span class="n">seqfile</span><span class="p">)</span>
+ <span class="c1"># loading the alignment, switch for gzip</span>
<span class="n">readfile</span> <span class="o">=</span> <span class="n">seqfile</span>
<span class="k">if</span> <span class="n">is_gz</span><span class="p">:</span>
- <span class="n">unzip_file</span> <span class="o">=</span> <span class="n">_TmpForGZip</span><span class="p">(</span><span class="n">seqfile</span><span class="p">,</span> <span class="s">'.fas'</span><span class="p">,</span> <span class="s">"Alignment"</span><span class="p">)</span>
+ <span class="n">unzip_file</span> <span class="o">=</span> <span class="n">_TmpForGZip</span><span class="p">(</span><span class="n">seqfile</span><span class="p">,</span> <span class="s1">'.fas'</span><span class="p">,</span> <span class="s2">"Alignment"</span><span class="p">)</span>
<span class="n">readfile</span> <span class="o">=</span> <span class="n">unzip_file</span><span class="o">.</span><span class="n">name</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">aln</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadAlignment</span><span class="p">(</span><span class="n">readfile</span><span class="p">,</span> <span class="n">format</span><span class="o">=</span><span class="n">format</span><span class="p">)</span>
- <span class="k">except</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">exc</span><span class="p">:</span> <span class="c">#pylint: disable=broad-except</span>
- <span class="k">if</span> <span class="n">exc</span><span class="o">.</span><span class="n">message</span> <span class="ow">in</span> <span class="p">[</span><span class="s">'Bad FASTA file: File is empty'</span><span class="p">,</span>
- <span class="s">'Bad CLUSTAL file: File is empty'</span><span class="p">]:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s">" refers to an empty file or "</span> <span class="o">+</span>
- <span class="s">"its in the wrong format."</span><span class="p">,</span> <span class="mi">15</span><span class="p">)</span>
+ <span class="k">except</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">exc</span><span class="p">:</span> <span class="c1">#pylint: disable=broad-except</span>
+ <span class="k">if</span> <span class="n">exc</span><span class="o">.</span><span class="n">message</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'Bad FASTA file: File is empty'</span><span class="p">,</span>
+ <span class="s1">'Bad CLUSTAL file: File is empty'</span><span class="p">]:</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s2">" refers to an empty file or "</span> <span class="o">+</span>
+ <span class="s2">"its in the wrong format."</span><span class="p">,</span> <span class="mi">15</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s">": error when reading alignment "</span><span class="o">+</span>
- <span class="s">"file: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">exc</span><span class="p">),</span> <span class="mi">18</span><span class="p">)</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s2">": error when reading alignment "</span><span class="o">+</span>
+ <span class="s2">"file: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">exc</span><span class="p">),</span> <span class="mi">18</span><span class="p">)</span>
<span class="k">finally</span><span class="p">:</span>
<span class="k">if</span> <span class="n">is_gz</span><span class="p">:</span>
<span class="n">unzip_file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
- <span class="c"># checking the alignment</span>
+ <span class="c1"># checking the alignment</span>
<span class="k">if</span> <span class="n">aln</span><span class="o">.</span><span class="n">GetCount</span><span class="p">()</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s">" points to an alignment with only "</span> <span class="o">+</span>
- <span class="s">"1 sequence."</span><span class="p">,</span> <span class="mi">16</span><span class="p">)</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s2">" points to an alignment with only "</span> <span class="o">+</span>
+ <span class="s2">"1 sequence."</span><span class="p">,</span> <span class="mi">16</span><span class="p">)</span>
<span class="k">if</span> <span class="n">aln</span><span class="o">.</span><span class="n">GetCount</span><span class="p">()</span> <span class="o">></span> <span class="mi">2</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">allow_multitemplate</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s">" points to an alignment with more "</span> <span class="o">+</span>
- <span class="s">"than 2 sequences and we do not allow this."</span><span class="p">,</span> <span class="mi">16</span><span class="p">)</span>
- <span class="c"># identify target</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s2">" points to an alignment with more "</span> <span class="o">+</span>
+ <span class="s2">"than 2 sequences and we do not allow this."</span><span class="p">,</span> <span class="mi">16</span><span class="p">)</span>
+ <span class="c1"># identify target</span>
<span class="n">target_idx</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">sequences</span> <span class="o">=</span> <span class="p">[(</span><span class="n">s</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">strip</span><span class="p">(),</span><span class="n">s</span><span class="o">.</span><span class="n">string</span><span class="p">)</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">aln</span><span class="o">.</span><span class="n">sequences</span><span class="p">]</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">s</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">sequences</span><span class="p">):</span>
- <span class="k">if</span> <span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="p">[</span><span class="s">'trg'</span><span class="p">,</span> <span class="s">'target'</span><span class="p">]:</span>
+ <span class="k">if</span> <span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="p">[</span><span class="s1">'trg'</span><span class="p">,</span> <span class="s1">'target'</span><span class="p">]:</span>
<span class="k">if</span> <span class="n">target_idx</span> <span class="o">>=</span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s">": multiple targets found!"</span><span class="p">,</span> <span class="mi">17</span><span class="p">)</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s2">": multiple targets found!"</span><span class="p">,</span> <span class="mi">17</span><span class="p">)</span>
<span class="n">target_idx</span> <span class="o">=</span> <span class="n">i</span>
- <span class="c"># reshuffle</span>
+ <span class="c1"># reshuffle</span>
<span class="k">if</span> <span class="n">target_idx</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">sequences</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">sequences</span><span class="p">[</span><span class="n">target_idx</span><span class="p">])</span>
<span class="k">del</span> <span class="n">sequences</span><span class="p">[</span><span class="n">target_idx</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span>
- <span class="c"># generate alignment</span>
+ <span class="c1"># generate alignment</span>
<span class="n">new_aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">()</span>
<span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">sequences</span><span class="p">:</span>
<span class="n">new_aln</span><span class="o">.</span><span class="n">AddSequence</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="n">s</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">s</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
- <span class="n">new_aln</span><span class="o">.</span><span class="n">SetSequenceRole</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="s">'TARGET'</span><span class="p">)</span>
+ <span class="n">new_aln</span><span class="o">.</span><span class="n">SetSequenceRole</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="s1">'TARGET'</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">new_aln</span><span class="o">.</span><span class="n">GetCount</span><span class="p">()):</span>
- <span class="n">new_aln</span><span class="o">.</span><span class="n">SetSequenceRole</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="s">'TEMPLATE'</span><span class="p">)</span>
+ <span class="n">new_aln</span><span class="o">.</span><span class="n">SetSequenceRole</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="s1">'TEMPLATE'</span><span class="p">)</span>
<span class="k">return</span> <span class="n">new_aln</span>
<span class="k">def</span> <span class="nf">_LoadPDB</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
<span class="sd">"""Load PDB file from filename and return it."""</span>
- <span class="n">argstr</span> <span class="o">=</span> <span class="s">"'--pdb "</span> <span class="o">+</span> <span class="n">filename</span> <span class="o">+</span> <span class="s">"'"</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s">"PDB Structure"</span><span class="p">,</span> <span class="mi">32</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
+ <span class="n">argstr</span> <span class="o">=</span> <span class="s2">"'--pdb "</span> <span class="o">+</span> <span class="n">filename</span> <span class="o">+</span> <span class="s2">"'"</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s2">"PDB Structure"</span><span class="p">,</span> <span class="mi">32</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">ent</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
- <span class="k">except</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">exc</span><span class="p">:</span> <span class="c">#pylint: disable=broad-except</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s">": failure to parse PDB file: "</span> <span class="o">+</span>
+ <span class="k">except</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">exc</span><span class="p">:</span> <span class="c1">#pylint: disable=broad-except</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s2">": failure to parse PDB file: "</span> <span class="o">+</span>
<span class="nb">str</span><span class="p">(</span><span class="n">exc</span><span class="p">),</span> <span class="mi">33</span><span class="p">)</span>
<span class="k">return</span> <span class="n">ent</span>
<span class="k">def</span> <span class="nf">_LoadEntity</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
<span class="sd">"""Load generic structure file from filename and return it."""</span>
- <span class="n">argstr</span> <span class="o">=</span> <span class="s">"'--entity "</span> <span class="o">+</span> <span class="n">filename</span> <span class="o">+</span> <span class="s">"'"</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s">"Structure"</span><span class="p">,</span> <span class="mi">32</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
+ <span class="n">argstr</span> <span class="o">=</span> <span class="s2">"'--entity "</span> <span class="o">+</span> <span class="n">filename</span> <span class="o">+</span> <span class="s2">"'"</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s2">"Structure"</span><span class="p">,</span> <span class="mi">32</span><span class="p">,</span> <span class="n">filename</span><span class="p">)</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">ent</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadEntity</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
- <span class="k">except</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">exc</span><span class="p">:</span> <span class="c">#pylint: disable=broad-except</span>
- <span class="k">if</span> <span class="n">exc</span><span class="o">.</span><span class="n">message</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">'no suitable entity io handler found'</span><span class="p">):</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s">": not a supported format "</span> <span class="o">+</span>
+ <span class="k">except</span> <span class="ne">Exception</span><span class="p">,</span> <span class="n">exc</span><span class="p">:</span> <span class="c1">#pylint: disable=broad-except</span>
+ <span class="k">if</span> <span class="n">exc</span><span class="o">.</span><span class="n">message</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s1">'no suitable entity io handler found'</span><span class="p">):</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s2">": not a supported format "</span> <span class="o">+</span>
<span class="nb">str</span><span class="p">(</span><span class="n">exc</span><span class="p">),</span> <span class="mi">34</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s">": failure to parse PDB file: "</span> <span class="o">+</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="n">argstr</span> <span class="o">+</span> <span class="s2">": failure to parse PDB file: "</span> <span class="o">+</span>
<span class="nb">str</span><span class="p">(</span><span class="n">exc</span><span class="p">),</span> <span class="mi">33</span><span class="p">)</span>
<span class="k">return</span> <span class="n">ent</span>
<span class="k">def</span> <span class="nf">_GetChains</span><span class="p">(</span><span class="n">structures</span><span class="p">,</span> <span class="n">structure_sources</span><span class="p">):</span>
<span class="sd">"""Get chain id to entity view (single chain) mapping (dict)."""</span>
- <span class="c"># IDs: (file_base = base file name with no extensions)</span>
- <span class="c"># - file_base.chain_name</span>
- <span class="c"># - file_base (iff only one chain in file)</span>
- <span class="c"># - chain_name (iff only one file)</span>
- <span class="c"># - note: single entry with key 'UNIQUE' created if only one chain in total!</span>
+ <span class="c1"># IDs: (file_base = base file name with no extensions)</span>
+ <span class="c1"># - file_base.chain_name</span>
+ <span class="c1"># - file_base (iff only one chain in file)</span>
+ <span class="c1"># - chain_name (iff only one file)</span>
+ <span class="c1"># - note: single entry with key 'UNIQUE' created if only one chain in total!</span>
<span class="n">chain_entities</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
<span class="n">single_file</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">structure_sources</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span>
- <span class="c"># parse structures</span>
+ <span class="c1"># parse structures</span>
<span class="k">for</span> <span class="n">file_name</span><span class="p">,</span> <span class="n">ent</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">structure_sources</span><span class="p">,</span> <span class="n">structures</span><span class="p">):</span>
- <span class="c"># get pure file name with no extension</span>
+ <span class="c1"># get pure file name with no extension</span>
<span class="n">file_base</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">file_name</span><span class="p">)</span>
<span class="n">file_split</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">file_base</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">file_split</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s">'.gz'</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">file_split</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'.gz'</span><span class="p">:</span>
<span class="n">file_base</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">file_split</span><span class="p">[</span><span class="mi">0</span><span class="p">])[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">file_base</span> <span class="o">=</span> <span class="n">file_split</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
- <span class="c"># get chainnames</span>
- <span class="n">prot</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"peptide=True"</span><span class="p">)</span>
+ <span class="c1"># get chainnames</span>
+ <span class="n">prot</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"peptide=True"</span><span class="p">)</span>
<span class="n">single_chain</span> <span class="o">=</span> <span class="n">prot</span><span class="o">.</span><span class="n">chain_count</span> <span class="o">==</span> <span class="mi">1</span>
<span class="n">chain_names</span> <span class="o">=</span> <span class="p">[</span><span class="n">ch</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">ch</span> <span class="ow">in</span> <span class="n">prot</span><span class="o">.</span><span class="n">chains</span><span class="p">]</span>
- <span class="c"># fill dict</span>
+ <span class="c1"># fill dict</span>
<span class="k">if</span> <span class="n">single_file</span> <span class="ow">and</span> <span class="n">single_chain</span><span class="p">:</span>
- <span class="n">chain_entities</span><span class="p">[</span><span class="s">'UNIQUE'</span><span class="p">]</span> <span class="o">=</span> <span class="n">prot</span>
+ <span class="n">chain_entities</span><span class="p">[</span><span class="s1">'UNIQUE'</span><span class="p">]</span> <span class="o">=</span> <span class="n">prot</span>
<span class="k">elif</span> <span class="n">single_chain</span><span class="p">:</span>
- <span class="n">chain_entities</span><span class="p">[</span><span class="n">file_base</span> <span class="o">+</span> <span class="s">'.'</span> <span class="o">+</span> <span class="n">chain_names</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">prot</span>
+ <span class="n">chain_entities</span><span class="p">[</span><span class="n">file_base</span> <span class="o">+</span> <span class="s1">'.'</span> <span class="o">+</span> <span class="n">chain_names</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span> <span class="o">=</span> <span class="n">prot</span>
<span class="n">chain_entities</span><span class="p">[</span><span class="n">file_base</span><span class="p">]</span> <span class="o">=</span> <span class="n">prot</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">for</span> <span class="n">chain_name</span> <span class="ow">in</span> <span class="n">chain_names</span><span class="p">:</span>
- <span class="n">ch_ent</span> <span class="o">=</span> <span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"cname="</span> <span class="o">+</span> <span class="n">chain_name</span><span class="p">)</span>
- <span class="n">chain_entities</span><span class="p">[</span><span class="n">file_base</span> <span class="o">+</span> <span class="s">'.'</span> <span class="o">+</span> <span class="n">chain_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">ch_ent</span>
+ <span class="n">ch_ent</span> <span class="o">=</span> <span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"cname="</span> <span class="o">+</span> <span class="n">chain_name</span><span class="p">)</span>
+ <span class="n">chain_entities</span><span class="p">[</span><span class="n">file_base</span> <span class="o">+</span> <span class="s1">'.'</span> <span class="o">+</span> <span class="n">chain_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">ch_ent</span>
<span class="k">if</span> <span class="n">single_file</span><span class="p">:</span>
<span class="n">chain_entities</span><span class="p">[</span><span class="n">chain_name</span><span class="p">]</span> <span class="o">=</span> <span class="n">ch_ent</span>
<span class="k">return</span> <span class="n">chain_entities</span>
@@ -312,34 +314,34 @@
<span class="sd">"""Attach views to tpl. sequences in aln according to sequence names."""</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">aln</span><span class="o">.</span><span class="n">GetCount</span><span class="p">()):</span>
<span class="n">seq_name</span> <span class="o">=</span> <span class="n">aln</span><span class="o">.</span><span class="n">GetSequence</span><span class="p">(</span><span class="n">i</span><span class="p">)</span><span class="o">.</span><span class="n">GetName</span><span class="p">()</span>
- <span class="c"># extract offset</span>
- <span class="n">my_split</span> <span class="o">=</span> <span class="n">seq_name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'|'</span><span class="p">)</span>
+ <span class="c1"># extract offset</span>
+ <span class="n">my_split</span> <span class="o">=</span> <span class="n">seq_name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'|'</span><span class="p">)</span>
<span class="n">tpl_id</span> <span class="o">=</span> <span class="n">my_split</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">my_split</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span> <span class="ow">and</span> <span class="n">my_split</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">isdigit</span><span class="p">():</span>
- <span class="c"># set offset</span>
+ <span class="c1"># set offset</span>
<span class="n">tpl_offset</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">my_split</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">())</span>
- <span class="c"># mismatch with existing one?</span>
+ <span class="c1"># mismatch with existing one?</span>
<span class="n">old_offset</span> <span class="o">=</span> <span class="n">aln</span><span class="o">.</span><span class="n">GetSequenceOffset</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
<span class="k">if</span> <span class="n">old_offset</span> <span class="o">></span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">old_offset</span> <span class="o">!=</span> <span class="n">tpl_offset</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"Inconsistent offsets between seq. name"</span><span class="o">+</span>
- <span class="s">" and seq. in alignment for "</span> <span class="o">+</span> <span class="n">seq_name</span><span class="p">,</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"Inconsistent offsets between seq. name"</span><span class="o">+</span>
+ <span class="s2">" and seq. in alignment for "</span> <span class="o">+</span> <span class="n">seq_name</span><span class="p">,</span>
<span class="mi">42</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">aln</span><span class="o">.</span><span class="n">SetSequenceOffset</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">tpl_offset</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">my_split</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">my_split</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">isdigit</span><span class="p">():</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"Non-integer offset defined in seq. name "</span><span class="o">+</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"Non-integer offset defined in seq. name "</span><span class="o">+</span>
<span class="n">seq_name</span><span class="p">,</span> <span class="mi">43</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">my_split</span><span class="p">)</span> <span class="o">></span> <span class="mi">2</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"Too many '|' in seq. name "</span> <span class="o">+</span> <span class="n">seq_name</span><span class="p">,</span> <span class="mi">44</span><span class="p">)</span>
- <span class="c"># identify chain and attach view</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"Too many '|' in seq. name "</span> <span class="o">+</span> <span class="n">seq_name</span><span class="p">,</span> <span class="mi">44</span><span class="p">)</span>
+ <span class="c1"># identify chain and attach view</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">chain_entities</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
- <span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">chain_entities</span><span class="p">[</span><span class="s">'UNIQUE'</span><span class="p">]</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
+ <span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">chain_entities</span><span class="p">[</span><span class="s1">'UNIQUE'</span><span class="p">]</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
<span class="k">elif</span> <span class="n">chain_entities</span><span class="o">.</span><span class="n">has_key</span><span class="p">(</span><span class="n">tpl_id</span><span class="p">):</span>
<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">chain_entities</span><span class="p">[</span><span class="n">tpl_id</span><span class="p">]</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"Could not find chain with ID "</span> <span class="o">+</span> <span class="n">tpl_id</span> <span class="o">+</span>
- <span class="s">" (should be <FILE>.<CHAIN>) to attach to"</span><span class="o">+</span>
- <span class="s">" sequence named "</span> <span class="o">+</span> <span class="n">seq_name</span><span class="p">,</span> <span class="mi">45</span><span class="p">)</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"Could not find chain with ID "</span> <span class="o">+</span> <span class="n">tpl_id</span> <span class="o">+</span>
+ <span class="s2">" (should be <FILE>.<CHAIN>) to attach to"</span><span class="o">+</span>
+ <span class="s2">" sequence named "</span> <span class="o">+</span> <span class="n">seq_name</span><span class="p">,</span> <span class="mi">45</span><span class="p">)</span>
<div class="viewcode-block" id="PM3ArgumentParser"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser">[docs]</a><span class="k">class</span> <span class="nc">PM3ArgumentParser</span><span class="p">(</span><span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">):</span>
<span class="sd">"""</span>
@@ -385,10 +387,10 @@
<span class="n">formatter_class</span><span class="o">=</span>\
<span class="n">argparse</span><span class="o">.</span><span class="n">RawDescriptionHelpFormatter</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">action</span> <span class="o">=</span> <span class="n">action</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">activate</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span>
-</div>
+ <span class="bp">self</span><span class="o">.</span><span class="n">activate</span> <span class="o">=</span> <span class="nb">set</span><span class="p">()</span></div>
+
<span class="k">def</span> <span class="nf">_print_message</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="nb">file</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
- <span class="c">#pylint: disable=redefined-builtin</span>
+ <span class="c1">#pylint: disable=redefined-builtin</span>
<span class="sd">"""</span>
<span class="sd"> This is like a welcome message to the "country of bad style"... we are</span>
<span class="sd"> overwriting a "_" function from the parent-class. Those guys should not</span>
@@ -397,7 +399,7 @@
<span class="sd"> """</span>
<span class="k">if</span> <span class="n">message</span><span class="p">:</span>
<span class="n">no_nl_msg</span> <span class="o">=</span> <span class="n">message</span>
- <span class="k">if</span> <span class="n">message</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s">'</span><span class="se">\n</span><span class="s">'</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">message</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'</span><span class="se">\n</span><span class="s1">'</span><span class="p">:</span>
<span class="n">no_nl_msg</span> <span class="o">=</span> <span class="n">message</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="k">if</span> <span class="nb">file</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> <span class="nb">file</span> <span class="ow">is</span> <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="p">:</span>
<span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="n">no_nl_msg</span><span class="p">)</span>
@@ -424,8 +426,8 @@
<span class="bp">self</span><span class="o">.</span><span class="n">parse_args</span><span class="p">(</span><span class="n">args</span><span class="o">=</span><span class="n">args</span><span class="p">,</span> <span class="n">namespace</span><span class="o">=</span><span class="n">opts</span><span class="p">)</span>
<span class="n">opts</span><span class="o">.</span><span class="n">PostProcess</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="p">)</span>
- <span class="k">return</span> <span class="n">opts</span>
-</div>
+ <span class="k">return</span> <span class="n">opts</span></div>
+
<div class="viewcode-block" id="PM3ArgumentParser.AssembleParser"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AssembleParser">[docs]</a> <span class="k">def</span> <span class="nf">AssembleParser</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> When adding options via the :meth:`Add*` methods, call this after you</span>
@@ -434,11 +436,11 @@
<span class="sd"> :meth:`AssembleParser` will put everything in place, in the right order</span>
<span class="sd"> and with the right constraints.</span>
<span class="sd"> """</span>
- <span class="k">if</span> <span class="s">'ALIGNMENT'</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="p">:</span>
+ <span class="k">if</span> <span class="s1">'ALIGNMENT'</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_AssembleAlignment</span><span class="p">()</span>
- <span class="k">if</span> <span class="s">'STRUCTURE'</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">_AssembleStructure</span><span class="p">()</span>
-</div>
+ <span class="k">if</span> <span class="s1">'STRUCTURE'</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">_AssembleStructure</span><span class="p">()</span></div>
+
<div class="viewcode-block" id="PM3ArgumentParser.AddAlignment"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment">[docs]</a> <span class="k">def</span> <span class="nf">AddAlignment</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">allow_multitemplate</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">"""Commandline options for alignments.</span>
@@ -507,10 +509,10 @@
<span class="sd"> * 28 - JSON object 'alignmentlist' 'target'/'template' has a value of</span>
<span class="sd"> wrong type</span>
<span class="sd"> """</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s">'ALIGNMENT'</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s1">'ALIGNMENT'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">allow_multitemplate</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s">'ALLOW_MULTITEMPLATE'</span><span class="p">)</span>
-</div>
+ <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s1">'ALLOW_MULTITEMPLATE'</span><span class="p">)</span></div>
+
<div class="viewcode-block" id="PM3ArgumentParser.AddStructure"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.AddStructure">[docs]</a> <span class="k">def</span> <span class="nf">AddStructure</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">attach_views</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">"""Commandline options for structures.</span>
@@ -568,52 +570,52 @@
<span class="sd"> * 44 - too many "|" in seq. name</span>
<span class="sd"> * 45 - chain to attach to sequence could not be identified</span>
<span class="sd"> """</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s">'STRUCTURE'</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s1">'STRUCTURE'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">attach_views</span><span class="p">:</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s">'ATTACH_VIEWS'</span><span class="p">)</span>
-</div>
+ <span class="bp">self</span><span class="o">.</span><span class="n">activate</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s1">'ATTACH_VIEWS'</span><span class="p">)</span></div>
+
<span class="k">def</span> <span class="nf">_AssembleAlignment</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""Actually add alignment arguments/options."""</span>
<span class="n">aln_grp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_mutually_exclusive_group</span><span class="p">(</span><span class="n">required</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
- <span class="c"># fasta input</span>
- <span class="n">aln_grp</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s">'-f'</span><span class="p">,</span> <span class="s">'--fasta'</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="p">(</span><span class="s">'<FILE>'</span><span class="p">),</span>
- <span class="n">help</span><span class="o">=</span><span class="s">'Target-template alignment in FASTA format. '</span><span class="o">+</span>
- <span class="s">'Target sequence is either named "trg" or '</span><span class="o">+</span>
- <span class="s">'"target" or the first sequence is used. '</span><span class="o">+</span>
- <span class="s">'File can be plain or gzipped.'</span><span class="p">,</span>
- <span class="n">action</span><span class="o">=</span><span class="s">'append'</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span>
- <span class="c"># clustal input</span>
- <span class="n">aln_grp</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s">'-c'</span><span class="p">,</span> <span class="s">'--clustal'</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="p">(</span><span class="s">'<FILE>'</span><span class="p">),</span>
- <span class="n">help</span><span class="o">=</span><span class="s">'Target-template alignment in CLUSTAL format. '</span><span class="o">+</span>
- <span class="s">'Target sequence is either named "trg" or '</span><span class="o">+</span>
- <span class="s">'"target" or the first sequence is used. '</span><span class="o">+</span>
- <span class="s">'File can be plain or gzipped.'</span><span class="p">,</span>
- <span class="n">action</span><span class="o">=</span><span class="s">'append'</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span>
- <span class="c"># JSON input</span>
- <span class="n">aln_grp</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s">'-j'</span><span class="p">,</span> <span class="s">'--json'</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="s">'<OBJECT>|<FILE>'</span><span class="p">,</span>
- <span class="n">help</span><span class="o">=</span><span class="s">'Alignments provided as JSON file/object. '</span><span class="o">+</span>
- <span class="s">'File can be plain or gzipped.'</span><span class="p">,</span>
- <span class="n">action</span><span class="o">=</span><span class="s">'append'</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span>
+ <span class="c1"># fasta input</span>
+ <span class="n">aln_grp</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-f'</span><span class="p">,</span> <span class="s1">'--fasta'</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="p">(</span><span class="s1">'<FILE>'</span><span class="p">),</span>
+ <span class="n">help</span><span class="o">=</span><span class="s1">'Target-template alignment in FASTA format. '</span><span class="o">+</span>
+ <span class="s1">'Target sequence is either named "trg" or '</span><span class="o">+</span>
+ <span class="s1">'"target" or the first sequence is used. '</span><span class="o">+</span>
+ <span class="s1">'File can be plain or gzipped.'</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span>
+ <span class="c1"># clustal input</span>
+ <span class="n">aln_grp</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-c'</span><span class="p">,</span> <span class="s1">'--clustal'</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="p">(</span><span class="s1">'<FILE>'</span><span class="p">),</span>
+ <span class="n">help</span><span class="o">=</span><span class="s1">'Target-template alignment in CLUSTAL format. '</span><span class="o">+</span>
+ <span class="s1">'Target sequence is either named "trg" or '</span><span class="o">+</span>
+ <span class="s1">'"target" or the first sequence is used. '</span><span class="o">+</span>
+ <span class="s1">'File can be plain or gzipped.'</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span>
+ <span class="c1"># JSON input</span>
+ <span class="n">aln_grp</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-j'</span><span class="p">,</span> <span class="s1">'--json'</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="s1">'<OBJECT>|<FILE>'</span><span class="p">,</span>
+ <span class="n">help</span><span class="o">=</span><span class="s1">'Alignments provided as JSON file/object. '</span><span class="o">+</span>
+ <span class="s1">'File can be plain or gzipped.'</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span>
<span class="k">def</span> <span class="nf">_AssembleStructure</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""Actually add structure arguments/options."""</span>
<span class="n">aln_grp</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">add_mutually_exclusive_group</span><span class="p">(</span><span class="n">required</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
- <span class="c"># pdb input</span>
- <span class="n">aln_grp</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s">'-p'</span><span class="p">,</span> <span class="s">'--pdb'</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="p">(</span><span class="s">'<FILE>'</span><span class="p">),</span>
- <span class="n">help</span><span class="o">=</span><span class="s">'Structure in PDB format. '</span><span class="o">+</span>
- <span class="s">'File can be plain or gzipped.'</span><span class="p">,</span>
- <span class="n">action</span><span class="o">=</span><span class="s">'append'</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span>
- <span class="c"># any OST entity</span>
- <span class="n">aln_grp</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s">'-e'</span><span class="p">,</span> <span class="s">'--entity'</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="p">(</span><span class="s">'<FILE>'</span><span class="p">),</span>
- <span class="n">help</span><span class="o">=</span><span class="s">"Structure in any format readable by OST's "</span><span class="o">+</span>
- <span class="s">"io.LoadEntity method. Format is chosen by file "</span><span class="o">+</span>
- <span class="s">"ending. Recognized File Extensions: .ent, .pdb, "</span><span class="o">+</span>
- <span class="s">".ent.gz, .pdb.gz, .cif, .cif.gz."</span><span class="p">,</span>
- <span class="n">action</span><span class="o">=</span><span class="s">'append'</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span>
-</div>
+ <span class="c1"># pdb input</span>
+ <span class="n">aln_grp</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-p'</span><span class="p">,</span> <span class="s1">'--pdb'</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="p">(</span><span class="s1">'<FILE>'</span><span class="p">),</span>
+ <span class="n">help</span><span class="o">=</span><span class="s1">'Structure in PDB format. '</span><span class="o">+</span>
+ <span class="s1">'File can be plain or gzipped.'</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span>
+ <span class="c1"># any OST entity</span>
+ <span class="n">aln_grp</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-e'</span><span class="p">,</span> <span class="s1">'--entity'</span><span class="p">,</span> <span class="n">metavar</span><span class="o">=</span><span class="p">(</span><span class="s1">'<FILE>'</span><span class="p">),</span>
+ <span class="n">help</span><span class="o">=</span><span class="s2">"Structure in any format readable by OST's "</span><span class="o">+</span>
+ <span class="s2">"io.LoadEntity method. Format is chosen by file "</span><span class="o">+</span>
+ <span class="s2">"ending. Recognized File Extensions: .ent, .pdb, "</span><span class="o">+</span>
+ <span class="s2">".ent.gz, .pdb.gz, .cif, .cif.gz."</span><span class="p">,</span>
+ <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">default</span><span class="o">=</span><span class="nb">list</span><span class="p">())</span></div>
+
<span class="k">class</span> <span class="nc">PM3OptionsNamespace</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
- <span class="c"># class will grow, so for the moment pylint is ignored</span>
- <span class="c">#pylint: disable=too-few-public-methods</span>
+ <span class="c1"># class will grow, so for the moment pylint is ignored</span>
+ <span class="c1">#pylint: disable=too-few-public-methods</span>
<span class="sd">"""Output of :meth:`PM3ArgumentParser.Parse`.</span>
<span class="sd"> Like output of :meth:`argparse.ArgumentParser.parse_args` with additional</span>
@@ -624,31 +626,31 @@
<span class="k">def</span> <span class="nf">PostProcess</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">activated</span><span class="p">):</span>
<span class="sd">"""Post processing of activated option packs."""</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">allow_multitemplate</span> <span class="o">=</span> <span class="s">'ALLOW_MULTITEMPLATE'</span> <span class="ow">in</span> <span class="n">activated</span>
- <span class="k">if</span> <span class="s">'ALIGNMENT'</span> <span class="ow">in</span> <span class="n">activated</span><span class="p">:</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">allow_multitemplate</span> <span class="o">=</span> <span class="s1">'ALLOW_MULTITEMPLATE'</span> <span class="ow">in</span> <span class="n">activated</span>
+ <span class="k">if</span> <span class="s1">'ALIGNMENT'</span> <span class="ow">in</span> <span class="n">activated</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_PostProcessAlignment</span><span class="p">()</span>
- <span class="k">if</span> <span class="s">'STRUCTURE'</span> <span class="ow">in</span> <span class="n">activated</span><span class="p">:</span>
+ <span class="k">if</span> <span class="s1">'STRUCTURE'</span> <span class="ow">in</span> <span class="n">activated</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_PostProcessStructure</span><span class="p">()</span>
- <span class="k">if</span> <span class="s">'ATTACH_VIEWS'</span> <span class="ow">in</span> <span class="n">activated</span><span class="p">:</span>
+ <span class="k">if</span> <span class="s1">'ATTACH_VIEWS'</span> <span class="ow">in</span> <span class="n">activated</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_AttachViews</span><span class="p">()</span>
<span class="k">def</span> <span class="nf">_PostProcessAlignment</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
- <span class="c">#pylint: disable=no-member</span>
- <span class="c">#pylint: disable=attribute-defined-outside-init</span>
+ <span class="c1">#pylint: disable=no-member</span>
+ <span class="c1">#pylint: disable=attribute-defined-outside-init</span>
<span class="sd">"""Get alignments from command line input."""</span>
<span class="bp">self</span><span class="o">.</span><span class="n">aln_sources</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">alignments</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">AlignmentList</span><span class="p">()</span>
- <span class="c"># parse fasta files</span>
+ <span class="c1"># parse fasta files</span>
<span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">fasta</span><span class="p">:</span>
- <span class="n">new_aln</span> <span class="o">=</span> <span class="n">_FetchAlnFromFile</span><span class="p">(</span><span class="n">src</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">allow_multitemplate</span><span class="p">,</span> <span class="s">"fasta"</span><span class="p">)</span>
+ <span class="n">new_aln</span> <span class="o">=</span> <span class="n">_FetchAlnFromFile</span><span class="p">(</span><span class="n">src</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">allow_multitemplate</span><span class="p">,</span> <span class="s2">"fasta"</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">alignments</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">new_aln</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">aln_sources</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">src</span><span class="p">)</span>
- <span class="c"># parse clustal files</span>
+ <span class="c1"># parse clustal files</span>
<span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">clustal</span><span class="p">:</span>
- <span class="n">new_aln</span> <span class="o">=</span> <span class="n">_FetchAlnFromFile</span><span class="p">(</span><span class="n">src</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">allow_multitemplate</span><span class="p">,</span> <span class="s">"clustal"</span><span class="p">)</span>
+ <span class="n">new_aln</span> <span class="o">=</span> <span class="n">_FetchAlnFromFile</span><span class="p">(</span><span class="n">src</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">allow_multitemplate</span><span class="p">,</span> <span class="s2">"clustal"</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">alignments</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">new_aln</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">aln_sources</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">src</span><span class="p">)</span>
- <span class="c"># parse JSON input</span>
+ <span class="c1"># parse JSON input</span>
<span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">json</span><span class="p">:</span>
<span class="n">json_obj</span> <span class="o">=</span> <span class="n">_GetJSONOBject</span><span class="p">(</span><span class="n">src</span><span class="p">)</span>
<span class="k">for</span> <span class="n">aln</span> <span class="ow">in</span> <span class="n">_GetAlnFromJSON</span><span class="p">(</span><span class="n">json_obj</span><span class="p">,</span> <span class="n">src</span><span class="p">):</span>
@@ -656,41 +658,41 @@
<span class="bp">self</span><span class="o">.</span><span class="n">aln_sources</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">src</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_PostProcessStructure</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
- <span class="c">#pylint: disable=attribute-defined-outside-init</span>
+ <span class="c1">#pylint: disable=attribute-defined-outside-init</span>
<span class="sd">"""Get structures from command line input."""</span>
<span class="bp">self</span><span class="o">.</span><span class="n">structures</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="bp">self</span><span class="o">.</span><span class="n">structure_sources</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
- <span class="c"># parse pdb files</span>
+ <span class="c1"># parse pdb files</span>
<span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">pdb</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">structures</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_LoadPDB</span><span class="p">(</span><span class="n">src</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">structure_sources</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">src</span><span class="p">)</span>
- <span class="c"># parse generic structures</span>
+ <span class="c1"># parse generic structures</span>
<span class="k">for</span> <span class="n">src</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">entity</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">structures</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">_LoadEntity</span><span class="p">(</span><span class="n">src</span><span class="p">))</span>
<span class="bp">self</span><span class="o">.</span><span class="n">structure_sources</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">src</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_AttachViews</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""Attach views to tpl. sequences according to sequence names."""</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">'structures'</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s">'alignments'</span><span class="p">)):</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"Need to have structures and alignments to "</span><span class="o">+</span>
- <span class="s">"attach views."</span><span class="p">,</span> <span class="mi">41</span><span class="p">)</span>
- <span class="c"># get chain id to entity view (single chain) mapping (dict)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">'structures'</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">hasattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="s1">'alignments'</span><span class="p">)):</span>
+ <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"Need to have structures and alignments to "</span><span class="o">+</span>
+ <span class="s2">"attach views."</span><span class="p">,</span> <span class="mi">41</span><span class="p">)</span>
+ <span class="c1"># get chain id to entity view (single chain) mapping (dict)</span>
<span class="n">chain_entities</span> <span class="o">=</span> <span class="n">_GetChains</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structures</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_sources</span><span class="p">)</span>
- <span class="c"># go through all templates in all alignments</span>
+ <span class="c1"># go through all templates in all alignments</span>
<span class="k">for</span> <span class="n">aln</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">alignments</span><span class="p">:</span>
<span class="n">_AttachViewsToAln</span><span class="p">(</span><span class="n">aln</span><span class="p">,</span> <span class="n">chain_entities</span><span class="p">)</span>
-<span class="c"># LocalWords: param attr prog argparse ArgumentParser bool sys os init str</span>
-<span class="c"># LocalWords: progattr descattr argpinit argv formatter meth args namespace</span>
-<span class="c"># LocalWords: ArgumentDefaultsHelpFormatter sysargv AssembleParser fasta io</span>
-<span class="c"># LocalWords: metavar trg tpl FastA gzip tempfile ost promod aln stderr src</span>
-<span class="c"># LocalWords: AssembleTrgTplAln CreateSequence SetSequenceOffset LogError</span>
-<span class="c"># LocalWords: LogScript OptionsNamespace PostProcess AssembleAlignment JSON</span>
-<span class="c"># LocalWords: AddAlignment AlignmentList SEQNAME whitespaces nargs trgname</span>
-<span class="c"># LocalWords: PostProcessAlignment startswith seqfile elif MsgErrorAndExit</span>
-<span class="c"># LocalWords: len FileExists gz FileGzip readfile fh NamedTemporaryFile fas</span>
-<span class="c"># LocalWords: LoadAlignment exc GetCount fst GetSequence snd</span>
+<span class="c1"># LocalWords: param attr prog argparse ArgumentParser bool sys os init str</span>
+<span class="c1"># LocalWords: progattr descattr argpinit argv formatter meth args namespace</span>
+<span class="c1"># LocalWords: ArgumentDefaultsHelpFormatter sysargv AssembleParser fasta io</span>
+<span class="c1"># LocalWords: metavar trg tpl FastA gzip tempfile ost promod aln stderr src</span>
+<span class="c1"># LocalWords: AssembleTrgTplAln CreateSequence SetSequenceOffset LogError</span>
+<span class="c1"># LocalWords: LogScript OptionsNamespace PostProcess AssembleAlignment JSON</span>
+<span class="c1"># LocalWords: AddAlignment AlignmentList SEQNAME whitespaces nargs trgname</span>
+<span class="c1"># LocalWords: PostProcessAlignment startswith seqfile elif MsgErrorAndExit</span>
+<span class="c1"># LocalWords: len FileExists gz FileGzip readfile fh NamedTemporaryFile fas</span>
+<span class="c1"># LocalWords: LoadAlignment exc GetCount fst GetSequence snd</span>
</pre></div>
</div>
@@ -716,9 +718,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -726,11 +725,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/_modules/promod3/modelling/_closegaps.html b/doc/html/_modules/promod3/modelling/_closegaps.html
index fa180db91e0932f68fa4b7ad39facb3667f5385f..85c8c033bdc62ac51dc8c0529b0e2ca2ad5f1f0f 100644
--- a/doc/html/_modules/promod3/modelling/_closegaps.html
+++ b/doc/html/_modules/promod3/modelling/_closegaps.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._closegaps — ProMod3 1.1.0 documentation</title>
+ <title>promod3.modelling._closegaps — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,14 +23,16 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../../../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
+ <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -38,90 +40,95 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._closegaps</h1><div class="highlight"><pre>
-<span class="sd">'''High-level functionality for modelling module to close gaps. Added in the</span>
+<span></span><span class="sd">'''High-level functionality for modelling module to close gaps. Added in the</span>
<span class="sd">__init__.py file. To be used directly by passing a ModellingHandle instance</span>
<span class="sd">as argument.</span>
<span class="sd">'''</span>
-<span class="c"># internal</span>
+<span class="c1"># internal</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">core</span><span class="p">,</span> <span class="n">scoring</span>
<span class="kn">from</span> <span class="nn">_modelling</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">_ring_punches</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">_reconstruct_sidechains</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="c"># external</span>
+<span class="c1"># external</span>
<span class="kn">import</span> <span class="nn">ost</span>
<span class="kn">import</span> <span class="nn">sys</span>
-<span class="c">###############################################################################</span>
-<span class="c"># loop candidate selection setup</span>
+<span class="c1">###############################################################################</span>
+<span class="c1"># loop candidate selection setup</span>
<span class="k">def</span> <span class="nf">_GetBestLC</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">loop_candidates</span><span class="p">,</span> <span class="n">start_resnum</span><span class="p">,</span> <span class="n">chain_idx</span><span class="p">,</span>
- <span class="n">db_scores</span><span class="p">,</span> <span class="n">max_num_all_atom</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
- <span class="c"># returns (min_idx, min_score)</span>
+ <span class="n">db_scores</span><span class="p">,</span> <span class="n">max_num_all_atom</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">length_dep_weights</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
+ <span class="c1"># returns (min_idx, min_score)</span>
- <span class="c"># dummy check</span>
+ <span class="c1"># dummy check</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">loop_candidates</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
- <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">"Need at least 1 candidate to choose from!"</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"Need at least 1 candidate to choose from!"</span><span class="p">)</span>
- <span class="c"># setup weights</span>
+ <span class="c1"># setup weights</span>
<span class="n">with_db</span> <span class="o">=</span> <span class="p">(</span><span class="ow">not</span> <span class="n">db_scores</span><span class="o">.</span><span class="n">IsEmpty</span><span class="p">())</span>
<span class="n">with_aa</span> <span class="o">=</span> <span class="p">(</span><span class="n">max_num_all_atom</span> <span class="o">></span> <span class="mi">0</span><span class="p">)</span>
- <span class="n">weights</span> <span class="o">=</span> <span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetWeights</span><span class="p">(</span><span class="n">with_db</span><span class="p">,</span> <span class="n">with_aa</span><span class="p">)</span>
+ <span class="n">weights</span> <span class="o">=</span> <span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetWeights</span><span class="p">(</span><span class="n">with_db</span><span class="p">,</span> <span class="n">with_aa</span><span class="p">,</span>
+ <span class="n">length_dep_weights</span><span class="p">,</span>
+ <span class="nb">len</span><span class="p">(</span><span class="n">loop_candidates</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
- <span class="c"># setup all scores object (we collect needed scores there)</span>
- <span class="n">all_scores</span> <span class="o">=</span> <span class="n">db_scores</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span> <span class="c"># copy to avoid changing db_scores</span>
+ <span class="c1"># setup all scores object (we collect needed scores there)</span>
+ <span class="n">all_scores</span> <span class="o">=</span> <span class="n">db_scores</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span> <span class="c1"># copy to avoid changing db_scores</span>
- <span class="c"># add backbone scores</span>
- <span class="n">loop_candidates</span><span class="o">.</span><span class="n">CalculateBackboneScores</span><span class="p">(</span><span class="n">all_scores</span><span class="p">,</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer</span><span class="p">,</span>
+ <span class="c1"># add backbone scores</span>
+ <span class="n">loop_candidates</span><span class="o">.</span><span class="n">CalculateBackboneScores</span><span class="p">(</span><span class="n">all_scores</span><span class="p">,</span> <span class="n">mhandle</span><span class="p">,</span>
<span class="n">start_resnum</span><span class="p">,</span> <span class="n">chain_idx</span><span class="p">)</span>
- <span class="c"># add all atom scores?</span>
+ <span class="c1"># add all atom scores?</span>
<span class="k">if</span> <span class="n">with_aa</span><span class="p">:</span>
- <span class="c"># get best ones based on previous scores</span>
- <span class="n">non_aa_weights</span> <span class="o">=</span> <span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetWeights</span><span class="p">(</span><span class="n">with_db</span><span class="p">,</span> <span class="bp">False</span><span class="p">)</span>
+ <span class="c1"># get best ones based on previous scores</span>
+ <span class="n">non_aa_weights</span> <span class="o">=</span> <span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetWeights</span><span class="p">(</span><span class="n">with_db</span><span class="p">,</span> <span class="bp">False</span><span class="p">,</span>
+ <span class="n">length_dep_weights</span><span class="p">,</span>
+ <span class="nb">len</span><span class="p">(</span><span class="n">loop_candidates</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
+
<span class="n">non_aa_scores</span> <span class="o">=</span> <span class="n">all_scores</span><span class="o">.</span><span class="n">LinearCombine</span><span class="p">(</span><span class="n">non_aa_weights</span><span class="p">)</span>
<span class="n">arg_sorted_scores</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">([(</span><span class="n">v</span><span class="p">,</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">non_aa_scores</span><span class="p">)])</span>
<span class="n">min_indices</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span> <span class="k">for</span> <span class="n">v</span><span class="p">,</span><span class="n">i</span> <span class="ow">in</span> <span class="n">arg_sorted_scores</span><span class="p">[:</span><span class="n">max_num_all_atom</span><span class="p">]]</span>
- <span class="c"># extract relevant loop candidates and scores</span>
+ <span class="c1"># extract relevant loop candidates and scores</span>
<span class="n">aa_loop_candidates</span> <span class="o">=</span> <span class="n">loop_candidates</span><span class="o">.</span><span class="n">Extract</span><span class="p">(</span><span class="n">min_indices</span><span class="p">)</span>
<span class="n">all_scores</span> <span class="o">=</span> <span class="n">all_scores</span><span class="o">.</span><span class="n">Extract</span><span class="p">(</span><span class="n">min_indices</span><span class="p">)</span>
- <span class="c"># add all atom scores</span>
+ <span class="c1"># add all atom scores</span>
<span class="n">aa_loop_candidates</span><span class="o">.</span><span class="n">CalculateAllAtomScores</span><span class="p">(</span><span class="n">all_scores</span><span class="p">,</span> <span class="n">mhandle</span><span class="p">,</span>
<span class="n">start_resnum</span><span class="p">,</span> <span class="n">chain_idx</span><span class="p">)</span>
- <span class="c"># get / return best</span>
+ <span class="c1"># get / return best</span>
<span class="n">scores</span> <span class="o">=</span> <span class="n">all_scores</span><span class="o">.</span><span class="n">LinearCombine</span><span class="p">(</span><span class="n">weights</span><span class="p">)</span>
<span class="n">min_score</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">scores</span><span class="p">)</span>
<span class="n">min_idx</span> <span class="o">=</span> <span class="n">scores</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">min_score</span><span class="p">)</span>
- <span class="c"># translate to original indexing for all atom</span>
+ <span class="c1"># translate to original indexing for all atom</span>
<span class="k">if</span> <span class="n">with_aa</span><span class="p">:</span>
<span class="n">min_idx</span> <span class="o">=</span> <span class="n">min_indices</span><span class="p">[</span><span class="n">min_idx</span><span class="p">]</span>
<span class="k">return</span> <span class="p">(</span><span class="n">min_idx</span><span class="p">,</span> <span class="n">min_score</span><span class="p">)</span>
-<span class="c">###############################################################################</span>
-<span class="c"># helper functions</span>
+<span class="c1">###############################################################################</span>
+<span class="c1"># helper functions</span>
<span class="k">def</span> <span class="nf">_GetGapExtender</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">actual_gap</span><span class="p">,</span> <span class="n">use_scoring_extender</span><span class="p">,</span>
<span class="n">use_full_extender</span><span class="p">,</span> <span class="n">max_length</span><span class="o">=-</span><span class="mi">1</span><span class="p">):</span>
- <span class="c"># DO NOT USE full ext. with max_len = -1 as this can use LOTS of memory</span>
+ <span class="c1"># DO NOT USE full ext. with max_len = -1 as this can use LOTS of memory</span>
<span class="k">if</span> <span class="n">use_full_extender</span> <span class="ow">and</span> <span class="n">max_length</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
- <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">"Cannot use neg. max_length with full extender!"</span><span class="p">)</span>
- <span class="c"># return appropriate gap extender</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"Cannot use neg. max_length with full extender!"</span><span class="p">)</span>
+ <span class="c1"># return appropriate gap extender</span>
<span class="n">actual_chain_idx</span> <span class="o">=</span> <span class="n">actual_gap</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">()</span>
<span class="k">if</span> <span class="n">use_scoring_extender</span><span class="p">:</span>
- <span class="c"># get extender_penalties (note: changes as gaps filled)</span>
+ <span class="c1"># get extender_penalties (note: changes as gaps filled)</span>
<span class="n">extender_penalties</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">seqres</span><span class="p">[</span><span class="n">actual_chain_idx</span><span class="p">])</span>
<span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="n">actual_chain_idx</span><span class="p">]</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
<span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">GetSecStructure</span><span class="p">()</span><span class="o">.</span><span class="n">IsHelical</span><span class="p">()</span> <span class="ow">or</span> \
<span class="n">r</span><span class="o">.</span><span class="n">GetSecStructure</span><span class="p">()</span><span class="o">.</span><span class="n">IsExtended</span><span class="p">():</span>
<span class="n">num</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span>
<span class="n">extender_penalties</span><span class="p">[</span><span class="n">num</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="mf">1.0</span>
- <span class="c"># setup scoring extender</span>
+ <span class="c1"># setup scoring extender</span>
<span class="k">if</span> <span class="n">use_full_extender</span><span class="p">:</span>
<span class="k">return</span> <span class="n">ScoringGapExtender</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">,</span> <span class="mf">0.8</span><span class="p">,</span>
<span class="n">extender_penalties</span><span class="p">,</span>
<span class="n">mhandle</span><span class="o">.</span><span class="n">seqres</span><span class="p">[</span><span class="n">actual_chain_idx</span><span class="p">],</span>
<span class="n">max_length</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">"Cannot use ScoringGapExtender w/o max_length."</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"Cannot use ScoringGapExtender w/o max_length."</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">if</span> <span class="n">use_full_extender</span><span class="p">:</span>
<span class="k">return</span> <span class="n">FullGapExtender</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">,</span>
@@ -132,24 +139,25 @@
<span class="n">mhandle</span><span class="o">.</span><span class="n">seqres</span><span class="p">[</span><span class="n">actual_chain_idx</span><span class="p">])</span>
<span class="k">def</span> <span class="nf">_ResolveLogInfo</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">,</span> <span class="n">optimal_gap</span><span class="p">,</span> <span class="n">n_candidates</span><span class="p">,</span> <span class="n">with_db</span><span class="p">,</span> <span class="n">with_aa</span><span class="p">):</span>
- <span class="c"># helper for consistent logging...</span>
- <span class="n">scor_str</span> <span class="o">=</span> <span class="s">"BB"</span>
+ <span class="c1"># helper for consistent logging...</span>
+ <span class="n">scor_str</span> <span class="o">=</span> <span class="s2">"BB"</span>
<span class="k">if</span> <span class="n">with_db</span><span class="p">:</span>
- <span class="n">scor_str</span> <span class="o">+=</span> <span class="s">"_DB"</span>
+ <span class="n">scor_str</span> <span class="o">+=</span> <span class="s2">"_DB"</span>
<span class="k">if</span> <span class="n">with_aa</span><span class="p">:</span>
- <span class="n">scor_str</span> <span class="o">+=</span> <span class="s">"_AA"</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Resolved </span><span class="si">%s</span><span class="s"> by filling </span><span class="si">%s</span><span class="s"> (</span><span class="si">%d</span><span class="s"> candidates, </span><span class="si">%s</span><span class="s">)"</span> <span class="o">%</span> \
+ <span class="n">scor_str</span> <span class="o">+=</span> <span class="s2">"_AA"</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Resolved </span><span class="si">%s</span><span class="s2"> by filling </span><span class="si">%s</span><span class="s2"> (</span><span class="si">%d</span><span class="s2"> candidates, </span><span class="si">%s</span><span class="s2">)"</span> <span class="o">%</span> \
<span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">optimal_gap</span><span class="p">),</span> <span class="n">n_candidates</span><span class="p">,</span> <span class="n">scor_str</span><span class="p">))</span>
<span class="k">def</span> <span class="nf">_CloseLoopFrame</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">gap_orig</span><span class="p">,</span> <span class="n">actual_candidates</span><span class="p">,</span> <span class="n">actual_extended_gaps</span><span class="p">,</span>
- <span class="n">actual_db_scores</span><span class="o">=</span><span class="p">[],</span> <span class="n">max_num_all_atom</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
+ <span class="n">actual_db_scores</span><span class="o">=</span><span class="p">[],</span> <span class="n">max_num_all_atom</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
+ <span class="n">length_dep_weights</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">'''Rank candidates with "frame-approach".</span>
<span class="sd"> All found candidates are extended prior to scoring so they match in size.</span>
<span class="sd"> '''</span>
- <span class="c"># get chain for gap</span>
+ <span class="c1"># get chain for gap</span>
<span class="n">actual_chain_idx</span> <span class="o">=</span> <span class="n">actual_extended_gaps</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">()</span>
<span class="n">actual_chain</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="n">actual_chain_idx</span><span class="p">]</span>
- <span class="c"># get min_res_num, max_after_resnum</span>
+ <span class="c1"># get min_res_num, max_after_resnum</span>
<span class="n">min_before_resnum</span> <span class="o">=</span> <span class="n">sys</span><span class="o">.</span><span class="n">maxint</span>
<span class="n">max_after_resnum</span> <span class="o">=</span> <span class="o">-</span><span class="n">sys</span><span class="o">.</span><span class="n">maxint</span><span class="o">-</span><span class="mi">1</span>
<span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="n">actual_extended_gaps</span><span class="p">:</span>
@@ -158,9 +166,9 @@
<span class="n">max_after_resnum</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">max_after_resnum</span><span class="p">,</span>
<span class="n">g</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">())</span>
- <span class="c"># all loop candidates will be scored along the full max. extension ever</span>
- <span class="c"># reached in the search before, so we build an overall frame, where we</span>
- <span class="c"># insert the loops</span>
+ <span class="c1"># all loop candidates will be scored along the full max. extension ever</span>
+ <span class="c1"># reached in the search before, so we build an overall frame, where we</span>
+ <span class="c1"># insert the loops</span>
<span class="n">frame_seq</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">seqres</span><span class="p">[</span><span class="n">actual_chain_idx</span><span class="p">]</span>\
<span class="p">[</span><span class="n">min_before_resnum</span><span class="o">-</span><span class="mi">1</span><span class="p">:</span><span class="n">max_after_resnum</span><span class="p">]</span>
<span class="n">frame_backbone_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">frame_seq</span><span class="p">)</span>
@@ -171,7 +179,7 @@
<span class="n">frame_backbone_list</span><span class="o">.</span><span class="n">Set</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">actual_res</span><span class="p">,</span> <span class="n">frame_seq</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
<span class="n">actual_res_num</span> <span class="o">+=</span> <span class="mi">1</span>
- <span class="c"># prepare loop candidates for scoring</span>
+ <span class="c1"># prepare loop candidates for scoring</span>
<span class="n">final_loop_candidates</span> <span class="o">=</span> <span class="n">LoopCandidates</span><span class="p">(</span><span class="n">frame_seq</span><span class="p">)</span>
<span class="n">back_mapper</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">loop_candidates</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">actual_candidates</span><span class="p">):</span>
@@ -184,87 +192,88 @@
<span class="n">final_loop_candidates</span><span class="o">.</span><span class="n">Add</span><span class="p">(</span><span class="n">actual_frame_backbone_list</span><span class="p">)</span>
<span class="n">back_mapper</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">))</span>
- <span class="c"># db scores requested</span>
+ <span class="c1"># db scores requested</span>
<span class="n">db_scores</span> <span class="o">=</span> <span class="n">ScoreContainer</span><span class="p">()</span>
<span class="k">for</span> <span class="n">actual_scores</span> <span class="ow">in</span> <span class="n">actual_db_scores</span><span class="p">:</span>
<span class="n">db_scores</span><span class="o">.</span><span class="n">Extend</span><span class="p">(</span><span class="n">actual_scores</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">final_loop_candidates</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="c"># get best</span>
+ <span class="c1"># get best</span>
<span class="n">min_idx</span><span class="p">,</span> <span class="n">min_score</span> <span class="o">=</span> <span class="n">_GetBestLC</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">final_loop_candidates</span><span class="p">,</span>
<span class="n">min_before_resnum</span><span class="p">,</span> <span class="n">actual_chain_idx</span><span class="p">,</span>
- <span class="n">db_scores</span><span class="p">,</span> <span class="n">max_num_all_atom</span><span class="p">)</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s">"Gap </span><span class="si">%s</span><span class="s"> - </span><span class="si">%d</span><span class="s"> candidates, best (min) score </span><span class="si">%g</span><span class="s">"</span> <span class="o">%</span>
+ <span class="n">db_scores</span><span class="p">,</span> <span class="n">max_num_all_atom</span><span class="p">,</span>
+ <span class="n">length_dep_weights</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s2">"Gap </span><span class="si">%s</span><span class="s2"> - </span><span class="si">%d</span><span class="s2"> candidates, best (min) score </span><span class="si">%g</span><span class="s2">"</span> <span class="o">%</span>
<span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">),</span> <span class="nb">len</span><span class="p">(</span><span class="n">final_loop_candidates</span><span class="p">),</span> <span class="n">min_score</span><span class="p">))</span>
- <span class="c"># resolve loop</span>
+ <span class="c1"># resolve loop</span>
<span class="n">idx_a</span> <span class="o">=</span> <span class="n">back_mapper</span><span class="p">[</span><span class="n">min_idx</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span>
<span class="n">idx_b</span> <span class="o">=</span> <span class="n">back_mapper</span><span class="p">[</span><span class="n">min_idx</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span>
<span class="n">_ResolveLogInfo</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">,</span> <span class="n">actual_extended_gaps</span><span class="p">[</span><span class="n">idx_a</span><span class="p">],</span>
<span class="nb">len</span><span class="p">(</span><span class="n">final_loop_candidates</span><span class="p">),</span> <span class="nb">bool</span><span class="p">(</span><span class="n">actual_db_scores</span><span class="p">),</span>
<span class="n">max_num_all_atom</span> <span class="o">></span> <span class="mi">0</span><span class="p">)</span>
- <span class="c"># update model and clear gaps</span>
+ <span class="c1"># update model and clear gaps</span>
<span class="n">bb_list</span> <span class="o">=</span> <span class="n">actual_candidates</span><span class="p">[</span><span class="n">idx_a</span><span class="p">][</span><span class="n">idx_b</span><span class="p">]</span>
<span class="n">actual_gap</span> <span class="o">=</span> <span class="n">actual_extended_gaps</span><span class="p">[</span><span class="n">idx_a</span><span class="p">]</span>
- <span class="c"># will return -1 if last gap removed, else next gap idx</span>
+ <span class="c1"># will return -1 if last gap removed, else next gap idx</span>
<span class="k">return</span> <span class="n">InsertLoopClearGaps</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">,</span> <span class="n">actual_gap</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Failed at loop insertion (</span><span class="si">%s</span><span class="s">)"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">))</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Failed at loop insertion (</span><span class="si">%s</span><span class="s2">)"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">))</span>
<span class="k">return</span> <span class="o">-</span><span class="mi">2</span>
<span class="k">def</span> <span class="nf">_CloseLoopBare</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">gap_orig</span><span class="p">,</span> <span class="n">actual_candidates</span><span class="p">,</span> <span class="n">actual_extended_gaps</span><span class="p">,</span>
<span class="n">actual_db_scores</span><span class="o">=</span><span class="p">[],</span> <span class="n">penalize_length</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
- <span class="n">max_num_all_atom</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
+ <span class="n">max_num_all_atom</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">length_dep_weights</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">'''Rank candidates directly.</span>
<span class="sd"> All candidates are scored directly and optionally penalized for gap length.</span>
<span class="sd"> '''</span>
- <span class="c"># get chain for gap</span>
+ <span class="c1"># get chain for gap</span>
<span class="n">actual_chain_idx</span> <span class="o">=</span> <span class="n">actual_extended_gaps</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">()</span>
- <span class="c"># score loops as they are</span>
- <span class="n">min_score</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="s">"inf"</span><span class="p">)</span>
+ <span class="c1"># score loops as they are</span>
+ <span class="n">min_score</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="s2">"inf"</span><span class="p">)</span>
<span class="n">optimal_gap</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">optimal_candidate</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">n_candidates</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">loop_candidates</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">actual_candidates</span><span class="p">):</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">loop_candidates</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span> <span class="k">continue</span>
<span class="n">n_candidates</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">loop_candidates</span><span class="p">)</span>
- <span class="c"># get current best</span>
+ <span class="c1"># get current best</span>
<span class="n">before_resnum</span> <span class="o">=</span> <span class="n">actual_extended_gaps</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span>
<span class="n">db_scores</span> <span class="o">=</span> <span class="n">ScoreContainer</span><span class="p">()</span>
<span class="k">if</span> <span class="n">actual_db_scores</span><span class="p">:</span>
<span class="n">db_scores</span> <span class="o">=</span> <span class="n">actual_db_scores</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">best_idx</span><span class="p">,</span> <span class="n">score</span> <span class="o">=</span> <span class="n">_GetBestLC</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">loop_candidates</span><span class="p">,</span> <span class="n">before_resnum</span><span class="p">,</span>
<span class="n">actual_chain_idx</span><span class="p">,</span> <span class="n">db_scores</span><span class="p">,</span>
- <span class="n">max_num_all_atom</span><span class="p">)</span>
- <span class="c"># compare with others</span>
+ <span class="n">max_num_all_atom</span><span class="p">,</span> <span class="n">length_dep_weights</span><span class="p">)</span>
+ <span class="c1"># compare with others</span>
<span class="k">if</span> <span class="n">penalize_length</span><span class="p">:</span>
- <span class="c"># penalized by gap length</span>
+ <span class="c1"># penalized by gap length</span>
<span class="n">score</span> <span class="o">=</span> <span class="n">score</span> <span class="o">*</span> <span class="n">actual_extended_gaps</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">length</span>
<span class="k">if</span> <span class="n">score</span> <span class="o"><</span> <span class="n">min_score</span><span class="p">:</span>
- <span class="c"># keep best one</span>
+ <span class="c1"># keep best one</span>
<span class="n">min_score</span> <span class="o">=</span> <span class="n">score</span>
<span class="n">optimal_gap</span> <span class="o">=</span> <span class="n">actual_extended_gaps</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">optimal_candidate</span> <span class="o">=</span> <span class="n">loop_candidates</span><span class="p">[</span><span class="n">best_idx</span><span class="p">]</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s">"Gap </span><span class="si">%s</span><span class="s"> - </span><span class="si">%d</span><span class="s"> candidates, best (min) score </span><span class="si">%g</span><span class="s">"</span> <span class="o">%</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s2">"Gap </span><span class="si">%s</span><span class="s2"> - </span><span class="si">%d</span><span class="s2"> candidates, best (min) score </span><span class="si">%g</span><span class="s2">"</span> <span class="o">%</span>
<span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">),</span> <span class="n">n_candidates</span><span class="p">,</span> <span class="n">min_score</span><span class="p">))</span>
- <span class="c"># finally resolve loop</span>
+ <span class="c1"># finally resolve loop</span>
<span class="k">if</span> <span class="n">optimal_candidate</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
- <span class="c"># report</span>
+ <span class="c1"># report</span>
<span class="n">_ResolveLogInfo</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">,</span> <span class="n">optimal_gap</span><span class="p">,</span> <span class="n">n_candidates</span><span class="p">,</span>
<span class="nb">bool</span><span class="p">(</span><span class="n">actual_db_scores</span><span class="p">),</span> <span class="n">max_num_all_atom</span> <span class="o">></span> <span class="mi">0</span><span class="p">)</span>
- <span class="c"># update model and clear gaps</span>
- <span class="c"># will return -1 if last gap removed, else next gap idx</span>
+ <span class="c1"># update model and clear gaps</span>
+ <span class="c1"># will return -1 if last gap removed, else next gap idx</span>
<span class="k">return</span> <span class="n">InsertLoopClearGaps</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">optimal_candidate</span><span class="p">,</span> <span class="n">optimal_gap</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Failed at loop insertion (</span><span class="si">%s</span><span class="s">)"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">))</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Failed at loop insertion (</span><span class="si">%s</span><span class="s2">)"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">))</span>
<span class="k">return</span> <span class="o">-</span><span class="mi">2</span>
<span class="k">def</span> <span class="nf">_CloseLoop</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">gap_orig</span><span class="p">,</span> <span class="n">actual_candidates</span><span class="p">,</span>
<span class="n">actual_extended_gaps</span><span class="p">,</span> <span class="n">variant</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">actual_db_scores</span><span class="o">=</span><span class="p">[],</span>
- <span class="n">max_num_all_atom</span><span class="o">=</span><span class="mi">0</span><span class="p">):</span>
+ <span class="n">max_num_all_atom</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">length_dep_weights</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">'''Choose best scoring loop candidate and close loop in mhandle.</span>
<span class="sd"> :param gap_orig: Gap we actually wanted to close</span>
<span class="sd"> :param actual_candidates: List of LoopCandidates</span>
@@ -276,34 +285,35 @@
<span class="sd"> :param max_num_all_atom: Num. of all atom LC to consider</span>
<span class="sd"> :return: gap-index as returned by ClearGaps or -2 if fail.</span>
<span class="sd"> '''</span>
- <span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="s">'closegaps::_CloseLoop'</span><span class="p">)</span>
- <span class="c"># check consistency</span>
+ <span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="s1">'closegaps::_CloseLoop'</span><span class="p">)</span>
+ <span class="c1"># check consistency</span>
<span class="n">N</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">actual_extended_gaps</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">actual_candidates</span><span class="p">)</span> <span class="o">!=</span> <span class="n">N</span><span class="p">:</span>
- <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">"Inconsistent list-lengths in _CloseLoop "</span> \
- <span class="s">"(</span><span class="si">%d</span><span class="s">, </span><span class="si">%d</span><span class="s">)"</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">actual_candidates</span><span class="p">),</span> <span class="n">N</span><span class="p">))</span>
- <span class="c"># check for empty candidate list</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"Inconsistent list-lengths in _CloseLoop "</span> \
+ <span class="s2">"(</span><span class="si">%d</span><span class="s2">, </span><span class="si">%d</span><span class="s2">)"</span> <span class="o">%</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">actual_candidates</span><span class="p">),</span> <span class="n">N</span><span class="p">))</span>
+ <span class="c1"># check for empty candidate list</span>
<span class="k">if</span> <span class="n">N</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Failed at loop insertion (</span><span class="si">%s</span><span class="s">)"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">))</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Failed at loop insertion (</span><span class="si">%s</span><span class="s2">)"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">))</span>
<span class="k">return</span> <span class="o">-</span><span class="mi">2</span>
- <span class="c"># choose variant</span>
+ <span class="c1"># choose variant</span>
<span class="k">if</span> <span class="n">variant</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">return</span> <span class="n">_CloseLoopFrame</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">gap_orig</span><span class="p">,</span> <span class="n">actual_candidates</span><span class="p">,</span>
<span class="n">actual_extended_gaps</span><span class="p">,</span> <span class="n">actual_db_scores</span><span class="p">,</span>
- <span class="n">max_num_all_atom</span><span class="p">)</span>
+ <span class="n">max_num_all_atom</span><span class="p">,</span> <span class="n">length_dep_weights</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">variant</span> <span class="ow">in</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">]:</span>
<span class="k">return</span> <span class="n">_CloseLoopBare</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">gap_orig</span><span class="p">,</span> <span class="n">actual_candidates</span><span class="p">,</span>
<span class="n">actual_extended_gaps</span><span class="p">,</span> <span class="n">actual_db_scores</span><span class="p">,</span>
- <span class="n">variant</span> <span class="o">==</span> <span class="mi">2</span><span class="p">,</span> <span class="n">max_num_all_atom</span><span class="p">)</span>
+ <span class="n">variant</span> <span class="o">==</span> <span class="mi">2</span><span class="p">,</span> <span class="n">max_num_all_atom</span><span class="p">,</span>
+ <span class="n">length_dep_weights</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">"Unknown variant </span><span class="si">%d</span><span class="s">"</span> <span class="o">%</span> <span class="n">variant</span><span class="p">);</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"Unknown variant </span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="n">variant</span><span class="p">);</span>
<span class="k">def</span> <span class="nf">_InRange</span><span class="p">(</span><span class="n">gap</span><span class="p">,</span> <span class="n">chain_idx</span><span class="p">,</span> <span class="n">resnum_range</span><span class="p">):</span>
<span class="sd">'''Check if gap is in range to be processed.'''</span>
- <span class="c"># It is possible to specify exact ranges that should be resolved by</span>
- <span class="c"># the chain_idx and resnum_range parameters.</span>
- <span class="c"># Let's check whether we care for that particular gap in case of one</span>
- <span class="c"># parameter being set.</span>
+ <span class="c1"># It is possible to specify exact ranges that should be resolved by</span>
+ <span class="c1"># the chain_idx and resnum_range parameters.</span>
+ <span class="c1"># Let's check whether we care for that particular gap in case of one</span>
+ <span class="c1"># parameter being set.</span>
<span class="k">if</span> <span class="n">chain_idx</span> <span class="o">!=</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">gap</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">()</span> <span class="o">!=</span> <span class="n">chain_idx</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">False</span>
<span class="k">elif</span> <span class="n">resnum_range</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span>
@@ -316,13 +326,13 @@
<span class="n">n_stem_num</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span>
<span class="n">c_stem_num</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span>
<span class="k">if</span> <span class="n">n_stem_num</span> <span class="o"><=</span> <span class="n">resnum_range</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">and</span> <span class="n">c_stem_num</span> <span class="o">>=</span> <span class="n">resnum_range</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span>
- <span class="c"># full overlap => current gap is fully enclosing range</span>
+ <span class="c1"># full overlap => current gap is fully enclosing range</span>
<span class="k">return</span> <span class="bp">True</span>
<span class="k">elif</span> <span class="n">n_stem_num</span> <span class="o">>=</span> <span class="n">resnum_range</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">and</span> <span class="n">n_stem_num</span> <span class="o"><</span> <span class="n">resnum_range</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span>
- <span class="c"># partial overlap => n-stem is within range</span>
+ <span class="c1"># partial overlap => n-stem is within range</span>
<span class="k">return</span> <span class="bp">True</span>
<span class="k">elif</span> <span class="n">c_stem_num</span> <span class="o">></span> <span class="n">resnum_range</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="ow">and</span> <span class="n">c_stem_num</span> <span class="o"><=</span> <span class="n">resnum_range</span><span class="p">[</span><span class="mi">1</span><span class="p">]:</span>
- <span class="c"># partial overlap => c-stem is within range</span>
+ <span class="c1"># partial overlap => c-stem is within range</span>
<span class="k">return</span> <span class="bp">True</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span> <span class="bp">False</span>
@@ -330,13 +340,16 @@
<span class="k">return</span> <span class="bp">True</span>
<span class="k">def</span> <span class="nf">_GetMCWeights</span><span class="p">():</span>
- <span class="c"># get weights for Monte Carlo sampling (BB only)</span>
- <span class="k">return</span> <span class="p">{</span><span class="s">"reduced"</span><span class="p">:</span> <span class="mf">3.0</span><span class="p">,</span>
- <span class="s">"cb_packing"</span><span class="p">:</span> <span class="mf">2.0</span><span class="p">,</span>
- <span class="s">"hbond"</span><span class="p">:</span> <span class="mf">1.0</span><span class="p">,</span>
- <span class="s">"clash"</span><span class="p">:</span> <span class="mf">0.05</span><span class="p">}</span>
+ <span class="c1"># get weights for Monte Carlo sampling (subset of BB only scores for super </span>
+ <span class="c1"># fast sampling)</span>
+ <span class="n">bb_weights</span> <span class="o">=</span> <span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetWeights</span><span class="p">()</span>
+ <span class="n">return_weights</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
+ <span class="n">return_weights</span><span class="p">[</span><span class="s2">"reduced"</span><span class="p">]</span> <span class="o">=</span> <span class="n">bb_weights</span><span class="p">[</span><span class="s2">"reduced"</span><span class="p">]</span>
+ <span class="n">return_weights</span><span class="p">[</span><span class="s2">"cb_packing"</span><span class="p">]</span> <span class="o">=</span> <span class="n">bb_weights</span><span class="p">[</span><span class="s2">"cb_packing"</span><span class="p">]</span>
+ <span class="n">return_weights</span><span class="p">[</span><span class="s2">"clash"</span><span class="p">]</span> <span class="o">=</span> <span class="n">bb_weights</span><span class="p">[</span><span class="s2">"clash"</span><span class="p">]</span>
+ <span class="k">return</span> <span class="n">return_weights</span>
-<span class="c">###############################################################################</span>
+<span class="c1">###############################################################################</span>
<div class="viewcode-block" id="CloseSmallDeletions"><a class="viewcode-back" href="../../../modelling/pipeline.html#promod3.modelling.CloseSmallDeletions">[docs]</a><span class="k">def</span> <span class="nf">CloseSmallDeletions</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">max_extension</span><span class="o">=</span><span class="mi">9</span><span class="p">,</span> <span class="n">clash_thresh</span><span class="o">=</span><span class="mf">1.0</span><span class="p">,</span>
<span class="n">e_thresh</span><span class="o">=</span><span class="mi">200</span><span class="p">,</span> <span class="n">use_scoring_extender</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
@@ -375,7 +388,8 @@
<span class="sd"> For the scondary-structure-penalty to work,</span>
<span class="sd"> the model-template must have the appropriate</span>
<span class="sd"> information before :func:`BuildRawModel` is</span>
-<span class="sd"> called (e.g. with :mod:`ost.bindings.dssp`).</span>
+<span class="sd"> called (e.g. with </span>
+<span class="sd"> :meth:`ost.mol.alg.AssignSecStruct`).</span>
<span class="sd"> :type use_scoring_extender: :class:`bool`</span>
<span class="sd"> :param use_full_extender: True = use :class:`FullGapExtender` instead of</span>
@@ -402,48 +416,53 @@
<span class="sd"> :type ff_lookup: :class:`promod3.loop.ForcefieldLookup`</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'closegaps::CloseSmallDeletions'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'closegaps::CloseSmallDeletions'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Trying to close small deletions (no. of gap(s): </span><span class="si">%d</span><span class="s">)."</span> \
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Trying to close small deletions (no. of gap(s): </span><span class="si">%d</span><span class="s2">)."</span> \
<span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span>
- <span class="c"># check/setup scoring</span>
+ <span class="c1"># check/setup scoring</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">IsBackboneScoringSetUp</span><span class="p">(</span><span class="n">mhandle</span><span class="p">):</span>
<span class="n">SetupDefaultBackboneScoring</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
- <span class="n">clash_scorer</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer</span><span class="o">.</span><span class="n">Get</span><span class="p">(</span><span class="s">"clash"</span><span class="p">)</span>
+
+ <span class="c1"># we're only calculating clash scores here, so we copy the default</span>
+ <span class="c1"># env and only attach a clash scorer. </span>
+ <span class="n">clash_scorer_env</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer_env</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
+ <span class="n">clash_scorer</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">ClashScorer</span><span class="p">()</span>
+ <span class="n">clash_scorer</span><span class="o">.</span><span class="n">AttachEnvironment</span><span class="p">(</span><span class="n">clash_scorer_env</span><span class="p">)</span>
<span class="k">if</span> <span class="n">ff_lookup</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">ff_lookup</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">ForcefieldLookup</span><span class="o">.</span><span class="n">GetDefault</span><span class="p">()</span>
- <span class="c"># iterating mhandle.gaps. The number of gaps may change during the process,</span>
- <span class="c"># hence we run by 'while', comparing to the updated list of gaps. If a gap</span>
- <span class="c"># gets closed, it is deleted from mhandle.gaps, otherwise, current_gap_index</span>
- <span class="c"># as a counter is increased.</span>
+ <span class="c1"># iterating mhandle.gaps. The number of gaps may change during the process,</span>
+ <span class="c1"># hence we run by 'while', comparing to the updated list of gaps. If a gap</span>
+ <span class="c1"># gets closed, it is deleted from mhandle.gaps, otherwise, current_gap_index</span>
+ <span class="c1"># as a counter is increased.</span>
<span class="n">current_gap_index</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">while</span> <span class="n">current_gap_index</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">):</span>
- <span class="c"># in the end this determines if a gap was closed or not</span>
+ <span class="c1"># in the end this determines if a gap was closed or not</span>
<span class="n">success</span> <span class="o">=</span> <span class="bp">False</span>
- <span class="c"># work on a copy of the gap, if not closed in the end, no harm done</span>
+ <span class="c1"># work on a copy of the gap, if not closed in the end, no harm done</span>
<span class="n">current_gap</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">current_gap_index</span><span class="p">]</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
- <span class="c"># A deletion is a gap of size 0 in the template, this means that to</span>
- <span class="c"># transform the template sequence into the target sequence, aa's vanish,</span>
- <span class="c"># so the target sequence has gap characters, the template not.</span>
- <span class="c"># If we are not looking at a deletion, do nothing.</span>
+ <span class="c1"># A deletion is a gap of size 0 in the template, this means that to</span>
+ <span class="c1"># transform the template sequence into the target sequence, aa's vanish,</span>
+ <span class="c1"># so the target sequence has gap characters, the template not.</span>
+ <span class="c1"># If we are not looking at a deletion, do nothing.</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">current_gap</span><span class="o">.</span><span class="n">seq</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">IsTerminal</span><span class="p">()</span>\
<span class="ow">and</span> <span class="n">_InRange</span><span class="p">(</span><span class="n">current_gap</span><span class="p">,</span> <span class="n">chain_idx</span><span class="p">,</span> <span class="n">resnum_range</span><span class="p">):</span>
<span class="n">current_chain</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">GetChain</span><span class="p">()</span>
<span class="n">current_chain_index</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">()</span>
- <span class="c"># Try to close gap by relaxation: by checking how far we may extend</span>
- <span class="c"># the gap, we get the backbone to be stretched. If no more extension</span>
- <span class="c"># is possible, break out. On first successful relaxation for an</span>
- <span class="c"># extension, we successfully stop.</span>
+ <span class="c1"># Try to close gap by relaxation: by checking how far we may extend</span>
+ <span class="c1"># the gap, we get the backbone to be stretched. If no more extension</span>
+ <span class="c1"># is possible, break out. On first successful relaxation for an</span>
+ <span class="c1"># extension, we successfully stop.</span>
<span class="n">extender</span> <span class="o">=</span> <span class="n">_GetGapExtender</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">current_gap</span><span class="p">,</span>
<span class="n">use_scoring_extender</span><span class="p">,</span>
<span class="n">use_full_extender</span><span class="p">,</span>
@@ -451,8 +470,8 @@
<span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">max_extension</span><span class="p">):</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">extender</span><span class="o">.</span><span class="n">Extend</span><span class="p">():</span>
<span class="k">break</span>
- <span class="c"># gather residues for backbone relaxation, check that we get a</span>
- <span class="c"># bunch of actual residues, otherwise jump to next extension</span>
+ <span class="c1"># gather residues for backbone relaxation, check that we get a</span>
+ <span class="c1"># bunch of actual residues, otherwise jump to next extension</span>
<span class="n">res_list</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="n">n_stem_resnum</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span>
<span class="n">c_stem_resnum</span> <span class="o">=</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span>
@@ -467,34 +486,47 @@
<span class="n">idx</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">found_residues</span><span class="p">:</span>
<span class="k">continue</span>
- <span class="c"># backbone relaxation, for now we allow 300 steps or stop at</span>
- <span class="c"># max. force of 0.1</span>
+ <span class="c1"># backbone relaxation, for now we allow 300 steps or stop at</span>
+ <span class="c1"># max. force of 0.1</span>
<span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">current_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">,</span> <span class="n">res_list</span><span class="p">)</span>
<span class="n">bb_relaxer</span> <span class="o">=</span> <span class="n">BackboneRelaxer</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="n">ff_lookup</span><span class="p">)</span>
<span class="n">potential_e</span> <span class="o">=</span> <span class="n">bb_relaxer</span><span class="o">.</span><span class="n">Run</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="mi">300</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">)</span>
- <span class="c"># check for clashes</span>
- <span class="n">score</span> <span class="o">=</span> <span class="n">clash_scorer</span><span class="o">.</span><span class="n">CalculateScore</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span>
- <span class="n">n_stem_resnum</span><span class="o">.</span><span class="n">GetNum</span><span class="p">(),</span>
+ <span class="c1"># check for clashes</span>
+
+ <span class="c1"># its a bit problematic since we score loops that are shifting </span>
+ <span class="c1"># around... so we perform a stash operation for each scoring step</span>
+
+ <span class="n">clash_scorer_env</span><span class="o">.</span><span class="n">Stash</span><span class="p">(</span><span class="n">n_stem_resnum</span><span class="o">.</span><span class="n">GetNum</span><span class="p">(),</span>
+ <span class="nb">len</span><span class="p">(</span><span class="n">bb_list</span><span class="p">),</span> <span class="n">current_chain_index</span><span class="p">)</span>
+ <span class="n">clash_scorer_env</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="n">n_stem_resnum</span><span class="o">.</span><span class="n">GetNum</span><span class="p">(),</span>
+ <span class="n">current_chain_index</span><span class="p">)</span>
+ <span class="n">score</span> <span class="o">=</span> <span class="n">clash_scorer</span><span class="o">.</span><span class="n">CalculateScore</span><span class="p">(</span><span class="n">n_stem_resnum</span><span class="o">.</span><span class="n">GetNum</span><span class="p">(),</span>
+ <span class="nb">len</span><span class="p">(</span><span class="n">bb_list</span><span class="p">),</span>
<span class="n">current_chain_index</span><span class="p">)</span>
+ <span class="n">clash_scorer_env</span><span class="o">.</span><span class="n">Pop</span><span class="p">()</span>
- <span class="c"># if there is no clash and potential energy is low enough we</span>
- <span class="c"># just solved a gap, delete it and update the scorer for the</span>
- <span class="c"># changed model</span>
+ <span class="c1"># if there is no clash and potential energy is low enough we</span>
+ <span class="c1"># just solved a gap, delete it and update the scorer for the</span>
+ <span class="c1"># changed model</span>
<span class="k">if</span> <span class="n">score</span> <span class="o"><</span> <span class="n">clash_thresh</span> <span class="ow">and</span> \
<span class="n">potential_e</span> <span class="o"><</span> <span class="n">e_thresh</span> <span class="ow">and</span> \
<span class="n">bb_list</span><span class="o">.</span><span class="n">TransOmegaTorsions</span><span class="p">():</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Closed: </span><span class="si">%s</span><span class="s"> by relaxing </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> \
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Closed: </span><span class="si">%s</span><span class="s2"> by relaxing </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> \
<span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">current_gap_index</span><span class="p">],</span> <span class="n">current_gap</span><span class="p">))</span>
<span class="n">InsertLoopClearGaps</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">,</span> <span class="n">current_gap</span><span class="p">)</span>
+ <span class="n">clash_scorer_env</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span>
+ <span class="n">n_stem_resnum</span><span class="o">.</span><span class="n">GetNum</span><span class="p">(),</span>
+ <span class="n">current_chain_index</span><span class="p">)</span>
<span class="n">success</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">break</span>
- <span class="c"># On closed gap, it is removed so the no. of gaps goes down by itself.</span>
- <span class="c"># In case of no success, counter needs to be increased to jump to the</span>
- <span class="c"># next gap.</span>
+
+ <span class="c1"># On closed gap, it is removed so the no. of gaps goes down by itself.</span>
+ <span class="c1"># In case of no success, counter needs to be increased to jump to the</span>
+ <span class="c1"># next gap.</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">success</span><span class="p">:</span>
- <span class="n">current_gap_index</span> <span class="o">+=</span> <span class="mi">1</span>
-</div>
+ <span class="n">current_gap_index</span> <span class="o">+=</span> <span class="mi">1</span></div>
+
<div class="viewcode-block" id="MergeGapsByDistance"><a class="viewcode-back" href="../../../modelling/pipeline.html#promod3.modelling.MergeGapsByDistance">[docs]</a><span class="k">def</span> <span class="nf">MergeGapsByDistance</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">distance</span><span class="p">,</span> <span class="n">chain_idx</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">resnum_range</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">'''Merge 2 neighbouring gaps by deleting residues in-between.</span>
@@ -524,54 +556,54 @@
<span class="sd"> :type resnum_range: :class:`tuple` containing two :class:`int`</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'closegaps::MergeGapsByDistance'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'closegaps::MergeGapsByDistance'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span> <span class="o">></span> <span class="mi">1</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Trying to merge </span><span class="si">%d</span><span class="s"> gap(s) with distance </span><span class="si">%d</span><span class="s">."</span> <span class="o">%</span> \
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Trying to merge </span><span class="si">%d</span><span class="s2"> gap(s) with distance </span><span class="si">%d</span><span class="s2">."</span> <span class="o">%</span> \
<span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">),</span> <span class="n">distance</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span>
- <span class="c"># indicate if we merged gaps and should check for more</span>
+ <span class="c1"># indicate if we merged gaps and should check for more</span>
<span class="n">try_again</span> <span class="o">=</span> <span class="bp">True</span>
- <span class="c"># The number of gaps changes on merge, so we cannot just iterate them.</span>
- <span class="c"># If we merged gaps, we do not know if this was the last one so try_again</span>
- <span class="c"># is set to True. If no more gaps were merged, we stop by leaving try_again</span>
- <span class="c"># as False.</span>
+ <span class="c1"># The number of gaps changes on merge, so we cannot just iterate them.</span>
+ <span class="c1"># If we merged gaps, we do not know if this was the last one so try_again</span>
+ <span class="c1"># is set to True. If no more gaps were merged, we stop by leaving try_again</span>
+ <span class="c1"># as False.</span>
<span class="k">while</span> <span class="n">try_again</span><span class="p">:</span>
<span class="n">try_again</span> <span class="o">=</span> <span class="bp">False</span>
- <span class="c"># iterate all but the last gap, since we are always looking ahead</span>
+ <span class="c1"># iterate all but the last gap, since we are always looking ahead</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">):</span>
<span class="n">current_gap</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
<span class="n">next_gap</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
- <span class="c"># check that we are on the same chain</span>
+ <span class="c1"># check that we are on the same chain</span>
<span class="k">if</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">GetChain</span><span class="p">()</span> <span class="o">!=</span> <span class="n">next_gap</span><span class="o">.</span><span class="n">GetChain</span><span class="p">():</span>
<span class="k">continue</span>
- <span class="c"># check for range (if given)</span>
+ <span class="c1"># check for range (if given)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">_InRange</span><span class="p">(</span><span class="n">current_gap</span><span class="p">,</span> <span class="n">chain_idx</span><span class="p">,</span> <span class="n">resnum_range</span><span class="p">)</span> <span class="ow">and</span>\
<span class="n">_InRange</span><span class="p">(</span><span class="n">next_gap</span><span class="p">,</span> <span class="n">chain_idx</span><span class="p">,</span> <span class="n">resnum_range</span><span class="p">)):</span>
<span class="k">continue</span>
- <span class="c"># no merging of gaps at the end AND the start :)</span>
+ <span class="c1"># no merging of gaps at the end AND the start :)</span>
<span class="k">if</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">IsNTerminal</span><span class="p">()</span> <span class="ow">and</span> <span class="n">next_gap</span><span class="o">.</span><span class="n">IsCTerminal</span><span class="p">():</span>
<span class="k">continue</span>
- <span class="c"># get the distance between the gaps</span>
+ <span class="c1"># get the distance between the gaps</span>
<span class="n">dist</span> <span class="o">=</span> <span class="n">next_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span> \
<span class="o">-</span> <span class="n">current_gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span>
- <span class="c"># NOTE: -1 can currently only happen when fixing ring punches</span>
- <span class="c"># in _pipeline.BuildSidechains</span>
+ <span class="c1"># NOTE: -1 can currently only happen when fixing ring punches</span>
+ <span class="c1"># in _pipeline.BuildSidechains</span>
<span class="k">if</span> <span class="n">dist</span> <span class="o"><</span> <span class="o">-</span><span class="mi">1</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Non-sequential gaps found. Ignoring."</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Non-sequential gaps found. Ignoring."</span><span class="p">)</span>
<span class="k">continue</span>
<span class="k">if</span> <span class="n">dist</span> <span class="o"><=</span> <span class="n">distance</span><span class="p">:</span>
- <span class="c"># gaps are close enough, combine! combine!</span>
+ <span class="c1"># gaps are close enough, combine! combine!</span>
<span class="n">MergeGaps</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Merged gap </span><span class="si">%s</span><span class="s"> and </span><span class="si">%s</span><span class="s"> into </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> \
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Merged gap </span><span class="si">%s</span><span class="s2"> and </span><span class="si">%s</span><span class="s2"> into </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> \
<span class="p">(</span><span class="n">current_gap</span><span class="p">,</span> <span class="n">next_gap</span><span class="p">,</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">i</span><span class="p">]))</span>
<span class="n">try_again</span> <span class="o">=</span> <span class="bp">True</span>
- <span class="k">break</span>
-</div>
+ <span class="k">break</span></div>
+
<div class="viewcode-block" id="FillLoopsByDatabase"><a class="viewcode-back" href="../../../modelling/pipeline.html#promod3.modelling.FillLoopsByDatabase">[docs]</a><span class="k">def</span> <span class="nf">FillLoopsByDatabase</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">fragment_db</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">,</span>
<span class="n">torsion_sampler</span><span class="p">,</span> <span class="n">max_loops_to_search</span><span class="o">=</span><span class="mi">40</span><span class="p">,</span>
<span class="n">min_loops_required</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span> <span class="n">max_res_extension</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span>
@@ -579,7 +611,7 @@
<span class="n">use_full_extender</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> <span class="n">score_variant</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
<span class="n">ring_punch_detection</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">chain_idx</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
<span class="n">resnum_range</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">max_num_all_atom</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
- <span class="n">clash_thresh</span><span class="o">=-</span><span class="mi">1</span><span class="p">):</span>
+ <span class="n">clash_thresh</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span> <span class="n">length_dep_weights</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">'''Try to fill up loops from a structural database.</span>
<span class="sd"> Usually this will extend the gaps a bit to match candidates from the</span>
@@ -677,139 +709,148 @@
<span class="sd"> :param clash_thresh: If > 0, we only keep loop candidates which have a</span>
<span class="sd"> backbone clash score lower than this.</span>
<span class="sd"> :type clash_thresh: :class:`float`</span>
+
+<span class="sd"> :param length_dep_weights: :class:`ScoringWeights` provides different sets</span>
+<span class="sd"> of weights that have been trained on different</span>
+<span class="sd"> loop subsets. If this flag is true, the length</span>
+<span class="sd"> dependent weights are used to select the final </span>
+<span class="sd"> loops.</span>
+<span class="sd"> :type length_dep_weights: :class:`bool`</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'closegaps::FillLoopsByDatabase'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'closegaps::FillLoopsByDatabase'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Trying to fill </span><span class="si">%d</span><span class="s"> gap(s) by database."</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Trying to fill </span><span class="si">%d</span><span class="s2"> gap(s) by database."</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span>
- <span class="c"># check/setup scoring</span>
+ <span class="c1"># check/setup scoring</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">IsBackboneScoringSetUp</span><span class="p">(</span><span class="n">mhandle</span><span class="p">):</span>
<span class="n">SetupDefaultBackboneScoring</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
<span class="k">if</span> <span class="n">max_num_all_atom</span> <span class="o">></span> <span class="mi">0</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">IsAllAtomScoringSetUp</span><span class="p">(</span><span class="n">mhandle</span><span class="p">):</span>
<span class="n">SetupDefaultAllAtomScoring</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
- <span class="c"># some score variants cannot deal with multiple insertions in one "gap"</span>
+ <span class="c1"># some score variants cannot deal with multiple insertions in one "gap"</span>
<span class="n">disallow_ins_merge</span> <span class="o">=</span> <span class="p">(</span><span class="n">score_variant</span> <span class="o">==</span> <span class="mi">0</span><span class="p">)</span>
- <span class="c"># do we want DB features?</span>
+ <span class="c1"># do we want DB features?</span>
<span class="n">add_db_features</span> <span class="o">=</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">profiles</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">)</span>
- <span class="c"># check min_loops_required</span>
+ <span class="c1"># check min_loops_required</span>
<span class="k">if</span> <span class="n">min_loops_required</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">min_loops_required</span> <span class="o">=</span> <span class="n">max_loops_to_search</span>
- <span class="c"># get biggest loop (w/o stems) stored in db</span>
+ <span class="c1"># get biggest loop (w/o stems) stored in db</span>
<span class="n">max_db_loop_len</span> <span class="o">=</span> <span class="n">fragment_db</span><span class="o">.</span><span class="n">MaxFragLength</span><span class="p">()</span> <span class="o">-</span> <span class="mi">2</span>
- <span class="c"># point to the current gap</span>
+ <span class="c1"># point to the current gap</span>
<span class="n">gap_idx</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="c"># Iterate all gaps. Since the number of gaps may change, always compare to</span>
- <span class="c"># an updated list. gap_idx is only increased when necessary, e.g. current</span>
- <span class="c"># gap could not be removed.</span>
+ <span class="c1"># Iterate all gaps. Since the number of gaps may change, always compare to</span>
+ <span class="c1"># an updated list. gap_idx is only increased when necessary, e.g. current</span>
+ <span class="c1"># gap could not be removed.</span>
<span class="k">while</span> <span class="n">gap_idx</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span> <span class="ow">and</span> <span class="n">gap_idx</span> <span class="o">>=</span> <span class="mi">0</span><span class="p">:</span>
- <span class="c"># keep copy of original gap</span>
+ <span class="c1"># keep copy of original gap</span>
<span class="n">gap_orig</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">gap_idx</span><span class="p">]</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
<span class="k">if</span> <span class="n">disallow_ins_merge</span><span class="p">:</span>
<span class="n">gap_ins</span> <span class="o">=</span> <span class="n">CountEnclosedInsertions</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">gap_orig</span><span class="p">)</span>
- <span class="c"># ignore terminal gaps and out-of-range (if range given)</span>
+ <span class="c1"># ignore terminal gaps and out-of-range (if range given)</span>
<span class="k">if</span> <span class="n">gap_orig</span><span class="o">.</span><span class="n">IsTerminal</span><span class="p">()</span> \
<span class="ow">or</span> <span class="ow">not</span> <span class="n">_InRange</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">,</span> <span class="n">chain_idx</span><span class="p">,</span> <span class="n">resnum_range</span><span class="p">):</span>
<span class="n">gap_idx</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">continue</span>
- <span class="c">##################################</span>
- <span class="c"># find loop candidates</span>
- <span class="c">##################################</span>
- <span class="c"># list of LoopCandidates to fill gap</span>
+ <span class="c1">##################################</span>
+ <span class="c1"># find loop candidates</span>
+ <span class="c1">##################################</span>
+ <span class="c1"># list of LoopCandidates to fill gap</span>
<span class="n">actual_candidates</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
- <span class="c"># list of StructuralGap corresponding to actual_candidates</span>
+ <span class="c1"># list of StructuralGap corresponding to actual_candidates</span>
<span class="n">actual_extended_gaps</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
- <span class="c"># list of dicts with DB specific scores</span>
- <span class="c"># -> empty if not add_db_features</span>
+ <span class="c1"># list of dicts with DB specific scores</span>
+ <span class="c1"># -> empty if not add_db_features</span>
<span class="n">actual_db_scores</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
- <span class="c"># number of loops found (stop if >= max_loops_to_search)</span>
+ <span class="c1"># number of loops found (stop if >= max_loops_to_search)</span>
<span class="n">found_loops</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="c"># maximal length for this gap</span>
+ <span class="c1"># maximal length for this gap</span>
<span class="k">if</span> <span class="n">max_res_extension</span> <span class="o">>=</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">max_gap_length</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">gap_orig</span><span class="o">.</span><span class="n">length</span> <span class="o">+</span> <span class="n">max_res_extension</span><span class="p">,</span>
<span class="n">max_db_loop_len</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">max_gap_length</span> <span class="o">=</span> <span class="n">max_db_loop_len</span>
- <span class="c"># currently extended gap and gap-extender</span>
+ <span class="c1"># currently extended gap and gap-extender</span>
<span class="n">actual_gap</span> <span class="o">=</span> <span class="n">gap_orig</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
<span class="n">actual_extender</span> <span class="o">=</span> <span class="n">_GetGapExtender</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">actual_gap</span><span class="p">,</span>
<span class="n">use_scoring_extender</span><span class="p">,</span>
<span class="n">use_full_extender</span><span class="p">,</span>
<span class="n">max_gap_length</span><span class="p">)</span>
- <span class="c"># iteratively extend actual_gap until we have enough loops</span>
+ <span class="c1"># iteratively extend actual_gap until we have enough loops</span>
<span class="n">first_iteration</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">while</span> <span class="n">actual_gap</span><span class="o">.</span><span class="n">length</span> <span class="o"><=</span> <span class="n">max_gap_length</span><span class="p">:</span>
- <span class="c"># check if we have enough</span>
+ <span class="c1"># check if we have enough</span>
<span class="k">if</span> <span class="n">found_loops</span> <span class="o">>=</span> <span class="n">max_loops_to_search</span><span class="p">:</span>
<span class="k">break</span>
- <span class="c"># extend the gap</span>
+ <span class="c1"># extend the gap</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">first_iteration</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">actual_extender</span><span class="o">.</span><span class="n">Extend</span><span class="p">():</span>
<span class="k">break</span>
<span class="n">first_iteration</span> <span class="o">=</span> <span class="bp">False</span>
- <span class="c"># ensure both stems are valid</span>
+ <span class="c1"># ensure both stems are valid</span>
<span class="n">n_stem</span> <span class="o">=</span> <span class="n">actual_gap</span><span class="o">.</span><span class="n">before</span>
<span class="n">c_stem</span> <span class="o">=</span> <span class="n">actual_gap</span><span class="o">.</span><span class="n">after</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">n_stem</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">c_stem</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
<span class="k">break</span>
- <span class="c"># skip if we try to merge insertions when disallowed</span>
+ <span class="c1"># skip if we try to merge insertions when disallowed</span>
<span class="k">if</span> <span class="n">disallow_ins_merge</span> <span class="ow">and</span> \
<span class="n">CountEnclosedInsertions</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">actual_gap</span><span class="p">)</span> <span class="o">!=</span> <span class="n">gap_ins</span><span class="p">:</span>
<span class="k">continue</span>
- <span class="c"># get candidates for the current loop</span>
+ <span class="c1"># get candidates for the current loop</span>
<span class="n">candidates</span> <span class="o">=</span> <span class="n">LoopCandidates</span><span class="o">.</span><span class="n">FillFromDatabase</span><span class="p">(</span>
<span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">,</span> <span class="n">actual_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">,</span>
<span class="n">fragment_db</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">,</span> <span class="n">extended_search</span><span class="p">)</span>
- <span class="c"># skip gaps with no loop candidates</span>
+ <span class="c1"># skip gaps with no loop candidates</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">continue</span>
- <span class="c"># check for stem rmsd before ApplyCCD</span>
+ <span class="c1"># check for stem rmsd before ApplyCCD</span>
<span class="k">if</span> <span class="n">add_db_features</span><span class="p">:</span>
<span class="n">db_scores</span> <span class="o">=</span> <span class="n">ScoreContainer</span><span class="p">()</span>
<span class="n">candidates</span><span class="o">.</span><span class="n">CalculateStemRMSDs</span><span class="p">(</span><span class="n">db_scores</span><span class="p">,</span> <span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">)</span>
- <span class="c"># try to close loops</span>
+ <span class="c1"># try to close loops</span>
<span class="k">try</span><span class="p">:</span>
- <span class="c">#pylint: disable=broad-except</span>
+ <span class="c1">#pylint: disable=broad-except</span>
<span class="n">orig_indices</span> <span class="o">=</span> <span class="n">candidates</span><span class="o">.</span><span class="n">ApplyCCD</span><span class="p">(</span><span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">,</span>
<span class="n">torsion_sampler</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span><span class="p">:</span>
- <span class="c"># CCD should work even if no residues exist before and/or after</span>
- <span class="c"># the stems. If this is not desired, you should skip those gaps.</span>
- <span class="c"># If anything else fails, the proposed gap is skipped.</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogWarning</span><span class="p">(</span><span class="s">"ApplyCCD failure for "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">))</span>
+ <span class="c1"># CCD should work even if no residues exist before and/or after</span>
+ <span class="c1"># the stems. If this is not desired, you should skip those gaps.</span>
+ <span class="c1"># If anything else fails, the proposed gap is skipped.</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogWarning</span><span class="p">(</span><span class="s2">"ApplyCCD failure for "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">))</span>
<span class="k">continue</span>
- <span class="c"># remove clashing ones if desired</span>
+ <span class="c1"># remove clashing ones if desired</span>
<span class="k">if</span> <span class="n">clash_thresh</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">scorer</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer</span><span class="o">.</span><span class="n">Get</span><span class="p">(</span><span class="s">"clash"</span><span class="p">)</span>
+ <span class="n">clash_score_container</span> <span class="o">=</span> <span class="n">ScoreContainer</span><span class="p">()</span>
+ <span class="n">candidates</span><span class="o">.</span><span class="n">CalculateBackboneScores</span><span class="p">(</span><span class="n">clash_score_container</span><span class="p">,</span>
+ <span class="n">mhandle</span><span class="p">,</span> <span class="p">[</span><span class="s2">"clash"</span><span class="p">],</span>
+ <span class="n">n_stem</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">(),</span>
+ <span class="n">actual_gap</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">())</span>
+ <span class="n">clash_scores</span> <span class="o">=</span> <span class="n">clash_score_container</span><span class="o">.</span><span class="n">Get</span><span class="p">(</span><span class="s2">"clash"</span><span class="p">)</span>
<span class="n">to_keep</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">bb_list</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">candidates</span><span class="p">):</span>
- <span class="n">score</span> <span class="o">=</span> <span class="n">scorer</span><span class="o">.</span><span class="n">CalculateScore</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span>
- <span class="n">n_stem</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">(),</span>
- <span class="n">actual_gap</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">())</span>
- <span class="k">if</span> <span class="n">score</span> <span class="o"><</span> <span class="n">clash_thresh</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">clash_scores</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o"><</span> <span class="n">clash_thresh</span><span class="p">:</span>
<span class="n">to_keep</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
<span class="n">candidates</span> <span class="o">=</span> <span class="n">candidates</span><span class="o">.</span><span class="n">Extract</span><span class="p">(</span><span class="n">to_keep</span><span class="p">)</span>
<span class="n">orig_indices</span> <span class="o">=</span> <span class="p">[</span><span class="n">orig_indices</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">to_keep</span><span class="p">]</span>
<span class="k">assert</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">orig_indices</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">))</span>
- <span class="c"># check for ring punchings</span>
+ <span class="c1"># check for ring punchings</span>
<span class="k">if</span> <span class="n">ring_punch_detection</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">FilterCandidates</span><span class="p">(</span><span class="n">candidates</span><span class="p">,</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span>
<span class="n">actual_gap</span><span class="p">,</span> <span class="n">orig_indices</span><span class="p">)</span>
@@ -817,16 +858,16 @@
<span class="n">FilterCandidatesWithSC</span><span class="p">(</span><span class="n">candidates</span><span class="p">,</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span>
<span class="n">actual_gap</span><span class="p">,</span> <span class="n">orig_indices</span><span class="p">)</span>
- <span class="c"># skip if no loop was successfully closed</span>
+ <span class="c1"># skip if no loop was successfully closed</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">continue</span>
- <span class="c"># deal with DB features</span>
+ <span class="c1"># deal with DB features</span>
<span class="k">if</span> <span class="n">add_db_features</span><span class="p">:</span>
- <span class="c"># get subset of stem rmsd scores</span>
+ <span class="c1"># get subset of stem rmsd scores</span>
<span class="k">assert</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">orig_indices</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">))</span>
<span class="n">db_scores</span> <span class="o">=</span> <span class="n">db_scores</span><span class="o">.</span><span class="n">Extract</span><span class="p">(</span><span class="n">orig_indices</span><span class="p">)</span>
- <span class="c"># add profile scores</span>
+ <span class="c1"># add profile scores</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">profiles</span><span class="p">[</span><span class="n">actual_gap</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">()]</span>
<span class="n">start_pos</span> <span class="o">=</span> <span class="n">n_stem</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span> <span class="o">-</span> <span class="mi">1</span>
<span class="n">candidates</span><span class="o">.</span><span class="n">CalculateSequenceProfileScores</span><span class="p">(</span><span class="n">db_scores</span><span class="p">,</span>
@@ -835,43 +876,44 @@
<span class="n">candidates</span><span class="o">.</span><span class="n">CalculateStructureProfileScores</span><span class="p">(</span><span class="n">db_scores</span><span class="p">,</span>
<span class="n">structure_db</span><span class="p">,</span>
<span class="n">prof</span><span class="p">,</span> <span class="n">start_pos</span><span class="p">)</span>
- <span class="c"># update list</span>
+ <span class="c1"># update list</span>
<span class="n">actual_db_scores</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">db_scores</span><span class="p">)</span>
- <span class="c"># update candidate lists</span>
+ <span class="c1"># update candidate lists</span>
<span class="n">actual_candidates</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">candidates</span><span class="p">)</span>
<span class="n">actual_extended_gaps</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">actual_gap</span><span class="o">.</span><span class="n">Copy</span><span class="p">())</span>
<span class="n">found_loops</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">)</span>
- <span class="c"># skip if we didn't find enough</span>
+ <span class="c1"># skip if we didn't find enough</span>
<span class="k">if</span> <span class="n">found_loops</span> <span class="o"><</span> <span class="n">min_loops_required</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Failed at loop insertion (</span><span class="si">%s</span><span class="s">), only </span><span class="si">%d</span><span class="s"> candidates"</span> <span class="o">%</span> \
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Failed at loop insertion (</span><span class="si">%s</span><span class="s2">), only </span><span class="si">%d</span><span class="s2"> candidates"</span> <span class="o">%</span> \
<span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">),</span> <span class="n">found_loops</span><span class="p">))</span>
<span class="n">gap_idx</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">continue</span>
- <span class="c">##################################</span>
- <span class="c"># close loop</span>
- <span class="c">##################################</span>
+ <span class="c1">##################################</span>
+ <span class="c1"># close loop</span>
+ <span class="c1">##################################</span>
<span class="n">new_idx</span> <span class="o">=</span> <span class="n">_CloseLoop</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">gap_orig</span><span class="p">,</span> <span class="n">actual_candidates</span><span class="p">,</span>
<span class="n">actual_extended_gaps</span><span class="p">,</span> <span class="n">score_variant</span><span class="p">,</span>
- <span class="n">actual_db_scores</span><span class="p">,</span> <span class="n">max_num_all_atom</span><span class="p">)</span>
+ <span class="n">actual_db_scores</span><span class="p">,</span> <span class="n">max_num_all_atom</span><span class="p">,</span>
+ <span class="n">length_dep_weights</span><span class="p">)</span>
<span class="k">if</span> <span class="n">new_idx</span> <span class="o">==</span> <span class="o">-</span><span class="mi">2</span><span class="p">:</span>
- <span class="c"># try next one if we failed</span>
+ <span class="c1"># try next one if we failed</span>
<span class="n">gap_idx</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
- <span class="c"># all good: fix sidechains if we're in ring-punch-mode and continue</span>
+ <span class="c1"># all good: fix sidechains if we're in ring-punch-mode and continue</span>
<span class="k">if</span> <span class="n">ring_punch_detection</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
- <span class="n">gap_idx</span> <span class="o">=</span> <span class="n">new_idx</span>
+ <span class="n">gap_idx</span> <span class="o">=</span> <span class="n">new_idx</span></div>
+
-</div>
<div class="viewcode-block" id="FillLoopsByMonteCarlo"><a class="viewcode-back" href="../../../modelling/pipeline.html#promod3.modelling.FillLoopsByMonteCarlo">[docs]</a><span class="k">def</span> <span class="nf">FillLoopsByMonteCarlo</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="p">,</span> <span class="n">max_loops_to_search</span><span class="o">=</span><span class="mi">6</span><span class="p">,</span>
<span class="n">max_extension</span><span class="o">=</span><span class="mi">30</span><span class="p">,</span> <span class="n">mc_num_loops</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">mc_steps</span><span class="o">=</span><span class="mi">5000</span><span class="p">,</span>
<span class="n">use_scoring_extender</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> <span class="n">use_full_extender</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
<span class="n">score_variant</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">ring_punch_detection</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">fragger_handles</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">chain_idx</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
- <span class="n">resnum_range</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+ <span class="n">resnum_range</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">length_dep_weights</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">'''Try to fill up loops with Monte Carlo sampling.</span>
<span class="sd"> This is meant as a "last-resort" approach when it is not possible to fill</span>
@@ -938,89 +980,96 @@
<span class="sd"> :param resnum_range: If not None, only gaps within this resnum range get</span>
<span class="sd"> processed</span>
<span class="sd"> :type resnum_range: :class:`tuple` containing two :class:`int`</span>
+
+<span class="sd"> :param length_dep_weights: :class:`ScoringWeights` provides different sets</span>
+<span class="sd"> of weights that have been trained on different</span>
+<span class="sd"> loop subsets. If this flag is true, the length</span>
+<span class="sd"> dependent weights are used to select the final </span>
+<span class="sd"> loops.</span>
+<span class="sd"> :type length_dep_weights: :class:`bool`</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'closegaps::FillLoopsByMonteCarlo'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'closegaps::FillLoopsByMonteCarlo'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Trying to fill </span><span class="si">%d</span><span class="s"> gap(s) by Monte Carlo."</span> \
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Trying to fill </span><span class="si">%d</span><span class="s2"> gap(s) by Monte Carlo."</span> \
<span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span>
- <span class="c"># check/setup scoring</span>
+ <span class="c1"># check/setup scoring</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">IsBackboneScoringSetUp</span><span class="p">(</span><span class="n">mhandle</span><span class="p">):</span>
<span class="n">SetupDefaultBackboneScoring</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
- <span class="c"># point to the current gap</span>
+ <span class="c1"># point to the current gap</span>
<span class="n">gap_idx</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="c"># Iterate all gaps. Since the number of gaps may change, always compare to</span>
- <span class="c"># an updated list. gap_idx is only increased when necessary, e.g. current</span>
- <span class="c"># gap could not be removed.</span>
+ <span class="c1"># Iterate all gaps. Since the number of gaps may change, always compare to</span>
+ <span class="c1"># an updated list. gap_idx is only increased when necessary, e.g. current</span>
+ <span class="c1"># gap could not be removed.</span>
<span class="k">while</span> <span class="n">gap_idx</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span> <span class="ow">and</span> <span class="n">gap_idx</span> <span class="o">>=</span> <span class="mi">0</span><span class="p">:</span>
- <span class="c"># keep copy of original gap</span>
+ <span class="c1"># keep copy of original gap</span>
<span class="n">gap_orig</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">gap_idx</span><span class="p">]</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
<span class="k">if</span> <span class="n">score_variant</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="n">gap_ins</span> <span class="o">=</span> <span class="n">CountEnclosedInsertions</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">gap_orig</span><span class="p">)</span>
- <span class="c"># ignore terminal gaps and out-of-range (if range given)</span>
+ <span class="c1"># ignore terminal gaps and out-of-range (if range given)</span>
<span class="k">if</span> <span class="n">gap_orig</span><span class="o">.</span><span class="n">IsTerminal</span><span class="p">()</span> \
<span class="ow">or</span> <span class="ow">not</span> <span class="n">_InRange</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">,</span> <span class="n">chain_idx</span><span class="p">,</span> <span class="n">resnum_range</span><span class="p">):</span>
<span class="n">gap_idx</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">continue</span>
- <span class="c">##################################</span>
- <span class="c"># find loop candidates</span>
- <span class="c">##################################</span>
- <span class="c"># list of LoopCandidates to fill gap</span>
+ <span class="c1">##################################</span>
+ <span class="c1"># find loop candidates</span>
+ <span class="c1">##################################</span>
+ <span class="c1"># list of LoopCandidates to fill gap</span>
<span class="n">actual_candidates</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
- <span class="c"># list of StructuralGap corresponding to actual_candidates</span>
+ <span class="c1"># list of StructuralGap corresponding to actual_candidates</span>
<span class="n">actual_extended_gaps</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
- <span class="c"># number of loops found (stop if >= max_loops_to_search)</span>
+ <span class="c1"># number of loops found (stop if >= max_loops_to_search)</span>
<span class="n">found_loops</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="c"># currently extended gap and gap-extender</span>
+ <span class="c1"># currently extended gap and gap-extender</span>
<span class="n">actual_gap</span> <span class="o">=</span> <span class="n">gap_orig</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
- <span class="c"># each extension can make it at most 1 longer...</span>
+ <span class="c1"># each extension can make it at most 1 longer...</span>
<span class="n">max_loop_len</span> <span class="o">=</span> <span class="n">gap_orig</span><span class="o">.</span><span class="n">length</span> <span class="o">+</span> <span class="n">max_extension</span>
<span class="n">actual_extender</span> <span class="o">=</span> <span class="n">_GetGapExtender</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">actual_gap</span><span class="p">,</span>
<span class="n">use_scoring_extender</span><span class="p">,</span>
<span class="n">use_full_extender</span><span class="p">,</span>
<span class="n">max_loop_len</span><span class="p">)</span>
<span class="n">actual_chain_idx</span> <span class="o">=</span> <span class="n">actual_gap</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">()</span>
- <span class="c"># iteratively extend actual_gap</span>
+ <span class="c1"># iteratively extend actual_gap</span>
<span class="n">ext_step</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">first_iteration</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">while</span> <span class="n">found_loops</span> <span class="o"><</span> <span class="n">max_loops_to_search</span> <span class="ow">and</span> <span class="n">ext_step</span> <span class="o"><</span> <span class="n">max_extension</span><span class="p">:</span>
- <span class="c"># extend the gap</span>
+ <span class="c1"># extend the gap</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">first_iteration</span><span class="p">:</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">actual_extender</span><span class="o">.</span><span class="n">Extend</span><span class="p">():</span>
<span class="k">break</span>
<span class="n">first_iteration</span> <span class="o">=</span> <span class="bp">False</span>
- <span class="c"># make sure, that the loop seq has at least length 3</span>
+ <span class="c1"># make sure, that the loop seq has at least length 3</span>
<span class="k">if</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">actual_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">):</span>
<span class="k">continue</span>
<span class="n">ext_step</span> <span class="o">+=</span> <span class="mi">1</span>
- <span class="c"># ensure both stems are valid</span>
+ <span class="c1"># ensure both stems are valid</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">actual_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">or</span> \
<span class="ow">not</span> <span class="n">actual_gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
<span class="k">break</span>
- <span class="c"># skip if we try to merge insertions with score_variant=0</span>
+ <span class="c1"># skip if we try to merge insertions with score_variant=0</span>
<span class="k">if</span> <span class="n">score_variant</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">and</span> \
<span class="n">CountEnclosedInsertions</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">actual_gap</span><span class="p">)</span> <span class="o">!=</span> <span class="n">gap_ins</span><span class="p">:</span>
<span class="k">continue</span>
- <span class="c"># setup sampler, closer, scorer and cooler for MC</span>
+ <span class="c1"># setup sampler, closer, scorer and cooler for MC</span>
<span class="k">if</span> <span class="n">fragger_handles</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">fragger_handle</span> <span class="o">=</span> <span class="n">fragger_handles</span><span class="p">[</span><span class="n">actual_chain_idx</span><span class="p">]</span>
<span class="k">try</span><span class="p">:</span>
- <span class="c"># choose sampler</span>
+ <span class="c1"># choose sampler</span>
<span class="k">if</span> <span class="n">fragger_handles</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> \
<span class="n">actual_gap</span><span class="o">.</span><span class="n">length</span> <span class="o"><</span> <span class="n">fragger_handle</span><span class="o">.</span><span class="n">fragment_length</span><span class="p">:</span>
<span class="n">mc_sampler</span> <span class="o">=</span> <span class="n">PhiPsiSampler</span><span class="p">(</span><span class="n">actual_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">,</span>
@@ -1039,66 +1088,69 @@
<span class="n">weights</span> <span class="o">=</span> <span class="n">_GetMCWeights</span><span class="p">()</span>
<span class="n">mc_scorer</span> <span class="o">=</span> <span class="n">LinearScorer</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer</span><span class="p">,</span>
+ <span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer_env</span><span class="p">,</span>
<span class="n">actual_gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">(),</span>
+ <span class="nb">len</span><span class="p">(</span><span class="n">actual_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">),</span>
<span class="n">actual_chain_idx</span><span class="p">,</span> <span class="n">weights</span><span class="p">)</span>
<span class="n">start_temperature</span> <span class="o">=</span> <span class="mi">100</span>
<span class="n">cooling_factor</span> <span class="o">=</span> <span class="mf">0.9</span>
- <span class="c"># the number of 109 is roughly the number of times we have to apply</span>
- <span class="c"># a factor of 0.9 to 100 until it reaches a value of 0.001</span>
+ <span class="c1"># the number of 109 is roughly the number of times we have to apply</span>
+ <span class="c1"># a factor of 0.9 to 100 until it reaches a value of 0.001</span>
<span class="n">cooling_interval</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="n">mc_steps</span><span class="o">/</span><span class="mf">109.0</span><span class="p">))</span>
<span class="n">mc_cooler</span> <span class="o">=</span> <span class="n">ExponentialCooler</span><span class="p">(</span><span class="n">cooling_interval</span><span class="p">,</span>
<span class="n">start_temperature</span><span class="p">,</span>
<span class="n">cooling_factor</span><span class="p">)</span>
<span class="k">except</span><span class="p">:</span>
- <span class="c"># something went terribly wrong...</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s">'Failed to set up MC components'</span><span class="p">)</span>
+ <span class="c1"># something went terribly wrong...</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s1">'Failed to set up MC components'</span><span class="p">)</span>
<span class="k">raise</span>
- <span class="c"># try to get candidates for the current loop</span>
+ <span class="c1"># try to get candidates for the current loop</span>
<span class="k">try</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s">"Firing MC for "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">))</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s2">"Firing MC for "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">))</span>
<span class="n">candidates</span> <span class="o">=</span> <span class="n">LoopCandidates</span><span class="o">.</span><span class="n">FillFromMonteCarloSampler</span><span class="p">(</span>
<span class="n">actual_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">,</span> <span class="n">mc_num_loops</span><span class="p">,</span> <span class="n">mc_steps</span><span class="p">,</span> <span class="n">mc_sampler</span><span class="p">,</span>
<span class="n">mc_closer</span><span class="p">,</span> <span class="n">mc_scorer</span><span class="p">,</span> <span class="n">mc_cooler</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">RuntimeError</span><span class="p">:</span>
- <span class="c"># monte carlo cannot be initialized when the stems are too far</span>
- <span class="c"># apart => we need further loop extension</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s">"Failed in setting up "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">)</span> <span class="o">+</span>
- <span class="s">" stems might be too far away..."</span><span class="p">)</span>
+ <span class="c1"># monte carlo cannot be initialized when the stems are too far</span>
+ <span class="c1"># apart => we need further loop extension</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s2">"Failed in setting up "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">)</span> <span class="o">+</span>
+ <span class="s2">" stems might be too far away..."</span><span class="p">)</span>
<span class="k">continue</span>
- <span class="c"># check for ring punchings</span>
+ <span class="c1"># check for ring punchings</span>
<span class="k">if</span> <span class="n">ring_punch_detection</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">FilterCandidates</span><span class="p">(</span><span class="n">candidates</span><span class="p">,</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">actual_gap</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">ring_punch_detection</span> <span class="o">==</span> <span class="mi">2</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">FilterCandidatesWithSC</span><span class="p">(</span><span class="n">candidates</span><span class="p">,</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">actual_gap</span><span class="p">)</span>
- <span class="c"># skip if nothing found</span>
+ <span class="c1"># skip if nothing found</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">continue</span>
- <span class="c"># update candidate lists</span>
+ <span class="c1"># update candidate lists</span>
<span class="n">actual_candidates</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">candidates</span><span class="p">)</span>
<span class="n">actual_extended_gaps</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">actual_gap</span><span class="o">.</span><span class="n">Copy</span><span class="p">())</span>
<span class="n">found_loops</span> <span class="o">+=</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">)</span>
- <span class="c">##################################</span>
- <span class="c"># close loop</span>
- <span class="c">##################################</span>
+ <span class="c1">##################################</span>
+ <span class="c1"># close loop</span>
+ <span class="c1">##################################</span>
<span class="n">new_idx</span> <span class="o">=</span> <span class="n">_CloseLoop</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">gap_orig</span><span class="p">,</span> <span class="n">actual_candidates</span><span class="p">,</span>
- <span class="n">actual_extended_gaps</span><span class="p">,</span> <span class="n">score_variant</span><span class="p">)</span>
+ <span class="n">actual_extended_gaps</span><span class="p">,</span> <span class="n">score_variant</span><span class="p">,</span>
+ <span class="n">length_dep_weights</span><span class="o">=</span><span class="n">length_dep_weights</span><span class="p">)</span>
<span class="k">if</span> <span class="n">new_idx</span> <span class="o">==</span> <span class="o">-</span><span class="mi">2</span><span class="p">:</span>
- <span class="c"># try next one if we failed</span>
+ <span class="c1"># try next one if we failed</span>
<span class="n">gap_idx</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
- <span class="c"># all good: fix sidechains if we're in ring-punch-mode and continue</span>
+ <span class="c1"># all good: fix sidechains if we're in ring-punch-mode and continue</span>
<span class="k">if</span> <span class="n">ring_punch_detection</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
<span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
- <span class="n">gap_idx</span> <span class="o">=</span> <span class="n">new_idx</span>
+ <span class="n">gap_idx</span> <span class="o">=</span> <span class="n">new_idx</span></div>
+
-</div>
<div class="viewcode-block" id="CloseGaps"><a class="viewcode-back" href="../../../modelling/pipeline.html#promod3.modelling.CloseGaps">[docs]</a><span class="k">def</span> <span class="nf">CloseGaps</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">merge_distance</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span> <span class="n">fragment_db</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">structure_db</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
<span class="n">torsion_sampler</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">fragger_handles</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">chain_idx</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
- <span class="n">resnum_range</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+ <span class="n">resnum_range</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">length_dep_weights</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">'''</span>
<span class="sd"> Tries to close all gaps in a model, except termini. It will go through</span>
<span class="sd"> following steps:</span>
@@ -1144,9 +1196,16 @@
<span class="sd"> :param resnum_range: If not None, only gaps within this resnum range get</span>
<span class="sd"> processed.</span>
<span class="sd"> :type resnum_range: :class:`tuple` containing two :class:`int` </span>
+
+<span class="sd"> :param length_dep_weights: :class:`ScoringWeights` provides different sets</span>
+<span class="sd"> of weights that have been trained on different</span>
+<span class="sd"> loop subsets. If this flag is true, the length</span>
+<span class="sd"> dependent weights are used to close loops with</span>
+<span class="sd"> database / Monte Carlo.</span>
+<span class="sd"> :type length_dep_weights: :class:`bool`</span>
<span class="sd"> '''</span>
- <span class="c"># load stuff if needed</span>
+ <span class="c1"># load stuff if needed</span>
<span class="k">if</span> <span class="n">fragment_db</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">fragment_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">()</span>
<span class="k">if</span> <span class="n">structure_db</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
@@ -1154,48 +1213,52 @@
<span class="k">if</span> <span class="n">torsion_sampler</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">torsion_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">()</span>
- <span class="c"># try to close small deletions by relaxing them</span>
+ <span class="c1"># try to close small deletions by relaxing them</span>
<span class="n">CloseSmallDeletions</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">chain_idx</span><span class="o">=</span><span class="n">chain_idx</span><span class="p">,</span>
<span class="n">resnum_range</span><span class="o">=</span><span class="n">resnum_range</span><span class="p">)</span>
- <span class="c"># iteratively merge gaps of distance i and fill loops by database</span>
+ <span class="c1"># iteratively merge gaps of distance i and fill loops by database</span>
<span class="k">for</span> <span class="n">distance</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">merge_distance</span><span class="p">):</span>
<span class="n">MergeGapsByDistance</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">distance</span><span class="p">,</span> <span class="n">chain_idx</span><span class="o">=</span><span class="n">chain_idx</span><span class="p">,</span>
<span class="n">resnum_range</span><span class="o">=</span><span class="n">resnum_range</span><span class="p">)</span>
<span class="n">FillLoopsByDatabase</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">fragment_db</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">,</span>
<span class="n">torsion_sampler</span><span class="p">,</span> <span class="n">min_loops_required</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span>
<span class="n">max_res_extension</span><span class="o">=</span><span class="mi">6</span><span class="p">,</span> <span class="n">chain_idx</span><span class="o">=</span><span class="n">chain_idx</span><span class="p">,</span>
- <span class="n">resnum_range</span><span class="o">=</span><span class="n">resnum_range</span><span class="p">,</span> <span class="n">clash_thresh</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
+ <span class="n">resnum_range</span><span class="o">=</span><span class="n">resnum_range</span><span class="p">,</span> <span class="n">clash_thresh</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span>
+ <span class="n">length_dep_weights</span><span class="o">=</span><span class="n">length_dep_weights</span><span class="p">)</span>
- <span class="c"># if above fails, try DB-fill with less restrictions</span>
+ <span class="c1"># if above fails, try DB-fill with less restrictions</span>
<span class="n">FillLoopsByDatabase</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">fragment_db</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">,</span>
<span class="n">torsion_sampler</span><span class="p">,</span> <span class="n">min_loops_required</span><span class="o">=-</span><span class="mi">1</span><span class="p">,</span>
<span class="n">chain_idx</span><span class="o">=</span><span class="n">chain_idx</span><span class="p">,</span> <span class="n">resnum_range</span><span class="o">=</span><span class="n">resnum_range</span><span class="p">,</span>
- <span class="n">clash_thresh</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
+ <span class="n">clash_thresh</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span>
+ <span class="n">length_dep_weights</span><span class="o">=</span><span class="n">length_dep_weights</span><span class="p">)</span>
<span class="n">FillLoopsByDatabase</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">fragment_db</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">,</span>
<span class="n">torsion_sampler</span><span class="p">,</span> <span class="n">chain_idx</span><span class="o">=</span><span class="n">chain_idx</span><span class="p">,</span>
- <span class="n">resnum_range</span><span class="o">=</span><span class="n">resnum_range</span><span class="p">)</span>
+ <span class="n">resnum_range</span><span class="o">=</span><span class="n">resnum_range</span><span class="p">,</span>
+ <span class="n">length_dep_weights</span><span class="o">=</span><span class="n">length_dep_weights</span><span class="p">)</span>
- <span class="c"># close remaining gaps by Monte Carlo</span>
+ <span class="c1"># close remaining gaps by Monte Carlo</span>
<span class="n">FillLoopsByMonteCarlo</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="p">,</span>
<span class="n">fragger_handles</span><span class="o">=</span><span class="n">fragger_handles</span><span class="p">,</span>
<span class="n">chain_idx</span><span class="o">=</span><span class="n">chain_idx</span><span class="p">,</span>
- <span class="n">resnum_range</span><span class="o">=</span><span class="n">resnum_range</span><span class="p">)</span>
+ <span class="n">resnum_range</span><span class="o">=</span><span class="n">resnum_range</span><span class="p">,</span>
+ <span class="n">length_dep_weights</span><span class="o">=</span><span class="n">length_dep_weights</span><span class="p">)</span>
- <span class="c"># last resort approach to close large deletions</span>
+ <span class="c1"># last resort approach to close large deletions</span>
<span class="n">CloseLargeDeletions</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">,</span> <span class="n">chain_idx</span><span class="o">=</span><span class="n">chain_idx</span><span class="p">,</span>
- <span class="n">resnum_range</span><span class="o">=</span><span class="n">resnum_range</span><span class="p">)</span>
+ <span class="n">resnum_range</span><span class="o">=</span><span class="n">resnum_range</span><span class="p">)</span></div>
+
+ <span class="c1"># NOTE:</span>
+ <span class="c1"># In the function above, we call :func:`FillLoopsByDatabase` multiple</span>
+ <span class="c1"># times. First, we try to close "easy" gaps which require few extensions</span>
+ <span class="c1"># (we wish to limit the damage we do on the template) and for which we have</span>
+ <span class="c1"># plenty of loop candidates. If some gaps cannot be closed like this, we try</span>
+ <span class="c1"># less restrictive options. This approach is helpful if neighboring gaps are</span>
+ <span class="c1"># close together and the one closer to the C-terminus is easier to close.</span>
+ <span class="c1"># Several variants were evaluated on 1752 target-template-pairs and this one</span>
+ <span class="c1"># worked best.</span>
- <span class="c"># NOTE:</span>
- <span class="c"># In the function above, we call :func:`FillLoopsByDatabase` multiple</span>
- <span class="c"># times. First, we try to close "easy" gaps which require few extensions</span>
- <span class="c"># (we wish to limit the damage we do on the template) and for which we have</span>
- <span class="c"># plenty of loop candidates. If some gaps cannot be closed like this, we try</span>
- <span class="c"># less restrictive options. This approach is helpful if neighboring gaps are</span>
- <span class="c"># close together and the one closer to the C-terminus is easier to close.</span>
- <span class="c"># Several variants were evaluated on 1752 target-template-pairs and this one</span>
- <span class="c"># worked best.</span>
-</div>
<div class="viewcode-block" id="ModelTermini"><a class="viewcode-back" href="../../../modelling/pipeline.html#promod3.modelling.ModelTermini">[docs]</a><span class="k">def</span> <span class="nf">ModelTermini</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="p">,</span> <span class="n">fragger_handles</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
<span class="n">mc_num_loops</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span> <span class="n">mc_steps</span><span class="o">=</span><span class="mi">5000</span><span class="p">):</span>
<span class="sd">'''Try to model termini with Monte Carlo sampling.</span>
@@ -1230,24 +1293,24 @@
<span class="sd"> :type mc_steps: :class:`int`</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'closegaps::ModelTermini'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'closegaps::ModelTermini'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
- <span class="c"># get terminal gaps (copies as we'll clear them as we go)</span>
+ <span class="c1"># get terminal gaps (copies as we'll clear them as we go)</span>
<span class="n">terminal_gaps</span> <span class="o">=</span> <span class="p">[</span><span class="n">g</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span> <span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span> <span class="k">if</span> <span class="n">g</span><span class="o">.</span><span class="n">IsTerminal</span><span class="p">()</span> <span class="ow">and</span> <span class="n">g</span><span class="o">.</span><span class="n">length</span> <span class="o">></span> <span class="mi">1</span><span class="p">]</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">terminal_gaps</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Trying to model </span><span class="si">%d</span><span class="s"> terminal gap(s)."</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">terminal_gaps</span><span class="p">))</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Trying to model </span><span class="si">%d</span><span class="s2"> terminal gap(s)."</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">terminal_gaps</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span>
- <span class="c"># check/setup scoring</span>
+ <span class="c1"># check/setup scoring</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">IsBackboneScoringSetUp</span><span class="p">(</span><span class="n">mhandle</span><span class="p">):</span>
<span class="n">SetupDefaultBackboneScoring</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
- <span class="c"># model them</span>
+ <span class="c1"># model them</span>
<span class="k">for</span> <span class="n">actual_gap</span> <span class="ow">in</span> <span class="n">terminal_gaps</span><span class="p">:</span>
- <span class="c"># extract info</span>
+ <span class="c1"># extract info</span>
<span class="k">if</span> <span class="n">actual_gap</span><span class="o">.</span><span class="n">IsNTerminal</span><span class="p">():</span>
<span class="n">start_resnum</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">else</span><span class="p">:</span>
@@ -1257,7 +1320,7 @@
<span class="k">if</span> <span class="n">fragger_handles</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">fragger_handle</span> <span class="o">=</span> <span class="n">fragger_handles</span><span class="p">[</span><span class="n">actual_chain_idx</span><span class="p">]</span>
- <span class="c"># choose sampler</span>
+ <span class="c1"># choose sampler</span>
<span class="k">if</span> <span class="n">fragger_handles</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> \
<span class="n">actual_gap</span><span class="o">.</span><span class="n">length</span> <span class="o"><</span> <span class="n">fragger_handle</span><span class="o">.</span><span class="n">fragment_length</span><span class="p">:</span>
<span class="n">mc_sampler</span> <span class="o">=</span> <span class="n">PhiPsiSampler</span><span class="p">(</span><span class="n">actual_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">,</span>
@@ -1268,50 +1331,51 @@
<span class="n">mc_sampler</span> <span class="o">=</span> <span class="n">FragmentSampler</span><span class="p">(</span><span class="n">actual_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">,</span> <span class="n">fragger_list</span><span class="p">,</span>
<span class="n">init_fragments</span><span class="o">=</span><span class="mi">5</span><span class="p">)</span>
- <span class="c"># choose closer</span>
+ <span class="c1"># choose closer</span>
<span class="k">if</span> <span class="n">actual_gap</span><span class="o">.</span><span class="n">IsNTerminal</span><span class="p">():</span>
<span class="n">mc_closer</span> <span class="o">=</span> <span class="n">NTerminalCloser</span><span class="p">(</span><span class="n">actual_gap</span><span class="o">.</span><span class="n">after</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">mc_closer</span> <span class="o">=</span> <span class="n">CTerminalCloser</span><span class="p">(</span><span class="n">actual_gap</span><span class="o">.</span><span class="n">before</span><span class="p">)</span>
- <span class="c"># setup scorer</span>
+ <span class="c1"># setup scorer</span>
<span class="n">weights</span> <span class="o">=</span> <span class="n">_GetMCWeights</span><span class="p">()</span>
- <span class="n">mc_scorer</span> <span class="o">=</span> <span class="n">LinearScorer</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer</span><span class="p">,</span> <span class="n">start_resnum</span><span class="p">,</span>
+ <span class="n">mc_scorer</span> <span class="o">=</span> <span class="n">LinearScorer</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer</span><span class="p">,</span>
+ <span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer_env</span><span class="p">,</span>
+ <span class="n">start_resnum</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">actual_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">),</span>
<span class="n">actual_chain_idx</span><span class="p">,</span> <span class="n">weights</span><span class="p">)</span>
- <span class="c"># setup cooler</span>
+ <span class="c1"># setup cooler</span>
<span class="n">start_temperature</span> <span class="o">=</span> <span class="mi">100</span>
<span class="n">cooling_factor</span> <span class="o">=</span> <span class="mf">0.9</span>
- <span class="c"># the number of 109 is roughly the number of times we have to apply</span>
- <span class="c"># a factor of 0.9 to 100 until it reaches a value of 0.001</span>
+ <span class="c1"># the number of 109 is roughly the number of times we have to apply</span>
+ <span class="c1"># a factor of 0.9 to 100 until it reaches a value of 0.001</span>
<span class="n">cooling_interval</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">round</span><span class="p">(</span><span class="n">mc_steps</span><span class="o">/</span><span class="mf">109.0</span><span class="p">))</span>
<span class="n">mc_cooler</span> <span class="o">=</span> <span class="n">ExponentialCooler</span><span class="p">(</span><span class="n">cooling_interval</span><span class="p">,</span> <span class="n">start_temperature</span><span class="p">,</span>
<span class="n">cooling_factor</span><span class="p">)</span>
- <span class="c"># try to get loop candidates</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s">"Firing MC for "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">))</span>
+ <span class="c1"># try to get loop candidates</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s2">"Firing MC for "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">))</span>
<span class="n">candidates</span> <span class="o">=</span> <span class="n">LoopCandidates</span><span class="o">.</span><span class="n">FillFromMonteCarloSampler</span><span class="p">(</span>
<span class="n">actual_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">,</span> <span class="n">mc_num_loops</span><span class="p">,</span> <span class="n">mc_steps</span><span class="p">,</span> <span class="n">mc_sampler</span><span class="p">,</span>
<span class="n">mc_closer</span><span class="p">,</span> <span class="n">mc_scorer</span><span class="p">,</span> <span class="n">mc_cooler</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="c"># score candidates</span>
+ <span class="c1"># score candidates</span>
<span class="n">bb_scores</span> <span class="o">=</span> <span class="n">ScoreContainer</span><span class="p">()</span>
- <span class="n">candidates</span><span class="o">.</span><span class="n">CalculateBackboneScores</span><span class="p">(</span><span class="n">bb_scores</span><span class="p">,</span>
- <span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer</span><span class="p">,</span>
+ <span class="n">candidates</span><span class="o">.</span><span class="n">CalculateBackboneScores</span><span class="p">(</span><span class="n">bb_scores</span><span class="p">,</span> <span class="n">mhandle</span><span class="p">,</span>
<span class="n">start_resnum</span><span class="p">,</span> <span class="n">actual_chain_idx</span><span class="p">)</span>
<span class="n">scores</span> <span class="o">=</span> <span class="n">bb_scores</span><span class="o">.</span><span class="n">LinearCombine</span><span class="p">(</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetWeights</span><span class="p">())</span>
<span class="n">min_score</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">scores</span><span class="p">)</span>
<span class="n">min_idx</span> <span class="o">=</span> <span class="n">scores</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">min_score</span><span class="p">)</span>
- <span class="c"># report</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Resolved terminal gap </span><span class="si">%s</span><span class="s"> (</span><span class="si">%d</span><span class="s"> candidates)"</span> <span class="o">%</span> \
+ <span class="c1"># report</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Resolved terminal gap </span><span class="si">%s</span><span class="s2"> (</span><span class="si">%d</span><span class="s2"> candidates)"</span> <span class="o">%</span> \
<span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">),</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">)))</span>
- <span class="c"># update model and clear gap</span>
+ <span class="c1"># update model and clear gap</span>
<span class="n">InsertLoopClearGaps</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">candidates</span><span class="p">[</span><span class="n">min_idx</span><span class="p">],</span> <span class="n">actual_gap</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Failed to model terminal gap (</span><span class="si">%s</span><span class="s">)"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">))</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Failed to model terminal gap (</span><span class="si">%s</span><span class="s2">)"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">))</span></div>
-</div>
+
<div class="viewcode-block" id="CloseLargeDeletions"><a class="viewcode-back" href="../../../modelling/pipeline.html#promod3.modelling.CloseLargeDeletions">[docs]</a><span class="k">def</span> <span class="nf">CloseLargeDeletions</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">,</span> <span class="n">linker_length</span><span class="o">=</span><span class="mi">8</span><span class="p">,</span>
<span class="n">num_fragments</span><span class="o">=</span><span class="mi">500</span><span class="p">,</span> <span class="n">use_scoring_extender</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
<span class="n">use_full_extender</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> <span class="n">chain_idx</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
@@ -1358,51 +1422,51 @@
<span class="sd"> :type resnum_range: :class:`tuple` containing two :class:`int`</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'closegaps::CloseLargeDeletions'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'closegaps::CloseLargeDeletions'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Trying to resolve large deletions (</span><span class="si">%d</span><span class="s"> gap(s) left) by "</span>
- <span class="s">"sampling a linker region."</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Trying to resolve large deletions (</span><span class="si">%d</span><span class="s2"> gap(s) left) by "</span>
+ <span class="s2">"sampling a linker region."</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="k">return</span>
- <span class="c"># check/setup scoring</span>
+ <span class="c1"># check/setup scoring</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">IsBackboneScoringSetUp</span><span class="p">(</span><span class="n">mhandle</span><span class="p">):</span>
<span class="n">SetupDefaultBackboneScoring</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
- <span class="c"># point to the current gap</span>
+ <span class="c1"># point to the current gap</span>
<span class="n">gap_idx</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="c"># Iterate all gaps. Since the number of gaps may change, always compare to</span>
- <span class="c"># an updated list. gap_idx is only increased when necessary, e.g. current</span>
- <span class="c"># gap could not be removed.</span>
+ <span class="c1"># Iterate all gaps. Since the number of gaps may change, always compare to</span>
+ <span class="c1"># an updated list. gap_idx is only increased when necessary, e.g. current</span>
+ <span class="c1"># gap could not be removed.</span>
<span class="k">while</span> <span class="n">gap_idx</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span> <span class="ow">and</span> <span class="n">gap_idx</span> <span class="o">>=</span> <span class="mi">0</span><span class="p">:</span>
- <span class="c"># keep copy of original gap</span>
+ <span class="c1"># keep copy of original gap</span>
<span class="n">gap_orig</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">gap_idx</span><span class="p">]</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
- <span class="c"># check whether we are in the desired range</span>
+ <span class="c1"># check whether we are in the desired range</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">_InRange</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">,</span> <span class="n">chain_idx</span><span class="p">,</span> <span class="n">resnum_range</span><span class="p">):</span>
<span class="n">gap_idx</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">continue</span>
- <span class="c"># get chain for gap</span>
+ <span class="c1"># get chain for gap</span>
<span class="n">actual_chain_idx</span> <span class="o">=</span> <span class="n">gap_orig</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">()</span>
<span class="n">actual_chain</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="n">actual_chain_idx</span><span class="p">]</span>
- <span class="c"># terminal gaps are not deletions...</span>
+ <span class="c1"># terminal gaps are not deletions...</span>
<span class="k">if</span> <span class="n">gap_orig</span><span class="o">.</span><span class="n">IsTerminal</span><span class="p">():</span>
<span class="n">gap_idx</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">continue</span>
- <span class="c"># check if too long</span>
+ <span class="c1"># check if too long</span>
<span class="k">if</span> <span class="n">gap_orig</span><span class="o">.</span><span class="n">length</span> <span class="o">></span> <span class="n">linker_length</span><span class="p">:</span>
<span class="n">gap_idx</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">continue</span>
- <span class="c"># the function only works, if there are no gaps (del. AND insert.)</span>
- <span class="c"># towards the n-ter in the same chain, except terminal gaps.</span>
+ <span class="c1"># the function only works, if there are no gaps (del. AND insert.)</span>
+ <span class="c1"># towards the n-ter in the same chain, except terminal gaps.</span>
<span class="n">clean_nter</span> <span class="o">=</span> <span class="bp">True</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">gap_idx</span><span class="p">):</span>
<span class="k">if</span> <span class="n">actual_chain_idx</span> <span class="o">==</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">():</span>
@@ -1413,47 +1477,47 @@
<span class="n">gap_idx</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">continue</span>
- <span class="c"># extend gap to desired length</span>
+ <span class="c1"># extend gap to desired length</span>
<span class="n">actual_gap</span> <span class="o">=</span> <span class="n">gap_orig</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
<span class="n">actual_extender</span> <span class="o">=</span> <span class="n">_GetGapExtender</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">actual_gap</span><span class="p">,</span>
<span class="n">use_scoring_extender</span><span class="p">,</span>
<span class="n">use_full_extender</span><span class="p">,</span>
<span class="n">linker_length</span><span class="p">)</span>
<span class="k">while</span> <span class="n">actual_gap</span><span class="o">.</span><span class="n">length</span> <span class="o"><</span> <span class="n">linker_length</span><span class="p">:</span>
- <span class="c"># extend the gap</span>
+ <span class="c1"># extend the gap</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">actual_extender</span><span class="o">.</span><span class="n">Extend</span><span class="p">():</span>
<span class="k">break</span>
- <span class="c"># FAIL (Fragger needs at least 3 residues)</span>
+ <span class="c1"># FAIL (Fragger needs at least 3 residues)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">actual_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Failed in CloseLargeDeletions (</span><span class="si">%s</span><span class="s">)"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">))</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Failed in CloseLargeDeletions (</span><span class="si">%s</span><span class="s2">)"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">))</span>
<span class="n">gap_idx</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="k">continue</span>
- <span class="c"># extract gap info</span>
+ <span class="c1"># extract gap info</span>
<span class="n">n_stem_res</span> <span class="o">=</span> <span class="n">actual_gap</span><span class="o">.</span><span class="n">before</span>
<span class="n">c_stem_res</span> <span class="o">=</span> <span class="n">actual_gap</span><span class="o">.</span><span class="n">after</span>
<span class="n">n_stem_res_num</span> <span class="o">=</span> <span class="n">n_stem_res</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span>
<span class="n">c_stem_res_num</span> <span class="o">=</span> <span class="n">c_stem_res</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span>
- <span class="c"># let's find fragments!</span>
+ <span class="c1"># let's find fragments!</span>
<span class="n">fragger</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">Fragger</span><span class="p">(</span><span class="n">actual_gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">)</span>
<span class="n">seqsim_matrix</span> <span class="o">=</span> <span class="n">ost</span><span class="o">.</span><span class="n">seq</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">BLOSUM62</span>
<span class="n">fragger</span><span class="o">.</span><span class="n">AddSeqSimParameters</span><span class="p">(</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">seqsim_matrix</span><span class="p">)</span>
<span class="n">fragger</span><span class="o">.</span><span class="n">Fill</span><span class="p">(</span><span class="n">structure_db</span><span class="p">,</span> <span class="mf">0.2</span><span class="p">,</span> <span class="n">num_fragments</span><span class="p">)</span>
- <span class="c"># We generate two backbonelists based on residues beginning from the </span>
- <span class="c"># n-terminus:</span>
- <span class="c"># - bb_list: covers the full thing being sampled (incl. stuff in gap)</span>
- <span class="c"># - initial_n_stem: n-stem residue before the fragment insertion</span>
- <span class="c">#</span>
- <span class="c"># After having found the ideal fragment, we cannot simply insert it into</span>
- <span class="c"># the model, since all sidechain information would be lost.</span>
- <span class="c"># We therefore need the initial_n_stem to store the initial N stem</span>
- <span class="c"># positions. We can then calculate a transformation in the end and </span>
- <span class="c"># apply it manually in the end for the according atom positions.</span>
-
- <span class="c"># only put valid residues in bb_seq</span>
+ <span class="c1"># We generate two backbonelists based on residues beginning from the </span>
+ <span class="c1"># n-terminus:</span>
+ <span class="c1"># - bb_list: covers the full thing being sampled (incl. stuff in gap)</span>
+ <span class="c1"># - initial_n_stem: n-stem residue before the fragment insertion</span>
+ <span class="c1">#</span>
+ <span class="c1"># After having found the ideal fragment, we cannot simply insert it into</span>
+ <span class="c1"># the model, since all sidechain information would be lost.</span>
+ <span class="c1"># We therefore need the initial_n_stem to store the initial N stem</span>
+ <span class="c1"># positions. We can then calculate a transformation in the end and </span>
+ <span class="c1"># apply it manually in the end for the according atom positions.</span>
+
+ <span class="c1"># only put valid residues in bb_seq</span>
<span class="n">first_num</span> <span class="o">=</span> <span class="n">actual_chain</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span>
<span class="n">bb_seq</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">seqres</span><span class="p">[</span><span class="n">actual_chain_idx</span><span class="p">][</span><span class="n">first_num</span><span class="o">-</span><span class="mi">1</span><span class="p">:</span><span class="n">c_stem_res_num</span><span class="p">]</span>
<span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">bb_seq</span><span class="p">)</span>
@@ -1464,43 +1528,45 @@
<span class="n">bb_list</span><span class="o">.</span><span class="n">Set</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">actual_res</span><span class="p">,</span> <span class="n">bb_seq</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
<span class="n">actual_res_num</span> <span class="o">+=</span> <span class="mi">1</span>
- <span class="c"># define region in fragger and region before, including the n_stem of </span>
- <span class="c"># the fragment</span>
+ <span class="c1"># define region in fragger and region before, including the n_stem of </span>
+ <span class="c1"># the fragment</span>
<span class="n">frag_start_idx</span> <span class="o">=</span> <span class="n">n_stem_res_num</span> <span class="o">-</span> <span class="n">first_num</span>
<span class="n">initial_n_stem</span> <span class="o">=</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">Extract</span><span class="p">(</span><span class="n">frag_start_idx</span><span class="p">,</span> <span class="n">frag_start_idx</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span>
- <span class="c"># all fragments get now sampled and scored</span>
- <span class="c"># the idea is to sample the fragments by moving the full part towards</span>
- <span class="c"># the n-terminus</span>
+ <span class="c1"># all fragments get now sampled and scored</span>
+ <span class="c1"># the idea is to sample the fragments by moving the full part towards</span>
+ <span class="c1"># the n-terminus</span>
<span class="n">closer</span> <span class="o">=</span> <span class="n">NTerminalCloser</span><span class="p">(</span><span class="n">c_stem_res</span><span class="p">)</span>
- <span class="n">best_score</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="s">"inf"</span><span class="p">)</span>
+ <span class="n">best_score</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="s2">"inf"</span><span class="p">)</span>
<span class="n">best_idx</span> <span class="o">=</span> <span class="mi">0</span>
- <span class="n">scorer_weights</span> <span class="o">=</span> <span class="p">{</span><span class="s">"clash"</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s">"reduced"</span><span class="p">:</span> <span class="mi">1</span><span class="p">}</span>
+ <span class="n">scorer_weights</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"clash"</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s2">"reduced"</span><span class="p">:</span> <span class="mi">1</span><span class="p">}</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fragger</span><span class="p">)):</span>
<span class="n">bb_list</span><span class="o">.</span><span class="n">ReplaceFragment</span><span class="p">(</span><span class="n">fragger</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">frag_start_idx</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
<span class="n">closer</span><span class="o">.</span><span class="n">Close</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">)</span>
- <span class="c"># a simple score gets calculated and best chosen</span>
+ <span class="c1"># a simple score gets calculated and best chosen</span>
+ <span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer_env</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="n">first_num</span><span class="p">,</span>
+ <span class="n">actual_chain_idx</span><span class="p">)</span>
<span class="n">score</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer</span><span class="o">.</span><span class="n">CalculateLinearCombination</span><span class="p">(</span>\
- <span class="n">scorer_weights</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">,</span> <span class="n">first_num</span><span class="p">,</span> <span class="n">actual_chain_idx</span><span class="p">)</span>
+ <span class="n">scorer_weights</span><span class="p">,</span> <span class="n">first_num</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">bb_list</span><span class="p">),</span> <span class="n">actual_chain_idx</span><span class="p">)</span>
<span class="k">if</span> <span class="n">score</span> <span class="o"><</span> <span class="n">best_score</span><span class="p">:</span>
<span class="n">best_score</span> <span class="o">=</span> <span class="n">score</span>
<span class="n">best_idx</span> <span class="o">=</span> <span class="n">i</span>
- <span class="c"># set best fragment into bb_list and </span>
+ <span class="c1"># set best fragment into bb_list and </span>
<span class="n">fragment</span> <span class="o">=</span> <span class="n">fragger</span><span class="p">[</span><span class="n">best_idx</span><span class="p">]</span>
<span class="n">bb_list</span><span class="o">.</span><span class="n">ReplaceFragment</span><span class="p">(</span><span class="n">fragment</span><span class="p">,</span> <span class="n">frag_start_idx</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
<span class="n">closer</span><span class="o">.</span><span class="n">Close</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">)</span>
- <span class="c"># reextract fragment, since the whole thing has undergone a </span>
- <span class="c"># transformation</span>
+ <span class="c1"># reextract fragment, since the whole thing has undergone a </span>
+ <span class="c1"># transformation</span>
<span class="n">fragment</span> <span class="o">=</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">Extract</span><span class="p">(</span><span class="n">frag_start_idx</span><span class="p">,</span> <span class="n">frag_start_idx</span> <span class="o">+</span>
<span class="nb">len</span><span class="p">(</span><span class="n">fragment</span><span class="p">))</span>
- <span class="c"># We finally calculate the transformation from the initial positions</span>
- <span class="c"># of all residues towards the n-terminus and apply it manually.</span>
- <span class="c"># this is done to not loose all the sidechain information</span>
+ <span class="c1"># We finally calculate the transformation from the initial positions</span>
+ <span class="c1"># of all residues towards the n-terminus and apply it manually.</span>
+ <span class="c1"># this is done to not loose all the sidechain information</span>
<span class="n">t</span> <span class="o">=</span> <span class="n">initial_n_stem</span><span class="o">.</span><span class="n">GetTransform</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">,</span> <span class="n">frag_start_idx</span><span class="p">)</span>
<span class="n">ed</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">EditXCS</span><span class="p">(</span><span class="n">ost</span><span class="o">.</span><span class="n">mol</span><span class="o">.</span><span class="n">BUFFERED_EDIT</span><span class="p">)</span>
<span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">actual_chain</span><span class="o">.</span><span class="n">residues</span><span class="p">[:</span><span class="n">frag_start_idx</span><span class="p">]:</span>
@@ -1509,26 +1575,26 @@
<span class="n">ed</span><span class="o">.</span><span class="n">SetAtomPos</span><span class="p">(</span><span class="n">a</span><span class="p">,</span> <span class="n">ost</span><span class="o">.</span><span class="n">geom</span><span class="o">.</span><span class="n">Vec3</span><span class="p">(</span><span class="n">new_pos</span><span class="p">))</span>
<span class="n">ed</span><span class="o">.</span><span class="n">UpdateICS</span><span class="p">()</span>
- <span class="c"># replace fragment part</span>
+ <span class="c1"># replace fragment part</span>
<span class="n">fragment</span><span class="o">.</span><span class="n">InsertInto</span><span class="p">(</span><span class="n">actual_chain</span><span class="p">,</span> <span class="n">n_stem_res_num</span><span class="p">)</span>
- <span class="c"># update score env. (manual to keep all atom sidechains)</span>
+ <span class="c1"># update score env. (manual to keep all atom sidechains)</span>
<span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer_env</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="n">first_num</span><span class="p">,</span>
<span class="n">actual_chain_idx</span><span class="p">)</span>
- <span class="c"># will return -1 if last gap removed</span>
+ <span class="c1"># will return -1 if last gap removed</span>
<span class="n">gap_idx</span> <span class="o">=</span> <span class="n">ClearGaps</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">actual_gap</span><span class="p">)</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Resolved </span><span class="si">%s</span><span class="s"> by sampling </span><span class="si">%s</span><span class="s"> as linker"</span> <span class="o">%</span> \
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Resolved </span><span class="si">%s</span><span class="s2"> by sampling </span><span class="si">%s</span><span class="s2"> as linker"</span> <span class="o">%</span> \
<span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">gap_orig</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">actual_gap</span><span class="p">)))</span>
- <span class="c"># reset all atom env. if it's set (changes are too drastic so we set all)</span>
+ <span class="c1"># reset all atom env. if it's set (changes are too drastic so we set all)</span>
<span class="k">if</span> <span class="n">IsAllAtomScoringSetUp</span><span class="p">(</span><span class="n">mhandle</span><span class="p">):</span>
- <span class="n">mhandle</span><span class="o">.</span><span class="n">all_atom_sidechain_env</span><span class="o">.</span><span class="n">SetInitialEnvironment</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">)</span>
+ <span class="n">mhandle</span><span class="o">.</span><span class="n">all_atom_sidechain_env</span><span class="o">.</span><span class="n">SetInitialEnvironment</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">)</span></div>
-<span class="c"># these methods will be exported into module</span></div>
-<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s">'CloseSmallDeletions'</span><span class="p">,</span> <span class="s">'MergeGapsByDistance'</span><span class="p">,</span> <span class="s">'FillLoopsByDatabase'</span><span class="p">,</span>
- <span class="s">'FillLoopsByMonteCarlo'</span><span class="p">,</span> <span class="s">'CloseGaps'</span><span class="p">,</span> <span class="s">'ModelTermini'</span><span class="p">,</span>
- <span class="s">'CloseLargeDeletions'</span><span class="p">)</span>
+<span class="c1"># these methods will be exported into module</span>
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s1">'CloseSmallDeletions'</span><span class="p">,</span> <span class="s1">'MergeGapsByDistance'</span><span class="p">,</span> <span class="s1">'FillLoopsByDatabase'</span><span class="p">,</span>
+ <span class="s1">'FillLoopsByMonteCarlo'</span><span class="p">,</span> <span class="s1">'CloseGaps'</span><span class="p">,</span> <span class="s1">'ModelTermini'</span><span class="p">,</span>
+ <span class="s1">'CloseLargeDeletions'</span><span class="p">)</span>
</pre></div>
</div>
@@ -1554,9 +1620,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -1564,11 +1627,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/_modules/promod3/modelling/_denovo.html b/doc/html/_modules/promod3/modelling/_denovo.html
index 22a3704651712098494a0b1ca7fafa8ddac8995e..b2100964e66fb6ebbc6d9f4a3a710767ffecfc50 100644
--- a/doc/html/_modules/promod3/modelling/_denovo.html
+++ b/doc/html/_modules/promod3/modelling/_denovo.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._denovo — ProMod3 1.1.0 documentation</title>
+ <title>promod3.modelling._denovo — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,14 +23,16 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../../../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
+ <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -38,7 +40,7 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._denovo</h1><div class="highlight"><pre>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">loop</span>
+<span></span><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">loop</span>
<span class="kn">from</span> <span class="nn">_modelling</span> <span class="kn">import</span> <span class="o">*</span>
<div class="viewcode-block" id="GenerateDeNovoTrajectories"><a class="viewcode-back" href="../../../modelling/algorithms.html#promod3.modelling.GenerateDeNovoTrajectories">[docs]</a><span class="k">def</span> <span class="nf">GenerateDeNovoTrajectories</span><span class="p">(</span><span class="n">sequence</span><span class="p">,</span>
@@ -48,6 +50,7 @@
<span class="n">psipred_prediction</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">fragment_handler</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">scorer</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
+ <span class="n">scorer_env</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">scoring_weights</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
<span class="sd">'''Example de novo modelling pipeline based on Fragment sampling and</span>
<span class="sd"> backbone scoring. Take this as a starting point for more advanced</span>
@@ -87,6 +90,10 @@
<span class="sd"> torsion and pairwise </span>
<span class="sd"> :type scorer: :class:`promod3.scoring.BackboneOverallScorer`</span>
+<span class="sd"> :param scorer_env: The scoring env that relates to **scorer**</span>
+<span class="sd"> This environment will be changed! </span>
+<span class="sd"> :type scorer_env: :class:`promod3.scoring.BackboneScoreEnv`</span>
+
<span class="sd"> :param scoring_weights: Linear weights for different scores. If not provided,</span>
<span class="sd"> the output of ScoringWeights.GetWeights() is used.</span>
<span class="sd"> Please note, that the weights must be consistent</span>
@@ -98,44 +105,47 @@
<span class="sd"> '''</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span> <span class="o"><</span> <span class="mi">9</span><span class="p">:</span>
- <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">"Seq too short for Denovo sampling (min length 9)"</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"Seq too short for Denovo sampling (min length 9)"</span><span class="p">)</span>
- <span class="c"># check whether profile / psipred_prediction are consistent if present</span>
+ <span class="c1"># check whether profile / psipred_prediction are consistent if present</span>
<span class="k">if</span> <span class="n">profile</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">if</span> <span class="n">profile</span><span class="o">.</span><span class="n">sequence</span> <span class="o">!=</span> <span class="n">sequence</span><span class="p">:</span>
- <span class="n">err</span> <span class="o">=</span> <span class="s">"Sequence of profile must match input sequence!"</span>
+ <span class="n">err</span> <span class="o">=</span> <span class="s2">"Sequence of profile must match input sequence!"</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="n">err</span><span class="p">)</span>
<span class="k">if</span> <span class="n">psipred_prediction</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">psipred_prediction</span><span class="p">):</span>
- <span class="n">err</span> <span class="o">=</span> <span class="s">"psipred_prediction must be consistent with the input sequence!"</span>
+ <span class="n">err</span> <span class="o">=</span> <span class="s2">"psipred_prediction must be consistent with the input sequence!"</span>
<span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="n">err</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">scorer</span> <span class="o">!=</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">scorer_env</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"Must provide an environment when you provide a scorer!"</span><span class="p">)</span>
+
<span class="k">if</span> <span class="n">fragment_handler</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
- <span class="c"># we first have to build our own handler</span>
+ <span class="c1"># we first have to build our own handler</span>
<span class="n">fragment_handler</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">FraggerHandle</span><span class="p">(</span><span class="n">sequence</span><span class="p">,</span>
<span class="n">profile</span> <span class="o">=</span> <span class="n">profile</span><span class="p">,</span>
<span class="n">psipred_pred</span> <span class="o">=</span> <span class="n">psipred_prediction</span><span class="p">)</span>
<span class="n">fragger_list</span> <span class="o">=</span> <span class="n">fragment_handler</span><span class="o">.</span><span class="n">GetList</span><span class="p">()</span>
<span class="k">if</span> <span class="n">scorer</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
- <span class="c"># Lets setup a scorer with empty environment</span>
+ <span class="c1"># Lets setup a scorer with empty environment</span>
<span class="n">scorer</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">BackboneOverallScorer</span><span class="p">()</span>
<span class="n">scorer_env</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">BackboneScoreEnv</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span>
- <span class="n">scorer</span><span class="p">[</span><span class="s">"clash"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">ClashScorer</span><span class="p">()</span>
- <span class="n">scorer</span><span class="p">[</span><span class="s">"reduced"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadReducedScorer</span><span class="p">()</span>
- <span class="n">scorer</span><span class="p">[</span><span class="s">"cb_packing"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadCBPackingScorer</span><span class="p">()</span>
- <span class="n">scorer</span><span class="p">[</span><span class="s">"hbond"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadHBondScorer</span><span class="p">()</span>
- <span class="n">scorer</span><span class="p">[</span><span class="s">"cbeta"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadCBetaScorer</span><span class="p">()</span>
- <span class="n">scorer</span><span class="p">[</span><span class="s">"torsion"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadTorsionScorer</span><span class="p">()</span>
- <span class="n">scorer</span><span class="p">[</span><span class="s">"pairwise"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">PairwiseScorer</span><span class="p">()</span>
+ <span class="n">scorer</span><span class="p">[</span><span class="s2">"clash"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">ClashScorer</span><span class="p">()</span>
+ <span class="n">scorer</span><span class="p">[</span><span class="s2">"reduced"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadReducedScorer</span><span class="p">()</span>
+ <span class="n">scorer</span><span class="p">[</span><span class="s2">"cb_packing"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadCBPackingScorer</span><span class="p">()</span>
+ <span class="n">scorer</span><span class="p">[</span><span class="s2">"hbond"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadHBondScorer</span><span class="p">()</span>
+ <span class="n">scorer</span><span class="p">[</span><span class="s2">"cbeta"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadCBetaScorer</span><span class="p">()</span>
+ <span class="n">scorer</span><span class="p">[</span><span class="s2">"torsion"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadTorsionScorer</span><span class="p">()</span>
+ <span class="n">scorer</span><span class="p">[</span><span class="s2">"pairwise"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">PairwiseScorer</span><span class="p">()</span>
<span class="n">scorer</span><span class="o">.</span><span class="n">AttachEnvironment</span><span class="p">(</span><span class="n">scorer_env</span><span class="p">)</span>
<span class="k">if</span> <span class="n">scoring_weights</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">scoring_weights</span> <span class="o">=</span> <span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetWeights</span><span class="p">()</span>
- <span class="c"># the number of 109 is roughly the number of times we have to apply</span>
- <span class="c"># a factor of 0.9 to 100 until it reaches a value of 0.001</span>
+ <span class="c1"># the number of 109 is roughly the number of times we have to apply</span>
+ <span class="c1"># a factor of 0.9 to 100 until it reaches a value of 0.001</span>
<span class="n">start_temperature</span> <span class="o">=</span> <span class="mi">100</span>
<span class="n">cooling_factor</span> <span class="o">=</span> <span class="mf">0.9</span>
<span class="n">sampling_steps</span> <span class="o">=</span> <span class="n">avg_sampling_per_position</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">fragger_list</span><span class="p">)</span>
@@ -144,7 +154,8 @@
<span class="n">mc_sampler</span> <span class="o">=</span> <span class="n">FragmentSampler</span><span class="p">(</span><span class="n">sequence</span><span class="p">,</span> <span class="n">fragger_list</span><span class="p">,</span>
<span class="n">init_fragments</span> <span class="o">=</span> <span class="mi">5</span><span class="p">)</span>
<span class="n">mc_closer</span> <span class="o">=</span> <span class="n">DeNovoCloser</span><span class="p">()</span>
- <span class="n">mc_scorer</span> <span class="o">=</span> <span class="n">LinearScorer</span><span class="p">(</span><span class="n">scorer</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">scoring_weights</span><span class="p">)</span>
+ <span class="n">mc_scorer</span> <span class="o">=</span> <span class="n">LinearScorer</span><span class="p">(</span><span class="n">scorer</span><span class="p">,</span> <span class="n">scorer_env</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">sequence</span><span class="p">),</span> <span class="mi">0</span><span class="p">,</span>
+ <span class="n">scoring_weights</span><span class="p">)</span>
<span class="n">mc_cooler</span> <span class="o">=</span> <span class="n">ExponentialCooler</span><span class="p">(</span><span class="n">start_temperature</span><span class="p">,</span>
<span class="n">cooling_interval</span><span class="p">,</span>
<span class="n">cooling_factor</span><span class="p">)</span>
@@ -182,9 +193,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -192,11 +200,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/_modules/promod3/modelling/_fragger_handle.html b/doc/html/_modules/promod3/modelling/_fragger_handle.html
index b364e59e84bdc161277db70d4fdd6d75b428d73a..0ef683b33454d388f4ec6354c16ddeef42fc101d 100644
--- a/doc/html/_modules/promod3/modelling/_fragger_handle.html
+++ b/doc/html/_modules/promod3/modelling/_fragger_handle.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._fragger_handle — ProMod3 1.1.0 documentation</title>
+ <title>promod3.modelling._fragger_handle — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,14 +23,16 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../../../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
+ <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -38,7 +40,7 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._fragger_handle</h1><div class="highlight"><pre>
-<span class="sd">'''Python functionality to generate fraggers.'''</span>
+<span></span><span class="sd">'''Python functionality to generate fraggers.'''</span>
<span class="kn">from</span> <span class="nn">promod3.loop</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">ost.conop</span> <span class="kn">import</span> <span class="n">OneLetterCodeToResidueName</span>
@@ -60,11 +62,11 @@
<span class="n">size_idx</span> <span class="o">=</span> <span class="n">_GetSizeIdx</span><span class="p">(</span><span class="n">frag_size</span><span class="p">)</span>
<span class="k">if</span> <span class="n">weight_group</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
- <span class="c"># group one, it's only sequence similarity...</span>
+ <span class="c1"># group one, it's only sequence similarity...</span>
<span class="k">return</span> <span class="p">[</span><span class="mf">1.0</span><span class="p">]</span>
<span class="k">elif</span> <span class="n">weight_group</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span>
- <span class="c"># group two: [sequence_profile_weight, structure_profile_weight]</span>
+ <span class="c1"># group two: [sequence_profile_weight, structure_profile_weight]</span>
<span class="k">if</span> <span class="n">size_idx</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">return</span> <span class="p">[</span><span class="o">-</span><span class="mf">1.0</span><span class="p">,</span> <span class="o">-</span><span class="mf">1.404</span><span class="p">]</span>
<span class="k">elif</span> <span class="n">size_idx</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
@@ -77,7 +79,7 @@
<span class="k">return</span> <span class="p">[</span><span class="o">-</span><span class="mf">1.0</span><span class="p">,</span> <span class="o">-</span><span class="mf">6.703</span><span class="p">]</span>
<span class="k">elif</span> <span class="n">weight_group</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span>
- <span class="c"># group_three: [ss_agreement_weight, torsion_weight, seqsim_weight] </span>
+ <span class="c1"># group_three: [ss_agreement_weight, torsion_weight, seqsim_weight] </span>
<span class="k">if</span> <span class="n">size_idx</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">return</span> <span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">71.467</span><span class="p">,</span> <span class="mf">2.276</span><span class="p">]</span>
<span class="k">elif</span> <span class="n">size_idx</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
@@ -90,8 +92,8 @@
<span class="k">return</span> <span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">5.784</span><span class="p">,</span> <span class="mf">4.618</span><span class="p">]</span>
<span class="k">elif</span> <span class="n">weight_group</span> <span class="o">==</span> <span class="mi">4</span><span class="p">:</span>
- <span class="c"># group_four: [ss_agreement_weight, torsion_weight, </span>
- <span class="c"># sequence_profile_weight, structure_profile_weight]</span>
+ <span class="c1"># group_four: [ss_agreement_weight, torsion_weight, </span>
+ <span class="c1"># sequence_profile_weight, structure_profile_weight]</span>
<span class="k">if</span> <span class="n">size_idx</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
<span class="k">return</span> <span class="p">[</span><span class="mf">1.0</span><span class="p">,</span> <span class="mf">17.219</span><span class="p">,</span> <span class="o">-</span><span class="mf">1.930</span><span class="p">,</span> <span class="o">-</span><span class="mf">3.328</span><span class="p">]</span>
<span class="k">elif</span> <span class="n">size_idx</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
@@ -226,21 +228,21 @@
<span class="n">torsion_sampler_coil</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">torsion_sampler_helix</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span>
<span class="n">torsion_sampler_extended</span> <span class="o">=</span> <span class="bp">None</span><span class="p">):</span>
- <span class="c"># check</span>
+ <span class="c1"># check</span>
<span class="k">if</span> <span class="n">profile</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span>
- <span class="c"># can either be a SequenceHandle or simple string...</span>
+ <span class="c1"># can either be a SequenceHandle or simple string...</span>
<span class="k">try</span><span class="p">:</span>
<span class="k">if</span> <span class="n">sequence</span><span class="o">.</span><span class="n">GetString</span><span class="p">()</span> <span class="o">!=</span> <span class="n">profile</span><span class="o">.</span><span class="n">sequence</span><span class="p">:</span>
- <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Sequence must be consistent with profile!"</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Sequence must be consistent with profile!"</span><span class="p">)</span>
<span class="k">except</span><span class="p">:</span>
<span class="k">if</span> <span class="n">sequence</span> <span class="o">!=</span> <span class="n">profile</span><span class="o">.</span><span class="n">sequence</span><span class="p">:</span>
- <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Sequence must be consistent with profile!"</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Sequence must be consistent with profile!"</span><span class="p">)</span>
<span class="k">if</span> <span class="n">psipred_pred</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span> <span class="o">!=</span> <span class="nb">len</span><span class="p">(</span><span class="n">psipred_pred</span><span class="p">):</span>
- <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Sequence must be consistent with PsipredPred!"</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Sequence must be consistent with PsipredPred!"</span><span class="p">)</span>
- <span class="c"># keep all objects</span>
+ <span class="c1"># keep all objects</span>
<span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="o">=</span> <span class="n">sequence</span>
<span class="bp">self</span><span class="o">.</span><span class="n">profile</span> <span class="o">=</span> <span class="n">profile</span>
<span class="bp">self</span><span class="o">.</span><span class="n">psipred_pred</span> <span class="o">=</span> <span class="n">psipred_pred</span>
@@ -254,7 +256,7 @@
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">structure_db</span> <span class="o">=</span> <span class="n">structure_db</span>
- <span class="c"># the torsion samplers are only required if we have a psipred prediction</span>
+ <span class="c1"># the torsion samplers are only required if we have a psipred prediction</span>
<span class="bp">self</span><span class="o">.</span><span class="n">samplers</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">torsion_sampler_coil</span> <span class="o">=</span> <span class="bp">None</span>
<span class="bp">self</span><span class="o">.</span><span class="n">torsion_sampler_helix</span> <span class="o">=</span> <span class="bp">None</span>
@@ -278,13 +280,13 @@
<span class="bp">self</span><span class="o">.</span><span class="n">samplers</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">torsion_sampler_coil</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">psipred_pred</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">psipred_pred</span><span class="p">)):</span>
- <span class="k">if</span> <span class="n">psipred_pred</span><span class="o">.</span><span class="n">GetPrediction</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">==</span> <span class="s">'H'</span> \
+ <span class="k">if</span> <span class="n">psipred_pred</span><span class="o">.</span><span class="n">GetPrediction</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">==</span> <span class="s1">'H'</span> \
<span class="ow">and</span> <span class="n">psipred_pred</span><span class="o">.</span><span class="n">GetConfidence</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">>=</span> <span class="mi">6</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">samplers</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">torsion_sampler_helix</span>
- <span class="k">if</span> <span class="n">psipred_pred</span><span class="o">.</span><span class="n">GetPrediction</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">==</span> <span class="s">'E'</span> \
+ <span class="k">if</span> <span class="n">psipred_pred</span><span class="o">.</span><span class="n">GetPrediction</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">==</span> <span class="s1">'E'</span> \
<span class="ow">and</span> <span class="n">psipred_pred</span><span class="o">.</span><span class="n">GetConfidence</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">>=</span> <span class="mi">6</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">samplers</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">torsion_sampler_extended</span>
- <span class="c"># prepare map</span>
+ <span class="c1"># prepare map</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fragger_map</span> <span class="o">=</span> <span class="n">FraggerMap</span><span class="p">()</span>
<div class="viewcode-block" id="FraggerHandle.Get"><a class="viewcode-back" href="../../../modelling/algorithms.html#promod3.modelling.FraggerHandle.Get">[docs]</a> <span class="k">def</span> <span class="nf">Get</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">frag_pos</span><span class="p">):</span>
@@ -295,12 +297,12 @@
<span class="sd"> :return: A :class:`Fragger` object.</span>
<span class="sd"> :raises: :exc:`~exceptions.ValueError` if index out-of-bounds.</span>
<span class="sd"> '''</span>
- <span class="c"># this is for ranges (i.e. last touched index is end_pos-1)</span>
+ <span class="c1"># this is for ranges (i.e. last touched index is end_pos-1)</span>
<span class="n">end_pos</span> <span class="o">=</span> <span class="n">frag_pos</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">fragment_length</span>
- <span class="c"># check</span>
+ <span class="c1"># check</span>
<span class="k">if</span> <span class="n">frag_pos</span> <span class="o"><</span> <span class="mi">0</span> <span class="ow">or</span> <span class="n">end_pos</span> <span class="o">></span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">):</span>
- <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s">"Invalid fragment position "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">frag_pos</span><span class="p">))</span>
- <span class="c"># get</span>
+ <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">"Invalid fragment position "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">frag_pos</span><span class="p">))</span>
+ <span class="c1"># get</span>
<span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">fragger_map</span><span class="o">.</span><span class="n">Contains</span><span class="p">(</span><span class="n">frag_pos</span><span class="p">):</span>
<span class="n">fragger</span> <span class="o">=</span> <span class="bp">None</span>
@@ -335,12 +337,12 @@
<span class="n">fragger</span><span class="o">.</span><span class="n">Fill</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">structure_db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">rmsd_thresh</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fragments_per_position</span><span class="p">)</span>
- <span class="c"># keep cached</span>
+ <span class="c1"># keep cached</span>
<span class="bp">self</span><span class="o">.</span><span class="n">fragger_map</span><span class="p">[</span><span class="n">frag_pos</span><span class="p">]</span> <span class="o">=</span> <span class="n">fragger</span>
- <span class="c"># get it back</span>
- <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">fragger_map</span><span class="p">[</span><span class="n">frag_pos</span><span class="p">]</span>
-</div>
+ <span class="c1"># get it back</span>
+ <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">fragger_map</span><span class="p">[</span><span class="n">frag_pos</span><span class="p">]</span></div>
+
<div class="viewcode-block" id="FraggerHandle.GetList"><a class="viewcode-back" href="../../../modelling/algorithms.html#promod3.modelling.FraggerHandle.GetList">[docs]</a> <span class="k">def</span> <span class="nf">GetList</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pos_start</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">pos_end</span><span class="o">=-</span><span class="mi">1</span><span class="p">):</span>
<span class="sd">'''Get List of fraggers covering sequence indices pos_start..pos_end.</span>
@@ -358,23 +360,23 @@
<span class="n">fragger_list</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="k">for</span> <span class="n">frag_pos</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">pos_start</span><span class="p">,</span> <span class="n">pos_end</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">fragment_length</span> <span class="o">+</span> <span class="mi">2</span><span class="p">):</span>
<span class="n">fragger_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">Get</span><span class="p">(</span><span class="n">frag_pos</span><span class="p">))</span>
- <span class="k">return</span> <span class="n">fragger_list</span>
-</div>
+ <span class="k">return</span> <span class="n">fragger_list</span></div>
+
<div class="viewcode-block" id="FraggerHandle.SaveCached"><a class="viewcode-back" href="../../../modelling/algorithms.html#promod3.modelling.FraggerHandle.SaveCached">[docs]</a> <span class="k">def</span> <span class="nf">SaveCached</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
<span class="sd">'''Save cached fraggers.'''</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">fragger_map</span><span class="o">.</span><span class="n">Save</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
-</div>
+ <span class="bp">self</span><span class="o">.</span><span class="n">fragger_map</span><span class="o">.</span><span class="n">Save</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span></div>
+
<div class="viewcode-block" id="FraggerHandle.LoadCached"><a class="viewcode-back" href="../../../modelling/algorithms.html#promod3.modelling.FraggerHandle.LoadCached">[docs]</a> <span class="k">def</span> <span class="nf">LoadCached</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
<span class="sd">'''Load fragger objects stored with :meth:`SaveCached`.</span>
<span class="sd"> Note that here we require that the same structure db is set as was</span>
<span class="sd"> used when `filename` was saved.'''</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">fragger_map</span> <span class="o">=</span> <span class="n">FraggerMap</span><span class="o">.</span><span class="n">Load</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_db</span><span class="p">)</span>
-</div>
+ <span class="bp">self</span><span class="o">.</span><span class="n">fragger_map</span> <span class="o">=</span> <span class="n">FraggerMap</span><span class="o">.</span><span class="n">Load</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">structure_db</span><span class="p">)</span></div>
+
<span class="k">def</span> <span class="nf">_GetAABefore</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">pos</span><span class="p">):</span>
<span class="k">if</span> <span class="n">pos</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">olc</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">pos</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">olc</span> <span class="o">=</span> <span class="s">'A'</span>
+ <span class="n">olc</span> <span class="o">=</span> <span class="s1">'A'</span>
<span class="n">aa_before</span> <span class="o">=</span> <span class="n">OneLetterCodeToResidueName</span><span class="p">(</span><span class="n">olc</span><span class="p">)</span>
<span class="k">return</span> <span class="n">aa_before</span>
@@ -382,13 +384,13 @@
<span class="k">if</span> <span class="n">pos</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span>
<span class="n">olc</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="n">pos</span> <span class="o">+</span> <span class="mi">1</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">olc</span> <span class="o">=</span> <span class="s">'A'</span>
+ <span class="n">olc</span> <span class="o">=</span> <span class="s1">'A'</span>
<span class="n">aa_after</span> <span class="o">=</span> <span class="n">OneLetterCodeToResidueName</span><span class="p">(</span><span class="n">olc</span><span class="p">)</span>
- <span class="k">return</span> <span class="n">aa_after</span>
+ <span class="k">return</span> <span class="n">aa_after</span></div>
-<span class="c"># these methods will be exported into module</span></div>
-<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s">'FraggerHandle'</span><span class="p">,)</span>
+<span class="c1"># these methods will be exported into module</span>
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s1">'FraggerHandle'</span><span class="p">,)</span>
</pre></div>
</div>
@@ -414,9 +416,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -424,11 +423,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/_modules/promod3/modelling/_molprobity.html b/doc/html/_modules/promod3/modelling/_molprobity.html
index 864c296f37a35cb8b8bf9fb528c6f438c7bffdad..b9441021b1cca2bd98ef90666bf96c15f20509f6 100644
--- a/doc/html/_modules/promod3/modelling/_molprobity.html
+++ b/doc/html/_modules/promod3/modelling/_molprobity.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._molprobity — ProMod3 1.1.0 documentation</title>
+ <title>promod3.modelling._molprobity — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,14 +23,16 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../../../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
+ <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -38,7 +40,7 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._molprobity</h1><div class="highlight"><pre>
-<span class="sd">'''Binding to external MolProbity tool to get scores.'''</span>
+<span></span><span class="sd">'''Binding to external MolProbity tool to get scores.'''</span>
<span class="kn">import</span> <span class="nn">ost</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">settings</span>
@@ -84,46 +86,46 @@
<span class="sd"> :raises: :class:`~ost.settings.FileNotFound` if the "phenix.molprobity"</span>
<span class="sd"> executable is not found.</span>
<span class="sd"> '''</span>
- <span class="c"># HELPER</span>
+ <span class="c1"># HELPER</span>
<span class="k">def</span> <span class="nf">GetStringValue</span><span class="p">(</span><span class="n">my_line</span><span class="p">):</span>
<span class="sd">"""Parse line formatted as ' bla = X ...' and return 'X' as string."""</span>
- <span class="k">return</span> <span class="n">my_line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">'='</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s">' '</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+ <span class="k">return</span> <span class="n">my_line</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">'='</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s1">' '</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
- <span class="c"># locate molprobity</span>
- <span class="n">molprobity_exec</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">Locate</span><span class="p">(</span><span class="s">"phenix.molprobity"</span><span class="p">,</span>
+ <span class="c1"># locate molprobity</span>
+ <span class="n">molprobity_exec</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">Locate</span><span class="p">(</span><span class="s2">"phenix.molprobity"</span><span class="p">,</span>
<span class="n">explicit_file_name</span><span class="o">=</span><span class="n">molprobity_bin</span><span class="p">,</span>
- <span class="n">env_name</span><span class="o">=</span><span class="s">'MOLPROBITY_EXECUTABLE'</span><span class="p">)</span>
- <span class="c"># run molprobity avoiding any file output</span>
- <span class="n">cmd</span> <span class="o">=</span> <span class="p">[</span><span class="n">molprobity_exec</span><span class="p">,</span> <span class="n">target_pdb</span><span class="p">,</span> <span class="s">"output.quiet=True"</span><span class="p">,</span> \
- <span class="s">"output.coot=False"</span><span class="p">,</span> <span class="s">"output.probe_dots=False"</span><span class="p">]</span>
+ <span class="n">env_name</span><span class="o">=</span><span class="s1">'MOLPROBITY_EXECUTABLE'</span><span class="p">)</span>
+ <span class="c1"># run molprobity avoiding any file output</span>
+ <span class="n">cmd</span> <span class="o">=</span> <span class="p">[</span><span class="n">molprobity_exec</span><span class="p">,</span> <span class="n">target_pdb</span><span class="p">,</span> <span class="s2">"output.quiet=True"</span><span class="p">,</span> \
+ <span class="s2">"output.coot=False"</span><span class="p">,</span> <span class="s2">"output.probe_dots=False"</span><span class="p">]</span>
<span class="n">job</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">Popen</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span> <span class="n">stdout</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">,</span> <span class="n">stderr</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">)</span>
<span class="n">sout</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">job</span><span class="o">.</span><span class="n">communicate</span><span class="p">()</span>
- <span class="c"># parse</span>
+ <span class="c1"># parse</span>
<span class="n">result</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
<span class="n">first_found</span> <span class="o">=</span> <span class="bp">False</span>
<span class="n">lines</span> <span class="o">=</span> <span class="n">sout</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>
<span class="k">for</span> <span class="n">line</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">:</span>
<span class="n">my_line</span> <span class="o">=</span> <span class="n">line</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
- <span class="k">if</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">"ramachandran outliers"</span><span class="p">):</span>
+ <span class="k">if</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"ramachandran outliers"</span><span class="p">):</span>
<span class="n">first_found</span> <span class="o">=</span> <span class="bp">True</span>
- <span class="n">result</span><span class="p">[</span><span class="s">"Ramachandran outliers"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
- <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">"favored"</span><span class="p">):</span>
- <span class="n">result</span><span class="p">[</span><span class="s">"Ramachandran favored"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
- <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">"rotamer outliers"</span><span class="p">):</span>
- <span class="n">result</span><span class="p">[</span><span class="s">"Rotamer outliers"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
- <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">"clashscore"</span><span class="p">):</span>
- <span class="n">result</span><span class="p">[</span><span class="s">"Clashscore"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
- <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">"c-beta deviations"</span><span class="p">):</span>
- <span class="n">result</span><span class="p">[</span><span class="s">"C-beta deviations"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
- <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">"molprobity score"</span><span class="p">):</span>
- <span class="n">result</span><span class="p">[</span><span class="s">"MolProbity score"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
- <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">"rms(bonds)"</span><span class="p">):</span>
- <span class="n">result</span><span class="p">[</span><span class="s">"RMS(bonds)"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
- <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s">"rms(angles)"</span><span class="p">):</span>
- <span class="n">result</span><span class="p">[</span><span class="s">"RMS(angles)"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
- <span class="k">return</span> <span class="n">result</span>
+ <span class="n">result</span><span class="p">[</span><span class="s2">"Ramachandran outliers"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
+ <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"favored"</span><span class="p">):</span>
+ <span class="n">result</span><span class="p">[</span><span class="s2">"Ramachandran favored"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
+ <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"rotamer outliers"</span><span class="p">):</span>
+ <span class="n">result</span><span class="p">[</span><span class="s2">"Rotamer outliers"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
+ <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"clashscore"</span><span class="p">):</span>
+ <span class="n">result</span><span class="p">[</span><span class="s2">"Clashscore"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
+ <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"c-beta deviations"</span><span class="p">):</span>
+ <span class="n">result</span><span class="p">[</span><span class="s2">"C-beta deviations"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
+ <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"molprobity score"</span><span class="p">):</span>
+ <span class="n">result</span><span class="p">[</span><span class="s2">"MolProbity score"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
+ <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"rms(bonds)"</span><span class="p">):</span>
+ <span class="n">result</span><span class="p">[</span><span class="s2">"RMS(bonds)"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
+ <span class="k">elif</span> <span class="n">first_found</span> <span class="ow">and</span> <span class="n">my_line</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"rms(angles)"</span><span class="p">):</span>
+ <span class="n">result</span><span class="p">[</span><span class="s2">"RMS(angles)"</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">GetStringValue</span><span class="p">(</span><span class="n">line</span><span class="p">))</span>
+ <span class="k">return</span> <span class="n">result</span></div>
+
-</div>
<div class="viewcode-block" id="RunMolProbityEntity"><a class="viewcode-back" href="../../../modelling/model_checking.html#promod3.modelling.RunMolProbityEntity">[docs]</a><span class="k">def</span> <span class="nf">RunMolProbityEntity</span><span class="p">(</span><span class="n">ost_ent</span><span class="p">,</span> <span class="n">molprobity_bin</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
<span class="sd">'''Run molprobity from phenix on given OST entity.</span>
<span class="sd"> </span>
@@ -132,29 +134,29 @@
<span class="sd"> :param ost_ent: OST entity on which to do analysis.</span>
<span class="sd"> :type ost_ent: :class:`Entity <ost.mol.EntityHandle>`</span>
<span class="sd"> '''</span>
- <span class="c"># store as PDB in a tmp. file</span>
- <span class="n">_</span><span class="p">,</span> <span class="n">tmpfile</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mkstemp</span><span class="p">(</span><span class="n">suffix</span><span class="o">=</span><span class="s">'.pdb'</span><span class="p">)</span>
+ <span class="c1"># store as PDB in a tmp. file</span>
+ <span class="n">_</span><span class="p">,</span> <span class="n">tmpfile</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">mkstemp</span><span class="p">(</span><span class="n">suffix</span><span class="o">=</span><span class="s1">'.pdb'</span><span class="p">)</span>
<span class="n">ost</span><span class="o">.</span><span class="n">PushVerbosityLevel</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="n">ost</span><span class="o">.</span><span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">ost_ent</span><span class="p">,</span> <span class="n">tmpfile</span><span class="p">)</span>
<span class="n">ost</span><span class="o">.</span><span class="n">PopVerbosityLevel</span><span class="p">()</span>
- <span class="c"># get result</span>
+ <span class="c1"># get result</span>
<span class="n">result</span> <span class="o">=</span> <span class="n">RunMolProbity</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">,</span> <span class="n">molprobity_bin</span><span class="p">)</span>
- <span class="c"># clean up</span>
+ <span class="c1"># clean up</span>
<span class="n">os</span><span class="o">.</span><span class="n">remove</span><span class="p">(</span><span class="n">tmpfile</span><span class="p">)</span>
- <span class="k">return</span> <span class="n">result</span>
-</div>
+ <span class="k">return</span> <span class="n">result</span></div>
+
<div class="viewcode-block" id="ReportMolProbityScores"><a class="viewcode-back" href="../../../modelling/model_checking.html#promod3.modelling.ReportMolProbityScores">[docs]</a><span class="k">def</span> <span class="nf">ReportMolProbityScores</span><span class="p">(</span><span class="n">scores</span><span class="p">):</span>
<span class="sd">'''Print MolProbity score and its components to LogInfo.</span>
<span class="sd"> </span>
<span class="sd"> :param scores: MolProbity scores as generated by :func:`RunMolProbity`.</span>
<span class="sd"> :type scores: :class:`dict`</span>
<span class="sd"> '''</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"MolProbity score: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">scores</span><span class="p">[</span><span class="s">"MolProbity score"</span><span class="p">]))</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"- Clashscore : "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">scores</span><span class="p">[</span><span class="s">"Clashscore"</span><span class="p">]))</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"- Rotamer outliers : "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">scores</span><span class="p">[</span><span class="s">"Rotamer outliers"</span><span class="p">])</span> <span class="o">+</span> <span class="s">" %"</span><span class="p">)</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"- Ramachandran favored: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">scores</span><span class="p">[</span><span class="s">"Ramachandran favored"</span><span class="p">])</span> <span class="o">+</span> <span class="s">" %"</span><span class="p">)</span>
-</div>
-<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s">'RunMolProbity'</span><span class="p">,</span> <span class="s">'RunMolProbityEntity'</span><span class="p">,</span> <span class="s">'ReportMolProbityScores'</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"MolProbity score: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">scores</span><span class="p">[</span><span class="s2">"MolProbity score"</span><span class="p">]))</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"- Clashscore : "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">scores</span><span class="p">[</span><span class="s2">"Clashscore"</span><span class="p">]))</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"- Rotamer outliers : "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">scores</span><span class="p">[</span><span class="s2">"Rotamer outliers"</span><span class="p">])</span> <span class="o">+</span> <span class="s2">" %"</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"- Ramachandran favored: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">scores</span><span class="p">[</span><span class="s2">"Ramachandran favored"</span><span class="p">])</span> <span class="o">+</span> <span class="s2">" %"</span><span class="p">)</span></div>
+
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s1">'RunMolProbity'</span><span class="p">,</span> <span class="s1">'RunMolProbityEntity'</span><span class="p">,</span> <span class="s1">'ReportMolProbityScores'</span><span class="p">)</span>
</pre></div>
</div>
@@ -180,9 +182,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -190,11 +189,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/_modules/promod3/modelling/_pipeline.html b/doc/html/_modules/promod3/modelling/_pipeline.html
index 2e1e714435baa559314bc1a202cddcfc87fe7177..3ea48e01d1e4a82180c71d72adbae5297ad85c69 100644
--- a/doc/html/_modules/promod3/modelling/_pipeline.html
+++ b/doc/html/_modules/promod3/modelling/_pipeline.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._pipeline — ProMod3 1.1.0 documentation</title>
+ <title>promod3.modelling._pipeline — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,14 +23,16 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../../../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
+ <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -38,25 +40,25 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._pipeline</h1><div class="highlight"><pre>
-<span class="sd">'''High-level functionality for modelling module to build pipelines. Added in </span>
+<span></span><span class="sd">'''High-level functionality for modelling module to build pipelines. Added in </span>
<span class="sd">the __init__.py file. To be used directly by passing a ModellingHandle instance</span>
<span class="sd">as argument.</span>
<span class="sd">'''</span>
-<span class="c"># internal</span>
+<span class="c1"># internal</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">sidechain</span><span class="p">,</span> <span class="n">core</span>
<span class="kn">from</span> <span class="nn">_modelling</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">_reconstruct_sidechains</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">_closegaps</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">_ring_punches</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="c"># external</span>
+<span class="c1"># external</span>
<span class="kn">import</span> <span class="nn">ost</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">mol</span><span class="p">,</span> <span class="n">conop</span>
<span class="kn">from</span> <span class="nn">ost.mol</span> <span class="kn">import</span> <span class="n">mm</span>
<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">math</span>
-<span class="c">###############################################################################</span>
-<span class="c"># helper functions</span>
+<span class="c1">###############################################################################</span>
+<span class="c1"># helper functions</span>
<span class="k">def</span> <span class="nf">_RemoveHydrogens</span><span class="p">(</span><span class="n">ent</span><span class="p">):</span>
<span class="sd">'''Hydrogen naming depends on the force field used.</span>
<span class="sd"> To be on the safe side, we simply remove all of them.</span>
@@ -64,7 +66,7 @@
<span class="sd"> when rebuilding sidechains.</span>
<span class="sd"> '''</span>
<span class="n">edi</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">EditXCS</span><span class="p">(</span><span class="n">mol</span><span class="o">.</span><span class="n">BUFFERED_EDIT</span><span class="p">)</span>
- <span class="n">ha</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">'ele=H'</span><span class="p">)</span>
+ <span class="n">ha</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s1">'ele=H'</span><span class="p">)</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">ha</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
<span class="n">edi</span><span class="o">.</span><span class="n">DeleteAtom</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">handle</span><span class="p">)</span>
<span class="n">edi</span><span class="o">.</span><span class="n">UpdateICS</span><span class="p">()</span>
@@ -84,53 +86,53 @@
<span class="sd"> Note: if successful, this will update ent (adding hydrogens).</span>
<span class="sd"> Set add_heuristic_hydrogens to True for ligands.</span>
<span class="sd"> '''</span>
- <span class="c"># try all force fields in order</span>
+ <span class="c1"># try all force fields in order</span>
<span class="k">for</span> <span class="n">i_ff</span><span class="p">,</span> <span class="n">ff</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">force_fields</span><span class="p">):</span>
<span class="n">settings</span><span class="o">.</span><span class="n">forcefield</span> <span class="o">=</span> <span class="n">ff</span>
<span class="k">try</span><span class="p">:</span>
- <span class="c"># check if we need to add hydrogens heuristically</span>
+ <span class="c1"># check if we need to add hydrogens heuristically</span>
<span class="k">if</span> <span class="n">add_heuristic_hydrogens</span><span class="p">:</span>
<span class="n">_AddHeuristicHydrogens</span><span class="p">(</span><span class="n">ent</span><span class="p">,</span> <span class="n">ff</span><span class="p">)</span>
- <span class="c"># ok now we try...</span>
+ <span class="c1"># ok now we try...</span>
<span class="n">topo</span> <span class="o">=</span> <span class="n">mm</span><span class="o">.</span><span class="n">TopologyCreator</span><span class="o">.</span><span class="n">Create</span><span class="p">(</span><span class="n">ent</span><span class="p">,</span> <span class="n">settings</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">ex</span><span class="p">:</span>
- <span class="c"># report only for debugging</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s">"Could not create mm topology for ff </span><span class="si">%d</span><span class="s">. </span><span class="si">%s</span><span class="s">"</span> \
- <span class="o">%</span> <span class="p">(</span><span class="n">i_ff</span><span class="p">,</span> <span class="nb">type</span><span class="p">(</span><span class="n">ex</span><span class="p">)</span><span class="o">.</span><span class="n">__name__</span> <span class="o">+</span> <span class="s">": "</span> <span class="o">+</span> <span class="n">ex</span><span class="o">.</span><span class="n">message</span><span class="p">))</span>
+ <span class="c1"># report only for debugging</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogVerbose</span><span class="p">(</span><span class="s2">"Could not create mm topology for ff </span><span class="si">%d</span><span class="s2">. </span><span class="si">%s</span><span class="s2">"</span> \
+ <span class="o">%</span> <span class="p">(</span><span class="n">i_ff</span><span class="p">,</span> <span class="nb">type</span><span class="p">(</span><span class="n">ex</span><span class="p">)</span><span class="o">.</span><span class="n">__name__</span> <span class="o">+</span> <span class="s2">": "</span> <span class="o">+</span> <span class="n">ex</span><span class="o">.</span><span class="n">message</span><span class="p">))</span>
<span class="k">continue</span>
<span class="k">else</span><span class="p">:</span>
- <span class="c"># all good</span>
+ <span class="c1"># all good</span>
<span class="k">return</span> <span class="n">topo</span>
- <span class="c"># if we got here, nothing worked</span>
+ <span class="c1"># if we got here, nothing worked</span>
<span class="k">return</span> <span class="bp">None</span>
<span class="k">def</span> <span class="nf">_AddLigands</span><span class="p">(</span><span class="n">ent</span><span class="p">,</span> <span class="n">top</span><span class="p">,</span> <span class="n">lig_ent</span><span class="p">,</span> <span class="n">settings</span><span class="p">,</span> <span class="n">force_fields</span><span class="p">):</span>
<span class="sd">'''Add ligands from lig_ent to topology top and update entity ent.'''</span>
- <span class="c"># connect them first</span>
+ <span class="c1"># connect them first</span>
<span class="n">proc</span> <span class="o">=</span> <span class="n">conop</span><span class="o">.</span><span class="n">RuleBasedProcessor</span><span class="p">(</span><span class="n">conop</span><span class="o">.</span><span class="n">GetDefaultLib</span><span class="p">())</span>
<span class="n">proc</span><span class="o">.</span><span class="n">Process</span><span class="p">(</span><span class="n">lig_ent</span><span class="p">)</span>
<span class="n">cur_res</span> <span class="o">=</span> <span class="n">lig_ent</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">lig_num</span> <span class="o">=</span> <span class="mi">1</span>
<span class="k">while</span> <span class="n">cur_res</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
- <span class="c"># setup connected components</span>
+ <span class="c1"># setup connected components</span>
<span class="n">cur_view</span> <span class="o">=</span> <span class="n">lig_ent</span><span class="o">.</span><span class="n">CreateEmptyView</span><span class="p">()</span>
<span class="n">cur_view</span><span class="o">.</span><span class="n">AddResidue</span><span class="p">(</span><span class="n">cur_res</span><span class="p">,</span> <span class="n">mol</span><span class="o">.</span><span class="n">INCLUDE_ATOMS</span><span class="p">)</span>
<span class="n">cur_res</span> <span class="o">=</span> <span class="n">cur_res</span><span class="o">.</span><span class="n">next</span>
<span class="k">while</span> <span class="n">cur_res</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">and</span> <span class="n">mol</span><span class="o">.</span><span class="n">InSequence</span><span class="p">(</span><span class="n">cur_res</span><span class="o">.</span><span class="n">prev</span><span class="p">,</span> <span class="n">cur_res</span><span class="p">):</span>
<span class="n">cur_view</span><span class="o">.</span><span class="n">AddResidue</span><span class="p">(</span><span class="n">cur_res</span><span class="p">,</span> <span class="n">mol</span><span class="o">.</span><span class="n">INCLUDE_ATOMS</span><span class="p">)</span>
<span class="n">cur_res</span> <span class="o">=</span> <span class="n">cur_res</span><span class="o">.</span><span class="n">next</span>
- <span class="c"># try to add topology with special named chain</span>
+ <span class="c1"># try to add topology with special named chain</span>
<span class="n">cur_ent</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">cur_view</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
<span class="n">edi</span> <span class="o">=</span> <span class="n">cur_ent</span><span class="o">.</span><span class="n">EditXCS</span><span class="p">()</span>
- <span class="n">edi</span><span class="o">.</span><span class="n">RenameChain</span><span class="p">(</span><span class="n">cur_ent</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'_'</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">lig_num</span><span class="p">))</span>
+ <span class="n">edi</span><span class="o">.</span><span class="n">RenameChain</span><span class="p">(</span><span class="n">cur_ent</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s1">'_'</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">lig_num</span><span class="p">))</span>
<span class="n">lig_num</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="n">cur_top</span> <span class="o">=</span> <span class="n">_GetTopology</span><span class="p">(</span><span class="n">cur_ent</span><span class="p">,</span> <span class="n">settings</span><span class="p">,</span> <span class="n">force_fields</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
<span class="k">if</span> <span class="n">cur_top</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">view_res_str</span> <span class="o">=</span> <span class="nb">str</span><span class="p">([</span><span class="nb">str</span><span class="p">(</span><span class="n">r</span><span class="p">)</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">cur_view</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s">"Failed to add ligands "</span> <span class="o">+</span> <span class="n">view_res_str</span> <span class="o">+</span> \
- <span class="s">" for energy minimization! Skipping..."</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s2">"Failed to add ligands "</span> <span class="o">+</span> <span class="n">view_res_str</span> <span class="o">+</span> \
+ <span class="s2">" for energy minimization! Skipping..."</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="c"># merge into main topology</span>
+ <span class="c1"># merge into main topology</span>
<span class="n">cur_top</span><span class="o">.</span><span class="n">SetFudgeLJ</span><span class="p">(</span><span class="n">top</span><span class="o">.</span><span class="n">GetFudgeLJ</span><span class="p">())</span>
<span class="n">cur_top</span><span class="o">.</span><span class="n">SetFudgeQQ</span><span class="p">(</span><span class="n">top</span><span class="o">.</span><span class="n">GetFudgeQQ</span><span class="p">())</span>
<span class="n">top</span><span class="o">.</span><span class="n">Merge</span><span class="p">(</span><span class="n">ent</span><span class="p">,</span> <span class="n">cur_top</span><span class="p">,</span> <span class="n">cur_ent</span><span class="p">)</span>
@@ -141,41 +143,41 @@
<span class="sd"> component in the ligand chain separately by evaluating the force fields in</span>
<span class="sd"> the same order as given. Ligands without force fields are skipped.</span>
<span class="sd"> '''</span>
- <span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="s">'pipeline::_SetupMmSimulation'</span><span class="p">)</span>
+ <span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="s1">'pipeline::_SetupMmSimulation'</span><span class="p">)</span>
- <span class="c"># get general settings </span>
+ <span class="c1"># get general settings </span>
<span class="n">settings</span> <span class="o">=</span> <span class="n">mm</span><span class="o">.</span><span class="n">Settings</span><span class="p">()</span>
<span class="n">settings</span><span class="o">.</span><span class="n">integrator</span> <span class="o">=</span> <span class="n">mm</span><span class="o">.</span><span class="n">LangevinIntegrator</span><span class="p">(</span><span class="mi">310</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mf">0.002</span><span class="p">)</span>
<span class="n">settings</span><span class="o">.</span><span class="n">init_temperature</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">settings</span><span class="o">.</span><span class="n">nonbonded_method</span> <span class="o">=</span> <span class="n">mm</span><span class="o">.</span><span class="n">NonbondedMethod</span><span class="o">.</span><span class="n">CutoffNonPeriodic</span>
<span class="n">settings</span><span class="o">.</span><span class="n">keep_ff_specific_naming</span> <span class="o">=</span> <span class="bp">False</span>
- <span class="c"># prepare entity with protein</span>
+ <span class="c1"># prepare entity with protein</span>
<span class="n">_RemoveHydrogens</span><span class="p">(</span><span class="n">model</span><span class="p">)</span>
- <span class="n">ent</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"cname!='_'"</span><span class="p">),</span> <span class="bp">True</span><span class="p">)</span>
+ <span class="n">ent</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"cname!='_'"</span><span class="p">),</span> <span class="bp">True</span><span class="p">)</span>
<span class="n">top</span> <span class="o">=</span> <span class="n">_GetTopology</span><span class="p">(</span><span class="n">ent</span><span class="p">,</span> <span class="n">settings</span><span class="p">,</span> <span class="n">force_fields</span><span class="p">)</span>
<span class="k">if</span> <span class="n">top</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
- <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">"Failed to setup protein for energy minimization!"</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"Failed to setup protein for energy minimization!"</span><span class="p">)</span>
- <span class="c"># prepare ligands: we reprocess them to ensure connectivity</span>
- <span class="n">lig_ent</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"cname='_'"</span><span class="p">),</span> <span class="bp">True</span><span class="p">)</span>
+ <span class="c1"># prepare ligands: we reprocess them to ensure connectivity</span>
+ <span class="n">lig_ent</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"cname='_'"</span><span class="p">),</span> <span class="bp">True</span><span class="p">)</span>
<span class="k">if</span> <span class="n">lig_ent</span><span class="o">.</span><span class="n">residue_count</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
<span class="n">_AddLigands</span><span class="p">(</span><span class="n">ent</span><span class="p">,</span> <span class="n">top</span><span class="p">,</span> <span class="n">lig_ent</span><span class="p">,</span> <span class="n">settings</span><span class="p">,</span> <span class="n">force_fields</span><span class="p">)</span>
- <span class="c"># use fast CPU platform by default</span>
- <span class="c"># NOTE: settings.platform only relevant for mm.Simulation!</span>
+ <span class="c1"># use fast CPU platform by default</span>
+ <span class="c1"># NOTE: settings.platform only relevant for mm.Simulation!</span>
<span class="n">settings</span><span class="o">.</span><span class="n">platform</span> <span class="o">=</span> <span class="n">mm</span><span class="o">.</span><span class="n">Platform</span><span class="o">.</span><span class="n">CPU</span>
<span class="k">if</span> <span class="n">mm</span><span class="o">.</span><span class="n">Simulation</span><span class="o">.</span><span class="n">IsPlatformAvailable</span><span class="p">(</span><span class="n">settings</span><span class="p">):</span>
- <span class="n">num_cpu_threads</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s">'PM3_OPENMM_CPU_THREADS'</span><span class="p">)</span>
+ <span class="n">num_cpu_threads</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s1">'PM3_OPENMM_CPU_THREADS'</span><span class="p">)</span>
<span class="k">if</span> <span class="n">num_cpu_threads</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
- <span class="n">settings</span><span class="o">.</span><span class="n">cpu_properties</span><span class="p">[</span><span class="s">"CpuThreads"</span><span class="p">]</span> <span class="o">=</span> <span class="s">"1"</span>
+ <span class="n">settings</span><span class="o">.</span><span class="n">cpu_properties</span><span class="p">[</span><span class="s2">"CpuThreads"</span><span class="p">]</span> <span class="o">=</span> <span class="s2">"1"</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">settings</span><span class="o">.</span><span class="n">cpu_properties</span><span class="p">[</span><span class="s">"CpuThreads"</span><span class="p">]</span> <span class="o">=</span> <span class="n">num_cpu_threads</span>
+ <span class="n">settings</span><span class="o">.</span><span class="n">cpu_properties</span><span class="p">[</span><span class="s2">"CpuThreads"</span><span class="p">]</span> <span class="o">=</span> <span class="n">num_cpu_threads</span>
<span class="k">else</span><span class="p">:</span>
- <span class="c"># switch to "mm.Platform.Reference" as fallback</span>
+ <span class="c1"># switch to "mm.Platform.Reference" as fallback</span>
<span class="n">settings</span><span class="o">.</span><span class="n">platform</span> <span class="o">=</span> <span class="n">mm</span><span class="o">.</span><span class="n">Platform</span><span class="o">.</span><span class="n">Reference</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogWarning</span><span class="p">(</span><span class="s">"Switched to slower reference platform of OpenMM!"</span><span class="p">)</span>
- <span class="c"># finally set up the simulation</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogWarning</span><span class="p">(</span><span class="s2">"Switched to slower reference platform of OpenMM!"</span><span class="p">)</span>
+ <span class="c1"># finally set up the simulation</span>
<span class="n">sim</span> <span class="o">=</span> <span class="n">mm</span><span class="o">.</span><span class="n">Simulation</span><span class="p">(</span><span class="n">top</span><span class="p">,</span> <span class="n">ent</span><span class="p">,</span> <span class="n">settings</span><span class="p">)</span>
<span class="k">return</span> <span class="n">sim</span>
@@ -183,24 +185,24 @@
<span class="k">def</span> <span class="nf">_GetSimEntity</span><span class="p">(</span><span class="n">sim</span><span class="p">):</span>
<span class="sd">'''Get Entity from mm sim and reverse ligand chain naming.'''</span>
<span class="n">ent</span> <span class="o">=</span> <span class="n">sim</span><span class="o">.</span><span class="n">GetEntity</span><span class="p">()</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
- <span class="c"># merge ligand chains into _</span>
+ <span class="c1"># merge ligand chains into _</span>
<span class="n">ent_ed</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">EditXCS</span><span class="p">(</span><span class="n">mol</span><span class="o">.</span><span class="n">BUFFERED_EDIT</span><span class="p">)</span>
<span class="n">chain_names</span> <span class="o">=</span> <span class="p">[</span><span class="n">ch</span><span class="o">.</span><span class="n">name</span> <span class="k">for</span> <span class="n">ch</span> <span class="ow">in</span> <span class="n">ent</span><span class="o">.</span><span class="n">chains</span><span class="p">]</span>
<span class="k">for</span> <span class="n">chain_name</span> <span class="ow">in</span> <span class="n">chain_names</span><span class="p">:</span>
- <span class="c"># all separate ligand chains start with _</span>
- <span class="k">if</span> <span class="n">chain_name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s">'_'</span><span class="p">:</span>
- <span class="c"># add to chain _</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">ent</span><span class="o">.</span><span class="n">FindChain</span><span class="p">(</span><span class="s">'_'</span><span class="p">)</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
- <span class="n">ent_ed</span><span class="o">.</span><span class="n">InsertChain</span><span class="p">(</span><span class="s">'_'</span><span class="p">)</span>
- <span class="n">lig_ch</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">FindChain</span><span class="p">(</span><span class="s">'_'</span><span class="p">)</span>
+ <span class="c1"># all separate ligand chains start with _</span>
+ <span class="k">if</span> <span class="n">chain_name</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="s1">'_'</span><span class="p">:</span>
+ <span class="c1"># add to chain _</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">ent</span><span class="o">.</span><span class="n">FindChain</span><span class="p">(</span><span class="s1">'_'</span><span class="p">)</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
+ <span class="n">ent_ed</span><span class="o">.</span><span class="n">InsertChain</span><span class="p">(</span><span class="s1">'_'</span><span class="p">)</span>
+ <span class="n">lig_ch</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">FindChain</span><span class="p">(</span><span class="s1">'_'</span><span class="p">)</span>
<span class="n">cur_ch</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">FindChain</span><span class="p">(</span><span class="n">chain_name</span><span class="p">)</span>
<span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">cur_ch</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
<span class="n">ent_ed</span><span class="o">.</span><span class="n">AppendResidue</span><span class="p">(</span><span class="n">lig_ch</span><span class="p">,</span> <span class="n">res</span><span class="p">,</span> <span class="n">deep</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
- <span class="c"># remove old chain</span>
+ <span class="c1"># remove old chain</span>
<span class="n">ent_ed</span><span class="o">.</span><span class="n">DeleteChain</span><span class="p">(</span><span class="n">cur_ch</span><span class="p">)</span>
<span class="n">ent_ed</span><span class="o">.</span><span class="n">UpdateICS</span><span class="p">()</span>
<span class="k">return</span> <span class="n">ent</span>
-<span class="c">###############################################################################</span>
+<span class="c1">###############################################################################</span>
<div class="viewcode-block" id="BuildSidechains"><a class="viewcode-back" href="../../../modelling/pipeline.html#promod3.modelling.BuildSidechains">[docs]</a><span class="k">def</span> <span class="nf">BuildSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">merge_distance</span><span class="o">=</span><span class="mi">4</span><span class="p">,</span> <span class="n">fragment_db</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span>
@@ -231,43 +233,43 @@
<span class="sd"> if None.</span>
<span class="sd"> :type torsion_sampler: :class:`~promod3.loop.TorsionSampler`</span>
<span class="sd"> '''</span>
- <span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="s">'pipeline::BuildSidechains'</span><span class="p">)</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Rebuilding sidechains."</span><span class="p">)</span>
+ <span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="s1">'pipeline::BuildSidechains'</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Rebuilding sidechains."</span><span class="p">)</span>
<span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
- <span class="c"># check for ring punches</span>
+ <span class="c1"># check for ring punches</span>
<span class="n">rings</span> <span class="o">=</span> <span class="n">GetRings</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">)</span>
<span class="n">ring_punches</span> <span class="o">=</span> <span class="n">GetRingPunches</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">)</span>
- <span class="c"># try to fix them</span>
+ <span class="c1"># try to fix them</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ring_punches</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Trying to fix </span><span class="si">%d</span><span class="s"> ring punch(es)."</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">ring_punches</span><span class="p">))</span>
- <span class="c"># backup old gaps</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Trying to fix </span><span class="si">%d</span><span class="s2"> ring punch(es)."</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">ring_punches</span><span class="p">))</span>
+ <span class="c1"># backup old gaps</span>
<span class="n">old_gaps</span> <span class="o">=</span> <span class="p">[</span><span class="n">g</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span> <span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">]</span>
- <span class="c"># new gaps for mhandle</span>
- <span class="c"># NOTE: we currently do not delete the punched residues here</span>
- <span class="c"># BUT they could be deleted when merging gaps below...</span>
+ <span class="c1"># new gaps for mhandle</span>
+ <span class="c1"># NOTE: we currently do not delete the punched residues here</span>
+ <span class="c1"># BUT they could be deleted when merging gaps below...</span>
<span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span> <span class="o">=</span> <span class="n">StructuralGapList</span><span class="p">()</span>
<span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">ring_punches</span><span class="p">:</span>
<span class="n">mygap</span> <span class="o">=</span> <span class="n">StructuralGap</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">prev</span><span class="p">,</span> <span class="n">res</span><span class="o">.</span><span class="n">next</span><span class="p">,</span> <span class="n">res</span><span class="o">.</span><span class="n">one_letter_code</span><span class="p">)</span>
<span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mygap</span><span class="p">)</span>
- <span class="c"># load stuff if needed</span>
+ <span class="c1"># load stuff if needed</span>
<span class="k">if</span> <span class="n">fragment_db</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">fragment_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">()</span>
<span class="k">if</span> <span class="n">structure_db</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
<span class="k">if</span> <span class="n">torsion_sampler</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">torsion_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">()</span>
- <span class="c"># fix it</span>
+ <span class="c1"># fix it</span>
<span class="n">MergeGapsByDistance</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">merge_distance</span><span class="p">)</span>
<span class="n">FillLoopsByDatabase</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">fragment_db</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">,</span>
<span class="n">torsion_sampler</span><span class="p">,</span> <span class="n">ring_punch_detection</span><span class="o">=</span><span class="mi">2</span><span class="p">)</span>
- <span class="c"># re-build sidechains</span>
+ <span class="c1"># re-build sidechains</span>
<span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
- <span class="c"># restore gaps</span>
+ <span class="c1"># restore gaps</span>
<span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span> <span class="o">=</span> <span class="n">StructuralGapList</span><span class="p">()</span>
<span class="k">for</span> <span class="n">g</span> <span class="ow">in</span> <span class="n">old_gaps</span><span class="p">:</span>
- <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">g</span><span class="p">)</span>
+ <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">g</span><span class="p">)</span></div>
-</div>
+
<div class="viewcode-block" id="MinimizeModelEnergy"><a class="viewcode-back" href="../../../modelling/pipeline.html#promod3.modelling.MinimizeModelEnergy">[docs]</a><span class="k">def</span> <span class="nf">MinimizeModelEnergy</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">max_iterations</span><span class="o">=</span><span class="mi">12</span><span class="p">,</span> <span class="n">max_iter_sd</span><span class="o">=</span><span class="mi">20</span><span class="p">,</span>
<span class="n">max_iter_lbfgs</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">use_amber_ff</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span>
<span class="n">extra_force_fields</span><span class="o">=</span><span class="nb">list</span><span class="p">()):</span>
@@ -311,47 +313,47 @@
<span class="sd"> :return: The model including all oxygens as used in the minimizer.</span>
<span class="sd"> :rtype: :class:`Entity <ost.mol.EntityHandle>`</span>
<span class="sd"> '''</span>
- <span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="s">'pipeline::MinimizeModelEnergy'</span><span class="p">)</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Minimize energy."</span><span class="p">)</span>
- <span class="c"># ignore LogInfo in stereochemical problems if output up to info done</span>
+ <span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="s1">'pipeline::MinimizeModelEnergy'</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Minimize energy."</span><span class="p">)</span>
+ <span class="c1"># ignore LogInfo in stereochemical problems if output up to info done</span>
<span class="n">ignore_stereo_log</span> <span class="o">=</span> <span class="p">(</span><span class="n">ost</span><span class="o">.</span><span class="n">GetVerbosityLevel</span><span class="p">()</span> <span class="o">==</span> <span class="mi">3</span><span class="p">)</span>
- <span class="c"># setup force fields</span>
+ <span class="c1"># setup force fields</span>
<span class="k">if</span> <span class="n">use_amber_ff</span><span class="p">:</span>
<span class="n">force_fields</span> <span class="o">=</span> <span class="p">[</span><span class="n">mm</span><span class="o">.</span><span class="n">LoadAMBERForcefield</span><span class="p">()]</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">force_fields</span> <span class="o">=</span> <span class="p">[</span><span class="n">mm</span><span class="o">.</span><span class="n">LoadCHARMMForcefield</span><span class="p">()]</span>
<span class="n">force_fields</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">extra_force_fields</span><span class="p">)</span>
- <span class="c"># setup mm simulation</span>
+ <span class="c1"># setup mm simulation</span>
<span class="n">sim</span> <span class="o">=</span> <span class="n">_SetupMmSimulation</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="n">force_fields</span><span class="p">)</span>
- <span class="c"># check for certain failure -> we get NaN if atoms are on top each other</span>
+ <span class="c1"># check for certain failure -> we get NaN if atoms are on top each other</span>
<span class="k">if</span> <span class="n">math</span><span class="o">.</span><span class="n">isnan</span><span class="p">(</span><span class="n">sim</span><span class="o">.</span><span class="n">GetEnergy</span><span class="p">()):</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s">"OpenMM could not minimize energy as atoms are on top of "</span>
- <span class="s">"each other!"</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s2">"OpenMM could not minimize energy as atoms are on top of "</span>
+ <span class="s2">"each other!"</span><span class="p">)</span>
<span class="k">return</span>
- <span class="c"># settings to check for stereochemical problems</span>
+ <span class="c1"># settings to check for stereochemical problems</span>
<span class="n">clashing_distances</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">DefaultClashingDistances</span><span class="p">()</span>
<span class="n">bond_stereo_chemical_param</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">DefaultBondStereoChemicalParams</span><span class="p">()</span>
<span class="n">angle_stereo_chemical_param</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">DefaultAngleStereoChemicalParams</span><span class="p">()</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">max_iterations</span><span class="p">):</span>
- <span class="c"># update atoms</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Perform energy minimization "</span>
- <span class="s">"(iteration </span><span class="si">%d</span><span class="s">, energy: </span><span class="si">%g</span><span class="s">)"</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="n">sim</span><span class="o">.</span><span class="n">GetEnergy</span><span class="p">()))</span>
+ <span class="c1"># update atoms</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Perform energy minimization "</span>
+ <span class="s2">"(iteration </span><span class="si">%d</span><span class="s2">, energy: </span><span class="si">%g</span><span class="s2">)"</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span> <span class="n">sim</span><span class="o">.</span><span class="n">GetEnergy</span><span class="p">()))</span>
<span class="n">sim</span><span class="o">.</span><span class="n">ApplySD</span><span class="p">(</span><span class="n">tolerance</span> <span class="o">=</span> <span class="mf">1.0</span><span class="p">,</span> <span class="n">max_iterations</span> <span class="o">=</span> <span class="n">max_iter_sd</span><span class="p">)</span>
<span class="n">sim</span><span class="o">.</span><span class="n">ApplyLBFGS</span><span class="p">(</span><span class="n">tolerance</span> <span class="o">=</span> <span class="mf">1.0</span><span class="p">,</span> <span class="n">max_iterations</span> <span class="o">=</span> <span class="n">max_iter_lbfgs</span><span class="p">)</span>
<span class="n">sim</span><span class="o">.</span><span class="n">UpdatePositions</span><span class="p">()</span>
- <span class="c"># check for stereochemical problems</span>
+ <span class="c1"># check for stereochemical problems</span>
<span class="k">if</span> <span class="n">ignore_stereo_log</span><span class="p">:</span>
<span class="n">ost</span><span class="o">.</span><span class="n">PushVerbosityLevel</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span>
<span class="n">temp_ent</span> <span class="o">=</span> <span class="n">sim</span><span class="o">.</span><span class="n">GetEntity</span><span class="p">()</span>
- <span class="n">temp_ent</span> <span class="o">=</span> <span class="n">temp_ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"aname!=OXT"</span><span class="p">)</span>
+ <span class="n">temp_ent</span> <span class="o">=</span> <span class="n">temp_ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"aname!=OXT"</span><span class="p">)</span>
<span class="n">temp_ent_clash_filtered</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">FilterClashes</span><span class="p">(</span>\
<span class="n">temp_ent</span><span class="p">,</span> <span class="n">clashing_distances</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
- <span class="c"># note: 10,10 parameters below are hard coded bond-/angle-tolerances</span>
+ <span class="c1"># note: 10,10 parameters below are hard coded bond-/angle-tolerances</span>
<span class="n">temp_ent_stereo_checked</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">CheckStereoChemistry</span><span class="p">(</span>\
<span class="n">temp_ent_clash_filtered</span><span class="p">,</span>
<span class="n">bond_stereo_chemical_param</span><span class="p">,</span>
@@ -359,91 +361,93 @@
<span class="mi">10</span><span class="p">,</span> <span class="mi">10</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
<span class="k">if</span> <span class="n">ignore_stereo_log</span><span class="p">:</span>
<span class="n">ost</span><span class="o">.</span><span class="n">PopVerbosityLevel</span><span class="p">()</span>
- <span class="c"># checks above would remove bad atoms</span>
- <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">temp_ent_stereo_checked</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"ele!=H"</span><span class="p">)</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span> \
- <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">temp_ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"ele!=H"</span><span class="p">)</span><span class="o">.</span><span class="n">atoms</span><span class="p">):</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"No more stereo-chemical problems "</span>
- <span class="s">"-> final energy: </span><span class="si">%g</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">sim</span><span class="o">.</span><span class="n">GetEnergy</span><span class="p">()))</span>
+ <span class="c1"># checks above would remove bad atoms</span>
+ <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">temp_ent_stereo_checked</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"ele!=H"</span><span class="p">)</span><span class="o">.</span><span class="n">atoms</span><span class="p">)</span> \
+ <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">temp_ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"ele!=H"</span><span class="p">)</span><span class="o">.</span><span class="n">atoms</span><span class="p">):</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"No more stereo-chemical problems "</span>
+ <span class="s2">"-> final energy: </span><span class="si">%g</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">sim</span><span class="o">.</span><span class="n">GetEnergy</span><span class="p">()))</span>
<span class="k">break</span>
- <span class="c"># update model</span>
+ <span class="c1"># update model</span>
<span class="n">simulation_ent</span> <span class="o">=</span> <span class="n">_GetSimEntity</span><span class="p">(</span><span class="n">sim</span><span class="p">)</span>
- <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">simulation_ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"ele!=H"</span><span class="p">),</span>
+ <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">simulation_ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"ele!=H"</span><span class="p">),</span>
<span class="bp">True</span><span class="p">)</span>
- <span class="c"># return model with hydrogens</span>
- <span class="k">return</span> <span class="n">simulation_ent</span>
-</div>
+ <span class="c1"># return model with hydrogens</span>
+ <span class="k">return</span> <span class="n">simulation_ent</span></div>
+
<div class="viewcode-block" id="CheckFinalModel"><a class="viewcode-back" href="../../../modelling/pipeline.html#promod3.modelling.CheckFinalModel">[docs]</a><span class="k">def</span> <span class="nf">CheckFinalModel</span><span class="p">(</span><span class="n">mhandle</span><span class="p">):</span>
<span class="sd">'''Performs samity checks on final models and reports problems.</span>
<span class="sd"> </span>
<span class="sd"> :param mhandle: Modelling handle for which to perform checks.</span>
<span class="sd"> :type mhandle: :class:`ModellingHandle`</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'pipeline::CheckFinalModel'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'pipeline::CheckFinalModel'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
- <span class="c"># report incomplete models</span>
+ <span class="c1"># report incomplete models</span>
<span class="k">for</span> <span class="n">chain</span> <span class="ow">in</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">chains</span><span class="p">:</span>
<span class="k">if</span> <span class="n">chain</span><span class="o">.</span><span class="n">residue_count</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogWarning</span><span class="p">(</span><span class="s">"Chain </span><span class="si">%s</span><span class="s"> of returned model contains only </span><span class="si">%d</span><span class="s"> "</span>\
- <span class="s">"residues! This typically indicates that the "</span>\
- <span class="s">"template is mostly a Calpha trace or contains "</span>\
- <span class="s">"too many D-peptides."</span>\
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogWarning</span><span class="p">(</span><span class="s2">"Chain </span><span class="si">%s</span><span class="s2"> of returned model contains only </span><span class="si">%d</span><span class="s2"> "</span>\
+ <span class="s2">"residues! This typically indicates that the "</span>\
+ <span class="s2">"template is mostly a Calpha trace or contains "</span>\
+ <span class="s2">"too many D-peptides."</span>\
<span class="o">%</span> <span class="p">(</span><span class="n">chain</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">chain</span><span class="o">.</span><span class="n">residue_count</span><span class="p">))</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogWarning</span><span class="p">(</span><span class="s">"Failed to close </span><span class="si">%d</span><span class="s"> gap(s). Returning incomplete model!"</span>\
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogWarning</span><span class="p">(</span><span class="s2">"Failed to close </span><span class="si">%d</span><span class="s2"> gap(s). Returning incomplete model!"</span>\
<span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
- <span class="c"># check sequences</span>
+ <span class="c1"># check sequences</span>
<span class="k">for</span> <span class="n">chain</span><span class="p">,</span> <span class="n">seq</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">chains</span><span class="p">,</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">seqres</span><span class="p">):</span>
<span class="n">a</span> <span class="o">=</span> <span class="n">chain</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span>
<span class="n">b</span> <span class="o">=</span> <span class="n">chain</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span>
<span class="n">expected_seq</span> <span class="o">=</span> <span class="n">seq</span><span class="p">[</span><span class="n">a</span><span class="o">-</span><span class="mi">1</span><span class="p">:</span><span class="n">b</span><span class="p">]</span>
- <span class="n">actual_seq</span> <span class="o">=</span> <span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">chain</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
+ <span class="n">actual_seq</span> <span class="o">=</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">chain</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
<span class="k">if</span> <span class="n">expected_seq</span> <span class="o">!=</span> <span class="n">actual_seq</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogWarning</span><span class="p">(</span><span class="s">"Sequence mismatch in chain </span><span class="si">%s</span><span class="s">!"</span>\
- <span class="s">" Expected '</span><span class="si">%s</span><span class="s">'. Got '</span><span class="si">%s</span><span class="s">'"</span> \
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogWarning</span><span class="p">(</span><span class="s2">"Sequence mismatch in chain </span><span class="si">%s</span><span class="s2">!"</span>\
+ <span class="s2">" Expected '</span><span class="si">%s</span><span class="s2">'. Got '</span><span class="si">%s</span><span class="s2">'"</span> \
<span class="o">%</span> <span class="p">(</span><span class="n">chain</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">expected_seq</span><span class="p">,</span> <span class="n">actual_seq</span><span class="p">))</span>
- <span class="c"># report ring punchings</span>
+ <span class="c1"># report ring punchings</span>
<span class="n">rings</span> <span class="o">=</span> <span class="n">GetRings</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">)</span>
<span class="n">ring_punches</span> <span class="o">=</span> <span class="n">GetRingPunches</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">)</span>
<span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">ring_punches</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogWarning</span><span class="p">(</span><span class="s">"Ring of "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">res</span><span class="p">)</span> <span class="o">+</span> <span class="s">" has been punched!"</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogWarning</span><span class="p">(</span><span class="s2">"Ring of "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">res</span><span class="p">)</span> <span class="o">+</span> <span class="s2">" has been punched!"</span><span class="p">)</span>
- <span class="c"># report stereo-chemical problems</span>
+ <span class="c1"># report stereo-chemical problems</span>
<span class="n">ost</span><span class="o">.</span><span class="n">PushVerbosityLevel</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
<span class="n">clashing_distances</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">DefaultClashingDistances</span><span class="p">()</span>
<span class="n">bond_stereo_chemical_param</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">DefaultBondStereoChemicalParams</span><span class="p">()</span>
<span class="n">angle_stereo_chemical_param</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">DefaultAngleStereoChemicalParams</span><span class="p">()</span>
- <span class="c"># extract problems</span>
- <span class="n">model_src</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"aname!=OXT"</span><span class="p">)</span>
+ <span class="c1"># extract problems</span>
+ <span class="n">model_src</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"aname!=OXT"</span><span class="p">)</span>
<span class="n">clash_info</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">FilterClashes</span><span class="p">(</span><span class="n">model_src</span><span class="p">,</span> <span class="n">clashing_distances</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
- <span class="c"># note: 10,10 parameters below are hard coded bond-/angle-tolerances</span>
+ <span class="c1"># note: 10,10 parameters below are hard coded bond-/angle-tolerances</span>
<span class="n">stereo_info</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">CheckStereoChemistry</span><span class="p">(</span><span class="n">model_src</span><span class="p">,</span>
<span class="n">bond_stereo_chemical_param</span><span class="p">,</span>
<span class="n">angle_stereo_chemical_param</span><span class="p">,</span>
<span class="mi">10</span><span class="p">,</span> <span class="mi">10</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">ost</span><span class="o">.</span><span class="n">PopVerbosityLevel</span><span class="p">()</span>
- <span class="c"># set bool props in model-residues</span>
+ <span class="c1"># set bool props in model-residues</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">GetFirstAtom</span><span class="p">()</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">clash_info</span><span class="o">.</span><span class="n">GetClashList</span><span class="p">()]</span>\
+ <span class="o">+</span> <span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">GetSecondAtom</span><span class="p">()</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">clash_info</span><span class="o">.</span><span class="n">GetClashList</span><span class="p">()]</span>\
<span class="o">+</span> <span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">GetFirstAtom</span><span class="p">()</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">stereo_info</span><span class="o">.</span><span class="n">GetBondViolationList</span><span class="p">()]</span>\
+ <span class="o">+</span> <span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">GetSecondAtom</span><span class="p">()</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">stereo_info</span><span class="o">.</span><span class="n">GetBondViolationList</span><span class="p">()]</span>\
<span class="o">+</span> <span class="p">[</span><span class="n">e</span><span class="o">.</span><span class="n">GetSecondAtom</span><span class="p">()</span> <span class="k">for</span> <span class="n">e</span> <span class="ow">in</span> <span class="n">stereo_info</span><span class="o">.</span><span class="n">GetAngleViolationList</span><span class="p">()]</span>
<span class="k">for</span> <span class="n">atomui</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
<span class="n">res</span> <span class="o">=</span> <span class="n">model_src</span><span class="o">.</span><span class="n">FindResidue</span><span class="p">(</span><span class="n">atomui</span><span class="o">.</span><span class="n">GetChainName</span><span class="p">(),</span> <span class="n">atomui</span><span class="o">.</span><span class="n">GetResNum</span><span class="p">())</span>
- <span class="n">res</span><span class="o">.</span><span class="n">SetBoolProp</span><span class="p">(</span><span class="s">"stereo_chemical_problem"</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">atomui</span><span class="o">.</span><span class="n">GetAtomName</span><span class="p">()</span> <span class="ow">in</span> <span class="p">[</span><span class="s">"CA"</span><span class="p">,</span> <span class="s">"N"</span><span class="p">,</span> <span class="s">"O"</span><span class="p">,</span> <span class="s">"C"</span><span class="p">]:</span>
- <span class="n">res</span><span class="o">.</span><span class="n">SetBoolProp</span><span class="p">(</span><span class="s">"stereo_chemical_problem_backbone"</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
- <span class="c"># report bad residues</span>
+ <span class="n">res</span><span class="o">.</span><span class="n">SetBoolProp</span><span class="p">(</span><span class="s2">"stereo_chemical_problem"</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">atomui</span><span class="o">.</span><span class="n">GetAtomName</span><span class="p">()</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">"CA"</span><span class="p">,</span> <span class="s2">"N"</span><span class="p">,</span> <span class="s2">"O"</span><span class="p">,</span> <span class="s2">"C"</span><span class="p">]:</span>
+ <span class="n">res</span><span class="o">.</span><span class="n">SetBoolProp</span><span class="p">(</span><span class="s2">"stereo_chemical_problem_backbone"</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
+ <span class="c1"># report bad residues</span>
<span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">model_src</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
- <span class="k">if</span> <span class="n">res</span><span class="o">.</span><span class="n">HasProp</span><span class="p">(</span><span class="s">"stereo_chemical_problem_backbone"</span><span class="p">)</span> <span class="ow">and</span>\
- <span class="n">res</span><span class="o">.</span><span class="n">GetBoolProp</span><span class="p">(</span><span class="s">"stereo_chemical_problem_backbone"</span><span class="p">):</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Stereo-chemical problem in backbone "</span> <span class="o">+</span> \
- <span class="s">"of residue "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">res</span><span class="p">))</span>
- <span class="k">elif</span> <span class="n">res</span><span class="o">.</span><span class="n">HasProp</span><span class="p">(</span><span class="s">"stereo_chemical_problem"</span><span class="p">)</span> <span class="ow">and</span>\
- <span class="n">res</span><span class="o">.</span><span class="n">GetBoolProp</span><span class="p">(</span><span class="s">"stereo_chemical_problem"</span><span class="p">):</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Stereo-chemical problem in sidechain "</span> <span class="o">+</span> \
- <span class="s">"of residue "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">res</span><span class="p">))</span>
-</div>
+ <span class="k">if</span> <span class="n">res</span><span class="o">.</span><span class="n">HasProp</span><span class="p">(</span><span class="s2">"stereo_chemical_problem_backbone"</span><span class="p">)</span> <span class="ow">and</span>\
+ <span class="n">res</span><span class="o">.</span><span class="n">GetBoolProp</span><span class="p">(</span><span class="s2">"stereo_chemical_problem_backbone"</span><span class="p">):</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Stereo-chemical problem in backbone "</span> <span class="o">+</span> \
+ <span class="s2">"of residue "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">res</span><span class="p">))</span>
+ <span class="k">elif</span> <span class="n">res</span><span class="o">.</span><span class="n">HasProp</span><span class="p">(</span><span class="s2">"stereo_chemical_problem"</span><span class="p">)</span> <span class="ow">and</span>\
+ <span class="n">res</span><span class="o">.</span><span class="n">GetBoolProp</span><span class="p">(</span><span class="s2">"stereo_chemical_problem"</span><span class="p">):</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Stereo-chemical problem in sidechain "</span> <span class="o">+</span> \
+ <span class="s2">"of residue "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">res</span><span class="p">))</span></div>
+
<div class="viewcode-block" id="BuildFromRawModel"><a class="viewcode-back" href="../../../modelling/pipeline.html#promod3.modelling.BuildFromRawModel">[docs]</a><span class="k">def</span> <span class="nf">BuildFromRawModel</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">use_amber_ff</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span> <span class="n">extra_force_fields</span><span class="o">=</span><span class="nb">list</span><span class="p">()):</span>
<span class="sd">'''Build a model starting with a raw model (see :func:`BuildRawModel`).</span>
@@ -484,46 +488,46 @@
<span class="sd"> :return: Delivers the model as an |ost_s| entity.</span>
<span class="sd"> :rtype: :class:`Entity <ost.mol.EntityHandle>`</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'pipeline::BuildFromRawModel'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'pipeline::BuildFromRawModel'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
- <span class="c"># ignore empty models</span>
+ <span class="c1"># ignore empty models</span>
<span class="k">if</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="o">.</span><span class="n">residue_count</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s">"Cannot perform modelling with an empty raw model."</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s2">"Cannot perform modelling with an empty raw model."</span><span class="p">)</span>
<span class="k">return</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s">"Starting modelling based on a raw model."</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogInfo</span><span class="p">(</span><span class="s2">"Starting modelling based on a raw model."</span><span class="p">)</span>
- <span class="c"># a bit of setup</span>
+ <span class="c1"># a bit of setup</span>
<span class="n">fragment_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">()</span>
<span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
<span class="n">torsion_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">()</span>
<span class="n">merge_distance</span> <span class="o">=</span> <span class="mi">4</span>
- <span class="c"># remove terminal gaps</span>
+ <span class="c1"># remove terminal gaps</span>
<span class="n">RemoveTerminalGaps</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
- <span class="c"># close gaps</span>
+ <span class="c1"># close gaps</span>
<span class="n">CloseGaps</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">merge_distance</span><span class="o">=</span><span class="n">merge_distance</span><span class="p">,</span>
<span class="n">fragment_db</span><span class="o">=</span><span class="n">fragment_db</span><span class="p">,</span> <span class="n">structure_db</span><span class="o">=</span><span class="n">structure_db</span><span class="p">,</span>
<span class="n">torsion_sampler</span><span class="o">=</span><span class="n">torsion_sampler</span><span class="p">)</span>
- <span class="c"># build sidechains</span>
+ <span class="c1"># build sidechains</span>
<span class="n">BuildSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">merge_distance</span><span class="p">,</span> <span class="n">fragment_db</span><span class="p">,</span>
<span class="n">structure_db</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="p">)</span>
- <span class="c"># minimize energy of final model using molecular mechanics</span>
+ <span class="c1"># minimize energy of final model using molecular mechanics</span>
<span class="n">MinimizeModelEnergy</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">use_amber_ff</span><span class="o">=</span><span class="n">use_amber_ff</span><span class="p">,</span>
<span class="n">extra_force_fields</span><span class="o">=</span><span class="n">extra_force_fields</span><span class="p">)</span>
- <span class="c"># sanity checks</span>
+ <span class="c1"># sanity checks</span>
<span class="n">CheckFinalModel</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
- <span class="c"># done</span>
- <span class="k">return</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span>
+ <span class="c1"># done</span>
+ <span class="k">return</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span></div>
-<span class="c"># these methods will be exported into module</span></div>
-<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s">'BuildFromRawModel'</span><span class="p">,</span> <span class="s">'BuildSidechains'</span><span class="p">,</span>
- <span class="s">'MinimizeModelEnergy'</span><span class="p">,</span> <span class="s">'CheckFinalModel'</span><span class="p">)</span>
+<span class="c1"># these methods will be exported into module</span>
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s1">'BuildFromRawModel'</span><span class="p">,</span> <span class="s1">'BuildSidechains'</span><span class="p">,</span>
+ <span class="s1">'MinimizeModelEnergy'</span><span class="p">,</span> <span class="s1">'CheckFinalModel'</span><span class="p">)</span>
</pre></div>
</div>
@@ -549,9 +553,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -559,11 +560,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html b/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
index 0f4481042177f9a9f53d2889255300e5216c678c..a8840922170b8f1448c05531aba3a51c444ff34e 100644
--- a/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
+++ b/doc/html/_modules/promod3/modelling/_reconstruct_sidechains.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._reconstruct_sidechains — ProMod3 1.1.0 documentation</title>
+ <title>promod3.modelling._reconstruct_sidechains — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,14 +23,16 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../../../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
+ <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -38,37 +40,37 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._reconstruct_sidechains</h1><div class="highlight"><pre>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">geom</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="n">conop</span>
+<span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">geom</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="n">conop</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">core</span><span class="p">,</span> <span class="n">sidechain</span>
+<span class="kn">import</span> <span class="nn">traceback</span>
-<span class="c">###############################################################################</span>
-<span class="c"># helper functions</span>
+<span class="c1">###############################################################################</span>
+<span class="c1"># helper functions</span>
<span class="k">def</span> <span class="nf">_GetRotamerIDs</span><span class="p">(</span><span class="n">res_list</span><span class="p">):</span>
<span class="sd">'''Return list (length = len(res_list)) of rotamer IDs for all residues.'''</span>
<span class="n">rotamer_ids</span> <span class="o">=</span> <span class="p">[</span><span class="n">sidechain</span><span class="o">.</span><span class="n">ALA</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_list</span><span class="p">)</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">r</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">res_list</span><span class="p">):</span>
<span class="n">rot_id</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">TLCToRotID</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">GetName</span><span class="p">())</span>
<span class="k">if</span> <span class="n">rot_id</span> <span class="o">==</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">XXX</span><span class="p">:</span>
- <span class="k">continue</span> <span class="c"># no idea what it is, so we stick with ALA </span>
- <span class="c"># => don't model sidechain</span>
+ <span class="k">continue</span> <span class="c1"># no idea what it is, so we stick with ALA </span>
<span class="n">rotamer_ids</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">rot_id</span>
<span class="k">return</span> <span class="n">rotamer_ids</span>
<span class="k">def</span> <span class="nf">_GetPhiAngle</span><span class="p">(</span><span class="n">r</span><span class="p">):</span>
<span class="sd">'''Extract phi angle for residue r.'''</span>
- <span class="c"># def. fallback = helix</span>
+ <span class="c1"># def. fallback = helix</span>
<span class="n">phi</span> <span class="o">=</span> <span class="o">-</span><span class="mf">1.0472</span>
- <span class="c"># try to get phi from torsion angles</span>
+ <span class="c1"># try to get phi from torsion angles</span>
<span class="n">tor</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">GetPhiTorsion</span><span class="p">()</span>
<span class="k">if</span> <span class="n">tor</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
<span class="n">phi</span> <span class="o">=</span> <span class="n">tor</span><span class="o">.</span><span class="n">GetAngle</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">r_prev</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">handle</span><span class="o">.</span><span class="n">prev</span>
<span class="k">if</span> <span class="n">r_prev</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">and</span> <span class="n">mol</span><span class="o">.</span><span class="n">InSequence</span><span class="p">(</span><span class="n">r_prev</span><span class="p">,</span> <span class="n">r</span><span class="o">.</span><span class="n">handle</span><span class="p">):</span>
- <span class="n">c_prev</span> <span class="o">=</span> <span class="n">r_prev</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"C"</span><span class="p">)</span>
- <span class="n">n</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"N"</span><span class="p">)</span>
- <span class="n">ca</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"CA"</span><span class="p">)</span>
- <span class="n">c</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"C"</span><span class="p">)</span>
+ <span class="n">c_prev</span> <span class="o">=</span> <span class="n">r_prev</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"C"</span><span class="p">)</span>
+ <span class="n">n</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"N"</span><span class="p">)</span>
+ <span class="n">ca</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"CA"</span><span class="p">)</span>
+ <span class="n">c</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"C"</span><span class="p">)</span>
<span class="k">if</span> <span class="n">c_prev</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">and</span> <span class="n">n</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">and</span> <span class="n">ca</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">and</span> <span class="n">c</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
<span class="n">phi</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">DihedralAngle</span><span class="p">(</span><span class="n">c_prev</span><span class="o">.</span><span class="n">GetPos</span><span class="p">(),</span><span class="n">n</span><span class="o">.</span><span class="n">GetPos</span><span class="p">(),</span>
<span class="n">ca</span><span class="o">.</span><span class="n">GetPos</span><span class="p">(),</span><span class="n">c</span><span class="o">.</span><span class="n">GetPos</span><span class="p">())</span>
@@ -76,19 +78,19 @@
<span class="k">def</span> <span class="nf">_GetPsiAngle</span><span class="p">(</span><span class="n">r</span><span class="p">):</span>
<span class="sd">'''Extract psi angle for residue r.'''</span>
- <span class="c"># def. fallback = helix </span>
+ <span class="c1"># def. fallback = helix </span>
<span class="n">psi</span> <span class="o">=</span> <span class="o">-</span><span class="mf">0.7854</span>
- <span class="c"># try to get psi from torsion angles</span>
+ <span class="c1"># try to get psi from torsion angles</span>
<span class="n">tor</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">GetPsiTorsion</span><span class="p">()</span>
<span class="k">if</span> <span class="n">tor</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
<span class="n">psi</span> <span class="o">=</span> <span class="n">tor</span><span class="o">.</span><span class="n">GetAngle</span><span class="p">()</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">r_next</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">handle</span><span class="o">.</span><span class="n">next</span>
<span class="k">if</span> <span class="n">r_next</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">and</span> <span class="n">mol</span><span class="o">.</span><span class="n">InSequence</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">handle</span><span class="p">,</span> <span class="n">r_next</span><span class="p">):</span>
- <span class="n">n</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"N"</span><span class="p">)</span>
- <span class="n">ca</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"CA"</span><span class="p">)</span>
- <span class="n">c</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"C"</span><span class="p">)</span>
- <span class="n">n_next</span> <span class="o">=</span> <span class="n">r_next</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"N"</span><span class="p">)</span>
+ <span class="n">n</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"N"</span><span class="p">)</span>
+ <span class="n">ca</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"CA"</span><span class="p">)</span>
+ <span class="n">c</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"C"</span><span class="p">)</span>
+ <span class="n">n_next</span> <span class="o">=</span> <span class="n">r_next</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"N"</span><span class="p">)</span>
<span class="k">if</span> <span class="n">n</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">and</span> <span class="n">ca</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">and</span> <span class="n">c</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">and</span> <span class="n">n_next</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
<span class="n">psi</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">DihedralAngle</span><span class="p">(</span><span class="n">n</span><span class="o">.</span><span class="n">GetPos</span><span class="p">(),</span> <span class="n">ca</span><span class="o">.</span><span class="n">GetPos</span><span class="p">(),</span>
<span class="n">c</span><span class="o">.</span><span class="n">GetPos</span><span class="p">(),</span> <span class="n">n_next</span><span class="o">.</span><span class="n">GetPos</span><span class="p">())</span>
@@ -98,7 +100,7 @@
<span class="sd">'''Extract dihedral angles for all residues.</span>
<span class="sd"> Returns phi and psi angles as 2 lists with length = len(res_list).</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'sidechain::_GetDihedrals'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'sidechain::_GetDihedrals'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
<span class="n">phi_angles</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_list</span><span class="p">)</span>
<span class="n">psi_angles</span> <span class="o">=</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">]</span> <span class="o">*</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_list</span><span class="p">)</span>
@@ -114,8 +116,8 @@
<span class="k">try</span><span class="p">:</span>
<span class="n">frame_residue</span> <span class="o">=</span> <span class="n">rotamer_constructor</span><span class="o">.</span><span class="n">ConstructBackboneFrameResidue</span><span class="p">(</span>\
<span class="n">r</span><span class="o">.</span><span class="n">handle</span><span class="p">,</span> <span class="n">rotamer_ids</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">i</span><span class="p">,</span>
- <span class="n">phi_angles</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">r</span><span class="o">.</span><span class="n">HasProp</span><span class="p">(</span><span class="s">"n_ter"</span><span class="p">),</span>
- <span class="n">r</span><span class="o">.</span><span class="n">HasProp</span><span class="p">(</span><span class="s">"c_ter"</span><span class="p">))</span>
+ <span class="n">phi_angles</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">r</span><span class="o">.</span><span class="n">HasProp</span><span class="p">(</span><span class="s2">"n_ter"</span><span class="p">),</span>
+ <span class="n">r</span><span class="o">.</span><span class="n">HasProp</span><span class="p">(</span><span class="s2">"c_ter"</span><span class="p">))</span>
<span class="n">frame_residues</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">frame_residue</span><span class="p">)</span>
<span class="k">except</span><span class="p">:</span>
<span class="k">continue</span>
@@ -124,15 +126,15 @@
<span class="sd">'''Update frame_residues (list) with FrameResidues for res. in ent_lig.</span>
<span class="sd"> Set offset >= number of non-ligand residues (used for residue_index).</span>
<span class="sd"> '''</span>
- <span class="c"># parse ligand residues</span>
+ <span class="c1"># parse ligand residues</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">res</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">ent_lig</span><span class="o">.</span><span class="n">residues</span><span class="p">):</span>
<span class="n">res_idx</span> <span class="o">=</span> <span class="n">offset</span> <span class="o">+</span> <span class="n">i</span>
<span class="n">is_done</span> <span class="o">=</span> <span class="bp">False</span>
- <span class="c"># special treatment for peptides</span>
+ <span class="c1"># special treatment for peptides</span>
<span class="k">if</span> <span class="n">res</span><span class="o">.</span><span class="n">IsPeptideLinking</span><span class="p">():</span>
<span class="n">rot_id</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">TLCToRotID</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">GetName</span><span class="p">())</span>
<span class="k">if</span> <span class="n">rot_id</span> <span class="o">!=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">XXX</span><span class="p">:</span>
- <span class="c"># get more info</span>
+ <span class="c1"># get more info</span>
<span class="n">phi</span> <span class="o">=</span> <span class="n">_GetPhiAngle</span><span class="p">(</span><span class="n">res</span><span class="p">)</span>
<span class="n">r_prev</span> <span class="o">=</span> <span class="n">res</span><span class="o">.</span><span class="n">handle</span><span class="o">.</span><span class="n">prev</span>
<span class="n">n_ter</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">r_prev</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> \
@@ -140,29 +142,28 @@
<span class="n">r_next</span> <span class="o">=</span> <span class="n">res</span><span class="o">.</span><span class="n">handle</span><span class="o">.</span><span class="n">next</span>
<span class="n">c_ter</span> <span class="o">=</span> <span class="ow">not</span> <span class="n">r_next</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> \
<span class="ow">or</span> <span class="ow">not</span> <span class="n">mol</span><span class="o">.</span><span class="n">InSequence</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">handle</span><span class="p">,</span> <span class="n">r_next</span><span class="p">)</span>
- <span class="c"># try to add frame residues (ignore exceptions)</span>
+ <span class="c1"># try to add frame residues (ignore exceptions)</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">fr1</span> <span class="o">=</span> <span class="n">rotamer_constructor</span><span class="o">.</span><span class="n">ConstructBackboneFrameResidue</span><span class="p">(</span>\
<span class="n">res</span><span class="o">.</span><span class="n">handle</span><span class="p">,</span> <span class="n">rot_id</span><span class="p">,</span> <span class="n">res_idx</span><span class="p">,</span>
<span class="n">phi</span><span class="p">,</span> <span class="n">n_ter</span><span class="p">,</span> <span class="n">c_ter</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">rot_id</span> <span class="o">!=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ALA</span> <span class="ow">and</span> <span class="n">rot_id</span> <span class="o">!=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">GLY</span><span class="p">:</span>
- <span class="n">fr2</span> <span class="o">=</span> <span class="n">rotamer_constructor</span><span class="o">.</span><span class="n">ConstructSidechainFrameResidue</span><span class="p">(</span>\
- <span class="n">res</span><span class="o">.</span><span class="n">handle</span><span class="p">,</span> <span class="n">rot_id</span><span class="p">,</span> <span class="n">res_idx</span><span class="p">)</span>
- <span class="n">frame_residues</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="n">fr1</span><span class="p">,</span><span class="n">fr2</span><span class="p">])</span>
- <span class="k">else</span><span class="p">:</span>
- <span class="n">frame_residues</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">fr1</span><span class="p">)</span>
+
+ <span class="n">fr2</span> <span class="o">=</span> <span class="n">rotamer_constructor</span><span class="o">.</span><span class="n">ConstructSidechainFrameResidue</span><span class="p">(</span>\
+ <span class="n">res</span><span class="o">.</span><span class="n">handle</span><span class="p">,</span> <span class="n">rot_id</span><span class="p">,</span> <span class="n">res_idx</span><span class="p">)</span>
+
+ <span class="n">frame_residues</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="n">fr1</span><span class="p">,</span><span class="n">fr2</span><span class="p">])</span>
<span class="k">except</span><span class="p">:</span>
- <span class="k">pass</span> <span class="c"># ignore peptide treatment and treat below</span>
+ <span class="k">pass</span> <span class="c1"># ignore peptide treatment and treat below</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">is_done</span> <span class="o">=</span> <span class="bp">True</span>
- <span class="c"># if it failed, treat it as an unknown entity</span>
+ <span class="c1"># if it failed, treat it as an unknown entity</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">is_done</span><span class="p">:</span>
- <span class="c"># try to add frame residues (skip exceptions)</span>
+ <span class="c1"># try to add frame residues (skip exceptions)</span>
<span class="k">try</span><span class="p">:</span>
- <span class="c"># NOTES:</span>
- <span class="c"># - ConstructFrameResidueHeuristic has fall back if res unknown</span>
- <span class="c"># - it only deals with few possible ligand cases and has not</span>
- <span class="c"># been tested extensively!</span>
+ <span class="c1"># NOTES:</span>
+ <span class="c1"># - ConstructFrameResidueHeuristic has fall back if res unknown</span>
+ <span class="c1"># - it only deals with few possible ligand cases and has not</span>
+ <span class="c1"># been tested extensively!</span>
<span class="n">comp_lib</span> <span class="o">=</span> <span class="n">conop</span><span class="o">.</span><span class="n">GetDefaultLib</span><span class="p">()</span>
<span class="n">fr</span> <span class="o">=</span> <span class="n">rotamer_constructor</span><span class="o">.</span><span class="n">ConstructFrameResidueHeuristic</span><span class="p">(</span>\
<span class="n">res</span><span class="o">.</span><span class="n">handle</span><span class="p">,</span> <span class="n">res_idx</span><span class="p">,</span> <span class="n">comp_lib</span><span class="p">)</span>
@@ -179,18 +180,15 @@
<span class="sd"> Each residue can only end up in one of the 3 lists.</span>
<span class="sd"> '''</span>
<span class="k">if</span> <span class="n">keep_sidechains</span><span class="p">:</span>
- <span class="c"># try to generate frame residues for all existing side chains</span>
- <span class="c"># skip non-existing sidechains and CYS (if cystein_indices) and update</span>
- <span class="c"># incomplete_sidechains and cystein_indices</span>
+ <span class="c1"># try to generate frame residues for all existing side chains</span>
+ <span class="c1"># skip non-existing sidechains and CYS (if cystein_indices) and update</span>
+ <span class="c1"># incomplete_sidechains and cystein_indices</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">r</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">res_list</span><span class="p">):</span>
<span class="k">if</span> <span class="n">cystein_indices</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">rotamer_ids</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">==</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">CYS</span><span class="p">:</span>
<span class="n">cystein_indices</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
<span class="k">continue</span>
- <span class="k">if</span> <span class="n">rotamer_ids</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">==</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ALA</span> <span class="ow">or</span> <span class="n">rotamer_ids</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">==</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">GLY</span><span class="p">:</span>
- <span class="k">continue</span> <span class="c"># no sidechain to model</span>
-
<span class="k">try</span><span class="p">:</span>
<span class="n">frame_residue</span> <span class="o">=</span> <span class="n">rotamer_constructor</span><span class="o">.</span><span class="n">ConstructSidechainFrameResidue</span><span class="p">(</span>\
<span class="n">r</span><span class="o">.</span><span class="n">handle</span><span class="p">,</span> <span class="n">rotamer_ids</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">i</span><span class="p">)</span>
@@ -198,17 +196,14 @@
<span class="k">except</span><span class="p">:</span>
<span class="n">incomplete_sidechains</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="c"># no frame residues to create, just update incomplete_sidechains</span>
- <span class="c"># and cystein_indices if needed</span>
+ <span class="c1"># no frame residues to create, just update incomplete_sidechains</span>
+ <span class="c1"># and cystein_indices if needed</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">r</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">res_list</span><span class="p">):</span>
<span class="k">if</span> <span class="n">cystein_indices</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">rotamer_ids</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">==</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">CYS</span><span class="p">:</span>
<span class="n">cystein_indices</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
<span class="k">continue</span>
- <span class="k">if</span> <span class="n">rotamer_ids</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">==</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ALA</span> <span class="ow">or</span> <span class="n">rotamer_ids</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">==</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">GLY</span><span class="p">:</span>
- <span class="k">continue</span> <span class="c"># no sidechain to model</span>
-
<span class="n">incomplete_sidechains</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
<span class="k">def</span> <span class="nf">_AddCysteinFrameResidues</span><span class="p">(</span><span class="n">frame_residues</span><span class="p">,</span> <span class="n">incomplete_sidechains</span><span class="p">,</span>
@@ -220,19 +215,19 @@
<span class="sd"> Some cysteins (in disulfid_indices) get special treatment as disulfid</span>
<span class="sd"> bridges (disulfid_indices, disulfid_rotamers from _GetDisulfidBridges).</span>
<span class="sd"> '''</span>
- <span class="c"># handle cysteins participating in a disulfid bond</span>
+ <span class="c1"># handle cysteins participating in a disulfid bond</span>
<span class="k">for</span> <span class="n">cys_idx</span><span class="p">,</span> <span class="n">cys_rot</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">disulfid_indices</span><span class="p">,</span> <span class="n">disulfid_rotamers</span><span class="p">):</span>
- <span class="c"># add FrameResidue</span>
+ <span class="c1"># add FrameResidue</span>
<span class="n">frame_residues</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cys_rot</span><span class="o">.</span><span class="n">ToFrameResidue</span><span class="p">(</span><span class="n">cys_idx</span><span class="p">))</span>
- <span class="c"># set the position in the proteins residues</span>
+ <span class="c1"># set the position in the proteins residues</span>
<span class="n">cys_rot</span><span class="o">.</span><span class="n">ApplyOnResidue</span><span class="p">(</span><span class="n">res_list</span><span class="p">[</span><span class="n">cys_idx</span><span class="p">]</span><span class="o">.</span><span class="n">handle</span><span class="p">,</span>
<span class="n">consider_hydrogens</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
<span class="n">sidechain</span><span class="o">.</span><span class="n">ConnectSidechain</span><span class="p">(</span><span class="n">res_list</span><span class="p">[</span><span class="n">cys_idx</span><span class="p">]</span><span class="o">.</span><span class="n">handle</span><span class="p">,</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">CYS</span><span class="p">)</span>
- <span class="c"># add remaining ones according the given flags</span>
+ <span class="c1"># add remaining ones according the given flags</span>
<span class="k">for</span> <span class="n">idx</span> <span class="ow">in</span> <span class="n">cystein_indices</span><span class="p">:</span>
<span class="k">if</span> <span class="n">idx</span> <span class="ow">in</span> <span class="n">disulfid_indices</span><span class="p">:</span>
- <span class="k">continue</span> <span class="c"># already handled</span>
+ <span class="k">continue</span> <span class="c1"># already handled</span>
<span class="k">if</span> <span class="n">keep_sidechains</span><span class="p">:</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">frame_residue</span> <span class="o">=</span> <span class="n">rot_constructor</span><span class="o">.</span><span class="n">ConstructSidechainFrameResidue</span><span class="p">(</span>\
@@ -271,27 +266,24 @@
<span class="n">phi_angles</span><span class="p">,</span> <span class="n">psi_angles</span><span class="p">,</span> <span class="n">use_frm</span><span class="p">,</span> <span class="n">bbdep</span><span class="p">,</span> <span class="n">frame_residues</span><span class="p">):</span>
<span class="sd">'''Get list of rotamer groups from subset of res_list.</span>
<span class="sd"> Residues are chosen as res_list[i] for i in indices and only if a rotamer</span>
-<span class="sd"> group can be created (e.g. no ALA, GLY).</span>
+<span class="sd"> group can be created.</span>
<span class="sd"> Rotamer groups are filtered to keep only best ones (given frame).</span>
<span class="sd"> Returns list of rotamer groups and list of res. indices they belong to.</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'sidechain::_GetRotamerGroups'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'sidechain::_GetRotamerGroups'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
- <span class="c"># res.index (res_list[i]) for each modelled sc</span>
+ <span class="c1"># res.index (res_list[i]) for each modelled sc</span>
<span class="n">residues_with_rotamer_group</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
- <span class="c"># linked to residue in residues_with_rotamer_group</span>
+ <span class="c1"># linked to residue in residues_with_rotamer_group</span>
<span class="n">rotamer_groups</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
- <span class="c"># get frame for score evaluation</span>
+ <span class="c1"># get frame for score evaluation</span>
<span class="n">frame</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">Frame</span><span class="p">(</span><span class="n">frame_residues</span><span class="p">)</span>
- <span class="c"># build rotamers for chosen sidechains</span>
+ <span class="c1"># build rotamers for chosen sidechains</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">indices</span><span class="p">:</span>
- <span class="c"># get rotamer ID</span>
+ <span class="c1"># get rotamer ID</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">res_list</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="n">rot_id</span> <span class="o">=</span> <span class="n">rot_ids</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
-
- <span class="k">if</span> <span class="n">rot_id</span> <span class="o">==</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">ALA</span> <span class="ow">or</span> <span class="n">rot_id</span> <span class="o">==</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">GLY</span><span class="p">:</span>
- <span class="k">continue</span>
<span class="k">if</span> <span class="n">rot_id</span> <span class="o">==</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">CYS</span><span class="p">:</span>
<span class="n">rot_id</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">CYH</span>
@@ -302,34 +294,34 @@
<span class="k">if</span> <span class="n">tor</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
<span class="n">omega</span> <span class="o">=</span> <span class="n">tor</span><span class="o">.</span><span class="n">GetAngle</span><span class="p">()</span>
<span class="k">elif</span> <span class="n">i</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="c"># fallback computation of omega as in OST-code</span>
+ <span class="c1"># fallback computation of omega as in OST-code</span>
<span class="n">prev</span> <span class="o">=</span> <span class="n">res_list</span><span class="p">[</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="k">if</span> <span class="n">prev</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">and</span> <span class="n">prev</span><span class="o">.</span><span class="n">IsPeptideLinking</span><span class="p">():</span>
- <span class="n">ca_prev</span> <span class="o">=</span> <span class="n">prev</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"CA"</span><span class="p">)</span>
- <span class="n">c_prev</span> <span class="o">=</span> <span class="n">prev</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"C"</span><span class="p">)</span>
- <span class="n">n</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"N"</span><span class="p">)</span>
- <span class="n">ca</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"CA"</span><span class="p">)</span>
+ <span class="n">ca_prev</span> <span class="o">=</span> <span class="n">prev</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"CA"</span><span class="p">)</span>
+ <span class="n">c_prev</span> <span class="o">=</span> <span class="n">prev</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"C"</span><span class="p">)</span>
+ <span class="n">n</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"N"</span><span class="p">)</span>
+ <span class="n">ca</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"CA"</span><span class="p">)</span>
<span class="n">valid</span> <span class="o">=</span> <span class="n">ca_prev</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">and</span> <span class="n">c_prev</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> \
<span class="ow">and</span> <span class="n">n</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">and</span> <span class="n">ca</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span>
<span class="k">if</span> <span class="n">valid</span> <span class="ow">and</span> <span class="n">mol</span><span class="o">.</span><span class="n">BondExists</span><span class="p">(</span><span class="n">c_prev</span><span class="o">.</span><span class="n">handle</span><span class="p">,</span> <span class="n">n</span><span class="o">.</span><span class="n">handle</span><span class="p">):</span>
<span class="n">omega</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">DihedralAngle</span><span class="p">(</span><span class="n">ca_prev</span><span class="o">.</span><span class="n">GetPos</span><span class="p">(),</span>
<span class="n">c_prev</span><span class="o">.</span><span class="n">GetPos</span><span class="p">(),</span>
<span class="n">n</span><span class="o">.</span><span class="n">GetPos</span><span class="p">(),</span> <span class="n">ca</span><span class="o">.</span><span class="n">GetPos</span><span class="p">())</span>
- <span class="c"># omega not set if prev. res. missing</span>
+ <span class="c1"># omega not set if prev. res. missing</span>
<span class="k">if</span> <span class="n">omega</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
<span class="k">if</span> <span class="nb">abs</span><span class="p">(</span><span class="n">omega</span><span class="p">)</span> <span class="o"><</span> <span class="mf">1.57</span><span class="p">:</span>
<span class="n">rot_id</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">CPR</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">rot_id</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">TPR</span>
- <span class="c"># get RotamerGroup</span>
+ <span class="c1"># get RotamerGroup</span>
<span class="k">try</span><span class="p">:</span>
<span class="n">rot_group</span> <span class="o">=</span> <span class="n">_GetRotamerGroup</span><span class="p">(</span><span class="n">r</span><span class="o">.</span><span class="n">handle</span><span class="p">,</span> <span class="n">rot_id</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">rot_lib</span><span class="p">,</span>
<span class="n">rot_constructor</span><span class="p">,</span> <span class="n">phi_angles</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
<span class="n">psi_angles</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">use_frm</span><span class="p">,</span> <span class="n">bbdep</span><span class="p">)</span>
<span class="k">except</span><span class="p">:</span>
<span class="k">continue</span>
- <span class="c"># keep best ones</span>
+ <span class="c1"># keep best ones</span>
<span class="n">rot_group</span><span class="o">.</span><span class="n">SetFrameEnergy</span><span class="p">(</span><span class="n">frame</span><span class="p">)</span>
<span class="n">rot_group</span><span class="o">.</span><span class="n">ApplySelfEnergyThresh</span><span class="p">()</span>
<span class="n">rotamer_groups</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rot_group</span><span class="p">)</span>
@@ -345,40 +337,40 @@
<span class="sd"> Returns: disulfid_indices: list of res. index in bridge,</span>
<span class="sd"> disulfid_rotamers: list of rotamers (best one for bridge).</span>
<span class="sd"> '''</span>
- <span class="c"># this is required for the disulfid score evaluation</span>
+ <span class="c1"># this is required for the disulfid score evaluation</span>
<span class="n">frame</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">Frame</span><span class="p">(</span><span class="n">frame_residues</span><span class="p">)</span>
- <span class="c"># some info we have to keep track of when evaluating disulfid bonds</span>
+ <span class="c1"># some info we have to keep track of when evaluating disulfid bonds</span>
<span class="n">cystein_rot_groups</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="n">cys_ca_positions</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="n">cys_cb_positions</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="n">indices_with_rot_groups</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">cystein_indices</span><span class="p">:</span>
- <span class="c"># check ca, cb</span>
+ <span class="c1"># check ca, cb</span>
<span class="n">r</span> <span class="o">=</span> <span class="n">res_list</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
- <span class="n">ca</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"CA"</span><span class="p">)</span>
- <span class="n">cb</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"CB"</span><span class="p">)</span>
+ <span class="n">ca</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"CA"</span><span class="p">)</span>
+ <span class="n">cb</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"CB"</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="n">ca</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">and</span> <span class="n">cb</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()):</span>
<span class="k">continue</span>
<span class="n">cys_ca_positions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ca</span><span class="o">.</span><span class="n">GetPos</span><span class="p">())</span>
<span class="n">cys_cb_positions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cb</span><span class="o">.</span><span class="n">GetPos</span><span class="p">())</span>
- <span class="c"># get RotamerGroup in case of cysteins, we do FRM in any case...</span>
- <span class="c"># If we're suposed to keep the existing sidechains and the processed</span>
- <span class="c"># cystein contains all required atoms, we manually construct an FRM</span>
- <span class="c"># rotamer to still allow the rotamer to enter the disulfid bridge </span>
- <span class="c"># resolving algorithm. </span>
+ <span class="c1"># get RotamerGroup in case of cysteins, we do FRM in any case...</span>
+ <span class="c1"># If we're suposed to keep the existing sidechains and the processed</span>
+ <span class="c1"># cystein contains all required atoms, we manually construct an FRM</span>
+ <span class="c1"># rotamer to still allow the rotamer to enter the disulfid bridge </span>
+ <span class="c1"># resolving algorithm. </span>
<span class="n">rot_group</span> <span class="o">=</span> <span class="bp">None</span>
<span class="k">if</span> <span class="n">keep_sidechains</span><span class="p">:</span>
- <span class="n">sg</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s">"SG"</span><span class="p">)</span>
+ <span class="n">sg</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">FindAtom</span><span class="p">(</span><span class="s2">"SG"</span><span class="p">)</span>
<span class="k">if</span> <span class="n">sg</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
<span class="n">particle</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">Particle</span><span class="p">(</span><span class="n">sidechain</span><span class="o">.</span><span class="n">SidechainParticle</span><span class="o">.</span><span class="n">SParticle</span><span class="p">,</span>
<span class="n">sg</span><span class="o">.</span><span class="n">GetPos</span><span class="p">(),</span>
- <span class="o">-</span><span class="mf">0.19</span><span class="p">,</span> <span class="s">"SG"</span><span class="p">)</span>
+ <span class="o">-</span><span class="mf">0.19</span><span class="p">,</span> <span class="s2">"SG"</span><span class="p">)</span>
<span class="n">particle_list</span> <span class="o">=</span> <span class="p">[</span><span class="n">particle</span><span class="p">]</span>
- <span class="c"># The temperature and self internal_e_prefactor parameter have </span>
- <span class="c"># been copied from the SCWRLRotamerConstructor. Hacky...</span>
+ <span class="c1"># The temperature and self internal_e_prefactor parameter have </span>
+ <span class="c1"># been copied from the SCWRLRotamerConstructor. Hacky...</span>
<span class="n">frm_rotamer</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">FRMRotamer</span><span class="p">(</span><span class="n">particle_list</span><span class="p">,</span>
<span class="mf">1.69</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mf">4.07</span><span class="p">)</span>
<span class="n">frm_rotamer</span><span class="o">.</span><span class="n">AddSubrotamerDefinition</span><span class="p">([</span><span class="mi">0</span><span class="p">])</span>
@@ -401,7 +393,7 @@
<span class="n">cys_cb_positions</span><span class="p">,</span> <span class="mf">45.0</span><span class="p">,</span>
<span class="bp">True</span><span class="p">)</span>
- <span class="c"># get CYS with disulfid bonds and the chosen rotamers</span>
+ <span class="c1"># get CYS with disulfid bonds and the chosen rotamers</span>
<span class="n">disulfid_indices</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="n">disulfid_rotamers</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
@@ -414,10 +406,10 @@
<span class="k">return</span> <span class="n">disulfid_indices</span><span class="p">,</span> <span class="n">disulfid_rotamers</span>
-<span class="c">###############################################################################</span>
+<span class="c1">###############################################################################</span>
<div class="viewcode-block" id="ReconstructSidechains"><a class="viewcode-back" href="../../../modelling/sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains">[docs]</a><span class="k">def</span> <span class="nf">ReconstructSidechains</span><span class="p">(</span><span class="n">ent</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span> <span class="n">build_disulfids</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
- <span class="n">rotamer_model</span><span class="o">=</span><span class="s">"frm"</span><span class="p">,</span> <span class="n">consider_ligands</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
+ <span class="n">rotamer_model</span><span class="o">=</span><span class="s2">"frm"</span><span class="p">,</span> <span class="n">consider_ligands</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
<span class="n">rotamer_library</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">optimize_subrotamers</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
<span class="n">graph_max_complexity</span><span class="o">=</span><span class="mi">100000000</span><span class="p">,</span>
<span class="n">graph_initial_epsilon</span><span class="o">=</span><span class="mf">0.02</span><span class="p">):</span>
@@ -465,16 +457,16 @@
<span class="sd"> :meth:`RotamerGraph.TreeSolve`.</span>
<span class="sd"> :type graph_intial_epsilon: :class:`float`</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'modelling::ReconstructSidechains'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'modelling::ReconstructSidechains'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
- <span class="c"># setup settings</span>
- <span class="k">if</span> <span class="n">rotamer_model</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">"frm"</span><span class="p">:</span>
+ <span class="c1"># setup settings</span>
+ <span class="k">if</span> <span class="n">rotamer_model</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s2">"frm"</span><span class="p">:</span>
<span class="n">use_frm</span> <span class="o">=</span> <span class="bp">True</span>
- <span class="k">elif</span> <span class="n">rotamer_model</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">"rrm"</span><span class="p">:</span>
+ <span class="k">elif</span> <span class="n">rotamer_model</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s2">"rrm"</span><span class="p">:</span>
<span class="n">use_frm</span> <span class="o">=</span> <span class="bp">False</span>
<span class="k">else</span><span class="p">:</span>
- <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">"Only </span><span class="se">\"</span><span class="s">rrm</span><span class="se">\"</span><span class="s"> and </span><span class="se">\"</span><span class="s">frm</span><span class="se">\"</span><span class="s"> allowed for rotamer_model!"</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"Only </span><span class="se">\"</span><span class="s2">rrm</span><span class="se">\"</span><span class="s2"> and </span><span class="se">\"</span><span class="s2">frm</span><span class="se">\"</span><span class="s2"> allowed for rotamer_model!"</span><span class="p">)</span>
<span class="k">if</span> <span class="n">rotamer_library</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">rotamer_library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadDunbrackLib</span><span class="p">()</span>
@@ -482,66 +474,66 @@
<span class="k">if</span> <span class="nb">type</span><span class="p">(</span><span class="n">rotamer_library</span><span class="p">)</span> <span class="ow">is</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">BBDepRotamerLib</span><span class="p">:</span>
<span class="n">bbdep</span> <span class="o">=</span> <span class="bp">True</span>
- <span class="n">rotamer_constructor</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">SCWRLRotamerConstructor</span><span class="p">()</span>
+ <span class="n">rotamer_constructor</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">SCWRLRotamerConstructor</span><span class="p">(</span><span class="bp">False</span><span class="p">)</span>
- <span class="c"># take out ligand chain and any non-peptides</span>
- <span class="n">prot</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"peptide=true and cname!='_'"</span><span class="p">)</span>
+ <span class="c1"># take out ligand chain and any non-peptides</span>
+ <span class="n">prot</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"peptide=true and cname!='_'"</span><span class="p">)</span>
- <span class="c"># parse residues (all lists of length len(prot.residues))</span>
+ <span class="c1"># parse residues (all lists of length len(prot.residues))</span>
<span class="n">rotamer_ids</span> <span class="o">=</span> <span class="n">_GetRotamerIDs</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">)</span>
<span class="n">phi_angles</span><span class="p">,</span> <span class="n">psi_angles</span> <span class="o">=</span> <span class="n">_GetDihedrals</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">)</span>
- <span class="c"># set nter and cter (needed in _AddBackboneFrameResidues)</span>
+ <span class="c1"># set nter and cter (needed in _AddBackboneFrameResidues)</span>
<span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">prot</span><span class="o">.</span><span class="n">chains</span><span class="p">:</span>
- <span class="n">c</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">SetIntProp</span><span class="p">(</span><span class="s">"n_ter"</span><span class="p">,</span><span class="mi">1</span><span class="p">)</span>
- <span class="n">c</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">SetIntProp</span><span class="p">(</span><span class="s">"c_ter"</span><span class="p">,</span><span class="mi">1</span><span class="p">)</span>
+ <span class="n">c</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">SetIntProp</span><span class="p">(</span><span class="s2">"n_ter"</span><span class="p">,</span><span class="mi">1</span><span class="p">)</span>
+ <span class="n">c</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">SetIntProp</span><span class="p">(</span><span class="s2">"c_ter"</span><span class="p">,</span><span class="mi">1</span><span class="p">)</span>
- <span class="c"># build up frame</span>
- <span class="n">frame_residues</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span> <span class="c"># list of frame residues connected to frame</span>
- <span class="n">incomplete_sidechains</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span> <span class="c"># residue indices</span>
+ <span class="c1"># build up frame</span>
+ <span class="n">frame_residues</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span> <span class="c1"># list of frame residues connected to frame</span>
+ <span class="n">incomplete_sidechains</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span> <span class="c1"># residue indices</span>
<span class="n">_AddBackboneFrameResidues</span><span class="p">(</span><span class="n">frame_residues</span><span class="p">,</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">,</span> <span class="n">rotamer_ids</span><span class="p">,</span>
<span class="n">rotamer_constructor</span><span class="p">,</span> <span class="n">phi_angles</span><span class="p">)</span>
- <span class="c"># add ligands?</span>
+ <span class="c1"># add ligands?</span>
<span class="k">if</span> <span class="n">consider_ligands</span><span class="p">:</span>
- <span class="n">ligs</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"cname='_'"</span><span class="p">)</span>
+ <span class="n">ligs</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"cname='_'"</span><span class="p">)</span>
<span class="n">offset</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">)</span>
<span class="n">_AddLigandFrameResidues</span><span class="p">(</span><span class="n">frame_residues</span><span class="p">,</span> <span class="n">ligs</span><span class="p">,</span> <span class="n">rotamer_constructor</span><span class="p">,</span> <span class="n">offset</span><span class="p">)</span>
- <span class="c"># check special handling of cysteins</span>
+ <span class="c1"># check special handling of cysteins</span>
<span class="k">if</span> <span class="n">build_disulfids</span><span class="p">:</span>
- <span class="c"># residue indices of cysteins</span>
+ <span class="c1"># residue indices of cysteins</span>
<span class="n">cystein_indices</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
- <span class="c"># update frame_residues, incomplete_sidechains, cystein_indices</span>
+ <span class="c1"># update frame_residues, incomplete_sidechains, cystein_indices</span>
<span class="n">_AddSidechainFrameResidues</span><span class="p">(</span><span class="n">frame_residues</span><span class="p">,</span> <span class="n">incomplete_sidechains</span><span class="p">,</span>
<span class="n">keep_sidechains</span><span class="p">,</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">,</span> <span class="n">rotamer_ids</span><span class="p">,</span>
<span class="n">rotamer_constructor</span><span class="p">,</span> <span class="n">cystein_indices</span><span class="p">)</span>
- <span class="c"># update frame_residues, incomplete_sidechains with cysteins (if needed)</span>
+ <span class="c1"># update frame_residues, incomplete_sidechains with cysteins (if needed)</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">cystein_indices</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="c"># get disulfid bridges and according rotamers</span>
+ <span class="c1"># get disulfid bridges and according rotamers</span>
<span class="n">disulfid_indices</span><span class="p">,</span> <span class="n">disulfid_rotamers</span> <span class="o">=</span> \
<span class="n">_GetDisulfidBridges</span><span class="p">(</span><span class="n">frame_residues</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="p">,</span>
<span class="n">cystein_indices</span><span class="p">,</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">,</span>
<span class="n">rotamer_library</span><span class="p">,</span> <span class="n">use_frm</span><span class="p">,</span> <span class="n">bbdep</span><span class="p">,</span>
<span class="n">rotamer_constructor</span><span class="p">,</span> <span class="n">phi_angles</span><span class="p">,</span> <span class="n">psi_angles</span><span class="p">)</span>
- <span class="c"># update frame_residues, incomplete_sidechains</span>
+ <span class="c1"># update frame_residues, incomplete_sidechains</span>
<span class="n">_AddCysteinFrameResidues</span><span class="p">(</span><span class="n">frame_residues</span><span class="p">,</span> <span class="n">incomplete_sidechains</span><span class="p">,</span>
<span class="n">keep_sidechains</span><span class="p">,</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">,</span> <span class="n">rotamer_ids</span><span class="p">,</span>
<span class="n">rotamer_constructor</span><span class="p">,</span> <span class="n">cystein_indices</span><span class="p">,</span>
<span class="n">disulfid_indices</span><span class="p">,</span> <span class="n">disulfid_rotamers</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
- <span class="c"># update frame_residues, incomplete_sidechains</span>
+ <span class="c1"># update frame_residues, incomplete_sidechains</span>
<span class="n">_AddSidechainFrameResidues</span><span class="p">(</span><span class="n">frame_residues</span><span class="p">,</span> <span class="n">incomplete_sidechains</span><span class="p">,</span>
<span class="n">keep_sidechains</span><span class="p">,</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">,</span> <span class="n">rotamer_ids</span><span class="p">,</span>
<span class="n">rotamer_constructor</span><span class="p">)</span>
- <span class="c"># get rotamer groups and residues they're linked to</span>
+ <span class="c1"># get rotamer groups and residues they're linked to</span>
<span class="n">rotamer_groups</span><span class="p">,</span> <span class="n">residues_with_rotamer_group</span> <span class="o">=</span> \
<span class="n">_GetRotamerGroups</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">,</span> <span class="n">rotamer_ids</span><span class="p">,</span> <span class="n">incomplete_sidechains</span><span class="p">,</span>
<span class="n">rotamer_library</span><span class="p">,</span> <span class="n">rotamer_constructor</span><span class="p">,</span> <span class="n">phi_angles</span><span class="p">,</span>
<span class="n">psi_angles</span><span class="p">,</span> <span class="n">use_frm</span><span class="p">,</span> <span class="n">bbdep</span><span class="p">,</span> <span class="n">frame_residues</span><span class="p">)</span>
- <span class="c"># set up graph and solve to get best rotamers</span>
+ <span class="c1"># set up graph and solve to get best rotamers</span>
<span class="k">if</span> <span class="n">use_frm</span><span class="p">:</span>
<span class="n">graph</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">RotamerGraph</span><span class="o">.</span><span class="n">CreateFromFRMList</span><span class="p">(</span><span class="n">rotamer_groups</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
@@ -557,7 +549,7 @@
<span class="n">rotamers_to_optimize</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rot_group</span><span class="p">[</span><span class="n">sol</span><span class="p">])</span>
<span class="n">sidechain</span><span class="o">.</span><span class="n">SubrotamerOptimizer</span><span class="p">(</span><span class="n">rotamers_to_optimize</span><span class="p">)</span>
- <span class="c"># update structure</span>
+ <span class="c1"># update structure</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">rot_group</span><span class="p">,</span> <span class="n">sol</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">residues_with_rotamer_group</span><span class="p">,</span> <span class="n">rotamer_groups</span><span class="p">,</span>
<span class="n">solution</span><span class="p">):</span>
<span class="k">try</span><span class="p">:</span>
@@ -565,11 +557,11 @@
<span class="n">rot_group</span><span class="p">[</span><span class="n">sol</span><span class="p">]</span><span class="o">.</span><span class="n">ApplyOnResidue</span><span class="p">(</span><span class="n">res_handle</span><span class="p">,</span> <span class="n">consider_hydrogens</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
<span class="n">sidechain</span><span class="o">.</span><span class="n">ConnectSidechain</span><span class="p">(</span><span class="n">res_handle</span><span class="p">,</span> <span class="n">rotamer_ids</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
<span class="k">except</span><span class="p">:</span>
- <span class="k">print</span> <span class="s">"there is a backbone atom missing... "</span><span class="p">,</span> \
- <span class="n">res_handle</span><span class="o">.</span><span class="n">GetQualifiedName</span><span class="p">()</span>
+ <span class="k">print</span> <span class="s2">"there is a backbone atom missing... "</span><span class="p">,</span> \
+ <span class="n">res_handle</span><span class="o">.</span><span class="n">GetQualifiedName</span><span class="p">()</span></div>
-<span class="c"># these methods will be exported into module</span></div>
-<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s">'ReconstructSidechains'</span><span class="p">,)</span>
+<span class="c1"># these methods will be exported into module</span>
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s1">'ReconstructSidechains'</span><span class="p">,)</span>
</pre></div>
</div>
@@ -595,9 +587,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -605,11 +594,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/_modules/promod3/modelling/_ring_punches.html b/doc/html/_modules/promod3/modelling/_ring_punches.html
index 5d01cf28297385b05f35c93061be5b2e7b6ec8ce..a443928984846cc8360ea5a3b7339d0c45757d85 100644
--- a/doc/html/_modules/promod3/modelling/_ring_punches.html
+++ b/doc/html/_modules/promod3/modelling/_ring_punches.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>promod3.modelling._ring_punches — ProMod3 1.1.0 documentation</title>
+ <title>promod3.modelling._ring_punches — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,14 +23,16 @@
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../../../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../../../index.html" />
<link rel="up" title="promod3" href="../../promod3.html" />
+ <link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -38,7 +40,7 @@
<div class="body" role="main">
<h1>Source code for promod3.modelling._ring_punches</h1><div class="highlight"><pre>
-<span class="sd">'''Helper functions to deal with ring punchings.'''</span>
+<span></span><span class="sd">'''Helper functions to deal with ring punchings.'''</span>
<span class="kn">import</span> <span class="nn">ost</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">geom</span>
<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">core</span>
@@ -47,8 +49,8 @@
<span class="k">def</span> <span class="nf">_AddRing</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">res</span><span class="p">,</span> <span class="n">atom_names</span><span class="p">):</span>
<span class="sd">'''Try to add ring for given atoms in residue res to rings.'''</span>
- <span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="s">"ring_punches::_AddRing"</span><span class="p">)</span>
- <span class="c"># get exisiting atom positions</span>
+ <span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="s2">"ring_punches::_AddRing"</span><span class="p">)</span>
+ <span class="c1"># get exisiting atom positions</span>
<span class="n">N</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">atom_names</span><span class="p">)</span>
<span class="k">assert</span><span class="p">(</span><span class="n">N</span> <span class="o">>=</span> <span class="mi">3</span><span class="p">)</span>
<span class="n">pos</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
@@ -59,34 +61,34 @@
<span class="n">pos</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">GetPos</span><span class="p">())</span>
<span class="n">center</span> <span class="o">+=</span> <span class="n">a</span><span class="o">.</span><span class="n">GetPos</span><span class="p">()</span>
- <span class="c"># all good?</span>
+ <span class="c1"># all good?</span>
<span class="n">allgood</span> <span class="o">=</span> <span class="bp">False</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pos</span><span class="p">)</span> <span class="o">==</span> <span class="n">N</span><span class="p">:</span>
- <span class="c"># all the ring there -> good</span>
+ <span class="c1"># all the ring there -> good</span>
<span class="n">center</span> <span class="o">=</span> <span class="n">center</span><span class="o">/</span><span class="n">N</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">Plane</span><span class="p">(</span><span class="n">pos</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">pos</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">center</span><span class="p">)</span>
<span class="n">allgood</span> <span class="o">=</span> <span class="bp">True</span>
- <span class="k">elif</span> <span class="n">res</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="o">==</span> <span class="s">'P'</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">pos</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span>
- <span class="c"># incomplete proline: 3 BB-pos there</span>
- <span class="c"># get ring-plane from 3 pos</span>
+ <span class="k">elif</span> <span class="n">res</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="o">==</span> <span class="s1">'P'</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">pos</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span>
+ <span class="c1"># incomplete proline: 3 BB-pos there</span>
+ <span class="c1"># get ring-plane from 3 pos</span>
<span class="n">plane</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">Plane</span><span class="p">(</span><span class="n">pos</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">pos</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">pos</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
- <span class="c"># fit circle in plane through 3 points:</span>
- <span class="c"># - build 2 planes normal to ring-plane and vector connecting 2 points</span>
- <span class="c"># - intersect 2 planes and resulting line with ring-plane -> DONE</span>
+ <span class="c1"># fit circle in plane through 3 points:</span>
+ <span class="c1"># - build 2 planes normal to ring-plane and vector connecting 2 points</span>
+ <span class="c1"># - intersect 2 planes and resulting line with ring-plane -> DONE</span>
<span class="n">plane1</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">Plane</span><span class="p">((</span><span class="n">pos</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">+</span> <span class="n">pos</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span> <span class="n">pos</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">-</span> <span class="n">pos</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="n">plane2</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">Plane</span><span class="p">((</span><span class="n">pos</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">+</span> <span class="n">pos</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span> <span class="n">pos</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">-</span> <span class="n">pos</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
<span class="n">i_line</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">IntersectionLine</span><span class="p">(</span><span class="n">plane1</span><span class="p">,</span> <span class="n">plane2</span><span class="p">)</span>
<span class="n">center</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">IntersectionPoint</span><span class="p">(</span><span class="n">i_line</span><span class="p">,</span> <span class="n">plane</span><span class="p">)</span>
<span class="n">allgood</span> <span class="o">=</span> <span class="bp">True</span>
- <span class="c"># add ring</span>
+ <span class="c1"># add ring</span>
<span class="k">if</span> <span class="n">allgood</span><span class="p">:</span>
- <span class="c"># get ring radius</span>
+ <span class="c1"># get ring radius</span>
<span class="n">radius</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">p</span> <span class="ow">in</span> <span class="n">pos</span><span class="p">:</span>
<span class="n">radius</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">radius</span><span class="p">,</span> <span class="n">geom</span><span class="o">.</span><span class="n">Length</span><span class="p">(</span><span class="n">p</span> <span class="o">-</span> <span class="n">center</span><span class="p">))</span>
- <span class="c"># append to list</span>
- <span class="n">Ring</span> <span class="o">=</span> <span class="n">namedtuple</span><span class="p">(</span><span class="s">'Ring'</span><span class="p">,</span> <span class="s">'center plane radius residue'</span><span class="p">)</span>
+ <span class="c1"># append to list</span>
+ <span class="n">Ring</span> <span class="o">=</span> <span class="n">namedtuple</span><span class="p">(</span><span class="s1">'Ring'</span><span class="p">,</span> <span class="s1">'center plane radius residue'</span><span class="p">)</span>
<span class="n">rings</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">Ring</span><span class="p">(</span><span class="n">center</span><span class="p">,</span> <span class="n">plane</span><span class="p">,</span> <span class="n">radius</span><span class="p">,</span> <span class="n">res</span><span class="o">.</span><span class="n">handle</span><span class="p">))</span>
<span class="k">def</span> <span class="nf">_IgnoreAtom</span><span class="p">(</span><span class="n">ring</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
@@ -97,22 +99,22 @@
<span class="sd">'''Check all bonds of atom for punches through ring.</span>
<span class="sd"> Atom is ignored if it's in ring-residue or direct neighbors.</span>
<span class="sd"> Return true if punch found.'''</span>
- <span class="c"># check this atom (can be view or handle!)</span>
+ <span class="c1"># check this atom (can be view or handle!)</span>
<span class="n">a1</span> <span class="o">=</span> <span class="n">atom</span><span class="o">.</span><span class="n">handle</span>
<span class="k">if</span> <span class="n">_IgnoreAtom</span><span class="p">(</span><span class="n">ring</span><span class="p">,</span> <span class="n">a1</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">False</span>
<span class="n">p1</span> <span class="o">=</span> <span class="n">a1</span><span class="o">.</span><span class="n">GetPos</span><span class="p">()</span>
<span class="n">d1</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">Dot</span><span class="p">(</span><span class="n">p1</span> <span class="o">-</span> <span class="n">ring</span><span class="o">.</span><span class="n">center</span><span class="p">,</span> <span class="n">ring</span><span class="o">.</span><span class="n">plane</span><span class="o">.</span><span class="n">normal</span><span class="p">)</span>
- <span class="c"># check all bonded partners</span>
+ <span class="c1"># check all bonded partners</span>
<span class="k">for</span> <span class="n">a_other</span> <span class="ow">in</span> <span class="n">atom</span><span class="o">.</span><span class="n">GetBondPartners</span><span class="p">():</span>
<span class="n">a2</span> <span class="o">=</span> <span class="n">a_other</span><span class="o">.</span><span class="n">handle</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">a_other</span><span class="o">.</span><span class="n">IsValid</span><span class="p">()</span> <span class="ow">or</span> <span class="n">_IgnoreAtom</span><span class="p">(</span><span class="n">ring</span><span class="p">,</span> <span class="n">a2</span><span class="p">):</span>
<span class="k">continue</span>
- <span class="c"># two bonded atoms on diff. sides of the plane?</span>
+ <span class="c1"># two bonded atoms on diff. sides of the plane?</span>
<span class="n">p2</span> <span class="o">=</span> <span class="n">a2</span><span class="o">.</span><span class="n">GetPos</span><span class="p">()</span>
<span class="n">d2</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">Dot</span><span class="p">(</span><span class="n">p2</span> <span class="o">-</span> <span class="n">ring</span><span class="o">.</span><span class="n">center</span><span class="p">,</span> <span class="n">ring</span><span class="o">.</span><span class="n">plane</span><span class="o">.</span><span class="n">normal</span><span class="p">)</span>
<span class="k">if</span> <span class="n">d1</span><span class="o">*</span><span class="n">d2</span> <span class="o"><</span> <span class="mi">0</span><span class="p">:</span>
- <span class="c"># get intersect</span>
+ <span class="c1"># get intersect</span>
<span class="n">line</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">Line3</span><span class="p">(</span><span class="n">p1</span><span class="p">,</span> <span class="n">p2</span><span class="p">)</span>
<span class="n">pi</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">IntersectionPoint</span><span class="p">(</span><span class="n">line</span><span class="p">,</span> <span class="n">ring</span><span class="o">.</span><span class="n">plane</span><span class="p">)</span>
<span class="k">if</span> <span class="n">geom</span><span class="o">.</span><span class="n">Length</span><span class="p">(</span><span class="n">pi</span> <span class="o">-</span> <span class="n">ring</span><span class="o">.</span><span class="n">center</span><span class="p">)</span> <span class="o"><</span> <span class="n">ring</span><span class="o">.</span><span class="n">radius</span><span class="p">:</span>
@@ -134,21 +136,21 @@
<span class="sd"> radius (:class:`float`),</span>
<span class="sd"> residue (:class:`~ost.mol.ResidueHandle`).</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'ring_punches::GetRings'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'ring_punches::GetRings'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
<span class="n">rings</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">ent</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
- <span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="ow">in</span> <span class="s">'YF'</span><span class="p">:</span>
- <span class="n">_AddRing</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="p">[</span><span class="s">"CG"</span><span class="p">,</span> <span class="s">"CD1"</span><span class="p">,</span> <span class="s">"CD2"</span><span class="p">,</span> <span class="s">"CE1"</span><span class="p">,</span> <span class="s">"CE2"</span><span class="p">,</span> <span class="s">"CZ"</span><span class="p">])</span>
- <span class="k">elif</span> <span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="o">==</span> <span class="s">'W'</span><span class="p">:</span>
- <span class="n">_AddRing</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="p">[</span><span class="s">"CG"</span><span class="p">,</span> <span class="s">"CD1"</span><span class="p">,</span> <span class="s">"NE1"</span><span class="p">,</span> <span class="s">"CD2"</span><span class="p">,</span> <span class="s">"CE2"</span><span class="p">])</span>
- <span class="n">_AddRing</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="p">[</span><span class="s">"CD2"</span><span class="p">,</span> <span class="s">"CE2"</span><span class="p">,</span> <span class="s">"CE3"</span><span class="p">,</span> <span class="s">"CZ2"</span><span class="p">,</span> <span class="s">"CZ3"</span><span class="p">,</span> <span class="s">"CH2"</span><span class="p">])</span>
- <span class="k">elif</span> <span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="o">==</span> <span class="s">'H'</span><span class="p">:</span>
- <span class="n">_AddRing</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="p">[</span><span class="s">"CG"</span><span class="p">,</span> <span class="s">"CD2"</span><span class="p">,</span> <span class="s">"ND1"</span><span class="p">,</span> <span class="s">"CE1"</span><span class="p">,</span> <span class="s">"NE2"</span><span class="p">])</span>
- <span class="k">elif</span> <span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="o">==</span> <span class="s">'P'</span><span class="p">:</span>
- <span class="n">_AddRing</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="p">[</span><span class="s">"N"</span><span class="p">,</span> <span class="s">"CA"</span><span class="p">,</span> <span class="s">"CB"</span><span class="p">,</span> <span class="s">"CD"</span><span class="p">,</span> <span class="s">"CG"</span><span class="p">])</span>
- <span class="k">return</span> <span class="n">rings</span>
-</div>
+ <span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="ow">in</span> <span class="s1">'YF'</span><span class="p">:</span>
+ <span class="n">_AddRing</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="p">[</span><span class="s2">"CG"</span><span class="p">,</span> <span class="s2">"CD1"</span><span class="p">,</span> <span class="s2">"CD2"</span><span class="p">,</span> <span class="s2">"CE1"</span><span class="p">,</span> <span class="s2">"CE2"</span><span class="p">,</span> <span class="s2">"CZ"</span><span class="p">])</span>
+ <span class="k">elif</span> <span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="o">==</span> <span class="s1">'W'</span><span class="p">:</span>
+ <span class="n">_AddRing</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="p">[</span><span class="s2">"CG"</span><span class="p">,</span> <span class="s2">"CD1"</span><span class="p">,</span> <span class="s2">"NE1"</span><span class="p">,</span> <span class="s2">"CD2"</span><span class="p">,</span> <span class="s2">"CE2"</span><span class="p">])</span>
+ <span class="n">_AddRing</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="p">[</span><span class="s2">"CD2"</span><span class="p">,</span> <span class="s2">"CE2"</span><span class="p">,</span> <span class="s2">"CE3"</span><span class="p">,</span> <span class="s2">"CZ2"</span><span class="p">,</span> <span class="s2">"CZ3"</span><span class="p">,</span> <span class="s2">"CH2"</span><span class="p">])</span>
+ <span class="k">elif</span> <span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="o">==</span> <span class="s1">'H'</span><span class="p">:</span>
+ <span class="n">_AddRing</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="p">[</span><span class="s2">"CG"</span><span class="p">,</span> <span class="s2">"CD2"</span><span class="p">,</span> <span class="s2">"ND1"</span><span class="p">,</span> <span class="s2">"CE1"</span><span class="p">,</span> <span class="s2">"NE2"</span><span class="p">])</span>
+ <span class="k">elif</span> <span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="o">==</span> <span class="s1">'P'</span><span class="p">:</span>
+ <span class="n">_AddRing</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="p">[</span><span class="s2">"N"</span><span class="p">,</span> <span class="s2">"CA"</span><span class="p">,</span> <span class="s2">"CB"</span><span class="p">,</span> <span class="s2">"CD"</span><span class="p">,</span> <span class="s2">"CG"</span><span class="p">])</span>
+ <span class="k">return</span> <span class="n">rings</span></div>
+
<div class="viewcode-block" id="GetRingPunches"><a class="viewcode-back" href="../../../modelling/model_checking.html#promod3.modelling.GetRingPunches">[docs]</a><span class="k">def</span> <span class="nf">GetRingPunches</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">ent</span><span class="p">):</span>
<span class="sd">'''Get list of residues with rings that are punched by the given structure.</span>
@@ -159,20 +161,20 @@
<span class="sd"> :return: :class:`list` of residues (:class:`~ost.mol.ResidueHandle`) which</span>
<span class="sd"> have a punched ring.</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'ring_punches::GetRingPunches'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'ring_punches::GetRingPunches'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
<span class="n">ring_punches</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="k">for</span> <span class="n">ring</span> <span class="ow">in</span> <span class="n">rings</span><span class="p">:</span>
- <span class="c"># we don't need to add residues multiple times</span>
+ <span class="c1"># we don't need to add residues multiple times</span>
<span class="k">if</span> <span class="n">ring</span><span class="o">.</span><span class="n">residue</span> <span class="ow">in</span> <span class="n">ring_punches</span><span class="p">:</span>
<span class="k">continue</span>
- <span class="c"># check neighborhood (3A should be enough)</span>
+ <span class="c1"># check neighborhood (3A should be enough)</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">ent</span><span class="o">.</span><span class="n">FindWithin</span><span class="p">(</span><span class="n">ring</span><span class="o">.</span><span class="n">center</span><span class="p">,</span> <span class="mi">3</span><span class="p">):</span>
<span class="k">if</span> <span class="n">_CheckAtomVsRing</span><span class="p">(</span><span class="n">ring</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
<span class="n">ring_punches</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ring</span><span class="o">.</span><span class="n">residue</span><span class="p">)</span>
<span class="k">break</span>
- <span class="k">return</span> <span class="n">ring_punches</span>
-</div>
+ <span class="k">return</span> <span class="n">ring_punches</span></div>
+
<div class="viewcode-block" id="HasRingPunches"><a class="viewcode-back" href="../../../modelling/model_checking.html#promod3.modelling.HasRingPunches">[docs]</a><span class="k">def</span> <span class="nf">HasRingPunches</span><span class="p">(</span><span class="n">rings</span><span class="p">,</span> <span class="n">ent</span><span class="p">):</span>
<span class="sd">'''Check if any ring is punched by the given structure.</span>
<span class="sd"> This check is faster than using :func:`GetRingPunches`.</span>
@@ -184,15 +186,15 @@
<span class="sd"> :return: True, iff any ring is punched</span>
<span class="sd"> :rtype: :class:`bool`</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'ring_punches::HasRingPunches'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'ring_punches::HasRingPunches'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
<span class="k">for</span> <span class="n">ring</span> <span class="ow">in</span> <span class="n">rings</span><span class="p">:</span>
- <span class="c"># check neighborhood (3A should be enough)</span>
+ <span class="c1"># check neighborhood (3A should be enough)</span>
<span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">ent</span><span class="o">.</span><span class="n">FindWithin</span><span class="p">(</span><span class="n">ring</span><span class="o">.</span><span class="n">center</span><span class="p">,</span> <span class="mi">3</span><span class="p">):</span>
<span class="k">if</span> <span class="n">_CheckAtomVsRing</span><span class="p">(</span><span class="n">ring</span><span class="p">,</span> <span class="n">atom</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">True</span>
- <span class="k">return</span> <span class="bp">False</span>
-</div>
+ <span class="k">return</span> <span class="bp">False</span></div>
+
<div class="viewcode-block" id="FilterCandidates"><a class="viewcode-back" href="../../../modelling/model_checking.html#promod3.modelling.FilterCandidates">[docs]</a><span class="k">def</span> <span class="nf">FilterCandidates</span><span class="p">(</span><span class="n">candidates</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">gap</span><span class="p">,</span> <span class="n">orig_indices</span><span class="o">=</span><span class="p">[]):</span>
<span class="sd">'''Remove loop candidates if they cause ring punches.</span>
@@ -207,23 +209,23 @@
<span class="sd"> must have as many elements as *candidates*.</span>
<span class="sd"> :type orig_indices: :class:`list`</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'ring_punches::FilterCandidates'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'ring_punches::FilterCandidates'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
<span class="n">start_resnum</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span>
<span class="n">chain_idx</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">()</span>
- <span class="c"># precompute rings and range of rings to replace</span>
+ <span class="c1"># precompute rings and range of rings to replace</span>
<span class="n">chain_name</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">GetChainName</span><span class="p">()</span>
<span class="n">end_resnum</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span>
- <span class="n">myqueryin</span> <span class="o">=</span> <span class="s">"cname="</span> <span class="o">+</span> <span class="n">chain_name</span> <span class="o">+</span> <span class="s">" and rnum="</span> <span class="o">+</span>\
- <span class="nb">str</span><span class="p">(</span><span class="n">start_resnum</span><span class="p">)</span> <span class="o">+</span> <span class="s">":"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">end_resnum</span><span class="p">)</span>
- <span class="n">myqueryout</span> <span class="o">=</span> <span class="s">"cname!="</span> <span class="o">+</span> <span class="n">chain_name</span> <span class="o">+</span> <span class="s">" or rnum<"</span> <span class="o">+</span>\
- <span class="nb">str</span><span class="p">(</span><span class="n">start_resnum</span><span class="p">)</span> <span class="o">+</span> <span class="s">" or rnum>"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">end_resnum</span><span class="p">)</span>
+ <span class="n">myqueryin</span> <span class="o">=</span> <span class="s2">"cname="</span> <span class="o">+</span> <span class="n">chain_name</span> <span class="o">+</span> <span class="s2">" and rnum="</span> <span class="o">+</span>\
+ <span class="nb">str</span><span class="p">(</span><span class="n">start_resnum</span><span class="p">)</span> <span class="o">+</span> <span class="s2">":"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">end_resnum</span><span class="p">)</span>
+ <span class="n">myqueryout</span> <span class="o">=</span> <span class="s2">"cname!="</span> <span class="o">+</span> <span class="n">chain_name</span> <span class="o">+</span> <span class="s2">" or rnum<"</span> <span class="o">+</span>\
+ <span class="nb">str</span><span class="p">(</span><span class="n">start_resnum</span><span class="p">)</span> <span class="o">+</span> <span class="s2">" or rnum>"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">end_resnum</span><span class="p">)</span>
<span class="n">model_out</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="n">myqueryout</span><span class="p">)</span>
<span class="n">rings_out</span> <span class="o">=</span> <span class="n">GetRings</span><span class="p">(</span><span class="n">model_out</span><span class="p">)</span>
- <span class="c"># filter loop candidates</span>
+ <span class="c1"># filter loop candidates</span>
<span class="n">lc_idx</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">while</span> <span class="n">lc_idx</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">):</span>
- <span class="c"># get loop-entity for checks</span>
+ <span class="c1"># get loop-entity for checks</span>
<span class="n">new_loop</span> <span class="o">=</span> <span class="n">candidates</span><span class="p">[</span><span class="n">lc_idx</span><span class="p">]</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">()</span>
<span class="n">rings_new</span> <span class="o">=</span> <span class="n">GetRings</span><span class="p">(</span><span class="n">new_loop</span><span class="p">)</span>
<span class="n">check_punches</span> <span class="o">=</span> <span class="n">HasRingPunches</span><span class="p">(</span><span class="n">rings_out</span><span class="o">+</span><span class="n">rings_new</span><span class="p">,</span> <span class="n">new_loop</span><span class="p">)</span> <span class="ow">or</span>\
@@ -233,32 +235,32 @@
<span class="k">if</span> <span class="n">orig_indices</span><span class="p">:</span>
<span class="k">del</span> <span class="n">orig_indices</span><span class="p">[</span><span class="n">lc_idx</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">lc_idx</span> <span class="o">+=</span> <span class="mi">1</span>
-</div>
+ <span class="n">lc_idx</span> <span class="o">+=</span> <span class="mi">1</span></div>
+
<div class="viewcode-block" id="FilterCandidatesWithSC"><a class="viewcode-back" href="../../../modelling/model_checking.html#promod3.modelling.FilterCandidatesWithSC">[docs]</a><span class="k">def</span> <span class="nf">FilterCandidatesWithSC</span><span class="p">(</span><span class="n">candidates</span><span class="p">,</span> <span class="n">model</span><span class="p">,</span> <span class="n">gap</span><span class="p">,</span> <span class="n">orig_indices</span><span class="o">=</span><span class="p">[]):</span>
<span class="sd">'''Remove loop candidates if they (with sidechain) cause ring punches.</span>
<span class="sd"> See :func:`FilterCandidates`.</span>
<span class="sd"> '''</span>
- <span class="n">prof_name</span> <span class="o">=</span> <span class="s">'ring_punches::FilterCandidatesWithSC'</span>
+ <span class="n">prof_name</span> <span class="o">=</span> <span class="s1">'ring_punches::FilterCandidatesWithSC'</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">core</span><span class="o">.</span><span class="n">StaticRuntimeProfiler</span><span class="o">.</span><span class="n">StartScoped</span><span class="p">(</span><span class="n">prof_name</span><span class="p">)</span>
<span class="n">start_resnum</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">before</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span>
<span class="n">chain_idx</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">GetChainIndex</span><span class="p">()</span>
<span class="n">cur_model</span> <span class="o">=</span> <span class="n">model</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
- <span class="c"># precompute rings and range of rings to replace</span>
+ <span class="c1"># precompute rings and range of rings to replace</span>
<span class="n">chain_name</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">GetChainName</span><span class="p">()</span>
<span class="n">end_resnum</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">after</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span>
- <span class="n">myqueryin</span> <span class="o">=</span> <span class="s">"cname="</span> <span class="o">+</span> <span class="n">chain_name</span> <span class="o">+</span> <span class="s">" and rnum="</span> <span class="o">+</span>\
- <span class="nb">str</span><span class="p">(</span><span class="n">start_resnum</span><span class="p">)</span> <span class="o">+</span> <span class="s">":"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">end_resnum</span><span class="p">)</span>
- <span class="n">myqueryout</span> <span class="o">=</span> <span class="s">"cname!="</span> <span class="o">+</span> <span class="n">chain_name</span> <span class="o">+</span> <span class="s">" or rnum<"</span> <span class="o">+</span>\
- <span class="nb">str</span><span class="p">(</span><span class="n">start_resnum</span><span class="p">)</span> <span class="o">+</span> <span class="s">" or rnum>"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">end_resnum</span><span class="p">)</span>
+ <span class="n">myqueryin</span> <span class="o">=</span> <span class="s2">"cname="</span> <span class="o">+</span> <span class="n">chain_name</span> <span class="o">+</span> <span class="s2">" and rnum="</span> <span class="o">+</span>\
+ <span class="nb">str</span><span class="p">(</span><span class="n">start_resnum</span><span class="p">)</span> <span class="o">+</span> <span class="s2">":"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">end_resnum</span><span class="p">)</span>
+ <span class="n">myqueryout</span> <span class="o">=</span> <span class="s2">"cname!="</span> <span class="o">+</span> <span class="n">chain_name</span> <span class="o">+</span> <span class="s2">" or rnum<"</span> <span class="o">+</span>\
+ <span class="nb">str</span><span class="p">(</span><span class="n">start_resnum</span><span class="p">)</span> <span class="o">+</span> <span class="s2">" or rnum>"</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">end_resnum</span><span class="p">)</span>
<span class="n">rings_out</span> <span class="o">=</span> <span class="n">GetRings</span><span class="p">(</span><span class="n">cur_model</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="n">myqueryout</span><span class="p">))</span>
- <span class="c"># filter loop candidates</span>
+ <span class="c1"># filter loop candidates</span>
<span class="n">lc_idx</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">while</span> <span class="n">lc_idx</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">):</span>
- <span class="c"># insert loop into model-copy</span>
+ <span class="c1"># insert loop into model-copy</span>
<span class="n">bb_list</span> <span class="o">=</span> <span class="n">candidates</span><span class="p">[</span><span class="n">lc_idx</span><span class="p">]</span>
<span class="n">bb_list</span><span class="o">.</span><span class="n">InsertInto</span><span class="p">(</span><span class="n">cur_model</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="n">chain_idx</span><span class="p">],</span> <span class="n">start_resnum</span><span class="p">)</span>
- <span class="c"># add sidechains and check for clashes</span>
+ <span class="c1"># add sidechains and check for clashes</span>
<span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">cur_model</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
<span class="n">models_new</span> <span class="o">=</span> <span class="n">cur_model</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="n">myqueryin</span><span class="p">)</span>
<span class="n">rings_new</span> <span class="o">=</span> <span class="n">GetRings</span><span class="p">(</span><span class="n">models_new</span><span class="p">)</span>
@@ -269,11 +271,11 @@
<span class="k">if</span> <span class="n">orig_indices</span><span class="p">:</span>
<span class="k">del</span> <span class="n">orig_indices</span><span class="p">[</span><span class="n">lc_idx</span><span class="p">]</span>
<span class="k">else</span><span class="p">:</span>
- <span class="n">lc_idx</span> <span class="o">+=</span> <span class="mi">1</span>
+ <span class="n">lc_idx</span> <span class="o">+=</span> <span class="mi">1</span></div>
-<span class="c"># these methods will be exported into module</span></div>
-<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s">'GetRings'</span><span class="p">,</span> <span class="s">'GetRingPunches'</span><span class="p">,</span> <span class="s">'HasRingPunches'</span><span class="p">,</span> <span class="s">'FilterCandidates'</span><span class="p">,</span>
- <span class="s">'FilterCandidatesWithSC'</span><span class="p">)</span>
+<span class="c1"># these methods will be exported into module</span>
+<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span><span class="s1">'GetRings'</span><span class="p">,</span> <span class="s1">'GetRingPunches'</span><span class="p">,</span> <span class="s1">'HasRingPunches'</span><span class="p">,</span> <span class="s1">'FilterCandidates'</span><span class="p">,</span>
+ <span class="s1">'FilterCandidatesWithSC'</span><span class="p">)</span>
</pre></div>
</div>
@@ -299,9 +301,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -309,11 +308,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/_modules/test_actions.html b/doc/html/_modules/test_actions.html
index e28652fc4fab9827bcdfea9a5aab29b6a7725292..f9739b382679bc7bfe2aafe0e47bace71563dd75 100644
--- a/doc/html/_modules/test_actions.html
+++ b/doc/html/_modules/test_actions.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>test_actions — ProMod3 1.1.0 documentation</title>
+ <title>test_actions — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,14 +23,16 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="Module code" href="index.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -38,7 +40,7 @@
<div class="body" role="main">
<h1>Source code for test_actions</h1><div class="highlight"><pre>
-<span class="sd">"""</span>
+<span></span><span class="sd">"""</span>
<span class="sd">unittest.TestCase class providing common functionality for testing actions.</span>
<span class="sd">"""</span>
<span class="kn">import</span> <span class="nn">unittest</span>
@@ -46,7 +48,7 @@
<span class="kn">import</span> <span class="nn">subprocess</span>
<span class="kn">import</span> <span class="nn">ost</span>
-<span class="c"># set verbosity level here, is propagated to all others</span>
+<span class="c1"># set verbosity level here, is propagated to all others</span>
<span class="n">ost</span><span class="o">.</span><span class="n">PushVerbosityLevel</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span>
<div class="viewcode-block" id="ActionTestCase"><a class="viewcode-back" href="../actions/index_dev.html#test_actions.ActionTestCase">[docs]</a><span class="k">class</span> <span class="nc">ActionTestCase</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
@@ -77,11 +79,11 @@
<span class="sd">"""</span>
<span class="sd"> Convenience stuff for action testing.</span>
<span class="sd"> """</span>
- <span class="c"># Determining the pm binary to be called. Going hard-coded is a bad</span>
- <span class="c"># thing. But this is a unit test and we know where we are as all unit</span>
- <span class="c"># tests are run in "tests/MODULENAME" within build-folder.</span>
+ <span class="c1"># Determining the pm binary to be called. Going hard-coded is a bad</span>
+ <span class="c1"># thing. But this is a unit test and we know where we are as all unit</span>
+ <span class="c1"># tests are run in "tests/MODULENAME" within build-folder.</span>
<span class="n">bld_dir</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">getcwd</span><span class="p">())))</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">pm_bin</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">bld_dir</span><span class="p">,</span> <span class="s">'stage'</span><span class="p">,</span> <span class="s">'bin'</span><span class="p">,</span> <span class="s">'pm'</span><span class="p">)</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">pm_bin</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">bld_dir</span><span class="p">,</span> <span class="s1">'stage'</span><span class="p">,</span> <span class="s1">'bin'</span><span class="p">,</span> <span class="s1">'pm'</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pm_action</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
@@ -103,30 +105,30 @@
<span class="sd"> :returns: The exit code of the action (:class:`int`).</span>
<span class="sd"> """</span>
<span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">pm_action</span><span class="p">:</span>
- <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s">"A 'pm_action' attribute has to be defined by "</span><span class="o">+</span>
- <span class="s">"each subclass of 'test_actions.ActionTestCase'"</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">RuntimeError</span><span class="p">(</span><span class="s2">"A 'pm_action' attribute has to be defined by "</span><span class="o">+</span>
+ <span class="s2">"each subclass of 'test_actions.ActionTestCase'"</span><span class="p">)</span>
- <span class="c"># run the action with arguments, wait for the job to finish and capture</span>
- <span class="c"># output</span>
+ <span class="c1"># run the action with arguments, wait for the job to finish and capture</span>
+ <span class="c1"># output</span>
<span class="n">cmd</span> <span class="o">=</span> <span class="p">[</span><span class="bp">self</span><span class="o">.</span><span class="n">pm_bin</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">pm_action</span><span class="p">]</span> <span class="o">+</span> <span class="n">arguments</span>
<span class="n">job</span> <span class="o">=</span> <span class="n">subprocess</span><span class="o">.</span><span class="n">Popen</span><span class="p">(</span><span class="n">cmd</span><span class="p">,</span>
<span class="n">stdout</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">,</span> <span class="n">stderr</span><span class="o">=</span><span class="n">subprocess</span><span class="o">.</span><span class="n">PIPE</span><span class="p">)</span>
<span class="n">sout</span><span class="p">,</span> <span class="n">serr</span> <span class="o">=</span> <span class="n">job</span><span class="o">.</span><span class="n">communicate</span><span class="p">()</span>
<span class="k">if</span> <span class="n">verbose</span><span class="p">:</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogScript</span><span class="p">(</span><span class="s">"stdout of '</span><span class="si">%s</span><span class="s">'"</span> <span class="o">%</span> <span class="s">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cmd</span><span class="p">))</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogScript</span><span class="p">(</span><span class="s">"------"</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogScript</span><span class="p">(</span><span class="s2">"stdout of '</span><span class="si">%s</span><span class="s2">'"</span> <span class="o">%</span> <span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cmd</span><span class="p">))</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogScript</span><span class="p">(</span><span class="s2">"------"</span><span class="p">)</span>
<span class="n">lines</span> <span class="o">=</span> <span class="n">sout</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>
<span class="k">for</span> <span class="n">out_l</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">:</span>
<span class="n">ost</span><span class="o">.</span><span class="n">LogScript</span><span class="p">(</span><span class="n">out_l</span><span class="p">)</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogScript</span><span class="p">(</span><span class="s">"------"</span><span class="p">)</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s">"stderr of '</span><span class="si">%s</span><span class="s">'"</span> <span class="o">%</span> <span class="s">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cmd</span><span class="p">))</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s">"------"</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogScript</span><span class="p">(</span><span class="s2">"------"</span><span class="p">)</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s2">"stderr of '</span><span class="si">%s</span><span class="s2">'"</span> <span class="o">%</span> <span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cmd</span><span class="p">))</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s2">"------"</span><span class="p">)</span>
<span class="n">lines</span> <span class="o">=</span> <span class="n">serr</span><span class="o">.</span><span class="n">splitlines</span><span class="p">()</span>
<span class="k">for</span> <span class="n">err_l</span> <span class="ow">in</span> <span class="n">lines</span><span class="p">:</span>
<span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="n">err_l</span><span class="p">)</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s">"------"</span><span class="p">)</span>
- <span class="k">return</span> <span class="n">job</span><span class="o">.</span><span class="n">returncode</span>
-</div>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="s2">"------"</span><span class="p">)</span>
+ <span class="k">return</span> <span class="n">job</span><span class="o">.</span><span class="n">returncode</span></div>
+
<div class="viewcode-block" id="ActionTestCase.RunExitStatusTest"><a class="viewcode-back" href="../actions/index_dev.html#test_actions.ActionTestCase.RunExitStatusTest">[docs]</a> <span class="k">def</span> <span class="nf">RunExitStatusTest</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">exit_code</span><span class="p">,</span> <span class="n">arguments</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Run the action with given arguments and check the exit code.</span>
@@ -142,12 +144,12 @@
<span class="sd"> """</span>
<span class="n">exit_code_run</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">RunAction</span><span class="p">(</span><span class="n">arguments</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="n">verbose</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">exit_code</span><span class="p">,</span> <span class="n">exit_code_run</span><span class="p">,</span>
- <span class="n">msg</span><span class="o">=</span><span class="s">"Exit code of '</span><span class="si">%s</span><span class="s">' "</span> <span class="o">%</span> <span class="s">' '</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">pm_bin</span><span class="p">,</span>
+ <span class="n">msg</span><span class="o">=</span><span class="s2">"Exit code of '</span><span class="si">%s</span><span class="s2">' "</span> <span class="o">%</span> <span class="s1">' '</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">pm_bin</span><span class="p">,</span>
<span class="bp">self</span><span class="o">.</span><span class="n">pm_action</span><span class="p">]</span><span class="o">+</span>
<span class="n">arguments</span><span class="p">)</span><span class="o">+</span>
- <span class="s">"is supposed to be '</span><span class="si">%d</span><span class="s">' "</span> <span class="o">%</span> <span class="n">exit_code</span><span class="o">+</span>
- <span class="s">"but returned as '</span><span class="si">%d</span><span class="s">'."</span> <span class="o">%</span> <span class="n">exit_code_run</span><span class="p">)</span>
-</div>
+ <span class="s2">"is supposed to be '</span><span class="si">%d</span><span class="s2">' "</span> <span class="o">%</span> <span class="n">exit_code</span><span class="o">+</span>
+ <span class="s2">"but returned as '</span><span class="si">%d</span><span class="s2">'."</span> <span class="o">%</span> <span class="n">exit_code_run</span><span class="p">)</span></div>
+
<div class="viewcode-block" id="ActionTestCase.testPMExists"><a class="viewcode-back" href="../actions/index_dev.html#test_actions.ActionTestCase.testPMExists">[docs]</a> <span class="k">def</span> <span class="nf">testPMExists</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> This is an internal test, executed when the source code of the test</span>
@@ -155,16 +157,16 @@
<span class="sd"> file (also complains if a directory is found instead).</span>
<span class="sd"> """</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">pm_bin</span><span class="p">),</span> <span class="bp">True</span><span class="p">,</span>
- <span class="n">msg</span><span class="o">=</span><span class="s">"Could not find 'pm' bin at '</span><span class="si">%s</span><span class="s">', "</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">pm_bin</span><span class="o">+</span>
- <span class="s">"cannot proceed unit tests."</span><span class="p">)</span>
-</div></div>
-<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">"__main__"</span><span class="p">:</span>
+ <span class="n">msg</span><span class="o">=</span><span class="s2">"Could not find 'pm' bin at '</span><span class="si">%s</span><span class="s2">', "</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">pm_bin</span><span class="o">+</span>
+ <span class="s2">"cannot proceed unit tests."</span><span class="p">)</span></div></div>
+
+<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
<span class="kn">import</span> <span class="nn">sys</span>
<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">testutils</span>
<span class="n">sys</span><span class="o">.</span><span class="n">dont_write_bytecode</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">testutils</span><span class="o">.</span><span class="n">RunTests</span><span class="p">()</span>
-<span class="c"># LocalWords: attr meth ActionTestCase init str stdout stderr param bool</span>
+<span class="c1"># LocalWords: attr meth ActionTestCase init str stdout stderr param bool</span>
</pre></div>
</div>
@@ -188,9 +190,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -198,11 +197,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/_sources/buildsystem.txt b/doc/html/_sources/buildsystem.txt
index 4bb192686d60b60c60d52e9c0e8fb56b3334a91e..a601d619b695a46a2f15352e312e4bdaf91ab90f 100644
--- a/doc/html/_sources/buildsystem.txt
+++ b/doc/html/_sources/buildsystem.txt
@@ -143,11 +143,11 @@ safely delete the whole source folder.
.. |qmean| replace:: QMEAN
.. |eigen3| replace:: Eigen 3
.. |openmm| replace:: OpenMM
-.. _qmean: http://swissmodel.expasy.org/qmean/cgi/index.cgi?
-.. _ost_l: http://www.OpenStructure.org
+.. _qmean: https://swissmodel.expasy.org/qmean/
+.. _ost_l: https://www.OpenStructure.org
.. _cmake: https://cmake.org/
.. _python: https://www.python.org/
-.. _boost: http://www.boost.org/
+.. _boost: https://www.boost.org/
.. _eigen3: http://eigen.tuxfamily.org/index.php?title=Main_Page
.. _openmm: http://openmm.org
diff --git a/doc/html/_sources/changelog.txt b/doc/html/_sources/changelog.txt
index aec8ac1362e2dbbf2f1e4d06a6ec6422e921b3d3..20e7a36a38c83e77511d058c8e9f459732964672 100644
--- a/doc/html/_sources/changelog.txt
+++ b/doc/html/_sources/changelog.txt
@@ -5,7 +5,36 @@
Changelog
================================================================================
-Release 1.1
+Release 1.2.0
+--------------------------------------------------------------------------------
+
+* Graph optimizer has been separated from the sidechain module and can now be
+ used for arbitrary optimization problems. Available optimization algorithms
+ are TreePack, AStar and MonteCarlo.
+* Make it possible to distinguish between the scores of a loop towards a constant
+ environment (external scores) and the scores within the loop itself
+ (internal scores).
+* Most scores based on pairwise interactions are now pairwise decomposable.
+* Disconnected loops at several locations can be scored at once.
+* Avoid the usage of the DSSP executable and use the OpenStructure internal
+ secondary structure assignment instead.
+* Allow to decide whether the CB atom belongs to the actual rotamer or to the
+ constant frame in sidechain optimization. This can be useful in design
+ questions, where the identity of a rotamer is not given and you want to
+ allow glycine or alanine.
+* The naming of the entries in the StructureDB is not strictly limited to
+ 4 letter codes anymore, arbitrary strings can be used instead.
+* Adding coordinates to the StructureDB does not require external tools anymore
+ (msms, dssp etc.), internal implementations are used instead.
+* The data that is stored in a StructureDB can be controlled at initialization,
+ everything except the sequence and the actual coordinates is optional.
+* Entries in the StructureDB can be removed again.
+* Allow to search positions of arbitrary copies in DynamicSpatialOrganizer
+ by providing RT operators.
+* Several minor bug fixes, improvements, and speed-ups
+
+
+Release 1.1.0
--------------------------------------------------------------------------------
* Updated dependencies: need Eigen 3.3.0 and OST 1.7
diff --git a/doc/html/_sources/contributing.txt b/doc/html/_sources/contributing.txt
index 832af70cc2e46a71d3850967a075a8f423ece6d8..ae3c842c641522624e55d208c51e6a146773a033 100644
--- a/doc/html/_sources/contributing.txt
+++ b/doc/html/_sources/contributing.txt
@@ -201,7 +201,7 @@ sporting a single monolithic :file:`test_sidechain_reconstruction.py`.
|python| code is evaluated using its own :py_docs:`unit testing framework
<library/unittest.html>` with a little help from |ost_s|_ (|C++| uses the
|boost| `Test Library
-<http://www.boost.org/doc/libs/1_47_0/libs/test/doc/html/index.html>`_). The
+<https://www.boost.org/doc/libs/1_53_0/libs/test/doc/html/index.html>`_). The
basic scheme is to import your module, subclass :class:`unittest.TestCase` and
make the whole file runnable as script using the most common |nameattr|_
attribute. As an example we test the
@@ -477,7 +477,7 @@ repository comes with a top-level :file:`doc` directory.
While you should not spend to much time thinking about how to format
documentation, here is a helpful list of standard formatters:
-http://sphinx-doc.org/markup/inline.html
+http://sphinx-doc.org/en/stable/markup/inline.html
If you write new functionality for |project|, or fix bugs, feel free to extend
the :file:`CHANGELOG` file. It will be automatically pulled into the
diff --git a/doc/html/_sources/core/graph_minimizer.txt b/doc/html/_sources/core/graph_minimizer.txt
new file mode 100644
index 0000000000000000000000000000000000000000..a1ddb9639f2816086ee62f64861e5e2e5b9dacb2
--- /dev/null
+++ b/doc/html/_sources/core/graph_minimizer.txt
@@ -0,0 +1,235 @@
+Graph Minimizer
+================================================================================
+
+.. currentmodule:: promod3.core
+
+The graph minimizer solves an energy minimization problem where we have n
+nodes :math:`N_i`, with each node having several possible solutions.
+Every solution has a self energy :math:`E_{self}` and pairwise energies in between nodes
+are possible. The goal is to select exactly one solution per node to obtain
+a set :math:`X=[x_1, x_2, ..., x_n]` that minimizes:
+
+.. math::
+ F(X)=\displaystyle\sum_iE_{self}(N_i[x_i]) +\displaystyle \sum_i \displaystyle \sum_{j>i}E_{pair}(N_i[x_i], N_j[x_j])
+
+
+
+.. class:: GraphMinimizer
+
+ .. method:: AddNode(self_energies)
+
+ Adds a node to the graph.
+
+ :param self_energies: Directly controls the number of possible solutions in that
+ node and assigns the corresponding self energies
+ :type self_energies: :class:`list` of :class:`float`
+
+ :returns: The idx of the added node
+ :rtype: :class:`int`
+
+
+ .. method:: AddEdge(node_idx_one, node_idx_two, pairwise_energies)
+
+ Adds an edge between the specified nodes.
+
+ :param node_idx_one: Index of the first node
+ :param node_idx_two: Index of the second node
+ :param pairwise_energies: The pairwise energies that contribute to the
+ overall energy function. There must be a list for
+ every possible solution in node one. All of those
+ lists must have exactly the length of possible
+ solutions in node two.
+
+ :type node_idx_one: :class:`int`
+ :type node_idx_two: :class:`int`
+ :type pairwise_energies: :class:`list` of :class:`list` of :class:`float`
+
+ :returns: The idx of the added edge
+ :rtype: :class:`int`
+ :raises: :exc:`~exceptions.RuntimeError` if *node_idx_one* or *node_idx_two*
+ specify non existent nodes or when *pairwise_energies* is
+ inconsistent with the number of solutions in the specified nodes.
+
+
+ .. method:: ApplyDEE(node_idx, [e_cut=0.0])
+
+ Applies dead end elimination on one particular node and potentially
+ deactivates certain solutions. The goldstein criterion is described in
+ [goldstein1994]_.
+
+ :param node_idx: Node to apply dead end elimination
+ :param e_cut: If set to
+ 0.0, the default goldstein criterion is applied =>
+ a solution is removed if it's dominated by all other
+ solutions in the same node. If you increase this value,
+ a solution must be dominated by at least this **e_cut**.
+
+ :type node_idx: :class:`int`
+ :type e_cut: :class:`float`
+
+ :returns: :class:`bool` whether any solution has been deactivated.
+
+
+ .. method:: ApplyEdgeDecomposition(edge_idx, epsilon)
+
+ Applies edge decomposition on one particular edge and potentially
+ deactivates it. The exact decomposition procedure is described in
+ [krivov2009]_.
+
+ :param edge_idx: Edge to decompose.
+ :param epsilon: The energy threshold to perform edge decomposition.
+
+ :type edge_idx: :class:`int`
+ :type epsilon: :class:`float`
+
+
+ :returns: :class:`bool` whether the edge has been decomposed and
+ deactivated
+
+
+
+ .. method:: Prune(epsilon, [e_cut=0.0, consider_all_nodes=False])
+
+ Performs edge decomposition followed by dead end elimination in an
+ iterative manner until no changes can be observed anymore given
+ **epsilon**.
+
+ :param epsilon: The energy threshold to perform edge decomposition.
+ :param e_cut: Parameter to control dead end elimination.
+ :param consider_all_nodes: Flag, wether the dead end elimination should be
+ applied to all nodes, or only those who are
+ connected with an edge removed by edge
+ decomposition. This is useful if already a Prune
+ operation has been performed => only those nodes
+ connected to a removed edge have the chance for
+ successful dead end elimination.
+
+ :type epsilon: :class:`float`
+ :type e_cut: :class:`float`
+ :type consider_all_nodes: :class:`bool`
+
+
+ .. method:: Reset()
+
+ Resets the graph by undoing any pruning operation (DEE and edge decomposition)
+
+
+ .. method:: TreeSolve([max_complexity=inf, initial_epsilon=0.02])
+
+ The method solves a graph using a minimal width tree decomposition
+ approach in an iterative manner. In every iteration, the algorithm performs
+ a pruning step (DEE / Edge Decomposition) and subsequently tries to solve
+ each connected component in the graph separately.
+ If the number of possible enumerations in the tree constructetd from a
+ particular connected component is is larger **max_complexity**,
+ this component is solved in a later iteration. The algorithm iterates until
+ all connected components are solved and steadily increases the epsilon value
+ resulting in a more and more agressive edge decomposition.
+ Algorithm further descsribed in [krivov2009]_.
+
+ :param max_complexity: Max number of possible permutations, that have to
+ be enumerated in the resulting tree after tree
+ decomposition.
+
+ :param initial_epsilon: The initial energy threshold to perform edge
+ decomposition.
+
+ :type max_complexity: :class:`int`
+ :type initial_epsilon: :class:`float`
+
+ :returns: A tuple with the first element being a list of indices
+ representing the single solutions minimizing
+ the overall energy function.
+ The second element is the according energy value.
+
+
+ .. method:: AStarSolve(e_thresh, [max_n=100, max_visited_nodes=100000000])
+
+ The method solves a graph using the A\* algorithm. Besides creating the
+ minimal energy solution, the function produces a maximum of **max_n**
+ solutions sorted by energy. It aborts as soon as it sees the first solution
+ with an energy difference of **e_thresh** to the optimal solution or hits
+ **max_n**. If you're only interested in the optimal solution you should use
+ the TreeSolve function since it's much faster and uses less memory.
+ There is no automatic pruning of the graph using DEE or edge decomposition,
+ so you have to do it by yourself, otherwise you'll have a looooooong
+ runtime or even hit the **max_visited_nodes** parameter that caps the memory
+ usage.
+ To have a valid solution you have to take care that you set the **e_cut**
+ parameter in the pruning function to **e_tresh**.
+ Algorithm is described in [leach1998]_.
+
+ :param e_thresh: Maximal energy difference of a solution to the
+ optimal solution to be considered.
+
+ :param max_n: The maximum number of solutions that will be generated.
+
+ :param max_visited_nodes: Caps the memory usage of the algorithm. Besides
+ The memory used for pairwise energies and self
+ energies, the algorithm uses about
+ **max_visited_nodes** * 20 bytes.
+
+
+ :type e_thresh: :class:`float`
+ :type max_n: :class:`int`
+ :type max_visited_nodes: :class:`int`
+
+ :returns: A tuple with the first element being a list of
+ solutions. The second element is a list
+ of energies for the according solutions.
+
+
+ .. method:: MCSolve([n=100, mc_steps=100000, start_temperature=1000.0, \\
+ change_frequency=1000, cooling_factor=0.9, seed=0])
+
+ Does a total of **n** Monte Carlo runs to find low energy solutions
+ of the graph. Each run starts with a random
+ configuration. At each of the **mc_steps** steps, a random node and
+ a random solution at that location is selected and an energy difference
+ of that random selection relative to the current configuration is
+ estimated. If the difference in energy is negative, the step is
+ accepted. If not, the step is accepted with a probability given by
+ the temperature dependent Metropolis criterion
+ :math:`exp^{\left(\frac{-e_{diff}}{T}\right)}`.
+ The temperature for every run starts with **start_temperature**
+ and is multiplied every **change_frequency** steps with **cooling_factor**
+ to achieve a simulated annealing effect.
+ There is no automatic pruning of the graph using DEE or edge decomposition,
+ you have to do that by yourself.
+
+ :param n: Number of Monte Carlo runs
+ :param mc_steps: Number of Monte Carlo steps per run
+ :param start_temperature: Start temperature for the temperature dependent
+ Metropolis criterion
+ :param change_frequency: Number of steps the temperature stays the same
+ :param cooling_factor: Factor to multiply temperature each
+ **change_frequency** steps
+ :param seed: Seed for random number generator
+
+ :type n: :class:`int`
+ :type mc_steps: :class:`int`
+ :type start_temperature: :class:`float`
+ :type change_frequency: :class:`int`
+ :type cooling_factor: :class:`float`
+ :type seed: :class:`float`
+
+ :returns: A tuple with the first element being a list of
+ solutions. The second element is a list
+ of energies for the according solutions.
+
+ .. method:: NaiveSolve()
+
+ Don't even think of using this... This function only exists for debug
+ purposes and does the full enumeration of the solution space.
+ It might become faster with the appropriate
+ `techniques <https://www.youtube.com/watch?v=fQGbXmkSArs>`_.
+
+ :returns: A tuple with the first element being a list of indices
+ representing the single solutions minimizing
+ the overall energy function.
+ The second element is the according energy value.
+
+
+.. [goldstein1994] Goldstein RF (1994). Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys J.
+
+.. [leach1998] Leach AR, Lemon AP (1998). Explring the conformational space of prootein side chains using dead-end elimination and the A* algorithm. Proteins.
diff --git a/doc/html/_sources/core/index.txt b/doc/html/_sources/core/index.txt
index 17f9534aea783a5b313ec58c5ba52b4b9d199fcc..2af5fca9cace92deef375d4857a1c9b55f9ec0d5 100644
--- a/doc/html/_sources/core/index.txt
+++ b/doc/html/_sources/core/index.txt
@@ -16,3 +16,4 @@ Contents:
helper
geometry
runtime_profiling
+ graph_minimizer
diff --git a/doc/html/_sources/loop/structure_db.txt b/doc/html/_sources/loop/structure_db.txt
index 631811ed79575c01da39b5dba4b94ad6a54729b2..a967d08a3823e6ae0eba26410ba7bdfa313ba358 100644
--- a/doc/html/_sources/loop/structure_db.txt
+++ b/doc/html/_sources/loop/structure_db.txt
@@ -3,30 +3,37 @@ Structural Data
.. currentmodule:: promod3.loop
-The structural database serves as a container for structural backbone
-and profile data. It can be filled with chains of pdb structures with their
-corresponding profiles as they are produced by the HHSuite tools [soding2005]_.
-Structural and profile data get complemented by with additional information.
-Following features get stored on a per residue basis:
-
-* The amino acid one letter code
-* The coordinates of the backbone atoms (N,CA,C,O)
-* The phi/psi dihedral angles
-* The secondary structure state as defined by dssp
-* The solvent accessibility in square Angstrom
-* The residue depth defined as the average distance from all atoms of a
- residue to the closest surface vertex as calculated by msms [sanner1996]_.
- This is a simplified version of the residue depth as discussed in
- [chakravarty1999]_ and gets directly calculated when structural information
- gets added to the StructureDB.
-* The amino acid frequencies as given by an input sequence profile
-* The amino acid frequency derived from structural alignments as described
- in [zhou2005]_ - Since the calculation of such a profile already requires a
- StructureDB, we end up in a hen and egg problem here... When adding
- structural information to the StructureDB, the according memory gets
- just allocated and set to zero. The usage of this information
- is therefore only meaningful if you calculate these profiles
- and manually set them (or load the provided default database).
+The structural database serves as a container for structural backbone and
+sequence data. Custom accessor objects can be implemented that relate
+arbitrary features to structural data. Examples provided by ProMod3 include
+accession using matching stem geometry (see: :class:`FragDB`) or sequence
+features (see: :class:`Fragger`).
+Besides backbone and sequence data, derived features can
+optionally be stored. E.g. sequence profiles or secondary structure information.
+Optional data includes:
+
+ * The phi/psi dihedral angles
+ * The secondary structure state as defined by dssp
+ * The solvent accessibility in square Angstrom
+ * The amino acid frequencies as given by an input sequence profile
+ * The residue depth - The residue depth is defined as the minimum distance of
+ a residue towards any of the exposed residues.
+ Distances are calculated using CB positions (artificially constructed in case
+ of glycine) and exposed is defined as:
+ relative solvent accessibility > 25% and at least one atom being exposed
+ to the OUTER surface. To determine whether an atom is part of that outer
+ surface, the full structure is placed into a 3D grid and a flood fill
+ algorithm is used to determine the atoms of interest.
+ Internal cavities are excluded by using this approach. This is a simplified
+ version of the residue depth as discussed in [chakravarty1999]_ and gets
+ directly calculated when structural information is added to the StructureDB.
+ * The amino acid frequency derived from structural alignments as described
+ in [zhou2005]_ - Since the calculation of such a profile already requires a
+ StructureDB, we end up in a hen and egg problem here... When adding
+ structural information to the StructureDB, the according memory gets
+ just allocated and set to zero. The usage of this information
+ is therefore only meaningful if you calculate these profiles
+ and manually set them (or load the provided default database).
Defining Chains and Fragments
--------------------------------------------------------------------------------
@@ -34,27 +41,45 @@ Defining Chains and Fragments
.. class:: CoordInfo()
The CoordInfo gets automatically generated when new chains are added to
- the structural database. It contains internal information of how
- the according chain is stored in the database.
+ the structural database. It contains internal information of how a
+ connected stretch of residues is stored in the database.
- .. attribute:: pdb_id
+ .. attribute:: id
- A character residue string containing the 4 character pdb_id and the
- 1 character chain_id. (:class:`str`)
+ An id string specified when adding the corresponding stretch to the
+ structure db
+
+ .. attribute:: chain_name
+
+ A chain name string specified when adding the corresponding stretch to the
+ structure db
.. attribute:: offset
- All residues of the added structures are stored in a linear memory layout.
- The offset parameter tells us where it exactly starts. (:class:`int`)
+ All residues of the added stretch are stored in a linear memory layout.
+ The offset parameter tells us where it exactly starts in the global data
+ structure. (:class:`int`)
.. attribute:: size
- The length of the stretch of residues. (:class:`int`)
+ The number of residues in that stretch (:class:`int`)
+
+ .. attribute:: start_resnum
+
+ Residue number of first residue in the added stretch. The residue number
+ is relative to the SEQRES provided in the input profile when adding the
+ stuff to the structure db.
+
+ .. attribute:: shift
+
+ Translation from original coordinates that has been applied before storing
+ structural information in db.
.. class:: FragmentInfo(chain_index, offset, length)
- The FragmentInfo defines a fragment in the structural database.
+ The FragmentInfo defines any fragment in the structural database. If you
+ implement your own accessor object, thats the information you want to store.
:param chain_index: Fills :attr:`chain_index`
@@ -64,17 +89,19 @@ Defining Chains and Fragments
.. attribute:: chain_index
- The index of the chain (defined by :class:`CoordInfo`) in the structure db this particle belongs to. (:class:`int`)
+ The index of the chain (defined by :class:`CoordInfo`) in the structure db
+ this particle belongs to. (:class:`int`)
.. attribute:: offset
- Index of residue in **chain** the fragment starts. (:class:`int`)
+ Index of residue in **chain** the fragment starts. (0-based, :class:`int`)
.. attribute:: length
Length of the fragment (:class:`int`)
+
The Structure Database
--------------------------------------------------------------------------------
@@ -83,18 +110,46 @@ and fill it with content.
.. literalinclude:: ../../../tests/doc/scripts/loop_structure_db.py
-Calculating the structural profiles is highly expensive and heavily depends on
+Calculating the structural profiles is expensive and heavily depends on
the size of the database used as source. If you want to do this for a larger
database, you might want to consider two things:
-1. Use a database of limited size as structural source (something
+1. Use a database of limited size to generate the actual profiles (something
in between 5000 and 10000 nonredundant chains is enough)
2. Use the :class:`ost.seq.ProfileDB` to gather profiles produced from jobs
running in parallel
-.. class:: StructureDB()
- .. staticmethod:: Load(filename, load_frequencies=True)
+.. class:: StructureDBDataType
+
+ The StructureDBDataType enum has to be passed at initialization of a
+ StructureDB in order to define what data you want to store additionally
+ to backbone coordinates and sequence.
+ If you want to store all data possible, use All. If you only want a subset,
+ you can combine some of the datatypes with a bitwise or operation
+ (see example script for StructureDB). One important note:
+ If you enable AAFrequenciesStruct, the actual information is not automatically
+ assigned. Only the according memory is allocated and set to zero, the actual
+ information must be assigned manually (see example script again...).
+
+ All, Dihedrals, SolventAccessibilities, ResidueDepths, DSSP, AAFrequencies,
+ AAFrequenciesStruct
+
+
+.. class:: StructureDB(data_to_store)
+
+ Generates an empty StructureDB that can be filled with content through
+ :func:`AddCoordinates`. The information extracted there is defined by
+ *data_to_store*. Have a look at the :class:`StructureDBDataType`
+ documentation and at the example script...
+
+ :param data_to_store: Specifies what data to store in the database, several
+ flags can be combined with a bitwise or operator.
+ :type data_to_store: :class:`StructureDBDataType`
+
+
+
+ .. staticmethod:: Load(filename)
LoadPortable(filename)
Loads raw binary file generated with :meth:`Save` (optimized for fast
@@ -103,13 +158,6 @@ database, you might want to consider two things:
:param filename: Path to the file from which to load the database.
:type filename: :class:`str`
- :param load_frequencies: If True, the full database including profile
- information for every position gets loaded.
- A database without profiles loads faster and
- requires less memory. But it's not possible
- to add new coordinates or call one of the
- profile dependent functions.
- :type load_frequencies: :class:`bool`
:returns: The loaded data base
:rtype: :class:`StructureDB`
@@ -117,6 +165,7 @@ database, you might want to consider two things:
:raises: :exc:`~exceptions.RuntimeError` if file cannot be opened or if
file cannot be parsed (see :ref:`here <portableIO>` for details).
+
.. method:: Save(filename)
SavePortable(filename)
@@ -127,73 +176,127 @@ database, you might want to consider two things:
:param filename: Path to the file where the database will be saved
:type filename: :class:`str`
- :raises: :exc:`~exceptions.RuntimeError` if file cannot be opened or if
- db has been loaded with load_frequencies=False (enforces only
- complete databases to be saved down)
-
- .. method:: AddCoordinates(pdb_id, chain_name, chain, surf, prof, \
- solvent_accessibility_string="solvent_accessibility")
-
- This method takes a structural chain and searches the longest stretch of
- connected residues containing all necessary backbone atoms. This stretch
- gets then added to the database. Due to technical reasons, The maximal
- extent along one of the base axis cannot exceed 650 A.
- Following features are expected to be set on a per residue level in *chain*:
- The secondary structure (e.g. call :meth:`ost.mol.alg.AssignSecStruct` on the
- full :class:`ost.mol.EntityView` the *chain* belongs to) and
- the solvent accessibility assigned using a float property with name
- *solvent_accessibility_string* as name on a per residue level (e.g. call
- :meth:`ost.mol.alg.Accessibility` on the full :class:`ost.mol.EntityView`
- the chain belongs to and take care to pass the appropriate
- *solvent_accessibility_string*).
-
- :param pdb_id: 4-letter code of the structure the chain belongs to
- :param chain_name: Name of the chain consisting of one letter
- :param chain: The actual chain
- :param surf: A surface describing the solvent accessible surface
- (we advise you to provide a surface estimated with the
- full :class:`ost.mol.EntityView` the *chain* belongs to)
- :param prof: Profile information for this *chain*.
- :param solvent_accessibility_string: Name of float property where the
- solvent accessibilities are stored
- on a per residue basis in *chain*
-
- :type pdb_id: :class:`str`
+ :raises: :exc:`~exceptions.RuntimeError` if file cannot be opened
+
+
+ .. method:: HasData(data_type)
+
+ Checks, whether requested data type is available in the current database.
+
+ :param data_type: Data type to check
+ :type data_type: :class:`StructureDBDataType`
+
+ :returns: Whether the requested datatype is available
+ :rtype: :class:`bool`
+
+
+ .. method:: AddCoordinates(id, chain_name, ent, seqres, prof=None, \
+ only_longest_stretch=True)
+
+ This method takes an entity and adds coordinates and the sequence
+ of one of its chains to the structural database. Additionally, all
+ data as specified at the initialization of the database is extracted
+ fully automatically by considering the full *ent* (e.g. when
+ calculating solvent accessibilities etc.).
+ The only exception is AAFrequencies, where a valid sequence profile
+ is expected in *prof* that has matching sequence with *seqres*
+ All residues in chain with name *chain_name* must have residue numbers
+ that directly relate them to the *seqres* with an indexing scheme
+ starting from one.
+ If this is not the case, an error gets thrown. You might want to
+ consider to use :meth:`ost.seq.Renumber` for proper numbering.
+ Based on consecutive numbering and additionally checking for valid
+ peptide bonds, connected stretches are identified
+ and every added connected stretch gets its own entry with
+ :class:`CoordInfo` as a descriptor.
+ To avoid cluttering the database with many small fragments, the flag:
+ *only_longest_stretch* can be used. Set it to False if all
+ connected stretches of chain with name *chain_name* should be added.
+ There is one final catch you have to consider: Due to the internal
+ lossy data compression for the positions, the extent in x, y and
+ z - direction for every connected stretch is limited to 655A. This should
+ be sufficient for most structures, but stretches exceeding this maximum
+ are discarded. For storing the structural data given these restraints,
+ a translation is applied that gets stored as the *shift* attribute
+ in the according :class:`CoordInfo` object.
+
+ :param id: identifier of the added structure (e.g. pdb id)
+ :param chain_name: Name of the chain in *ent* you want to add
+ :param ent: The full entity that must contain a chain named
+ as specified by *chain_name*.
+ :param seqres: The reference sequence of chain with name *chain_name*
+ :param prof: Profile information for the chain with name
+ *chain_name*. The profile sequence must match *seqres*.
+ :param only_longest_stretch: Flag whether you want to add only the longest
+ connected stretch of residues are all connected
+ stretches of residues
+
+ :type id: :class:`str`
:type chain_name: :class:`str`
- :type chain: :class:`ost.mol.ChainView`
- :type surf: :class:`ost.mol.SurfaceHandle`
+ :type ent: :class:`ost.mol.EntityView`
+ :type seqres: :class:`ost.seq.SequenceHandle`
:type prof: :class:`ost.seq.ProfileHandle`
- :type solvent_accessibility_string: :class:`str`
+ :type only_longest_strech: :class:`bool`
- :returns: DB index of added chain.
- :rtype: :class:`int`
+ :returns: indices of added stretches in db
+ :rtype: :class:`list` of `int`
- :raises: :exc:`~exceptions.RuntimeError` if size of chain is too large,
- when db has been loaded with load_frequencies=False or when the
- ATOMSEQ form the *chain* can't be aligned with the SEQRES from
- the *prof*.
+ :raises: :exc:`~exceptions.RuntimeError` if the residues in chain with
+ name *chain_name* do not match *seqres* given the
+ residue numbers, when AAFrequencies have to to be extracted and
+ the sequence in *prof* does not match the *seqres* or *prof* is
+ invalid.
- .. method:: GetCoordIndex(pdb_id, chain_name)
- :returns: The StructureDB index (in [0, :meth:`GetNumCoords`-1]) of the
- chain of interest, -1 if it cannot be found.
- :rtype: :class:`int`
+ .. method:: RemoveCoordinates(coord_idx)
+
+ Removes coordinates at specified location and all its associated data. This
+ has an impact on the offset values of all :class:`CoordInfo` objects
+ that are internally stored afterwards and on the actual coord indices
+ (all shifted by one). So make sure that you adapt your data access
+ accordingly!
+
+ :param coord_idx: Specifies coordinates to be removed
+ :type coord_idx: :class:`int`
- :param pdb_id: 4-letter code of the structure the chain belongs to
- :param chain_name: Name of the chain consisting of one letter
+ :raises: :exc:`~exceptions.RuntimeError` if *coord_idx* is invalid
+
+ .. method:: GetCoordIdx(id, chain_name)
+
+ :returns: The StructureDB indices (in [0, :meth:`GetNumCoords`-1]) of
+ of all coords (connected stretches) with matching
+ *id* / *chain_name*.
+ :rtype: :class:`list` of :class:`int`
+
+ :param id: Identifier given when calling :meth:`AddCoordinates`
+ :param chain_name: Name of chain given when calling :meth:`AddCoordinates`
:type pdb_id: :class:`str`
:type chain_name: :class:`str`
+
.. method:: GetCoordInfo(idx)
- :returns: Object describing the chain with index *idx*.
+ :returns: Object describing the stretch of connected residues with
+ index *idx*.
:rtype: :class:`CoordInfo`
:param idx: The StructureDB index (in [0, :meth:`GetNumCoords`-1])
:type idx: :class:`int`
+ .. method:: GetNumCoords()
+
+ :returns: Number of connected stretches of residues that have been added to
+ the database.
+ :rtype: :class:`int`
+
+
+ .. method:: PrintStatistics()
+
+ Prints out some information about the db.
+
+
.. method:: GetBackboneList(fragment, sequence)
GetBackboneList(n_stem, c_stem, fragment, sequence)
@@ -212,20 +315,9 @@ database, you might want to consider two things:
:type c_stem: :class:`ost.mol.ResidueHandle`
:raises: :exc:`~exceptions.RuntimeError` if fragment is invalid (happens
- if the fragment does not fully fit into one of the chains in the
- database) or if *sequence* contains a one letter code which is not
- one of the 20 default amino acids.
-
-
- .. method:: GetNumCoords()
-
- :returns: Number of chains that have been added to the database.
- :rtype: :class:`int`
-
-
- .. method:: PrintStatistics()
-
- Prints out some information about the db.
+ if the fragment does not fully fit into one of the connected
+ stretches in the database) or if *sequence* contains a one letter
+ code which is not one of the 20 default amino acids.
.. method:: GetSequence(fragment)
@@ -238,7 +330,7 @@ database, you might want to consider two things:
:raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
+ connected stretches of residues in the database.
.. method:: GetDSSPStates(fragment)
@@ -249,9 +341,10 @@ database, you might want to consider two things:
:param fragment: Fragment definition from which to extract the states.
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain dssp
+ data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
+ connected stretches of residues in the database.
.. method:: GetDihedralAngles(fragment)
@@ -262,9 +355,11 @@ database, you might want to consider two things:
:param fragment: Fragment definition from which to extract the dihedrals.
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ dihedral angle data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
+ connected stretches of residues in the database.
+
.. method:: GetResidueDepths(fragment)
@@ -275,9 +370,11 @@ database, you might want to consider two things:
depths
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ residue depth data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
+ connected stretches of residues in the database.
+
.. method:: GetSolventAccessibilitites(fragment)
@@ -289,9 +386,11 @@ database, you might want to consider two things:
accessibilities
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ solvent accessibility data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
+ connected stretches of residues in the database.
+
.. method:: GetSequenceProfile(fragment)
@@ -304,10 +403,12 @@ database, you might want to consider two things:
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
+ :raises: :exc:`~exceptions.RuntimeError` if database does not cotain
+ aa frequency data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
-
+ connected stretches of residues in the database.
+
+
.. method:: GetStructureProfile(fragment)
:returns: The structure profile for the residues defined by *fragment* with
@@ -319,44 +420,50 @@ database, you might want to consider two things:
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ aa frequencies struct data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
+ connected stretches of residues in the database.
- .. method:: GenerateStructureProfile(other_db, fragment)
- Takes the CA positions and residue depths for *fragment* defined from
- *other_db* to calculate a structure profile using the full internal
- structural data of this database with their corresponding residue depths.
+ .. method:: GenerateStructureProfile(bb_list, residue_depths)
- :param fragment: Fragment definition from *other_db*.
- :type fragment: :class:`FragmentInfo`
- :param other_db: Structural database from which we extract CA positions and
- residue depths for *fragment*.
- :type other_db: :class:`StructureDB`
+ Calculates a structure profile for *bb_list* with given *residue_depths*
+ using the full internal data of this StructureDB.
+
+ :param bb_list: Positions for which to calculate the structural profile
+ :type bb_list: :class:`BackboneList`
+ :param residue_depths: The residue depth for each residue in *bb_list*
+ as you would extract it from any StructureDB
+ containing that data.
+ :type residue_depths: :class:`list` of :class:`float`
:returns: The structure profile for the input with the BLOSUM62
probabilities as NULL model.
:rtype: :class:`ost.seq.ProfileHandle`
:raises: :exc:`~exceptions.RuntimeError` if *bb_list* and
- *residue_depths* differ in size or when their size is 0
+ *residue_depths* differ in size, when their size is 0
+ or when database does not contain aa frequencies struct data.
- .. method:: SetStructureProfile(chain_idx, prof)
+
+ .. method:: SetStructureProfile(coord_idx, prof)
Takes the *prof* and sets the corresponding StructureProfile
- frequencies in entry with *chain_idx*
+ frequencies in entry with *coord_idx*
:param prof: Source of profile frequencies
- :param chain_idx: StructureDB index of entry for which to set frequencies
+ :param coord_idx: StructureDB index of entry for which to set frequencies
(in [0, :meth:`GetNumCoords`-1])
:type prof: :class:`ost.seq.ProfileHandle`
- :type chain_idx: :class:`int`
+ :type coord_idx: :class:`int`
+
+ :raises: :exc:`~exceptions.RuntimeError` if *coord_idx* does not match
+ any entry in the db, when the size of the *prof* does not
+ exactly match the size of entry at *coord_idx* or when database
+ does not contain aa frequency struct data.
- :raises: :exc:`~exceptions.RuntimeError` if *chain_idx* does not match
- any entry in the db or when the size of the *prof* does not
- exactly match the size of entry at *chain_idx*
.. method:: GetSubDB(indices)
@@ -437,6 +544,7 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
:return: The bin size
:rtype: :class:`float`
+
.. method:: AddFragments(fragment_length, rmsd_cutoff, structure_db)
Iterates over all fragments of length **fragment_length** in the given structural database and adds them to the fragment database. Fragments will be skipped if there is already a fragment in the database that has an RMSD to the one being added smaller than **rmsd_cutoff**.
@@ -870,7 +978,6 @@ The PsipredPrediction class
.. [soding2005] Söding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.
-.. [sanner1996] Sanner M, Olson AJ, Spehner JC (1996). Reduced Surface: an Efficient Way to Compute Molecular Surfaces. Biopolymers 38 (3): 305-320.
.. [chakravarty1999] Chakravarty S, Varadarajan R (1999). Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7 (7): 723–732.
.. [zhou2005] Zhou H, Zhou Y (2005). Fold Recognition by Combining Sequence Profiles Derived From Evolution and From Depth-Dependent Structural Alignment of Fragments. Proteins 58 (2): 321–328.
.. [Jones1999] Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.
diff --git a/doc/html/_sources/modelling/algorithms.txt b/doc/html/_sources/modelling/algorithms.txt
index 439fd2d9009650a24933a6ccaebb0a6d567c8528..7ff5ae3a33e08ccccdf6d98f87abe2748e1d0d19 100644
--- a/doc/html/_sources/modelling/algorithms.txt
+++ b/doc/html/_sources/modelling/algorithms.txt
@@ -24,11 +24,9 @@ iterative superposition multiple times by using a sliding window to select the
initial subset and gathers all unique results. These results can be very
similar and only differ by single positions. The algorithm therefore reduces
the amount of solutions by merging them based on a threshold of similarity.
-If the sum of matching positions within the distance threshold divided by
-the maximum length of the two solutions is above a cluster thresh, the two
-solutions get merged by producing a common solution containing the shared
-positions. As a final result, the algorithm therefore detects common rigid
-subsets of positions.
+The similarity is defined by the fraction of positions in solution A that are
+also present in solution B. As a final result, the algorithm therefore detects
+common rigid subsets of positions.
.. method:: RigidBlocks(bb_list_one, bb_list_two, [window_length = 12, max_iterations=20, distance_thresh=3.0, cluster_thresh=0.9])
diff --git a/doc/html/_sources/modelling/loop_candidates.txt b/doc/html/_sources/modelling/loop_candidates.txt
index dc3b5c96a28b7320d2fbb4dbdf47fe2492b49ff1..d0711c5a7c89292a61e3f1547ed28af62841382b 100644
--- a/doc/html/_sources/modelling/loop_candidates.txt
+++ b/doc/html/_sources/modelling/loop_candidates.txt
@@ -67,6 +67,12 @@ The LoopCandidates class
Uses Monte Carlo simulated annealing to sample the loop to be modelled.
If *initial_bb* is given, every Monte Carlo run starts from that configuration.
+
+ .. warning:: The :class:`~promod3.scoring.BackboneScoreEnv`
+ attached to *scorer* will be altered in the specified stretch.
+ You might consider the Stash / Pop mechanism of the
+ :class:`~promod3.scoring.BackboneScoreEnv` to restore to the
+ original state once the sampling is done.
:param initial_bb: Initial configuration used for the sampling
:param seq: The sequence of residues to be sampled
@@ -181,10 +187,14 @@ The LoopCandidates class
useful to keep track of scores and other data extracted before.
:rtype: :class:`list` of :class:`int`
- .. method:: CalculateBackboneScores(score_container, scorer, \
+ .. method:: CalculateBackboneScores(score_container, scorer, scorer_env,\
start_resnum, chain_idx=0)
- CalculateBackboneScores(score_container, scorer, keys, \
+ CalculateBackboneScores(score_container, scorer, scorer_env,\
+ keys, start_resnum, chain_idx=0)
+ CalculateBackboneScores(score_container, mhandle,\
start_resnum, chain_idx=0)
+ CalculateBackboneScores(score_container, mhandle,\
+ keys, start_resnum, chain_idx=0)
CalculateAllAtomScores(score_container, mhandle, \
start_resnum, chain_idx=0)
CalculateAllAtomScores(score_container, mhandle, keys, \
@@ -201,7 +211,10 @@ The LoopCandidates class
:param scorer: Backbone scoring object with set environment for the
particular loop modelling problem.
:type scorer: :class:`~promod3.scoring.BackboneOverallScorer`
- :param mhandle: Modelling handle set up for all atom scoring (see
+ :param scorer_env: The scoring environment attached to *scorer*
+ :type scorer_env: :class:`~promod3.scoring.BackboneScoreEnv`
+ :param mhandle: Modelling handle set up scoring (see
+ :func:`SetupDefaultBackboneScoring`
:func:`SetupDefaultAllAtomScoring`).
:type mhandle: :class:`ModellingHandle`
:param keys: Keys of the desired scorers. If not given, we use the set of
@@ -484,15 +497,25 @@ on loop candidates.
a consistent naming of keys used for backbone and all atom scorers as set up
by :func:`SetupDefaultBackboneScoring` and :func:`SetupDefaultAllAtomScoring`.
+ Different sets of weights are available. You can get general weights
+ that have been optimized for a non redundant set of loops with lengths [3,14]
+ (including stem residues). The alternative is to get weights that have only
+ been optimized on a length specific subset of loops. By default you get
+ different weights for following lengths: [0,1,2,3,4], [5,6], [7,8], [9,10],
+ [11,12], [13,14].
+
If you choose to modify the weights, please ensure to set consistently named
keys in here and to use consistently named scorers and scoring computations!
- .. staticmethod:: GetWeights(with_db=False, with_aa=False)
+ .. staticmethod:: GetWeights(with_db=False, with_aa=False,\
+ length_dependent=False, loop_length=-1)
:return: Named weights to be used when scoring loop candidates. The default
weights were optimized to give the best performance when choosing
the loop candidate with the lowest combined score. Each set of
- weights includes (different) backbone scoring weights.
+ weights includes (different) backbone scoring weights, that are
+ optionally only trained on a subset of loops with corresponding
+ loop length.
:rtype: :class:`dict` (keys: :class:`str`, values: :class:`float`)
:param with_db: True to choose a set of weights including DB specific scores
@@ -500,12 +523,21 @@ on loop candidates.
:type with_db: :class:`bool`
:param with_aa: True to choose a set of weights including all atom scores
:type with_aa: :class:`bool`
+ :param length_dependent: Whether to use general weights or their length
+ length dependent counterparts.
+ :type length_dependent: :class:`bool`
+ :param loop_length: Length of full loop. If no weights are available for
+ this length or when *loop_length* is -1, the general
+ weights are returned.
+ :type loop_length: :class:`int`
- .. staticmethod:: SetWeights(with_db, with_aa, weights)
+ .. staticmethod:: SetWeights(with_db, with_aa, weights,\
+ length_dependent=False, loop_length=-1)
Overwrite a set of weights as returned by :meth:`GetWeights`.
- .. staticmethod:: GetBackboneWeights(with_db=False, with_aa=False)
+ .. staticmethod:: GetBackboneWeights(with_db=False, with_aa=False,\
+ length_dependent=False, loop_length=-1)
:return: Subset of :meth:`GetWeights` for backbone scoring as in
:meth:`scoring.BackboneOverallScorer.CalculateLinearCombination`.
@@ -515,8 +547,13 @@ on loop candidates.
:type with_db: :class:`bool`
:param with_aa: As in :meth:`GetWeights`
:type with_aa: :class:`bool`
+ :param length_dependent: As in :meth:`GetWeights`
+ :type length_dependent: :class:`bool`
+ :param loop_length: As in :meth:`GetWeights`
+ :type loop_length: :class:`int`
- .. staticmethod:: GetAllAtomWeights(with_db=False)
+ .. staticmethod:: GetAllAtomWeights(with_db=False, length_dependent=False,\
+ loop_length=-1)
:return: Subset of :meth:`GetWeights` for all atom scoring as in
:meth:`scoring.AllAtomOverallScorer.CalculateLinearCombination`.
@@ -524,6 +561,10 @@ on loop candidates.
:param with_db: As in :meth:`GetWeights`
:type with_db: :class:`bool`
+ :param length_dependent: As in :meth:`GetWeights`
+ :type length_dependent: :class:`bool`
+ :param loop_length: As in :meth:`GetWeights`
+ :type loop_length: :class:`int`
.. staticmethod:: GetStemRMSDsKey()
diff --git a/doc/html/_sources/modelling/loop_closing.txt b/doc/html/_sources/modelling/loop_closing.txt
index 386458ba39abdf80e0b2289a35c5eb25b7cb6463..7ec7230b20a4e32fd9cc1f15a9e84ea7b549c113 100644
--- a/doc/html/_sources/modelling/loop_closing.txt
+++ b/doc/html/_sources/modelling/loop_closing.txt
@@ -197,7 +197,11 @@ the relaxer.
.. method:: Run(bb_list, steps=100, stop_criterion=0.01)
- Performs steepest descent on given BackboneList.
+ Performs steepest descent on given BackboneList. The function possibly fails
+ if there are particles (almost) on top of each other, resulting in NaN
+ positions in the OpenMM system. The positions of **bb_list** are not touched
+ in this case and the function returns an infinit potential energy.
+ In Python you can check for that with float("inf").
:param bb_list: To be relaxed
:param steps: number of steepest descent steps
@@ -209,7 +213,7 @@ the relaxer.
:type steps: :class:`int`
:type stop_criterion: :class:`float`
- :return: Forcefield energy upon relaxation
+ :return: Forcefield energy upon relaxation, infinity in case of OpenMM Error
:rtype: :class:`float`
:raises: :exc:`~exceptions.RuntimeError` if *bb_list* has not the same
@@ -332,7 +336,11 @@ Example usage:
.. method:: Run(sc_data, steps=100, stop_criterion=0.01)
Performs steepest descent for this system and writes updated positions into
- *sc_data.env_pos.all_pos*.
+ *sc_data.env_pos.all_pos*. The function possibly fails
+ if there are particles (almost) on top of each other, resulting in NaN
+ positions in the OpenMM system. The positions of *sc_data.env_pos.all_pos*
+ are not touched in this case and the function returns an infinit potential
+ energy. In Python you can check for that with float("inf").
:param sc_data: Sidechain reconstruction result to be updated
:type sc_data: :class:`~promod3.modelling.SidechainReconstructionData`
@@ -342,7 +350,7 @@ Example usage:
that threshold, the relaxation aborts.
:type stop_criterion: :class:`float`
- :return: Potential energy after relaxation
+ :return: Potential energy after relaxation, infinity in case of OpenMM Error
:rtype: :class:`float`
:raises: :exc:`~exceptions.RuntimeError` if *sc_data* is incompatible with
diff --git a/doc/html/_sources/modelling/monte_carlo.txt b/doc/html/_sources/modelling/monte_carlo.txt
index 328b73d366cf8ce5a6affe7cce3d27a1d6325036..56e572a8788749bde35c415893a964126c5e67b9 100644
--- a/doc/html/_sources/modelling/monte_carlo.txt
+++ b/doc/html/_sources/modelling/monte_carlo.txt
@@ -402,18 +402,29 @@ The scorer asses a proposed conformation and are intended to return a pseudo
energy, the lower the better.
-.. class:: LinearScorer(scorer, start_resnum, chain_idx, linear_weights)
+.. class:: LinearScorer(scorer, scorer_env, start_resnum, num_residues,
+ chain_idx, linear_weights)
The LinearScorer allows to combine the scores available from
:class:`~promod3.scoring.BackboneOverallScorer` in a linear manner. See
:meth:`~promod3.scoring.BackboneOverallScorer.CalculateLinearCombination` for a
detailed description of the arguments.
+ .. warning:: The provided *scorer_env* will be altered in every
+ :func:`GetScore` call.
+ You might consider the Stash / Pop mechanism of the
+ :class:`~promod3.scoring.BackboneScoreEnv` to restore to the
+ original state once the sampling is done.
+
:param scorer: Scorer Object with set environment for the particular loop
modelling problem.
:type scorer: :class:`~promod3.scoring.BackboneOverallScorer`
+ :param scorer_env: The environment that is linked to the *scorer*
+ :type scorer_env: :class:`~promod3.scoring.BackboneScoreEnv`
:param start_resnum: Res. number defining the position in the SEQRES.
:type start_resnum: :class:`int`
+ :param num_residues: Number of residues to score
+ :type num_residues: :class:`int`
:param chain_idx: Index of chain the loop(s) belong to.
:type chain_idx: :class:`int`
:param linear_weights: Weights for each desired scorer.
diff --git a/doc/html/_sources/modelling/pipeline.txt b/doc/html/_sources/modelling/pipeline.txt
index db7dc9d5bf060bf81fcca1e3b918b9824d6d145d..175b65c5d6554d15f76076e3bd3c530595a7cf64 100644
--- a/doc/html/_sources/modelling/pipeline.txt
+++ b/doc/html/_sources/modelling/pipeline.txt
@@ -236,10 +236,8 @@ Modelling Steps
- "reduced": :class:`~promod3.scoring.ReducedScorer`
- "clash": :class:`~promod3.scoring.ClashScorer`
- "hbond": :class:`~promod3.scoring.HBondScorer`
- - "ss_agreement": :class:`~promod3.scoring.SSAgreementScorer`
- "torsion": :class:`~promod3.scoring.TorsionScorer`
- "pairwise": :class:`~promod3.scoring.PairwiseScorer`
- - "density": :class:`~promod3.scoring.DensityScorer`
:param mhandle: The modelling handle. This will set the properties
:attr:`~ModellingHandle.backbone_scorer` and
diff --git a/doc/html/_sources/scoring/all_atom_scorers.txt b/doc/html/_sources/scoring/all_atom_scorers.txt
index 5637039287244c727e7e700670d182e2b64bacec..0a1b39b1613522dd671df0b73b32e98dcaac55eb 100644
--- a/doc/html/_sources/scoring/all_atom_scorers.txt
+++ b/doc/html/_sources/scoring/all_atom_scorers.txt
@@ -37,10 +37,10 @@ AllAtomOverallScorer class
:type env: :class:`~promod3.loop.AllAtomEnv`
.. method:: CalculateLinearCombination(linear_weights, start_resnum, \
- num_residues, chain_idx=0)
+ num_residues, chain_idx)
- Calculate linear combination of scores for the desired loop (extracted from
- environment) against the set environment (see
+ Calculate linear combination of scores for the desired loop(s) (extracted
+ from environment) against the set environment (see
:meth:`AllAtomScorer.CalculateScore`).
:param linear_weights: Weights for each desired scorer. You can add a
@@ -48,14 +48,14 @@ AllAtomOverallScorer class
with key "intercept".
:type linear_weights: :class:`dict` (keys: :class:`str`,
values: :class:`float`)
- :param start_resnum: Res. number defining the position in the SEQRES
+ :param start_resnum: Res. number(s) defining the position(s) in the SEQRES
(see :class:`~promod3.loop.AllAtomEnv` for indexing)
- :type start_resnum: :class:`int` / :class:`ost.mol.ResNum`
- :param num_residues: Length of loop.
- :type num_residues: :class:`int`
- :param chain_idx: Index of chain the loop belongs to
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Length of loop(s).
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :param chain_idx: Index of chain the loop(s) belongs to
(see :class:`~promod3.loop.AllAtomEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
:return: Score for the given set of atoms.
:rtype: :class:`float`
@@ -91,25 +91,20 @@ AllAtomScorer base class
:param env: Link scorer to this score environment.
:type env: :class:`~promod3.loop.AllAtomEnv`
- .. method:: CalculateScore(start_resnum, num_residues, chain_idx=0)
+ .. method:: CalculateScore(start_resnum, num_residues, chain_idx)
- Calculates score for the desired loop (extracted from environment) against
+ Calculates score for the desired loop(s) (extracted from environment) against
the set environment. Unless otherwise noted in the scorer, a lower "score"
is better!
- Note that the structural data of the loop is expected to be in the linked
- environment before calling this! This behavior is different from the
- corresponding function in :class:`BackboneScorer` as, for performance
- reasons, we require all the comparisons to be done against the environment.
-
- :param start_resnum: Res. number defining the position in the SEQRES
+ :param start_resnum: Res. number(s) defining the position(s) in the SEQRES
(see :class:`~promod3.loop.AllAtomEnv` for indexing)
- :type start_resnum: :class:`int` / :class:`ost.mol.ResNum`
- :param num_residues: Length of loop.
- :type num_residues: :class:`int`
- :param chain_idx: Index of chain the loop belongs to
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Length of loop(s).
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :param chain_idx: Index of chain the loop(s) belongs to
(see :class:`~promod3.loop.AllAtomEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
:return: Score for the given set of atoms.
:rtype: :class:`float`
@@ -121,25 +116,21 @@ AllAtomScorer base class
.. method:: CalculateScoreProfile(start_resnum, num_residues, chain_idx=0)
- Calculates per residue scores for the desired loop (extracted from
+ Calculates per residue scores for the desired loop(s) (extracted from
environment) against the set environment.
- Note that the structural data of the loop is expected to be in the linked
- environment before calling this! This behavior is different from the
- corresponding function in :class:`BackboneScorer` as, for performance
- reasons, we require all the comparisons to be done against the environment.
-
- :param start_resnum: Res. number defining the position in the SEQRES
+ :param start_resnum: Res. number(s) defining the position(s) in the SEQRES
(see :class:`~promod3.loop.AllAtomEnv` for indexing)
- :type start_resnum: :class:`int` / :class:`ost.mol.ResNum`
- :param num_residues: Length of loop.
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Length of loop(s).
:type num_residues: :class:`int`
- :param chain_idx: Index of chain the loop belongs to
+ :param chain_idx: Index of chain the loop(s) belongs to
(see :class:`~promod3.loop.AllAtomEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
- :return: Scores for the given loop, one for each residue.
- :rtype: :class:`list` of :class:`float`
+ :return: Scores for the given loop(s), one for each residue.
+ :rtype: :class:`list` of :class:`float` / :class:`list` of :class:`list`
+ of :class:`float`
:raises: same :exc:`~exceptions.RuntimeError` as :meth:`CalculateScore`.
@@ -154,8 +145,11 @@ AllAtomInteractionScorer class
*cutoff* and which are at least *seq_sep* residues apart. An energy is
assigned to each distance using equally sized bins and distinguishing all
possible pairs of atoms (usually the energy only differs for chemically
- distinguishable heavy atoms). The calculated score is normalized by the number
- of interacting atom pairs.
+ distinguishable heavy atoms).
+ By default, the scorer calculates the scores by
+ including everything, the stuff set in the environment and the coordinates
+ in the input loops. You can change this behaviour with the according
+ functions.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadAllAtomInteractionScorer`) or by setting all energies (see :meth:`SetEnergy`).
@@ -204,6 +198,10 @@ AllAtomInteractionScorer class
Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every pair of heavy atom types and for every *bin* < *bins*.
+ Internal symmetry is enforced => Calling SetEnergy(aaa1, aaa2, bin, energy) is
+ equivalent to calling SetEnergy(aaa1, aaa2, bin, energy) AND
+ SetEnergy(aaa2, aaa1, bin, energy).
+
:param aaa1: Heavy atom type for first interaction partner.
:type aaa1: :class:`~promod3.loop.AminoAcidAtom`
@@ -216,6 +214,24 @@ AllAtomInteractionScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoInternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions within the
+ loop. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoExternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions towards the
+ environment. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues in the input loop. True by default.
+ :type do_it: :class:`bool`
+
.. function:: LoadAllAtomInteractionScorer()
@@ -230,8 +246,7 @@ AllAtomPackingScorer class
Inherits all functionality of :class:`AllAtomScorer`. Evaluates pseudo
energies by counting surrounding atoms within a certain *cutoff* radius around
- all heavy atoms not belonging to the assessed residue itself. The calculated
- score is normalized by the number of atoms being assessed.
+ all heavy atoms not belonging to the assessed residue itself.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadAllAtomPackingScorer`) or by setting all energies (see
@@ -287,6 +302,12 @@ AllAtomPackingScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues in the input loop. True by default.
+ :type do_it: :class:`bool`
+
.. function:: LoadAllAtomPackingScorer()
@@ -302,5 +323,25 @@ AllAtomClashScorer class
Inherits all functionality of :class:`AllAtomScorer`. Calculates a simple
clash score of all atoms against the environment. There is no need to define
any parameters here as all interaction energies are fixed (see Eq. (11) in
- [canutescu2003b]_). The calculated score is normalized by the number of atoms
- being assessed.
+ [canutescu2003b]_). By default, the scorer calculates the scores by
+ including everything, the stuff set in the environment and the coordinates
+ in the input loops. You can change this behaviour with the according
+ functions.
+
+ .. method:: DoInternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions within the
+ loop. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoExternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions towards the
+ environment. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues in the input loop. True by default.
+ :type do_it: :class:`bool`
diff --git a/doc/html/_sources/scoring/backbone_score_env.txt b/doc/html/_sources/scoring/backbone_score_env.txt
index f9c1e18ce2d2537df02f053e2932ab28d24b7712..25980a4d34ba90890e7686c87838fa8dcd0f1679 100644
--- a/doc/html/_sources/scoring/backbone_score_env.txt
+++ b/doc/html/_sources/scoring/backbone_score_env.txt
@@ -12,10 +12,18 @@ BackboneScoreEnv class
used by the scorers. It is linked to a (list of) seqres (one per chain) at
construction. The idea is to initialize it at the beginning of the modelling
process with all known data (positions extracted from template, psipred
- prediction, density map, etc) and then update the environment whenever a new
- loop is being added. Note that, depending on the used scorers, some
- information must be provided for the score to make sense and any env. data can
- be set at any time before actually calculating a score.
+ prediction, etc). All scorers attached to that environment will see that data
+ and can calculate scores accordingly.
+ Scoring with this setup is a two step process:
+
+ * Set the positions you want to score in the environment to make it available
+ to all attached scorers
+ * Call the scorers to get the desired scores
+
+ One problem that might occur is that you mess around with the environment and
+ at some point you want to restore the original state. The
+ :class:`BackboneScoreEnv` provides a Stash / Pop mechanism to perform this
+ task.
:param seqres: Internal SEQRES to be set (single chain or list with one per
chain). Whenever setting structural data, consistency with this SEQRES is enforced.
@@ -94,17 +102,6 @@ BackboneScoreEnv class
inconsistent with the number of internal chains or when one of the
predictions' sizes is inconsistent with the internal SEQRES size.
- .. method:: SetMap(map, resolution, all_atom=False)
-
- Sets an internal density map, which is necessary to calculate some scores.
-
- :param map: The density map
- :type map: :class:`ost.img.ImageHandle`
- :param resolution: Expected resolution of the density map.
- :type resolution: :class:`float`
- :param all_atom: Whether the map is accurate enough to resolve all atoms.
- :type all_atom: :class:`bool`
-
.. method:: AddPairwiseFunction(function, function_type)
Adds a pairwise function that can be used in :meth:`ApplyPairwiseFunction`.
@@ -139,6 +136,26 @@ BackboneScoreEnv class
res. numbers is invalid, the interaction partners are the same
residue or when *f_idx* is an invalid index.
+ .. method:: Stash(start_rnum, num_residues, chain_idx)
+
+ FILO style stashing. You can perform up to 100 stash operations to save
+ the current state of certain stretches in the environment. This state can
+ be restored by calling :func:`Pop`. In one stash operation you can either
+ stash one stretch by providing integers as input or several stretches by
+ providing lists of integers.
+
+ :param start_rnum: start rnum of stretch to stash
+ :param num_residues: length of stretch to stash
+ :param chain_idx: chain idx of stretch to stash
+
+ :type start_rnum: :class:`int` / :class:`list` of :class:`int`
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
+
+ .. method:: Pop()
+
+ Remove and apply the the last stash operation.
+
.. method:: GetSeqres()
:return: SEQRES that was set in constructor (one sequence per chain).
diff --git a/doc/html/_sources/scoring/backbone_scorers.txt b/doc/html/_sources/scoring/backbone_scorers.txt
index ebb0bc300bd52033bb4a020ac0a5a63c390d3617..55a07ec77cc2e0ebc0b619c90c4ebaf824e9531a 100644
--- a/doc/html/_sources/scoring/backbone_scorers.txt
+++ b/doc/html/_sources/scoring/backbone_scorers.txt
@@ -36,55 +36,51 @@ BackboneOverallScorer class
:param env: Link all scorers to this score environment.
:type env: :class:`BackboneScoreEnv`
- .. method:: Calculate(key, bb_list, start_resnum, chain_idx=0)
+ .. method:: Calculate(key, start_resnum, num_residues, chain_idx=0)
- Calculate score(s) for one or many loop(s) with
- :meth:`BackboneScorer.CalculateScore`.
+ Calculate score for one or several stretches of amino acids given the
+ current scoring environment.
:param key: Key for desired scorer.
:type key: :class:`str`
- :param bb_list: Loop(s) for which to calculate the given score
- :type bb_list: :class:`~promod3.loop.BackboneList` / :class:`list` of
- :class:`~promod3.loop.BackboneList`
:param start_resnum: Res. number defining the position in the SEQRES
(see :class:`BackboneScoreEnv` for indexing)
- :type start_resnum: :class:`int`
- :param chain_idx: Index of chain the loop(s) belong to
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Number of residues in the stretch(es) to score
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :param chain_idx: Index of chain the stretch(es) belongs to
(see :class:`BackboneScoreEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
- :return: Score(s) calculated with the desired scorer for the given loop(s).
- In the case of multiple loops, the returned list has the same
- order as the input.
- :rtype: :class:`float` / :class:`list` of :class:`float`
+ :return: Score calculated with the desired scorer for the given stretch(es).
+ :rtype: :class:`float`
:raises: :exc:`~exceptions.RuntimeError` if there is no scorer with that
*key* or anything raised in :meth:`BackboneScorer.CalculateScore`.
- .. method:: CalculateLinearCombination(linear_weights, bb_list, start_resnum,\
- chain_idx=0)
+ .. method:: CalculateLinearCombination(linear_weights, start_resnum,\
+ num_residues, chain_idx=0)
- Calculate linear combination(s) of scores for one or many loop(s).
+ Calculate linear combination of scores for one or several stretches of
+ amino acids given the current scoring environment.
:param linear_weights: Weights for each desired scorer. You can add a
constant value to each score by defining a weight
with key "intercept".
:type linear_weights: :class:`dict` (keys: :class:`str`,
values: :class:`float`)
- :param bb_list: Loop(s) for which to calculate the given score
- :type bb_list: :class:`~promod3.loop.BackboneList` / :class:`list` of
- :class:`~promod3.loop.BackboneList`
:param start_resnum: Res. number defining the position in the SEQRES
(see :class:`BackboneScoreEnv` for indexing)
- :type start_resnum: :class:`int`
- :param chain_idx: Index of chain the loop(s) belong to
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Number of residues in the stretch(es) to score
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :param chain_idx: Index of chain the stretch(es) belongs to
(see :class:`BackboneScoreEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
- :return: Linear combination(s) of the scores calculated with the desired
- scorers for the given loop(s). In the case of multiple loops, the
- returned list has the same order as the input.
- :rtype: :class:`float` / :class:`list` of :class:`float`
+ :return: Linear combination of the scores calculated with the desired
+ scorers for the given stretch(es)
+ :rtype: :class:`float`
:raises: :exc:`~exceptions.RuntimeError` if *linear_weights* has a *key* for
which no scorer exists or anything raised in
@@ -103,7 +99,7 @@ BackboneOverallScorer class
:returns: Loads or creates the default scorers accessible through
following keys:
"cb_packing", "cbeta", "reduced", "clash", "hbond", "ss_agreement",\
- "torsion", "pairwise", "density"
+ "torsion", "pairwise"
:rtype: :class:`BackboneOverallScorer`
@@ -119,47 +115,46 @@ BackboneScorer base class
:param env: Link scorer to this score environment.
:type env: :class:`BackboneScoreEnv`
- .. method:: CalculateScore(bb_list, start_resnum, chain_idx=0)
+ .. method:: CalculateScore(start_resnum, num_residues, chain_idx=0)
- Calculates score for the given loop internally and against the set
- environment. Data in the environment, which overlaps with the given
- *bb_list* is ignored. Unless otherwise noted in the scorer, a lower "score"
- is better!
+ Calculates score for one or several stretches given the structural
+ information in the attached environment. Unless otherwise noted in the
+ scorer, a lower "score" is better!
- :param bb_list: Loop for which to calculate the given score
- :type bb_list: :class:`~promod3.loop.BackboneList`
:param start_resnum: Res. number defining the position in the SEQRES
(see :class:`BackboneScoreEnv` for indexing)
- :type start_resnum: :class:`int`
- :param chain_idx: Index of chain the loop belongs to
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Number of residues in the stretch(es) to score
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :param chain_idx: Index of chain the stretch(es) belongs to
(see :class:`BackboneScoreEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
- :return: Score for the given loop.
+ :return: Score for the given stretch(es).
:rtype: :class:`float`
:raises: (for most scorers) :exc:`~exceptions.RuntimeError` if scorer was
never attached to a score environment, if scorer has never been
- properly initialized or if *chain_index* / *start_resnum* lead to
- invalid positions.
+ properly initialized or if *start_resnum* / *num_residues* /
+ *chain_idx* lead to invalid positions.
- .. method:: CalculateScoreProfile(bb_list, start_resnum, chain_idx=0)
+ .. method:: CalculateScoreProfile(start_resnum, num_residues, chain_idx=0)
- Calculates per residue scores for the given loop internally and against the
- set environment. Data in the environment, which overlaps with the given
- *bb_list* is ignored.
+ Calculates per residue scores for one or several stretches given the
+ structural information in the attached environment.
- :param bb_list: Loop for which to calculate the given scores
- :type bb_list: :class:`~promod3.loop.BackboneList`
:param start_resnum: Res. number defining the position in the SEQRES
(see :class:`BackboneScoreEnv` for indexing)
- :type start_resnum: :class:`int`
- :param chain_idx: Index of chain the loop belongs to
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Number of residues in the stretch(es) to score
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :param chain_idx: Index of chain the stretch(es) belongs to
(see :class:`BackboneScoreEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
- :return: Scores for the given loop, one for each residue.
- :rtype: :class:`list` of :class:`float`
+ :return: Scores for the given stretch(es), one for each residue.
+ :rtype: :class:`list` of :class:`float` or :class:`list` of :class:`list`
+ of :class:`float`
:raises: same :exc:`~exceptions.RuntimeError` as :meth:`CalculateScore`.
@@ -171,25 +166,7 @@ CBPackingScorer class
Inherits all functionality of :class:`BackboneScorer`. Evaluates pseudo
energies by counting the number of other CB positions within a certain
- *cutoff* radius of the CB position of the residue to be evaluated. The
- calculated score is normalized by the number of residues in the loop.
- In the default mode, the scorer scores a :class:`promod3.loop.BackboneList`
- given the defined environment. By placing this
- :class:`promod3.loop.BackboneList`, the score of the residues in the
- environment also change. It is possible to honour this effect by using the
- "IncludeEnv" mode. In this alternative mode, every environment residue close
- to the input :class:`promod3.loop.BackboneList` also contributes
- to the final score by adding the difference in score when the environment
- residue sees the original environment and the score when the environment would
- be modified by the :class:`promod3.loop.BackboneList`. You choose the mode
- by specifically calling the according CalculateEnergy functions.
- If you call the CalculateScore function from the parent class
- (e.g. when the scorer is part of the :class:`BackboneOverallScorer`), it
- gets checked what mode is currently active. You can toggle the mode by calling
- the appropriate functions in this class. By default (when you load a scorer or
- when you create a new scorer) the classic version gets called. If you want to
- get per residue scores, the "IncludeEnv" mode makes not much sense and the
- scorer throws an error if a profile is requeset in this mode.
+ *cutoff* radius of the CB position of the residue to be evaluated.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadCBPackingScorer`) or by setting all energies (see
@@ -245,16 +222,12 @@ CBPackingScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
- .. method:: UseClassicMode()
+ .. method:: DoNormalize(do_it)
- If you call this function, the default mode is set to classic if the
- CalculateScore function from the parent class gets called.
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
- .. method:: UseIncludeEnvMode()
-
- If you call this function, the default mode is set to the
- described alternative mode if the CalculateScore function from the parent
- class gets called.
.. function:: LoadCBPackingScorer()
@@ -270,9 +243,8 @@ CBetaScorer class
Inherits all functionality of :class:`BackboneScorer`. Evaluates a pairwise
pseudo interaction energy between CB atoms which are located within a *cutoff*
and which are at least *seq_sep* residues apart. An energy is assigned to each
- distance using *bins* equally sized bins and distinguishing all possible pairs
- of amino acids. The calculated score is normalized by the number of
- interacting CB pairs.
+ distance using equally sized bins and distinguishing all possible pairs
+ of amino acids.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadCBetaScorer`) or by setting all energies (see :meth:`SetEnergy`).
@@ -321,6 +293,9 @@ CBetaScorer class
Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every pair of amino acids and for every *bin* < *bins*.
+ Internal symmetry is enforced => Calling SetEnergy(aa1, aa2, bin, energy) is
+ equivalent to calling SetEnergy(aa1, aa2, bin, energy) AND
+ SetEnergy(aa2, aa1, bin, energy).
:param aa1: Amino acid for first interaction partner.
:type aa1: :class:`ost.conop.AminoAcid`
@@ -333,6 +308,25 @@ CBetaScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoInternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions between
+ the scored residues. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoExternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions of the scored
+ residues towards the surrounding environment.
+ True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
+
.. function:: LoadCBetaScorer()
@@ -348,7 +342,7 @@ ReducedScorer class
Inherits all functionality of :class:`BackboneScorer`. Evaluates a pairwise
pseudo interaction energy between the reduced representation of residues.
Every residue gets represented by its CA position p and a directional
- component ``v = norm(ca_pos-n_pos) + norm (ca_pos-c_pos)``. Residues with CA
+ component ``v = norm(p-n_pos) + norm(p-c_pos)``. Residues with CA
distance < *cutoff* and which are at least *seq_sep* residues apart are
considered to be interacting. For interacting residues r1 and r2, we can
define a line l between p1 and p2. The potential then considers:
@@ -358,10 +352,6 @@ ReducedScorer class
* beta => angle between v2 and l
* gamma => dihedral between (p1+v1,p1,p2,p2+v2)
- Every pairwise interaction within the loop and to the environment gets
- evaluated according to the given parametrization, summed up and finally
- normalized by the number of total interactions.
-
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadReducedScorer`) or by setting all energies (see :meth:`SetEnergy`).
@@ -418,6 +408,11 @@ ReducedScorer class
called for every pair of amino acids, every *dist_bin* < *dist_bins*, every
*alpha_bin* < *angle_bins*, every *beta_bin* < *angle_bins* and every
*gamma_bin* < *dihedral_bins*.
+ Internal symmetry is enforced => Calling
+ SetEnergy(aa1, aa2, dist_bin, alpha_bin, beta_bin, energy) is
+ equivalent to calling
+ SetEnergy(aa1, aa2, dist_bin, alpha_bin, beta_bin, energy) AND
+ SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).
:param aa1: Amino acid for first interaction partner.
:type aa1: :class:`ost.conop.AminoAcid`
@@ -436,6 +431,24 @@ ReducedScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoInternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions between
+ the scored residues. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoExternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions of the scored
+ residues towards the surrounding environment.
+ True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
.. function:: LoadReducedScorer()
@@ -450,29 +463,27 @@ ClashScorer class
Inherits all functionality of :class:`BackboneScorer`. Calculates a simple
clash score of a loop itself and with the set environment. There is no need to
- define any parameters here as all interaction energies are fixed. The
- calculated score is normalized by the number of residues in the loop.
+ define any parameters here as all interaction energies are fixed (see Eq. (11)
+ in [canutescu2003b]_).
+ .. method:: DoInternalScores(do_it)
-DensityScorer class
---------------------------------------------------------------------------------
+ :param do_it: Whether to include pairwise interactions between
+ the scored residues. True by default.
+ :type do_it: :class:`bool`
-.. class:: DensityScorer
+ .. method:: DoExternalScores(do_it)
- Inherits all functionality of :class:`BackboneScorer`. Calculates the
- normalized cross correlation between a density generated from the input
- :class:`~promod3.loop.BackboneList` and a set map.
+ :param do_it: Whether to include pairwise interactions of the scored
+ residues towards the surrounding environment.
+ True by default.
+ :type do_it: :class:`bool`
- This scorer requires that the attached environment has a density map defined
- (see :meth:`BackboneScoreEnv.SetMap`) as soon as a score is to be calculated.
- The *resolution* and *all_atom* flags that were specified in SetMap determine
- how the backbone list is translated into an artificial density map. If
- *all_atom* is set to False (which is recommended for low resolution maps), the
- artificial map gets constructed by only using CA positions instead of all
- atoms.
+ .. method:: DoNormalize(do_it)
- Note that for this scorer a higher "score" is better! So take care when
- combining this to other scores, where it is commonly the other way around.
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
HBondScorer class
@@ -499,10 +510,6 @@ HBondScorer class
thats the one from which the energy is extracted. In all other cases, the
energy is extracted from the 0 state.
- Every pairwise interaction within the loop and to the environment gets
- evaluated according to the given parametrization, summed up and finally
- normalized by the number of residues in the loop.
-
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadHBondScorer`) or by setting all energies (see :meth:`SetEnergy`).
@@ -589,6 +596,25 @@ HBondScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoInternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions between
+ the scored residues. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoExternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions of the scored
+ residues towards the surrounding environment.
+ True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
+
.. function:: LoadHBondScorer()
@@ -607,8 +633,7 @@ SSAgreementScorer class
structure in the model. In every score evaluation, the secondary structure of
the loop is estimated by searching for hydrogen bonds leading to a secondary
structure as defined by dssp. The hbonds are searched internally in the loop
- as well as in the environment. The final score gets summed up over all
- residues in the loop and normalized by the number of residues.
+ as well as in the environment.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadSSAgreementScorer`) or by setting scores for all possible states
@@ -665,6 +690,11 @@ SSAgreementScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
.. function:: LoadSSAgreementScorer()
@@ -679,9 +709,7 @@ TorsionScorer class
Inherits all functionality of :class:`BackboneScorer`. Evaluates pseudo
energies based on the identity of three consecutive residues and the phi/psi
- dihedral angles of the central residue. Every residue gets evaluated according
- to the set parametrization and the final score gets normalized by the total
- number of summed pseudo energies. The first phi and last psi angle get
+ dihedral angles of the central residue. The first phi and last psi angle get
determined with the help of the environment if set.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
@@ -746,6 +774,11 @@ TorsionScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
.. function:: LoadTorsionScorer()
@@ -759,14 +792,28 @@ PairwiseScorer class
.. class:: PairwiseScorer
Inherits all functionality of :class:`BackboneScorer`. Evaluates a list of
- generic pairwise functions (see :class:`PairwiseFunction`). When evaluating a
- loop, the scores of all pairwise functions which involve a residue in the loop
- are summed up (the other residue can be either in the loop or in the env.) and
- normalized by the number of residues in the loop.
-
- This scorer assumes that the attached environment has pairwise functions
- defined (see :meth:`BackboneScoreEnv.ApplyPairwiseFunction`) as soon as a
- score is to be calculated.
+ generic pairwise functions (see :class:`PairwiseFunction`).
+ That are set in the attached scoring environment
+ (see :meth:`BackboneScoreEnv.ApplyPairwiseFunction`).
Note that for this scorer a higher "score" is better! So take care when
combining this to other scores, where it is commonly the other way around.
+
+ .. method:: DoInternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions between
+ the scored residues. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoExternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions of the scored
+ residues towards the surrounding environment.
+ True by default.
+ :type do_it: :class:`bool`, true by default.
+
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
diff --git a/doc/html/_sources/scoring/index.txt b/doc/html/_sources/scoring/index.txt
index 9b9a97882cf52c828b6d48133c6b721a34cb66b8..983d6b5587c5f70fc9088e6bdac386567fef16c3 100644
--- a/doc/html/_sources/scoring/index.txt
+++ b/doc/html/_sources/scoring/index.txt
@@ -9,8 +9,8 @@
Tools and algorithms to score loops. The scoring system is split between an
environment which contains model-specific data and scorers which evaluate loops.
-In this example, we load a structure, setup a score environment and a few
-scorers and finally score some loops:
+In this example, we load a structure, setup a score environment, link a few
+scorers to it and finally score some loops:
.. literalinclude:: ../../../tests/doc/scripts/scoring_main.py
@@ -22,3 +22,4 @@ Contents:
backbone_score_env
backbone_scorers
all_atom_scorers
+ other_scoring_functions
diff --git a/doc/html/_sources/scoring/other_scoring_functions.txt b/doc/html/_sources/scoring/other_scoring_functions.txt
new file mode 100644
index 0000000000000000000000000000000000000000..f505232e026655cdebf83d068269e805eb99fedd
--- /dev/null
+++ b/doc/html/_sources/scoring/other_scoring_functions.txt
@@ -0,0 +1,56 @@
+Other Scoring Functions
+================================================================================
+
+.. currentmodule:: promod3.scoring
+
+
+Scoring Functions from SCWRL3
+--------------------------------------------------------------------------------
+
+.. method:: SCWRL3PairwiseScore(d, Rij)
+
+ Pairwise score from the SCWRL3 sidechain construction algorithm
+ [canutescu2003b]_.
+
+ :param d: Distance between the two interacting particles
+ :param Rij: Summed hard-sphere radii of the interacting particles.
+ Suggestions from the paper:
+
+ - carbon: 1.6
+ - oxygen: 1.3
+ - nitrogen: 1.3
+ - sulfur: 1.7
+
+ :type d: :class:`float`
+ :type Rij: :class:`float`
+
+ :returns: The score
+ :rtype: :class:`float`
+
+
+.. method:: SCWRL3DisulfidScore(ca_pos_one, cb_pos_one, sg_pos_one\
+ ca_pos_two, cb_pos_two, sg_pos_two)
+
+ Implements the empirically derived disulfid score from the SCWRL3 sidechain
+ construction algorithm [canutescu2003b]_.
+
+ :param ca_pos_one: CA carbon position of first amino acid
+ :param cb_pos_one: CB carbon position of first amino acid
+ :param sg_pos_one: SG sulfur position of first amino acid
+ :param ca_pos_two: CA carbon position of second amino acid
+ :param cb_pos_two: CB carbon position of second amino acid
+ :param sg_pos_two: SG sulfur position of second amino acid
+
+ :type ca_pos_one: :class:`ost.geoom.Vec3`
+ :type cb_pos_one: :class:`ost.geoom.Vec3`
+ :type sg_pos_one: :class:`ost.geoom.Vec3`
+ :type ca_pos_two: :class:`ost.geoom.Vec3`
+ :type cb_pos_two: :class:`ost.geoom.Vec3`
+ :type sg_pos_two: :class:`ost.geoom.Vec3`
+
+ :returns: The score
+ :rtype: :class:`float`
+
+
+
+.. [canutescu2003b] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).
diff --git a/doc/html/_sources/sidechain/disulfid.txt b/doc/html/_sources/sidechain/disulfid.txt
index 5b330287975708bdf84fa008b20d2e63315f4895..1cee3075640728b8c205c8bf9d9ff0128d6eeb9d 100644
--- a/doc/html/_sources/sidechain/disulfid.txt
+++ b/doc/html/_sources/sidechain/disulfid.txt
@@ -7,8 +7,9 @@ When calculating the pairwise interaction energy between two rotamers building
a disulfid bond, one would get an unfavourable energy due to "clashes" between
the sulfur atoms. It is possible to improve performance in sidechain
reconstruction regarding cysteins when finding and separately handle
-disulfid bonds. PROMOD3 implements a simple geometrical description
-[canutescu2003b]_ . The paper proposes two rotamers to be in a disulfid
+disulfid bonds. The scoring module implements an empirically derived disulfid
+score (:func:`promod3.scoring.SCWRL3DisulfidScore`) as defined in
+[canutescu2003b]_. The paper proposes two rotamers to be in a disulfid
bonded state, if the resulting disulfid score plus the self energies of the
involved rotamers is below 45. If there are several cysteines close together,
this problem gets another layer of complexity. One has to assure, that
@@ -16,38 +17,18 @@ every cysteine only participates in one disulfid bond but the network
of disulfid bonds is geometrically optimal. SCWRL4 proposes an approach,
that has also been implemented here.
-.. method:: DisulfidRawScore(ca_pos_one, cb_pos_one, sg_pos_one, \
- ca_pos_two, cb_pos_two, sg_pos_two)
-
- Evaluates the geometric expression based on the input positions
-
- :param ca_pos_one: The CA position of first rotamer
- :param cb_pos_one: The CB position of first rotamer
- :param sg_pos_one: The gamma sulfur position of first rotamer
- :param ca_pos_two: The CA position of second rotamer
- :param cb_pos_two: The CB position of second rotamer
- :param sg_pos_two: The gamma sulfur position of second rotamer
-
- :type ca_pos_one: :class:`ost.geom.Vec3`
- :type cb_pos_one: :class:`ost.geom.Vec3`
- :type sg_pos_one: :class:`ost.geom.Vec3`
- :type ca_pos_two: :class:`ost.geom.Vec3`
- :type cb_pos_two: :class:`ost.geom.Vec3`
- :type sg_pos_two: :class:`ost.geom.Vec3`
-
- :returns: The result of the raw score
-
-
.. method:: DisulfidScore(rotamer_one, rotamer_two, ca_pos_one, cb_pos_one, \
ca_pos_two, cb_pos_two)
Directly extracts the positions of the gamma sulfurs from the rotamers by
- searching for particles with the name "SG". In case of :class:`RRMRotamer`
- It expects exactly one gamma sulfur per rotamer. In case of
- :class:`FRMRotamer` there can be an arbitrary number of gamma sulfurs per
- rotamer (at least one), it then evaluates the score for all possible
- combinations of gamma sulfurs and takes the minimum score.
+ searching for particles with the name "SG".
+ The found positions are then passed to
+ :func:`promod3.scoring.SCWRL3DisulfidScore`.
+ In case of :class:`RRMRotamer` it expects exactly one gamma sulfur per
+ rotamer. In case of :class:`FRMRotamer` there can be an arbitrary number
+ of gamma sulfurs per rotamer (at least one), it then evaluates the score
+ for all possible combinations of gamma sulfurs and takes the minimum score.
To get a final DisulfidScore, it finally adds the self energies of the
rotamers to the result of the geometric expression.
@@ -108,6 +89,3 @@ that has also been implemented here.
The tuples in the first list describe the indices of cysteins
participating in disulfid bonds. The tuples in the second list
describe the optimal rotamers in the according rotamer groups.
-
-
-.. [canutescu2003b] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).
diff --git a/doc/html/_sources/sidechain/graph.txt b/doc/html/_sources/sidechain/graph.txt
index 33f3da97bd5f34cd341d31a25f09b733b3b015df..118c72eabb98ed98acdc13eafcb6f3af4bbbb867 100644
--- a/doc/html/_sources/sidechain/graph.txt
+++ b/doc/html/_sources/sidechain/graph.txt
@@ -6,15 +6,15 @@ Rotamer Graph
Once having a frame representing the rigid parts, the internal energies in
rotamer groups can be calculated. To come to a final solution of the sidechain
modelling problem, the pairwise energies also have to be evaluated and an
-overall solution has to be found. PROMOD3 implements an interaction graph that
-takes a list of rotamer groups, calculates the pairwise energies, does edge
-decomposition and dead end elimination. Solutions can finally be found
-using Tree decomposition, AStar or Monte Carlo approaches.
+overall solution has to be found. PROMOD3 implements a
+:class:`promod3.core.GraphMinimizer` that allows to find solutions using
+tree decomposition, A* and Monte Carlo algorithms.
.. class:: RotamerGraph
- The Graph object has no constructor exported to python. It is meant to be
- constructed using the static create functions.
+ The :class:`RotamerGraph` objects inherits from
+ :class:`promod3.core.GraphMinimizer` and extends the minimizer by static
+ initialization functions.
.. staticmethod:: CreateFromRRMList(rotamer_groups)
@@ -27,276 +27,3 @@ using Tree decomposition, AStar or Monte Carlo approaches.
:type rotamer_groups: :class:`list`
- .. method:: Prune(epsilon, [e_cut=0.0, consider_all_nodes=False])
-
- Performs edge decomposition followed by dead end elimination in an
- iterative manner until no changes can be observed anymore given
- **epsilon**.
-
- :param epsilon: The energy threshold to perform edge decomposition.
-
- :param e_cut: Parameter to control dead end elimination. If set to
- 0.0, the default goldstein criterion is applied =>
- the rotamer gets removed if it's dominated by all other
- rotamers in the same node. If you increase this value,
- a rotamer must be dominated by at least this **e_cut**.
-
-
- :param consider_all_nodes: Flag, wether the dead end elimination should be
- applied to all nodes, or only those who are
- connected with an edge removed by edge
- decomposition. This is useful if already a Prune
- operation has been performed => only those nodes
- connected to a removed edge have the chance for
- successful dead end elimination.
-
- :type epsilon: :class:`float`
- :type e_cut: :class:`float`
- :type consider_all_nodes: :class:`bool`
-
-
- .. method:: ApplyDEE(node_idx, [e_cut=0.0])
-
- Applies dead end elimination on one particular node and potentially
- deactivates certain rotamers.
-
- :param node_idx: Node to apply dead end elimination
- :param e_cut: If set to
- 0.0, the default goldstein criterion is applied =>
- the rotamer gets removed if it's dominated by all other
- rotamers in the same node. If you increase this value,
- a rotamer must be dominated by at least this **e_cut**.
-
- :type node_idx: :class:`int`
- :type e_cut: :class:`float`
-
- :returns: :class:`bool` whether any rotamer has been deactivated.
-
-
-
- .. method:: ApplyEdgeDecomposition(edge_idx, epsilon)
-
- Applies edge decomposition on one particular edge and potentially
- deactivates it.
-
-
- :param edge_idx: Edge to decompose.
- the idx relates to the list you get back
- when calling the :meth:`GetEdges` function.
-
- :param epsilon: The energy threshold to perform edge decomposition.
-
- :type edge_idx: :class:`int`
- :type epsilon: :class:`float`
-
-
- :returns: :class:`bool` whether the edge has been decomposed and
- deactivated
-
-
- .. method:: Reset()
-
- Resets the graph by undoing any pruning operation (DEE and edge decomposition)
-
-
- .. method:: TreeSolve([max_complexity=inf, initial_epsilon=0.02])
-
- The method solves a rotamer graph using a minimal width tree decomposition
- approach in an iterative manner. In every iteration, the algorithm performs
- a pruning step (DEE / Edge Decomposition) and subsequently tries to solve
- each connected component in the graph separately.
- If the number of possible enumerations in the tree constructetd from a
- particular connected component is is larger **max_complexity**,
- this component is solved in a later iteration. The algorithm iterates until
- all connected components are solved and steadily increases the epsilon value
- resulting in a more and more agressive edge decomposition. This function
- assumes all self energies of the rotamers to be calculated and properly set!
-
- :param max_complexity: Max number of possible permutations, that have to
- be enumerated in the resulting tree after tree
- decomposition.
-
- :param initial_epsilon: The initial energy threshold to perform edge
- decomposition.
-
- :type max_complexity: :class:`int`
- :type initial_epsilon: :class:`float`
-
- :returns: A tuple with the first element being a list of indices
- representing the single rotamers minimizing
- the overall energy functions from every rotamer group.
- The second element is the according energy value.
-
-
- .. method:: AStarSolve(e_thresh, [max_n=100, max_visited_nodes=100000000])
-
- The method solves a rotamer graph using the A\* algorithm. Besides creating
- minimal energy solution, the function produces a maximum of **max_n**
- solutions sorted by energy. It aborts as soon as it sees the first solution
- with an energy difference of **e_thresh** to the optimal solution or hits
- **max_n**. If you're only interested in the optimal solution you should use
- the TreeSolve function since it's much faster and uses less memory.
- There is no automatic pruning of the graph using DEE or edge decomposition,
- so you have to do it by yourself, otherwise you'll have a looooooong
- runtime or even hit the **max_visited_nodes** parameter that caps the memory
- usage.
- To have a valid solution you have to take care that you set the **e_cut**
- parameter in the pruning function to **e_tresh**.
- This function assumes all self energies of the rotamers to be calculated
- and properly set!
-
- :param e_thresh: Maximal energy difference of a solution to the
- optimal solution to be considered.
-
- :param max_n: The maximum number of solutions that will be generated.
-
- :param max_visited_nodes: Caps the memory usage of the algorithm. Besides
- The memory used for pairwise energies and self
- energies, the algorithm uses about
- **max_visited_nodes** * 20 bytes.
-
-
- :type e_thresh: :class:`float`
- :type max_n: :class:`int`
- :type max_visited_nodes: :class:`int`
-
- :returns: A tuple with the first element being a list of
- solutions with indices representing the single rotamers
- selected for that solution. The second element is a list
- of energies for the according solutions.
-
-
- .. method:: MCSolve([n=100, mc_steps=100000, start_temperature=1000.0, \\
- change_frequency=1000, cooling_factor=0.9, seed=0])
-
- Does a total of **n** Monte Carlo runs to find low energy solutions
- of the RotamerGraph. Each run starts with a random rotamer
- configuration. At each of the **mc_steps** steps, a random location and
- a random rotamer at that location is selected and an energy difference
- of that random selection relative to the current configuration is
- estimated. If the difference in energy is negative, the step is
- accepted. If not, the step is accepted with a probability given by
- the temperature dependent Metropolis criterion (exp(-ediff/T)).
- The temperature for every run starts with **start_temperature**
- and is multiplied every **change_frequency** steps with **cooling_factor**
- to achieve a simulated annealing effect.
- There is no automatic pruning of the graph using DEE or edge decomposition,
- you have to do that by yourself.
- This function assumes all self energies of the rotamers to be calculated
- and properly set!
-
- :param n: Number of Monte Carlo runs
- :param mc_steps: Number of Monte Carlo steps per run
- :param start_temperature: Start temperature for the temperature dependent
- Metropolis criterion
- :param change_frequency: Number of steps the temperature stays the same
- :param cooling_factor: Factor to multiply temperature each
- **change_frequency** steps
- :param seed: Seed for random number generator
-
- :type n: :class:`int`
- :type mc_steps: :class:`int`
- :type start_temperature: :class:`float`
- :type change_frequency: :class:`int`
- :type cooling_factor: :class:`float`
- :type seed: :class:`float`
-
- :returns: A tuple with the first element being a list of
- solutions with indices representing the single rotamers
- selected for that solution. The second element is a list
- of energies for the according solutions.
-
-
-
- .. method:: GetNumNodes()
-
- :returns: The number of nodes in the graph
- => every RotamerGroup is a node
-
-
- .. method:: GetNumEdges()
-
- :returns: The number of edges in the graph, representing
- connections between nodes with at least one
- nonzero interaction
-
-
- .. method:: GetNumActiveNodes()
-
- :returns: The number of nodes having more than one active rotamer,
- even after performing pruning operations
-
-
- .. method:: GetNumActiveEdges()
-
- :returns: The number of edges representing nonzero interactions,
- even after performing pruning operations
-
-
- .. method:: GetNumRotamers()
-
- :returns: The total number of rotamers in the graph
-
-
- .. method:: GetNumActiveRotamers()
-
- :returns: The total number of active rotamers (Total number of
- rotamers minus those that have been deactivated by DEE)
-
-
- .. method:: GetEdges()
-
- :returns: A list of tuples describing the edges
- connecting nodes with nonzero pairwise interactions
-
-
- .. method:: GetActiveEdges()
-
- :returns: A :class:`list` of :class:`tuples` describing the edges
- connecting nodes with nonzero pairwise interactions
- (All edges minus those that have been deactived by edge
- decomposition)
-
-
- .. method:: GetActiveRotamers(node_idx)
-
- :param node_idx: Specifies node from which the active rotamers should be
- extracted
-
- :type node_idx: :class:`int`
-
- :returns: list of the rotamers that are active
- in specified node (all rotamers minus those that have
- been deactivated using DEE)
-
-
- .. method:: GetSelfEnergies(node_idx)
-
- :param node_idx: Specifies node from which the self energies should be
- extracted
-
- :type node_idx: :class:`int`
-
- :returns: list of self energies for all rotamers in
- specified node as they are fed into the solving
- algorithms. Note, that they might slightly differ
- from the original self energies in the input rotamers
- because of approximations introduced in edge
- decomposition.
-
-
- .. method:: GetPairwiseEnergies(edge_idx)
-
- :param edge_idx: Specifies edge from which the pairwise energies should
- be extracted, the idx relates to the list you get back
- when calling the :meth:`GetEdges` function.
-
- :type edge_idx: :class:`int`
-
- :returns: list of list where you can extract
- the energy of rotamer i in the first node in the
- edge with rotamer j in the second node in the edge
- with: e = pairwise_energies[i][j]
-
-
-
diff --git a/doc/html/_sources/sidechain/rotamer.txt b/doc/html/_sources/sidechain/rotamer.txt
index a62ca72acb66bab21f99740b7d46912eba07b18a..40f882320bb51f59b604a6ea7de7106d8582ca2a 100644
--- a/doc/html/_sources/sidechain/rotamer.txt
+++ b/doc/html/_sources/sidechain/rotamer.txt
@@ -156,7 +156,8 @@ Rotamers
Iterates over every particle and searches for the according atom in
**res**. If it's present, the position gets reset to the particle position.
- If not, a new atom gets added to **res**.
+ If not, a new atom gets added to **res**. No atoms are removed from **res**
+ in this process.
:param res: Residue to be reconstructed
:param consider_hydrogens: Flag, whether polar hydrogens should be added to
@@ -313,6 +314,7 @@ Rotamers
Iterates over every particle of the active subrotamer and searches for the
according atom in **res**. If it's present, the position gets reset to the
particle position. If not, a new atom gets added to **res**.
+ No atoms are removed from **res** in this process.
:param res: Residue to be reconstructed
:param consider_hydrogens: Flag, whether polar hydrogens should be added to
diff --git a/doc/html/_sources/sidechain/rotamer_constructor.txt b/doc/html/_sources/sidechain/rotamer_constructor.txt
index 316c0aba0559e2c0061d8a5ed23641967093a00f..36c76a2c0857dc5bdbd5b3257e24e8b2bde5eaac 100644
--- a/doc/html/_sources/sidechain/rotamer_constructor.txt
+++ b/doc/html/_sources/sidechain/rotamer_constructor.txt
@@ -11,22 +11,33 @@ Constructing Rotamers and Frame Residues
--------------------------------------------------------------------------------
-.. class:: SCWRLRotamerConstructor()
+.. class:: SCWRLRotamerConstructor(cb_in_sidechain)
Constructing rotamers and frame residues that are parametrized according to
the SCWRL4 method. They contain all heavy atoms, but also the
- polar hydrogens. The rotamers start after the CB atom (typically CG).
+ polar hydrogens.
In case of the :class:`FrameResidue` construction, the
constructor distinguishes between backbone and sidechain frame residues.
+ :param cb_in_sidechain: If set to true, all constructed rotamers will contain
+ the cb atom. This flag also affects the construction
+ of frame residues and controls whether the cb atom
+ shows up in the backbone frame residues or sidechain
+ frame residues.
+ This is useful when you want to represent ALA or
+ GLY with actual rotamers, but be aware of increased
+ runtime. This flag can be set to False for most
+ modeling applications and you just don't generate
+ any rotamers for ALA and GLY.
+
+ :type cb_in_sidechain: :class:`bool`
+
+
.. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib,\
[probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(all_atom_pos, aa_res_idx, id,\
residue_index, rot_lib,\
[probability_cutoff = 0.98])
- .. method:: ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos, id,\
- residue_index, rot_lib,\
- [probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib,\
[phi = -1.0472, psi = -0.7854,\
probability_cutoff = 0.98])
@@ -34,29 +45,19 @@ Constructing Rotamers and Frame Residues
residue_index, rot_lib,\
[phi = -1.0472, psi = -0.7854,\
probability_cutoff = 0.98])
- .. method:: ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos, id,\
- residue_index, rot_lib,\
- [phi = -1.0472, psi = -0.7854,\
- probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib_entries,\
[probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(all_atom_pos, aa_res_idx, id,\
residue_index, rot_lib_entries,\
[probability_cutoff = 0.98])
- .. method:: ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos, id,\
- residue_index, rot_lib_entries,\
- [probability_cutoff = 0.98])
All functions are also avaible for their flexible rotamer model counterpart.
=>ConstructFRMRotamerGroup(...) with exactly the same parameters.
- :param res: To extract the N, CA, CB backbone anchor
- :param all_atom_pos: To extract the N, CA, CB backbone anchor
+ :param res: To extract the required backbone atoms
+ :param all_atom_pos: To extract the required backbone atoms
:param aa_res_idx: Index of residue in **all_atom_pos** from which to
- extract the backbone anchor
- :param n_pos: To directly feed in the backbone anchor positions
- :param ca_pos: To directly feed in the backbone anchor positions
- :param cb_pos: To directly feed in the backbone anchor positions
+ extract the required backbone atoms
:param id: Identifies the sidechain.
:param residue_index: Important for the energy calculations towards the
:class:`Frame` you don't want to calculate a pairwise
@@ -82,9 +83,6 @@ Constructing Rotamers and Frame Residues
:type res: :class:`ost.mol.ResidueHandle`
:type all_atom_pos: :class:`promod3.loop.AllAtomPositions`
:type aa_res_idx: :class:`int`
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
:type id: :class:`RotamerID`
:type residue_index: :class:`int`
:type rot_lib: :class:`RotamerLib` / :class:`BBDepRotamerLib`
@@ -93,9 +91,8 @@ Constructing Rotamers and Frame Residues
:rtype: :class:`RRMRotamerGroup`
:raises: :exc:`~exceptions.RuntimeError` when not all required backbone
- atoms are present in **residue**, not all required atom
- positions are set in **all_atom_pos** or when the rotamer library
- does not contain any entries for **id**
+ atoms are present in **residue** or not all required atom
+ positions are set in **all_atom_pos**
.. method:: ConstructBackboneFrameResidue(res, id, residue_index, Real phi,\
@@ -105,13 +102,8 @@ Constructing Rotamers and Frame Residues
residue_index, Real phi,\
[n_ter = False, c_ter = False])
- .. method:: ConstructBackboneFrameResidue(n_pos, ca_pos, c_pos, o_pos, cb_pos,\
- id, residue_index, Real phi,\
- [n_ter = False, c_ter = False])
-
- Constructs backbone frame residues for amino acid residues. It extracts
- the n, ca, c, o and cb positions and constructs a frame residue based on
- the parametrizations of SCWRL4. In case of **n_ter**, there are additional
+ Constructs backbone frame residues for amino acid residues based on the
+ parametrizations of SCWRL4. In case of **n_ter**, there are additional
hydrogens added at the nitrogen to represent a proper n-terminus. The same
is true for **c_ter**, an additional oxygen is built instead. In any case,
a single hydrogen is added to the nitrogen (except proline), this is
@@ -121,11 +113,6 @@ Constructing Rotamers and Frame Residues
:param all_atom_pos: To extract the backbone positions
:param aa_res_idx: Index of residue in **all_atom_pos** from which to
extract the backbone positions
- :param n_pos: To directly feed in the backbone positions
- :param ca_pos: To directly feed in the backbone positions
- :param c_pos: To directly feed in the backbone positions
- :param o_pos: To directly feed in the backbone positions
- :param cb_pos: To directly feed in the backbone positions
:param id: Identifies the sidechain
:param residue_index: Important for the energy calculations towards the
:class:`Frame` you don't want to calculate a pairwise
@@ -141,11 +128,6 @@ Constructing Rotamers and Frame Residues
:type res: :class:`ost.mol.ResidueHandle`
:type all_atom_pos: :class:`promod3.loop.AllAtomPositions`
:type aa_res_idx: :class:`int`
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type c_pos: :class:`ost.geom.Vec3`
- :type o_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
:type id: :class:`RotamerID`
:type residue_index: :class:`int`
:type phi: :class:`float`
@@ -156,7 +138,7 @@ Constructing Rotamers and Frame Residues
:raises: :exc:`~exceptions.RuntimeError` when not all required backbone
- atoms are present in **residue**, not all required atom
+ atoms are present in **residue** or not all required atom
positions are set in **all_atom_pos**.
diff --git a/doc/html/_static/alabaster.css b/doc/html/_static/alabaster.css
index 07a9e2a42ae0c0d42495b844723754f80d111911..517cb43e58b2e57a766cbed1ca59eddbe7f4515c 100644
--- a/doc/html/_static/alabaster.css
+++ b/doc/html/_static/alabaster.css
@@ -28,6 +28,7 @@ body {
padding: 0;
}
+
div.document {
width: 940px;
margin: 30px auto 0 auto;
@@ -44,6 +45,8 @@ div.bodywrapper {
div.sphinxsidebar {
width: 220px;
+ font-size: 14px;
+ line-height: 1.5;
}
hr {
@@ -56,6 +59,10 @@ div.body {
padding: 0 30px 0 30px;
}
+div.body > .section {
+ text-align: left;
+}
+
div.footer {
width: 940px;
margin: 20px auto 30px auto;
@@ -68,6 +75,11 @@ div.footer a {
color: #888;
}
+p.caption {
+ font-family: ;
+ font-size: inherit;
+}
+
div.relations {
display: none;
@@ -84,11 +96,6 @@ div.sphinxsidebar a:hover {
border-bottom: 1px solid #999;
}
-div.sphinxsidebar {
- font-size: 14px;
- line-height: 1.5;
-}
-
div.sphinxsidebarwrapper {
padding: 18px 10px;
}
@@ -168,8 +175,8 @@ div.sphinxsidebar input {
div.sphinxsidebar hr {
border: none;
height: 1px;
- color: #999;
- background: #999;
+ color: #AAA;
+ background: #AAA;
text-align: left;
margin-left: 0;
@@ -350,8 +357,12 @@ table.field-list td {
padding: 0;
}
+table.field-list p {
+ margin-bottom: 0.8em;
+}
+
table.footnote td.label {
- width: 0px;
+ width: .1px;
padding: 0.3em 0 0.3em 0.5em;
}
@@ -374,6 +385,7 @@ blockquote {
}
ul, ol {
+ /* Matches the 30px from the narrow-screen "li > ul" selector below */
margin: 10px 0 10px 30px;
padding: 0;
}
@@ -411,6 +423,11 @@ a.reference {
border-bottom: 1px dotted #004B6B;
}
+/* Don't put an underline on images */
+a.image-reference, a.image-reference:hover {
+ border-bottom: none;
+}
+
a.reference:hover {
border-bottom: 1px solid #6D4100;
}
@@ -460,6 +477,11 @@ a:hover tt, a:hover code {
margin-left: 0;
}
+ li > ul {
+ /* Matches the 30px from the "ul, ol" selector above */
+ margin-left: 30px;
+ }
+
.document {
width: auto;
}
diff --git a/doc/html/_static/basic.css b/doc/html/_static/basic.css
index 9fa77d886d4f09c635c781bc3fadf10c8036c59e..65dfd7dfda92b36a93ea2b50d82d3917aec69c66 100644
--- a/doc/html/_static/basic.css
+++ b/doc/html/_static/basic.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
- * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -52,6 +52,8 @@ div.sphinxsidebar {
width: 230px;
margin-left: -100%;
font-size: 90%;
+ word-wrap: break-word;
+ overflow-wrap : break-word;
}
div.sphinxsidebar ul {
@@ -187,6 +189,13 @@ div.genindex-jumpbox {
/* -- general body styles --------------------------------------------------- */
+div.body p, div.body dd, div.body li, div.body blockquote {
+ -moz-hyphens: auto;
+ -ms-hyphens: auto;
+ -webkit-hyphens: auto;
+ hyphens: auto;
+}
+
a.headerlink {
visibility: hidden;
}
diff --git a/doc/html/_static/custom.css b/doc/html/_static/custom.css
new file mode 100644
index 0000000000000000000000000000000000000000..2a924f1d6a8bc930c5296bdb2d5c2d3e39b04a1c
--- /dev/null
+++ b/doc/html/_static/custom.css
@@ -0,0 +1 @@
+/* This file intentionally left blank. */
diff --git a/doc/html/_static/doctools.js b/doc/html/_static/doctools.js
index c7bfe760aa8b32cfa5676be000a43f465531ac0c..816349563588e87ca99c7cf2d6e54268e52e761d 100644
--- a/doc/html/_static/doctools.js
+++ b/doc/html/_static/doctools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for all documentation.
*
- * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@@ -124,6 +124,7 @@ var Documentation = {
this.fixFirefoxAnchorBug();
this.highlightSearchWords();
this.initIndexTable();
+
},
/**
@@ -252,6 +253,29 @@ var Documentation = {
});
var url = parts.join('/');
return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
+ },
+
+ initOnKeyListeners: function() {
+ $(document).keyup(function(event) {
+ var activeElementType = document.activeElement.tagName;
+ // don't navigate when in search box or textarea
+ if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') {
+ switch (event.keyCode) {
+ case 37: // left
+ var prevHref = $('link[rel="prev"]').prop('href');
+ if (prevHref) {
+ window.location.href = prevHref;
+ return false;
+ }
+ case 39: // right
+ var nextHref = $('link[rel="next"]').prop('href');
+ if (nextHref) {
+ window.location.href = nextHref;
+ return false;
+ }
+ }
+ }
+ });
}
};
@@ -260,4 +284,4 @@ _ = Documentation.gettext;
$(document).ready(function() {
Documentation.init();
-});
+});
\ No newline at end of file
diff --git a/doc/html/_static/pygments.css b/doc/html/_static/pygments.css
index 57eadc030ea86ea65a3747c27dfa3ef334f8f79a..8213e90bed399b1ddc4914808df328f5803e953f 100644
--- a/doc/html/_static/pygments.css
+++ b/doc/html/_static/pygments.css
@@ -4,8 +4,10 @@
.highlight .err { border: 1px solid #FF0000 } /* Error */
.highlight .k { color: #007020; font-weight: bold } /* Keyword */
.highlight .o { color: #666666 } /* Operator */
+.highlight .ch { color: #408090; font-style: italic } /* Comment.Hashbang */
.highlight .cm { color: #408090; font-style: italic } /* Comment.Multiline */
.highlight .cp { color: #007020 } /* Comment.Preproc */
+.highlight .cpf { color: #408090; font-style: italic } /* Comment.PreprocFile */
.highlight .c1 { color: #408090; font-style: italic } /* Comment.Single */
.highlight .cs { color: #408090; background-color: #fff0f0 } /* Comment.Special */
.highlight .gd { color: #A00000 } /* Generic.Deleted */
diff --git a/doc/html/_static/searchtools.js b/doc/html/_static/searchtools.js
index 0e794fd3e906970a10812199e11f9f159ab906b5..066857ce21b1b4b055f9a9308eb351237260fcca 100644
--- a/doc/html/_static/searchtools.js
+++ b/doc/html/_static/searchtools.js
@@ -2,14 +2,15 @@
* searchtools.js_t
* ~~~~~~~~~~~~~~~~
*
- * Sphinx JavaScript utilties for the full-text search.
+ * Sphinx JavaScript utilities for the full-text search.
*
- * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
+/* Non-minified version JS is _stemmer.js if file is provided */
/**
* Porter Stemmer
*/
@@ -373,8 +374,7 @@ var Search = {
}
// lookup as search terms in fulltext
- results = results.concat(this.performTermsSearch(searchterms, excluded, terms, Scorer.term))
- .concat(this.performTermsSearch(searchterms, excluded, titleterms, Scorer.title));
+ results = results.concat(this.performTermsSearch(searchterms, excluded, terms, titleterms));
// let the scorer override scores with a custom scoring function
if (Scorer.score) {
@@ -538,23 +538,47 @@ var Search = {
/**
* search for full-text terms in the index
*/
- performTermsSearch : function(searchterms, excluded, terms, score) {
+ performTermsSearch : function(searchterms, excluded, terms, titleterms) {
var filenames = this._index.filenames;
var titles = this._index.titles;
- var i, j, file, files;
+ var i, j, file;
var fileMap = {};
+ var scoreMap = {};
var results = [];
// perform the search on the required terms
for (i = 0; i < searchterms.length; i++) {
var word = searchterms[i];
+ var files = [];
+ var _o = [
+ {files: terms[word], score: Scorer.term},
+ {files: titleterms[word], score: Scorer.title}
+ ];
+
// no match but word was a required one
- if ((files = terms[word]) === undefined)
+ if ($u.every(_o, function(o){return o.files === undefined;})) {
break;
- if (files.length === undefined) {
- files = [files];
}
+ // found search word in contents
+ $u.each(_o, function(o) {
+ var _files = o.files;
+ if (_files === undefined)
+ return
+
+ if (_files.length === undefined)
+ _files = [_files];
+ files = files.concat(_files);
+
+ // set score for the word in each file to Scorer.term
+ for (j = 0; j < _files.length; j++) {
+ file = _files[j];
+ if (!(file in scoreMap))
+ scoreMap[file] = {}
+ scoreMap[file][word] = o.score;
+ }
+ });
+
// create the mapping
for (j = 0; j < files.length; j++) {
file = files[j];
@@ -576,7 +600,9 @@ var Search = {
// ensure that none of the excluded terms is in the search result
for (i = 0; i < excluded.length; i++) {
if (terms[excluded[i]] == file ||
- $u.contains(terms[excluded[i]] || [], file)) {
+ titleterms[excluded[i]] == file ||
+ $u.contains(terms[excluded[i]] || [], file) ||
+ $u.contains(titleterms[excluded[i]] || [], file)) {
valid = false;
break;
}
@@ -584,6 +610,9 @@ var Search = {
// if we have still a valid result we can add it to the result list
if (valid) {
+ // select one (max) score for the file.
+ // for better ranking, we should calculate ranking by using words statistics like basic tf-idf...
+ var score = $u.max($u.map(fileMap[file], function(w){return scoreMap[file][w]}));
results.push([filenames[file], titles[file], '', null, score]);
}
}
@@ -594,7 +623,7 @@ var Search = {
* helper function to return a node containing the
* search summary for a given text. keywords is a list
* of stemmed words, hlwords is the list of normal, unstemmed
- * words. the first one is used to find the occurance, the
+ * words. the first one is used to find the occurrence, the
* latter for highlighting it.
*/
makeSearchSummary : function(text, keywords, hlwords) {
diff --git a/doc/html/_static/websupport.js b/doc/html/_static/websupport.js
index 28d65db4aaf30db00ac3e591b88035ba434d4901..98e7f40b6327e673e382068cdfb3bf3674a06cca 100644
--- a/doc/html/_static/websupport.js
+++ b/doc/html/_static/websupport.js
@@ -2,9 +2,9 @@
* websupport.js
* ~~~~~~~~~~~~~
*
- * sphinx.websupport utilties for all documentation.
+ * sphinx.websupport utilities for all documentation.
*
- * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index 0a4e2803686157f938ff3a21635aadb3eadd0577..f83632f45740b0b6ed02b2d4176abe058c068625 100644
--- a/doc/html/actions/index.html
+++ b/doc/html/actions/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3 Actions — ProMod3 1.1.0 documentation</title>
+ <title>ProMod3 Actions — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Building ProMod3" href="../buildsystem.html" />
<link rel="prev" title="Getting Started" href="../gettingstarted.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -49,12 +51,12 @@ you can type <code class="docutils literal"><span class="pre">pm</span> <span cl
<span id="promod-build-model"></span><h2>Building models<a class="headerlink" href="#building-models" title="Permalink to this headline">¶</a></h2>
<p>You can run a full protein homology modelling pipeline from the command line
with</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> pm build-model <span class="o">[</span>-h<span class="o">]</span> <span class="o">(</span>-f <FILE> <span class="p">|</span> -c <FILE> <span class="p">|</span> -j <OBJECT><span class="p">|</span><FILE><span class="o">)</span>
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-model <span class="o">[</span>-h<span class="o">]</span> <span class="o">(</span>-f <FILE> <span class="p">|</span> -c <FILE> <span class="p">|</span> -j <OBJECT><span class="p">|</span><FILE><span class="o">)</span>
<span class="go"> (-p <FILE> | -e <FILE>) [-o <FILENAME>]</span>
</pre></div>
</div>
<p>Example usage:</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> pm build-model -f aln.fasta -p tpl.pdb
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm build-model -f aln.fasta -p tpl.pdb
</pre></div>
</div>
<p>This reads a target-template alignment from <code class="file docutils literal"><span class="pre">aln.fasta</span></code> and a matching
@@ -71,7 +73,7 @@ Notes on the input formats:</p>
<li><p class="first">Leading/trailing whitespaces of sequence names will always be deleted</p>
</li>
<li><p class="first">FASTA input example:</p>
-<div class="highlight-none"><div class="highlight"><pre>>target
+<div class="highlight-none"><div class="highlight"><pre><span></span>>target
HGFHVHEFGDNTNGCMSSGPHFNPYGKEHGAPVDENRHLG
>2jlp-1.A|55
RAIHVHQFGDLSQGCESTGPHYNPLAVPH------PQHPG
@@ -92,7 +94,7 @@ Those in turn are objects with keys
‘seqres’ (string for aligned sequence) and optionally for templates
‘offset’ (number of residues to skip in structure file attached to it).
Example:</p>
-<div class="highlight-json"><div class="highlight"><pre><span class="p">{</span><span class="nt">"alignmentlist"</span><span class="p">:</span> <span class="p">[</span> <span class="p">{</span>
+<div class="highlight-json"><div class="highlight"><pre><span></span><span class="p">{</span><span class="nt">"alignmentlist"</span><span class="p">:</span> <span class="p">[</span> <span class="p">{</span>
<span class="nt">"target"</span><span class="p">:</span> <span class="p">{</span>
<span class="nt">"name"</span><span class="p">:</span> <span class="s2">"mytrg"</span><span class="p">,</span>
<span class="nt">"seqres"</span><span class="p">:</span> <span class="s2">"HGFHVHEFGDNTNGCMSSGPHFNPYGKEHGAPVDENRHLG"</span>
@@ -108,7 +110,7 @@ Example:</p>
</li>
</ul>
<p>Structures can be provided in PDB (<code class="docutils literal"><span class="pre">-p</span></code>) or in any format readable by the
-<a class="reference external" href="http://www.openstructure.org/docs/dev/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.6.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
+<a class="reference external" href="https://www.openstructure.org/docs/dev/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.7.1)"><code class="xref py py-func docutils literal"><span class="pre">ost.io.LoadEntity()</span></code></a> method (<code class="docutils literal"><span class="pre">-e</span></code>). In the latter case, the format is
chosen by file ending. Recognized File Extensions: <code class="docutils literal"><span class="pre">.ent</span></code>, <code class="docutils literal"><span class="pre">.pdb</span></code>,
<code class="docutils literal"><span class="pre">.ent.gz</span></code>, <code class="docutils literal"><span class="pre">.pdb.gz</span></code>, <code class="docutils literal"><span class="pre">.cif</span></code>, <code class="docutils literal"><span class="pre">.cif.gz</span></code>. At least one structure must be
given and you cannot mix file formats. Multiple structures can be given and each
@@ -182,9 +184,6 @@ residue in the aligned sequence. Leading/trailing whitespaces of <CHAINID>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -192,11 +191,11 @@ residue in the aligned sequence. Leading/trailing whitespaces of <CHAINID>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/actions/index.txt"
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 5b85e1b17a59c30e08cf733e350e284590fc685f..7a72c1a6616b45888b696930be029d8e2cb467f2 100644
--- a/doc/html/actions/index_dev.html
+++ b/doc/html/actions/index_dev.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>test_actions - Testing Actions — ProMod3 1.1.0 documentation</title>
+ <title>test_actions - Testing Actions — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="ProMod3‘s Share Of CMake" href="../cmake/index.html" />
<link rel="prev" title="Contributing" href="../contributing.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -62,15 +64,15 @@ Python imports a module, its usually compiled into bytecode. This new file
would clutter up the source repository, it would always show up as untracked
file on <code class="docutils literal"><span class="pre">git</span> <span class="pre">status</span></code>. To prevent this, tell Python to stop producing
bytecode right at the beginning of your test-script:</p>
-<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
2
3
4
-5</pre></div></td><td class="code"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">sys</span>
+5</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">sys</span>
-<span class="c"># this is needed so there will be no test_actions.pyc created in the source</span>
-<span class="c"># directory</span>
-<span class="hll"><span class="n">sys</span><span class="o">.</span><span class="n">dont_write_bytecode</span> <span class="o">=</span> <span class="bp">True</span>
+<span class="c1"># this is needed so there will be no test_actions.pyc created in the source</span>
+<span class="c1"># directory</span>
+<span class="hll"><span class="n">sys</span><span class="o">.</span><span class="n">dont_write_bytecode</span> <span class="o">=</span> <span class="kc">True</span>
</span></pre></div>
</td></tr></table></div>
<p>Line 5 does the trick. This needs to be set by you in every action unit test
@@ -101,20 +103,20 @@ called <code class="docutils literal"><span class="pre">do-awesome</span></code>
action. So here we create a file <code class="file docutils literal"><span class="pre">test_action_do_awesome.py</span></code> (recognise
the underscore between <code class="docutils literal"><span class="pre">do</span></code> and <code class="docutils literal"><span class="pre">awesome</span></code> instead of a hyphen, that’s
<a class="reference external" href="https://www.python.org/dev/peps/pep-0008/">PEP 8</a>).</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> touch <SOURCE>/actions/tests/test_action_do_awesome.py
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> touch <SOURCE>/actions/tests/test_action_do_awesome.py
<span class="gp">$</span>
</pre></div>
</div>
<p>As a starter, we disable bytecode compilation in the script:</p>
-<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
+<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
2
3
4
-5</pre></div></td><td class="code"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">sys</span>
+5</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">sys</span>
-<span class="c"># this is needed so there will be no test_actions.pyc created in the source</span>
-<span class="c"># directory</span>
-<span class="n">sys</span><span class="o">.</span><span class="n">dont_write_bytecode</span> <span class="o">=</span> <span class="bp">True</span>
+<span class="c1"># this is needed so there will be no test_actions.pyc created in the source</span>
+<span class="c1"># directory</span>
+<span class="n">sys</span><span class="o">.</span><span class="n">dont_write_bytecode</span> <span class="o">=</span> <span class="kc">True</span>
</pre></div>
</td></tr></table></div>
</div>
@@ -130,7 +132,7 @@ add your new script:</p>
4
5
6
-7</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">set</span><span class="p">(</span><span class="s">ACTION_UNIT_TESTS</span>
+7</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="nb">set</span><span class="p">(</span><span class="s">ACTION_UNIT_TESTS</span>
<span class="s">test_action_help.py</span>
<span class="hll"> <span class="s">test_action_do_awesome.py</span>
</span> <span class="s">test_actions.py</span> <span class="c"># leave this as last item so it will be executed first!</span>
@@ -152,20 +154,20 @@ other action test script is run.</p>
tests. By spawning off from this you inherit a bunch of useful methods for your
testing. To make it work, the childclass needs to be set up properly. But
first, <code class="file docutils literal"><span class="pre">test_actions.py</span></code> has to be loaded as a module:</p>
-<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>6</pre></div></td><td class="code"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">test_actions</span>
+<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>6</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">test_actions</span>
</pre></div>
</td></tr></table></div>
<p>To showcase, the test cases, we explain how one would (and does) test the
<code class="docutils literal"><span class="pre">help</span></code> action of <code class="docutils literal"><span class="pre">pm</span></code>.
First, we create the childclass for the action.
Go for <code class="xref py py-class docutils literal"><span class="pre"><NAME>ActionTests</span></code> as a naming scheme:</p>
-<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 7
+<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 7
8
9
-10</pre></div></td><td class="code"><div class="highlight"><pre><span class="k">class</span> <span class="nc">HelpActionTests</span><span class="p">(</span><span class="n">test_actions</span><span class="o">.</span><span class="n">ActionTestCase</span><span class="p">):</span>
+10</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="k">class</span> <span class="nc">HelpActionTests</span><span class="p">(</span><span class="n">test_actions</span><span class="o">.</span><span class="n">ActionTestCase</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
<span class="n">test_actions</span><span class="o">.</span><span class="n">ActionTestCase</span><span class="o">.</span><span class="n">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">pm_action</span> <span class="o">=</span> <span class="s">'help'</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">pm_action</span> <span class="o">=</span> <span class="s1">'help'</span>
</pre></div>
</td></tr></table></div>
<p>Pay attention that in your own class, you must set <code class="xref py py-attr docutils literal"><span class="pre">pm_action</span></code> to make
@@ -178,8 +180,8 @@ is derived from the <a class="reference external" href="https://docs.python.org/
states will be placed in the userlevel documentation. This topic is already
covered in <a class="reference internal" href="#test_actions.ActionTestCase" title="test_actions.ActionTestCase"><code class="xref py py-class docutils literal"><span class="pre">test_actions.ActionTestCase</span></code></a> by <a class="reference internal" href="#test_actions.ActionTestCase.RunExitStatusTest" title="test_actions.ActionTestCase.RunExitStatusTest"><code class="xref py py-meth docutils literal"><span class="pre">RunExitStatusTest()</span></code></a>.
As an example, testing for <code class="docutils literal"><span class="pre">$?=0</span></code> could work like this:</p>
-<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
-12</pre></div></td><td class="code"><div class="highlight"><pre> <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
+12</pre></div></td><td class="code"><div class="highlight"><pre><span></span> <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">RunExitStatusTest</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">list</span><span class="p">())</span>
</pre></div>
</td></tr></table></div>
@@ -191,13 +193,13 @@ happens if a user throws dirty input data in.</p>
</div>
<div class="section" id="making-the-script-executable">
<h3>Making the Script Executable<a class="headerlink" href="#making-the-script-executable" title="Permalink to this headline">¶</a></h3>
-<p>In ProMod3, unit tests are run via <a class="reference external" href="http://www.OpenStructure.org">OST</a>‘s <a class="reference external" href="http://www.openstructure.org/docs/dev/base/testutils/#module-ost.testutils" title="(in OpenStructure v1.6.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.testutils</span></code></a> and Python‘s
+<p>In ProMod3, unit tests are run via <a class="reference external" href="https://www.OpenStructure.org">OST</a>‘s <a class="reference external" href="https://www.openstructure.org/docs/dev/base/testutils/#module-ost.testutils" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.testutils</span></code></a> and Python‘s
<a class="reference external" href="https://docs.python.org/2.7/library/unittest.html#unittest.TestCase" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">unittest.TestCase</span></code></a>. Those are called when the test module is executed
as a script:</p>
-<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
+<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
14
-15</pre></div></td><td class="code"><div class="highlight"><pre><span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">"__main__"</span><span class="p">:</span>
- <span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">testutils</span>
+15</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
+ <span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">testutils</span>
<span class="n">testutils</span><span class="o">.</span><span class="n">RunTests</span><span class="p">()</span>
</pre></div>
</td></tr></table></div>
@@ -208,7 +210,7 @@ as a script:</p>
<p>Unit tests are executed via <code class="docutils literal"><span class="pre">make</span> <span class="pre">check</span></code> and so are ProMod3 action tests.
But for every test script, we also provide a private <code class="docutils literal"><span class="pre">make</span></code> target, ending
with <code class="file docutils literal"><span class="pre">_run</span></code>. To solely run the tests for the awesome action, hit</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> make test_action_do_awesome.py_run
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make test_action_do_awesome.py_run
</pre></div>
</div>
</div>
@@ -225,20 +227,20 @@ parameter <code class="xref py py-attr docutils literal"><span class="pre">verbo
output onto the command line. The idea is to turn it on for development, but
once done, disable it to keep output of unit tests low.</p>
<p>To get the test for exit code <code class="docutils literal"><span class="pre">0</span></code> talking to you, just do</p>
-<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
-12</pre></div></td><td class="code"><div class="highlight"><pre> <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
- <span class="bp">self</span><span class="o">.</span><span class="n">RunExitStatusTest</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">list</span><span class="p">(),</span> <span class="n">verbose</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
+12</pre></div></td><td class="code"><div class="highlight"><pre><span></span> <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+ <span class="bp">self</span><span class="o">.</span><span class="n">RunExitStatusTest</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">list</span><span class="p">(),</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
</pre></div>
</td></tr></table></div>
<p>and</p>
-<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
-12</pre></div></td><td class="code"><div class="highlight"><pre> <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>11
+12</pre></div></td><td class="code"><div class="highlight"><pre><span></span> <span class="k">def</span> <span class="nf">testExit0</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">RunExitStatusTest</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">list</span><span class="p">())</span>
</pre></div>
</td></tr></table></div>
<p>keeps it silent (<code class="xref py py-attr docutils literal"><span class="pre">verbose</span></code> is set to <code class="docutils literal"><span class="pre">False</span></code> by default). If enabled,
output will be separated into <code class="file docutils literal"><span class="pre">stdout</span></code> and <code class="file docutils literal"><span class="pre">stderr</span></code>:</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> make test_action_do_awesome.py_run
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make test_action_do_awesome.py_run
<span class="go"><Lots of output from the build process></span>
<span class="go">running checks test_action_do_awesome.py</span>
<span class="go">stdout of '<BUILD>/stage/bin/pm do-awesome'</span>
@@ -401,9 +403,6 @@ file (also complains if a directory is found instead).</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -411,11 +410,11 @@ file (also complains if a directory is found instead).</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/actions/index_dev.txt"
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index a716f5434283bb2cfa80fb2322bbd42795c26a38..05f730f28a2e8349dffce5b4b7a0fcbfb68a61a0 100644
--- a/doc/html/buildsystem.html
+++ b/doc/html/buildsystem.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Building ProMod3 — ProMod3 1.1.0 documentation</title>
+ <title>Building ProMod3 — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Users" href="users.html" />
<link rel="next" title="modelling - Protein Modelling" href="modelling/index.html" />
<link rel="prev" title="ProMod3 Actions" href="actions/index.html" />
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -43,20 +45,20 @@
<span id="building-promod"></span><h1>Building ProMod3<a class="headerlink" href="#building-project" title="Permalink to this headline">¶</a></h1>
<div class="section" id="dependencies">
<h2>Dependencies<a class="headerlink" href="#dependencies" title="Permalink to this headline">¶</a></h2>
-<p>ProMod3 is build on top of <a class="reference external" href="http://www.OpenStructure.org">OpenStructure</a> (OST), requiring at least version
+<p>ProMod3 is build on top of <a class="reference external" href="https://www.OpenStructure.org">OpenStructure</a> (OST), requiring at least version
1.7. OST must be configured and compiled with <code class="docutils literal"><span class="pre">ENABLE_MM=1</span></code> to use <a class="reference external" href="http://openmm.org">OpenMM</a>.
To create the build system, <a class="reference external" href="https://cmake.org/">CMake</a> is required in version
2.8.7 or higher. <a class="reference external" href="https://www.python.org/">Python</a> works well from version 2.7. For OST and the
-C++ bit of ProMod3, <a class="reference external" href="http://www.boost.org/">Boost</a> is required in version 1.53.0 (the same as
+C++ bit of ProMod3, <a class="reference external" href="https://www.boost.org/">Boost</a> is required in version 1.53.0 (the same as
used for OST). Also <a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> is needed. To build
documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.2b1 is required.</p>
<p>The currently preferred versions are:</p>
<ul class="simple">
-<li><a class="reference external" href="http://www.OpenStructure.org">OST</a> 1.7</li>
+<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 1.7</li>
<li><a class="reference external" href="http://openmm.org">OpenMM</a> 7.1.1</li>
<li><a class="reference external" href="https://cmake.org/">CMake</a> 2.8.12</li>
<li><a class="reference external" href="https://www.python.org/">Python</a> 2.7.5</li>
-<li><a class="reference external" href="http://www.boost.org/">Boost</a> 1.53.0</li>
+<li><a class="reference external" href="https://www.boost.org/">Boost</a> 1.53.0</li>
<li><a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> 3.3.0</li>
<li><a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.3.1</li>
</ul>
@@ -68,9 +70,9 @@ and certain directories needed for building ProMod3. Basically it is called
right from a shell with the directory containing the top-level
<code class="file docutils literal"><span class="pre">CMakeLists.txt</span></code> as an argument. The preferred approach is to generate a
build folder and configure and compile in there:</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">#</span> execute this in the ProMod3 root folder
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">#</span> execute this in the ProMod3 root folder
<span class="gp">$</span> mkdir build
-<span class="gp">$</span> <span class="nb">cd </span>build
+<span class="gp">$</span> <span class="nb">cd</span> build
<span class="gp">$</span> cmake .. -DOST_ROOT<span class="o">=</span><PATH TO OST>
</pre></div>
</div>
@@ -115,7 +117,7 @@ really got rebuild and similar things required.</p>
<div class="section" id="running-make">
<h2>Running Make<a class="headerlink" href="#running-make" title="Permalink to this headline">¶</a></h2>
<p>After configuring, you want to build ProMod3 by</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> make
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make
</pre></div>
</div>
<p>to populate the <code class="file docutils literal"><span class="pre">stage</span></code> directory with a ready-to-go version of the
@@ -139,7 +141,7 @@ builder</li>
<h2>Installing ProMod3<a class="headerlink" href="#installing-project" title="Permalink to this headline">¶</a></h2>
<p>If you wish to install ProMod3 (note that you can also safely keep it all in
the <code class="file docutils literal"><span class="pre">stage</span></code> directory), you can use</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> make install
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> make install
</pre></div>
</div>
<p>By default, this will copy the <code class="file docutils literal"><span class="pre">stage</span></code> directory to <code class="file docutils literal"><span class="pre">/usr/local</span></code>. To
@@ -195,9 +197,6 @@ safely delete the whole source folder.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -205,11 +204,11 @@ safely delete the whole source folder.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/buildsystem.txt"
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 0893031cb90a205da543e19cea1f2bea928af80f..776b517f5d8af27418df83b927924c2b327d2a65 100644
--- a/doc/html/changelog.html
+++ b/doc/html/changelog.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Changelog — ProMod3 1.1.0 documentation</title>
+ <title>Changelog — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,14 +23,16 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
<link rel="prev" title="Using Binary Files In ProMod3" href="portableIO.html" />
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -39,8 +41,37 @@
<div class="section" id="changelog">
<h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="release-1-1">
-<h2>Release 1.1<a class="headerlink" href="#release-1-1" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="release-1-2-0">
+<h2>Release 1.2.0<a class="headerlink" href="#release-1-2-0" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li>Graph optimizer has been separated from the sidechain module and can now be
+used for arbitrary optimization problems. Available optimization algorithms
+are TreePack, AStar and MonteCarlo.</li>
+<li>Make it possible to distinguish between the scores of a loop towards a constant
+environment (external scores) and the scores within the loop itself
+(internal scores).</li>
+<li>Most scores based on pairwise interactions are now pairwise decomposable.</li>
+<li>Disconnected loops at several locations can be scored at once.</li>
+<li>Avoid the usage of the DSSP executable and use the OpenStructure internal
+secondary structure assignment instead.</li>
+<li>Allow to decide whether the CB atom belongs to the actual rotamer or to the
+constant frame in sidechain optimization. This can be useful in design
+questions, where the identity of a rotamer is not given and you want to
+allow glycine or alanine.</li>
+<li>The naming of the entries in the StructureDB is not strictly limited to
+4 letter codes anymore, arbitrary strings can be used instead.</li>
+<li>Adding coordinates to the StructureDB does not require external tools anymore
+(msms, dssp etc.), internal implementations are used instead.</li>
+<li>The data that is stored in a StructureDB can be controlled at initialization,
+everything except the sequence and the actual coordinates is optional.</li>
+<li>Entries in the StructureDB can be removed again.</li>
+<li>Allow to search positions of arbitrary copies in DynamicSpatialOrganizer
+by providing RT operators.</li>
+<li>Several minor bug fixes, improvements, and speed-ups</li>
+</ul>
+</div>
+<div class="section" id="release-1-1-0">
+<h2>Release 1.1.0<a class="headerlink" href="#release-1-1-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li>Updated dependencies: need Eigen 3.3.0 and OST 1.7</li>
<li>Changes in modelling pipeline: remove clashing loop candidates early, new
@@ -80,7 +111,8 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Changelog</a><ul>
-<li><a class="reference internal" href="#release-1-1">Release 1.1</a></li>
+<li><a class="reference internal" href="#release-1-2-0">Release 1.2.0</a></li>
+<li><a class="reference internal" href="#release-1-1-0">Release 1.1.0</a></li>
<li><a class="reference internal" href="#release-1-0">Release 1.0</a></li>
</ul>
</li>
@@ -108,9 +140,6 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -118,11 +147,11 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/changelog.txt"
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index 4f3556eef9038ea882168fed65877fa5ab20eacc..f80cc16828502e7b936f090bbb38cd803d3b88ee 100644
--- a/doc/html/cmake/index.html
+++ b/doc/html/cmake/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3‘s Share Of CMake — ProMod3 1.1.0 documentation</title>
+ <title>ProMod3‘s Share Of CMake — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Developers" href="../developers.html" />
<link rel="next" title="Using Binary Files In ProMod3" href="../portableIO.html" />
<link rel="prev" title="test_actions - Testing Actions" href="../actions/index_dev.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -73,7 +75,7 @@ various <code class="file docutils literal"><span class="pre">CMakeLists.txt</sp
<dl class="command">
<dt id="command:module">
<code class="descname">module</code><a class="headerlink" href="#command:module" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">module</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">module</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
<span class="s">SOURCES</span> <span class="s">source1</span> <span class="s">source2</span>
<span class="s">HEADERS</span> <span class="s">header1</span> <span class="s">header2</span> <span class="s">[IN_DIR</span> <span class="s">dir]</span>
<span class="s">[header3</span> <span class="s">header4</span> <span class="s">[IN_DIR</span> <span class="s">dir]]</span>
@@ -114,7 +116,7 @@ libraries here, such as <code class="docutils literal"><span class="pre">${OST_L
<dl class="command">
<dt id="command:pymod">
<code class="descname">pymod</code><a class="headerlink" href="#command:pymod" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">pymod</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">pymod</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
<span class="s">CPP</span> <span class="s">source1</span> <span class="s">source2</span>
<span class="s">PY</span> <span class="s">source</span> <span class="s">source2</span> <span class="s">[IN_DIR</span> <span class="s">dir]</span>
<span class="s">[source3</span> <span class="s">source4</span> <span class="s">[IN_DIR</span> <span class="s">dir]]</span>
@@ -162,7 +164,7 @@ headers in the <code class="file docutils literal"><span class="pre">config</spa
<dl class="command">
<dt id="command:convert_module_data">
<code class="descname">convert_module_data</code><a class="headerlink" href="#command:convert_module_data" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">convert_module_data</span><span class="p">(</span><span class="s">MODULE</span> <span class="s">name</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">convert_module_data</span><span class="p">(</span><span class="s">MODULE</span> <span class="s">name</span>
<span class="s">FILE</span> <span class="s">file</span>
<span class="s">SCRIPT</span> <span class="s">script</span>
<span class="s">[ARGS</span> <span class="s">args]</span><span class="p">)</span>
@@ -184,7 +186,7 @@ If given, <code class="docutils literal"><span class="pre">args</span></code> ca
<dl class="command">
<dt id="command:promod3_unittest">
<code class="descname">promod3_unittest</code><a class="headerlink" href="#command:promod3_unittest" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">promod3_unittest</span><span class="p">(</span><span class="s">MODULE</span> <span class="s">name</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">promod3_unittest</span><span class="p">(</span><span class="s">MODULE</span> <span class="s">name</span>
<span class="s">SOURCES</span> <span class="s">source1</span> <span class="s">[source2</span> <span class="s">...]</span>
<span class="s">[LINK</span> <span class="s">library1/</span> <span class="s">linker</span> <span class="s">flag1</span> <span class="s">[library2/</span> <span class="s">linker</span> <span class="s">flag2</span> <span class="s">...]]</span>
<span class="s">[DATA</span> <span class="s">data1</span> <span class="s">[data2</span> <span class="s">...]]</span>
@@ -240,7 +242,7 @@ By default all unit tests are registered to be executed with the
<dl class="command">
<dt id="command:add_doc_source">
<code class="descname">add_doc_source</code><a class="headerlink" href="#command:add_doc_source" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">add_doc_source</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">add_doc_source</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
<span class="s">RST</span> <span class="s">rst1</span> <span class="s">[rst2...]</span><span class="p">)</span>
</pre></div>
</div>
@@ -265,7 +267,7 @@ name or a CMake list.</dd>
<dl class="command">
<dt id="command:add_doc_dependency">
<code class="descname">add_doc_dependency</code><a class="headerlink" href="#command:add_doc_dependency" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">add_doc_dependency</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">add_doc_dependency</span><span class="p">(</span><span class="s">NAME</span> <span class="s">name</span>
<span class="s">DEP</span> <span class="s">dependency1</span> <span class="s">[dependency2...]</span><span class="p">)</span>
</pre></div>
</div>
@@ -292,7 +294,7 @@ absolute path.</dd>
<dl class="command">
<dt id="command:pm_action">
<code class="descname">pm_action</code><a class="headerlink" href="#command:pm_action" title="Permalink to this definition">¶</a></dt>
-<dd><div class="highlight-cmake"><div class="highlight"><pre><span class="nb">pm_action</span><span class="p">(</span><span class="s">ACTION</span> <span class="s">action-script</span>
+<dd><div class="highlight-cmake"><div class="highlight"><pre><span></span><span class="nb">pm_action</span><span class="p">(</span><span class="s">ACTION</span> <span class="s">action-script</span>
<span class="s">TARGET</span> <span class="s">target</span><span class="p">)</span>
</pre></div>
</div>
@@ -363,9 +365,6 @@ target has to be created <strong>before</strong> any action may be attached to i
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -373,11 +372,11 @@ target has to be created <strong>before</strong> any action may be attached to i
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/cmake/index.txt"
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index a603efdf074a16bb0b6c713c9757612dc40d17f5..069ec304aa26f141410c4fe3bfd06b0b7624cbce 100644
--- a/doc/html/contributing.html
+++ b/doc/html/contributing.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Contributing — ProMod3 1.1.0 documentation</title>
+ <title>Contributing — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="test_actions - Testing Actions" href="actions/index_dev.html" />
<link rel="prev" title="ProMod3 Setup" href="dev_setup.html" />
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -53,27 +55,27 @@ the repository into a directory and just changed into it.</p>
work fine with all the other new fellows waiting for release right from the
beginning. Therefore you need to switch branches as a first step. Git will
tell you for which branch you went, a story of failure otherwise.</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git checkout develop
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout develop
<span class="go">Switched to branch 'develop'</span>
</pre></div>
</div>
<p>Sitting on top of the right code basis, you should just spawn your own branch
from it. As an example, your feature will go by the name of ‘sidechain’.</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git checkout -b sidechain
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout -b sidechain
<span class="go">Switched to a new branch 'sidechain'</span>
</pre></div>
</div>
<p>This time, Git should tell you about going for <strong>a new</strong> branch.</p>
<p>Before starting to create anything for real, now is the perfect moment to
install our very own Git hook to check some coding rules on commit.</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> cp extras/pre_commit/pre-commit .git/hooks/
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> cp extras/pre_commit/pre-commit .git/hooks/
</pre></div>
</div>
<p>With that in place, changes which break our coding standards will abort any
commit.</p>
<p>Now create the directory structure where your project will live. Here is the
list of directories which are likely to be used in every project.</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> mkdir -p sidechain/doc
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> mkdir -p sidechain/doc
<span class="gp">$</span> mkdir -p sidechain/pymod
<span class="gp">$</span> mkdir -p sidechain/tests
</pre></div>
@@ -81,7 +83,7 @@ list of directories which are likely to be used in every project.</p>
<p>If you run <code class="docutils literal"><span class="pre">git</span> <span class="pre">status</span></code> at this point, you will see basically nothing. That
is, Git does not admire empty directories. Before you bring your module under
version control, create a couple of files which are always needed.</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> touch sidechain/pymod/__init__.py
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> touch sidechain/pymod/__init__.py
<span class="gp">$</span> <span class="nb">echo</span> <span class="s2">":mod:\`~promod3.sidechain\` - ProMod3 side chain optimiser"</span> >> sidechain/doc/index.rst
<span class="gp">$</span> <span class="nb">echo</span> <span class="s2">"================================================================================"</span> >> sidechain/doc/index.rst
</pre></div>
@@ -93,7 +95,7 @@ your documentation.</p>
<p>For integration with <strong class="command">make</strong>, the build system needs to now about the
new module and its members. This goes for setting up new CMake files and
extending some around the directory root.</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> touch sidechain/CMakeLists.txt
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> touch sidechain/CMakeLists.txt
<span class="gp">$</span> touch sidechain/pymod/CMakeLists.txt
<span class="gp">$</span> touch sidechain/doc/CMakeLists.txt
</pre></div>
@@ -101,7 +103,7 @@ extending some around the directory root.</p>
<p>Each of those files still needs a bit of content. The simplest one comes from
the module’s root, <code class="file docutils literal"><span class="pre">sidechain/CMakeLists.txt</span></code>:</p>
<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
-2</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">pymod</span><span class="p">)</span>
+2</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">pymod</span><span class="p">)</span>
<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">doc</span><span class="p">)</span>
</pre></div>
</td></tr></table></div>
@@ -113,7 +115,7 @@ configurations. The next level in <code class="file docutils literal"><span clas
2
3
4
-5</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAIN_RST</span>
+5</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAIN_RST</span>
<span class="s">index.rst</span>
<span class="p">)</span>
@@ -138,7 +140,7 @@ a couple of examples around in this repository. Here is the most basic
2
3
4
-5</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAIN_PYMOD</span>
+5</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAIN_PYMOD</span>
<span class="s">__init__.py</span>
<span class="p">)</span>
@@ -166,7 +168,7 @@ top level <code class="file docutils literal"><span class="pre">CMakeLists.txt</
12
13
14
-15</pre></div></td><td class="code"><div class="highlight"><pre><span class="c">## <lots of cmake commands...></span>
+15</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="c">## <lots of cmake commands...></span>
<span class="c">## sub dirs to be recognised by CMake</span>
<span class="c">## e.g. add_subdirectory(src), subdirs have their own CMakeLists.txt</span>
@@ -198,8 +200,8 @@ still can stay in your repository while being out of the source tree by using
sub-directories. ProMod3 comes with a dedicated prefix ‘build*’ in
<code class="file docutils literal"><span class="pre">.gitignore</span></code>. Have a directory <code class="file docutils literal"><span class="pre">build</span></code> and <code class="file docutils literal"><span class="pre">build-dbg</span></code> and it
will not show up in <code class="docutils literal"><span class="pre">git</span> <span class="pre">status</span></code>.</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> mkdir build
-<span class="gp">$</span> <span class="nb">cd </span>build
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> mkdir build
+<span class="gp">$</span> <span class="nb">cd</span> build
</pre></div>
</div>
<p>To actually create all the makefiles and generated files, you may use one of
@@ -208,7 +210,7 @@ those scripts only need to be pointed to an OST staging tree. Even if you
are on a system not covered by available scripts, their code may help you at
the CMake command. Once you managed to conquer a new system, feel free to add
a new configuration script. The following example assumes Fedora 19.</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> ../conf-scripts/fedora-19-conf ../../ost.git/stage
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> ../conf-scripts/fedora-19-conf ../../ost.git/stage
</pre></div>
</div>
<p>From this point, <strong class="command">make</strong> should work and you could start adding your
@@ -219,13 +221,13 @@ beginning. At some point, new code needs testing anyway to see if it does what
it should, so just do this by writing unit tests. Test sources are stored in
files with a prefix <code class="file docutils literal"><span class="pre">test_</span></code> and usually come per submodule instead of
sporting a single monolithic <code class="file docutils literal"><span class="pre">test_sidechain_reconstruction.py</span></code>.</p>
-<p>Python code is evaluated using its own <a class="reference external" href="https://docs.python.org/2.7/library/unittest.html">unit testing framework</a> with a little help from <a class="reference external" href="http://www.OpenStructure.org">OST</a> (C++ uses the
-Boost <a class="reference external" href="http://www.boost.org/doc/libs/1_47_0/libs/test/doc/html/index.html">Test Library</a>). The
+<p>Python code is evaluated using its own <a class="reference external" href="https://docs.python.org/2.7/library/unittest.html">unit testing framework</a> with a little help from <a class="reference external" href="https://www.OpenStructure.org">OST</a> (C++ uses the
+Boost <a class="reference external" href="https://www.boost.org/doc/libs/1_53_0/libs/test/doc/html/index.html">Test Library</a>). The
basic scheme is to import your module, subclass <a class="reference external" href="https://docs.python.org/2.7/library/unittest.html#unittest.TestCase" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">unittest.TestCase</span></code></a> and
make the whole file runnable as script using the most common <a class="reference external" href="https://docs.python.org/2.7/library/__main__.html"><code class="xref py py-attr docutils literal"><span class="pre">__name__</span></code></a>
attribute. As an example we test the
<a class="reference internal" href="modelling/sidechain_reconstruction.html#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal"><span class="pre">promod3.modelling.ReconstructSidechains()</span></code></a> function:</p>
-<div class="highlight-python"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
+<div class="highlight-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
2
3
4
@@ -243,24 +245,24 @@ attribute. As an example we test the
16
17
18
-19</pre></div></td><td class="code"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">unittest</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span><span class="n">mol</span>
+19</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">unittest</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span><span class="n">mol</span>
<span class="kn">import</span> <span class="nn">os</span>
<span class="k">class</span> <span class="nc">ReconstructTests</span><span class="p">(</span><span class="n">unittest</span><span class="o">.</span><span class="n">TestCase</span><span class="p">):</span>
<span class="k">def</span> <span class="nf">testReconstruct</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
- <span class="n">in_file</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s">'data'</span><span class="p">,</span> <span class="s">'1eye.pdb'</span><span class="p">)</span>
- <span class="n">ref_file</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s">'data'</span><span class="p">,</span> <span class="s">'1eye_rec.pdb'</span><span class="p">)</span>
- <span class="c"># get and reconstruct 1eye</span>
+ <span class="n">in_file</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">'data'</span><span class="p">,</span> <span class="s1">'1eye.pdb'</span><span class="p">)</span>
+ <span class="n">ref_file</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">'data'</span><span class="p">,</span> <span class="s1">'1eye_rec.pdb'</span><span class="p">)</span>
+ <span class="c1"># get and reconstruct 1eye</span>
<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="n">in_file</span><span class="p">)</span>
- <span class="n">modelling</span><span class="o">.</span><span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
- <span class="c"># compare with reference solution</span>
+ <span class="n">modelling</span><span class="o">.</span><span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+ <span class="c1"># compare with reference solution</span>
<span class="n">prot_rec</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="n">ref_file</span><span class="p">)</span>
<span class="bp">self</span><span class="o">.</span><span class="n">assertEqual</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">GetAtomCount</span><span class="p">(),</span> <span class="n">prot_rec</span><span class="o">.</span><span class="n">GetAtomCount</span><span class="p">())</span>
-<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">"__main__"</span><span class="p">:</span>
- <span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">testutils</span>
+<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
+ <span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">testutils</span>
<span class="n">testutils</span><span class="o">.</span><span class="n">RunTests</span><span class="p">()</span>
</pre></div>
</td></tr></table></div>
@@ -270,7 +272,7 @@ First, tell CMake to search <code class="file docutils literal"><span class="pre
by extending the list of sub-directories in <code class="file docutils literal"><span class="pre">sidechain/CMakeLists.txt</span></code>:</p>
<div class="highlight-cmake"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>1
2
-3</pre></div></td><td class="code"><div class="highlight"><pre> <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">pymod</span><span class="p">)</span>
+3</pre></div></td><td class="code"><div class="highlight"><pre><span></span> <span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">pymod</span><span class="p">)</span>
<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">doc</span><span class="p">)</span>
<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">tests</span><span class="p">)</span>
</pre></div>
@@ -289,7 +291,7 @@ you.</p>
9
10
11
-12</pre></div></td><td class="code"><div class="highlight"><pre><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAIN_UNIT_TESTS</span>
+12</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="nb">set</span><span class="p">(</span><span class="s">SIDECHAIN_UNIT_TESTS</span>
<span class="s">test_reconstruct_sidechains.py</span>
<span class="p">)</span>
@@ -314,10 +316,10 @@ you.</p>
launcher found in your staging directory at <code class="file docutils literal"><span class="pre">stage/bin/pm</span></code>. This little
guy helps keeping the shell environment in the right mood to carry out your
job. So usually you will start an action by</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> stage/bin/pm <span class="nb">help</span>
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> stage/bin/pm <span class="nb">help</span>
</pre></div>
</div>
-<p>To start your own action, follow <a class="reference internal" href="#how-to-start-your-own-module"><span>How To Start Your Own Module</span></a> until
+<p>To start your own action, follow <a class="reference internal" href="#how-to-start-your-own-module"><span class="std std-ref">How To Start Your Own Module</span></a> until
creating a directory structure for a new module. Also <strong>do</strong> go for a dedicated
branch for action-development. There you can produce intermediate commits while
other branches stay clean in case you have to do some work there which needs to
@@ -325,7 +327,7 @@ get public.</p>
<p>After preparing your repository its time to create a file for the action. That
is a bit different than for modules. Assuming we are sitting in the
repository’s root:</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> touch action/pm-awesome-action
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> touch action/pm-awesome-action
<span class="gp">$</span> chmod +x action/pm-awesome-action
</pre></div>
</div>
@@ -342,7 +344,7 @@ executable, which does not propagate if you do it <strong>after</strong> the fir
4
5
6
-7</pre></div></td><td class="code"><div class="highlight"><pre> <span class="nb">add_custom_target</span><span class="p">(</span><span class="s">actions</span> <span class="s">ALL</span><span class="p">)</span>
+7</pre></div></td><td class="code"><div class="highlight"><pre><span></span> <span class="nb">add_custom_target</span><span class="p">(</span><span class="s">actions</span> <span class="s">ALL</span><span class="p">)</span>
<span class="nb">add_subdirectory</span><span class="p">(</span><span class="s">tests</span><span class="p">)</span>
<span class="nb">pm_action_init</span><span class="p">()</span>
@@ -376,11 +378,11 @@ that’s enough to get everything just right.</p>
Your action will have own function definitions, variables and all the bells
and whistles. Hiding behind <a class="reference external" href="https://docs.python.org/2.7/library/__main__.html"><code class="xref py py-attr docutils literal"><span class="pre">__main__</span></code></a> keeps everything separated and makes
things easier when it gets to debugging. So just after</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">alot</span>
+<div class="highlight-python"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">alot</span>
<span class="k">def</span> <span class="nf">functions_specific_to_your_action</span><span class="p">(</span><span class="o">...</span><span class="p">):</span>
-<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">"__main__"</span><span class="p">:</span>
+<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
<span class="o"><</span><span class="n">put</span> <span class="n">together</span> <span class="n">what</span> <span class="n">your</span> <span class="n">action</span> <span class="n">should</span> <span class="n">do</span> <span class="n">here</span><span class="o">></span>
</pre></div>
</div>
@@ -463,7 +465,7 @@ and <code class="docutils literal"><span class="pre">ost</span></code> as in the
folder and adapt it for your purposes. First, you will have to fix the paths
to ProMod3 and OST in the <code class="file docutils literal"><span class="pre">Makefile</span></code> by changing the following
lines:</p>
-<div class="highlight-make"><div class="highlight"><pre><span class="c"># path to OST and ProMod3 stage</span>
+<div class="highlight-make"><div class="highlight"><pre><span></span><span class="c"># path to OST and ProMod3 stage</span>
<span class="nv">OST_ROOT</span> <span class="o">=</span> <DEFINEME>/ost/build/stage
<span class="nv">PROMOD3_ROOT</span> <span class="o">=</span> <DEFINEME>/ProMod3/build/stage
</pre></div>
@@ -518,7 +520,7 @@ crucial. For documentation which does not relate to a particular module, the
repository comes with a top-level <code class="file docutils literal"><span class="pre">doc</span></code> directory.</p>
<p>While you should not spend to much time thinking about how to format
documentation, here is a helpful list of standard formatters:
-<a class="reference external" href="http://sphinx-doc.org/markup/inline.html">http://sphinx-doc.org/markup/inline.html</a></p>
+<a class="reference external" href="http://sphinx-doc.org/en/stable/markup/inline.html">http://sphinx-doc.org/en/stable/markup/inline.html</a></p>
<p>If you write new functionality for ProMod3, or fix bugs, feel free to extend
the <code class="file docutils literal"><span class="pre">CHANGELOG</span></code> file. It will be automatically pulled into the
documentation.</p>
@@ -532,13 +534,13 @@ they can be included in the documentation using the
<a class="reference external" href="http://www.sphinx-doc.org/en/stable/markup/code.html#includes">literalinclude</a>
directive. For instance, if you add a new example code <code class="file docutils literal"><span class="pre">loop_main.py</span></code>,
you would add it in your module documentation as follows:</p>
-<div class="highlight-rest"><div class="highlight"><pre><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> ../../../tests/doc/scripts/loop_main.py
+<div class="highlight-rest"><div class="highlight"><pre><span></span><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> ../../../tests/doc/scripts/loop_main.py
</pre></div>
</div>
<p>If your example does not relate to a specific module and the documentation is
in the top-level <code class="file docutils literal"><span class="pre">doc</span></code> directory, you need to drop one of the <code class="docutils literal"><span class="pre">..</span></code> as
follows:</p>
-<div class="highlight-rest"><div class="highlight"><pre><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> ../../tests/doc/scripts/hello_world.py
+<div class="highlight-rest"><div class="highlight"><pre><span></span><span class="p">..</span> <span class="ow">literalinclude</span><span class="p">::</span> ../../tests/doc/scripts/hello_world.py
</pre></div>
</div>
<p>To ensure that the code examples keep on working, a unit test has to be defined
@@ -556,7 +558,7 @@ test.</li>
there is no need to compile ProMod3 to read it. Our policy is to keep that
folder in-sync with the latest documentation at least on the <code class="docutils literal"><span class="pre">master</span></code> branch
(i.e. for every release). You can use the following commands to do the update:</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> <span class="nb">cd</span> <PROMOD3_PATH>/build
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> <span class="nb">cd</span> <PROMOD3_PATH>/build
<span class="gp">$</span> make html
<span class="gp">$</span> rsync -iv -az --exclude<span class="o">=</span><span class="s2">".*"</span> --delete <span class="se">\</span>
<span class="go"> "stage/share/promod3/html/" "../doc/html"</span>
@@ -639,9 +641,6 @@ contributions to web pages using ProMod3.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -649,11 +648,11 @@ contributions to web pages using ProMod3.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/contributing.txt"
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index d5c2a5d69c5b5b2f98ed0b572ee1ea3d57f40a2a..3cdcb509f583cc24facb60b9bcd5c19e7db01f34 100644
--- a/doc/html/core/geometry.html
+++ b/doc/html/core/geometry.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Geometry functions — ProMod3 1.1.0 documentation</title>
+ <title>Geometry functions — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="Runtime profiling" href="runtime_profiling.html" />
<link rel="prev" title="helper - Shared Functionality For the Everything" href="helper.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -53,14 +55,14 @@
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rule</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Gromacs rule</li>
<li><strong>number</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Desired number of positions (max. 3)</li>
-<li><strong>anchors</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</li>
+<li><strong>anchors</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor positions (max. 4)</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Constructed <em>number</em> positions.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -76,16 +78,16 @@
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>c_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Positions of O and OXT atoms.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> of <a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -102,9 +104,9 @@ dihedral (A-B-C-D).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>A</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom A</li>
-<li><strong>B</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom B</li>
-<li><strong>C</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom C</li>
+<li><strong>A</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom A</li>
+<li><strong>B</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom B</li>
+<li><strong>C</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of atom C</li>
<li><strong>bond_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Bond length (C-D)</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle (B-C-D)</li>
<li><strong>dihedral</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Dihedral (A-B-C-D)</li>
@@ -114,7 +116,7 @@ dihedral (A-B-C-D).</p>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of atom D</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -131,16 +133,16 @@ C-alpha and c atoms.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of nitrogen atom</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C-alpha atom</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Position of C atom</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Position of C-beta atom</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -157,8 +159,8 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>axis</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
-<li><strong>anchor</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</li>
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
+<li><strong>anchor</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Anchor for rotation</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
</ul>
</td>
@@ -166,7 +168,7 @@ around a line defined by <cite>axis</cite> and <cite>anchor</cite>.</p>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Transformation matrix</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat4</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Mat4</span></code></a></p>
</td>
</tr>
</tbody>
@@ -183,7 +185,7 @@ going through the origin.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>axis</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
+<li><strong>axis</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Axis of rotation</li>
<li><strong>angle</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Angle (in radians in range [-pi,pi]) of rotation</li>
</ul>
</td>
@@ -191,7 +193,7 @@ going through the origin.</p>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Rotation matrix</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat3</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Mat3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -208,7 +210,7 @@ going through the origin.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue handle from which to extract N, CA and C coordinates.</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>res</em> does not contain N, CA and C
atoms.</td>
@@ -227,7 +229,7 @@ atoms.</td>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
</tr>
</tbody>
</table>
@@ -337,9 +339,6 @@ angles and one distance and is used in the fragment database for fast lookups.</
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -347,11 +346,11 @@ angles and one distance and is used in the fragment database for fast lookups.</
<div class="clearer"></div>
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+ ©2018, ProMod3 authors.
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+
+ <div class="section" id="graph-minimizer">
+<h1>Graph Minimizer<a class="headerlink" href="#graph-minimizer" title="Permalink to this headline">¶</a></h1>
+<p>The graph minimizer solves an energy minimization problem where we have n
+nodes <span class="math">N_i</span>, with each node having several possible solutions.
+Every solution has a self energy <span class="math">E_{self}</span> and pairwise energies in between nodes
+are possible. The goal is to select exactly one solution per node to obtain
+a set <span class="math">X=[x_1, x_2, ..., x_n]</span> that minimizes:</p>
+<div class="math">
+<p><span class="math">F(X)=\displaystyle\sum_iE_{self}(N_i[x_i]) +\displaystyle \sum_i \displaystyle \sum_{j>i}E_{pair}(N_i[x_i], N_j[x_j])</span></p>
+</div><dl class="class">
+<dt id="promod3.core.GraphMinimizer">
+<em class="property">class </em><code class="descclassname">promod3.core.</code><code class="descname">GraphMinimizer</code><a class="headerlink" href="#promod3.core.GraphMinimizer" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="method">
+<dt id="promod3.core.GraphMinimizer.AddNode">
+<code class="descname">AddNode</code><span class="sig-paren">(</span><em>self_energies</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AddNode" title="Permalink to this definition">¶</a></dt>
+<dd><p>Adds a node to the graph.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>self_energies</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Directly controls the number of possible solutions in that
+node and assigns the corresponding self energies</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The idx of the added node</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.core.GraphMinimizer.AddEdge">
+<code class="descname">AddEdge</code><span class="sig-paren">(</span><em>node_idx_one</em>, <em>node_idx_two</em>, <em>pairwise_energies</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AddEdge" title="Permalink to this definition">¶</a></dt>
+<dd><p>Adds an edge between the specified nodes.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>node_idx_one</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of the first node</li>
+<li><strong>node_idx_two</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of the second node</li>
+<li><strong>pairwise_energies</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The pairwise energies that contribute to the
+overall energy function. There must be a list for
+every possible solution in node one. All of those
+lists must have exactly the length of possible
+solutions in node two.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The idx of the added edge</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>node_idx_one</em> or <em>node_idx_two</em>
+specify non existent nodes or when <em>pairwise_energies</em> is
+inconsistent with the number of solutions in the specified nodes.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.core.GraphMinimizer.ApplyDEE">
+<code class="descname">ApplyDEE</code><span class="sig-paren">(</span><em>node_idx</em><span class="optional">[</span>, <em>e_cut=0.0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyDEE" title="Permalink to this definition">¶</a></dt>
+<dd><p>Applies dead end elimination on one particular node and potentially
+deactivates certain solutions. The goldstein criterion is described in
+<a class="reference internal" href="#goldstein1994" id="id1">[goldstein1994]</a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>node_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Node to apply dead end elimination</li>
+<li><strong>e_cut</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – If set to
+0.0, the default goldstein criterion is applied =>
+a solution is removed if it’s dominated by all other
+solutions in the same node. If you increase this value,
+a solution must be dominated by at least this <strong>e_cut</strong>.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> whether any solution has been deactivated.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.core.GraphMinimizer.ApplyEdgeDecomposition">
+<code class="descname">ApplyEdgeDecomposition</code><span class="sig-paren">(</span><em>edge_idx</em>, <em>epsilon</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.ApplyEdgeDecomposition" title="Permalink to this definition">¶</a></dt>
+<dd><p>Applies edge decomposition on one particular edge and potentially
+deactivates it. The exact decomposition procedure is described in
+<a class="reference internal" href="../sidechain/index.html#krivov2009" id="id2">[krivov2009]</a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>edge_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Edge to decompose.</li>
+<li><strong>epsilon</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The energy threshold to perform edge decomposition.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> whether the edge has been decomposed and
+deactivated</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.core.GraphMinimizer.Prune">
+<code class="descname">Prune</code><span class="sig-paren">(</span><em>epsilon</em><span class="optional">[</span>, <em>e_cut=0.0</em>, <em>consider_all_nodes=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.Prune" title="Permalink to this definition">¶</a></dt>
+<dd><p>Performs edge decomposition followed by dead end elimination in an
+iterative manner until no changes can be observed anymore given
+<strong>epsilon</strong>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>epsilon</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The energy threshold to perform edge decomposition.</li>
+<li><strong>e_cut</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Parameter to control dead end elimination.</li>
+<li><strong>consider_all_nodes</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, wether the dead end elimination should be
+applied to all nodes, or only those who are
+connected with an edge removed by edge
+decomposition. This is useful if already a Prune
+operation has been performed => only those nodes
+connected to a removed edge have the chance for
+successful dead end elimination.</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.core.GraphMinimizer.Reset">
+<code class="descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.Reset" title="Permalink to this definition">¶</a></dt>
+<dd><p>Resets the graph by undoing any pruning operation (DEE and edge decomposition)</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.core.GraphMinimizer.TreeSolve">
+<code class="descname">TreeSolve</code><span class="sig-paren">(</span><span class="optional">[</span><em>max_complexity=inf</em>, <em>initial_epsilon=0.02</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.TreeSolve" title="Permalink to this definition">¶</a></dt>
+<dd><p>The method solves a graph using a minimal width tree decomposition
+approach in an iterative manner. In every iteration, the algorithm performs
+a pruning step (DEE / Edge Decomposition) and subsequently tries to solve
+each connected component in the graph separately.
+If the number of possible enumerations in the tree constructetd from a
+particular connected component is is larger <strong>max_complexity</strong>,
+this component is solved in a later iteration. The algorithm iterates until
+all connected components are solved and steadily increases the epsilon value
+resulting in a more and more agressive edge decomposition.
+Algorithm further descsribed in <a class="reference internal" href="../sidechain/index.html#krivov2009" id="id3">[krivov2009]</a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>max_complexity</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max number of possible permutations, that have to
+be enumerated in the resulting tree after tree
+decomposition.</li>
+<li><strong>initial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The initial energy threshold to perform edge
+decomposition.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A tuple with the first element being a list of indices
+representing the single solutions minimizing
+the overall energy function.
+The second element is the according energy value.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.core.GraphMinimizer.AStarSolve">
+<code class="descname">AStarSolve</code><span class="sig-paren">(</span><em>e_thresh</em><span class="optional">[</span>, <em>max_n=100</em>, <em>max_visited_nodes=100000000</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.AStarSolve" title="Permalink to this definition">¶</a></dt>
+<dd><p>The method solves a graph using the A* algorithm. Besides creating the
+minimal energy solution, the function produces a maximum of <strong>max_n</strong>
+solutions sorted by energy. It aborts as soon as it sees the first solution
+with an energy difference of <strong>e_thresh</strong> to the optimal solution or hits
+<strong>max_n</strong>. If you’re only interested in the optimal solution you should use
+the TreeSolve function since it’s much faster and uses less memory.
+There is no automatic pruning of the graph using DEE or edge decomposition,
+so you have to do it by yourself, otherwise you’ll have a looooooong
+runtime or even hit the <strong>max_visited_nodes</strong> parameter that caps the memory
+usage.
+To have a valid solution you have to take care that you set the <strong>e_cut</strong>
+parameter in the pruning function to <strong>e_tresh</strong>.
+Algorithm is described in <a class="reference internal" href="#leach1998" id="id4">[leach1998]</a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>e_thresh</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal energy difference of a solution to the
+optimal solution to be considered.</li>
+<li><strong>max_n</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The maximum number of solutions that will be generated.</li>
+<li><strong>max_visited_nodes</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Caps the memory usage of the algorithm. Besides
+The memory used for pairwise energies and self
+energies, the algorithm uses about
+<strong>max_visited_nodes</strong> * 20 bytes.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A tuple with the first element being a list of
+solutions. The second element is a list
+of energies for the according solutions.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.core.GraphMinimizer.MCSolve">
+<code class="descname">MCSolve</code><span class="sig-paren">(</span><span class="optional">[</span><em>n=100</em>, <em>mc_steps=100000</em>, <em>start_temperature=1000.0</em>, <em>change_frequency=1000</em>, <em>cooling_factor=0.9</em>, <em>seed=0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.MCSolve" title="Permalink to this definition">¶</a></dt>
+<dd><p>Does a total of <strong>n</strong> Monte Carlo runs to find low energy solutions
+of the graph. Each run starts with a random
+configuration. At each of the <strong>mc_steps</strong> steps, a random node and
+a random solution at that location is selected and an energy difference
+of that random selection relative to the current configuration is
+estimated. If the difference in energy is negative, the step is
+accepted. If not, the step is accepted with a probability given by
+the temperature dependent Metropolis criterion
+<span class="math">exp^{\left(\frac{-e_{diff}}{T}\right)}</span>.
+The temperature for every run starts with <strong>start_temperature</strong>
+and is multiplied every <strong>change_frequency</strong> steps with <strong>cooling_factor</strong>
+to achieve a simulated annealing effect.
+There is no automatic pruning of the graph using DEE or edge decomposition,
+you have to do that by yourself.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>n</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of Monte Carlo runs</li>
+<li><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of Monte Carlo steps per run</li>
+<li><strong>start_temperature</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Start temperature for the temperature dependent
+Metropolis criterion</li>
+<li><strong>change_frequency</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of steps the temperature stays the same</li>
+<li><strong>cooling_factor</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Factor to multiply temperature each
+<strong>change_frequency</strong> steps</li>
+<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Seed for random number generator</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A tuple with the first element being a list of
+solutions. The second element is a list
+of energies for the according solutions.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.core.GraphMinimizer.NaiveSolve">
+<code class="descname">NaiveSolve</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.core.GraphMinimizer.NaiveSolve" title="Permalink to this definition">¶</a></dt>
+<dd><p>Don’t even think of using this... This function only exists for debug
+purposes and does the full enumeration of the solution space.
+It might become faster with the appropriate
+<a class="reference external" href="https://www.youtube.com/watch?v=fQGbXmkSArs">techniques</a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A tuple with the first element being a list of indices
+representing the single solutions minimizing
+the overall energy function.
+The second element is the according energy value.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<table class="docutils citation" frame="void" id="goldstein1994" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label"><a class="fn-backref" href="#id1">[goldstein1994]</a></td><td>Goldstein RF (1994). Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys J.</td></tr>
+</tbody>
+</table>
+<table class="docutils citation" frame="void" id="leach1998" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label"><a class="fn-backref" href="#id4">[leach1998]</a></td><td>Leach AR, Lemon AP (1998). Explring the conformational space of prootein side chains using dead-end elimination and the A* algorithm. Proteins.</td></tr>
+</tbody>
+</table>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper"><div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../users.html">Documentation For Users</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
+ <li>Previous: <a href="runtime_profiling.html" title="previous chapter">Runtime profiling</a></li>
+ <li>Next: <a href="setcompoundschemlib.html" title="next chapter"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
+ <div role="note" aria-label="source link">
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/core/graph_minimizer.txt"
+ rel="nofollow">Show Source</a></li>
+ </ul>
+ </div>
+<div id="searchbox" style="display: none" role="search">
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" />
+ <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
+ <input type="hidden" name="area" value="default" />
+ </form>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+ </div>
+ </div>
+ <div class="clearer"></div>
+ </div>
+ <div class="footer">
+ ©2018, ProMod3 authors.
+
+ |
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
+
+ |
+ <a href="../_sources/core/graph_minimizer.txt"
+ rel="nofollow">Page source</a>
+ </div>
+
+
+
+
+ </body>
+</html>
\ No newline at end of file
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index fbc111e15392a003d2646f3e8cfbb502a57fdf29..2ef049d9bc9fdc579ad7b7dffa6e9227371c6429 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>helper - Shared Functionality For the Everything — ProMod3 1.1.0 documentation</title>
+ <title>helper - Shared Functionality For the Everything — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="Geometry functions" href="geometry.html" />
<link rel="prev" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -48,15 +50,15 @@ rather empty modules left alone.</p>
</div>
<div class="section" id="messages">
<h2>Messages<a class="headerlink" href="#messages" title="Permalink to this headline">¶</a></h2>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">helper</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">promod3.core</span> <span class="k">import</span> <span class="n">helper</span>
-<span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">"Something failed!"</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s2">"Something failed!"</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
</pre></div>
</div>
<dl class="function">
<dt id="promod3.core.helper.MsgErrorAndExit">
<code class="descclassname">promod3.core.helper.</code><code class="descname">MsgErrorAndExit</code><span class="sig-paren">(</span><em>msg</em>, <em>exit_status</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/helper.html#MsgErrorAndExit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.helper.MsgErrorAndExit" title="Permalink to this definition">¶</a></dt>
-<dd><p>Send a messages to the OST <a class="reference external" href="http://www.openstructure.org/docs/dev/base/logging/">error log</a> and
+<dd><p>Send a messages to the OST <a class="reference external" href="https://www.openstructure.org/docs/dev/base/logging/">error log</a> and
exit the Python interpreter.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -81,20 +83,20 @@ traditionally reserved to successful commands.</li>
<h2>File Tests<a class="headerlink" href="#file-tests" title="Permalink to this headline">¶</a></h2>
<p>The following example parses an argument (call as <code class="docutils literal"><span class="pre">pm</span> <span class="pre">SCRIPTNAME</span> <span class="pre">FILENAME</span></code>) as
a file name and checks whether it is a <code class="docutils literal"><span class="pre">pdb</span></code> or <code class="docutils literal"><span class="pre">mmcif</span></code> file.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="sd">"""Test for file reading."""</span>
-<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">helper</span>
-<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">pm3argparse</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="sd">"""Test for file reading."""</span>
+<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="k">import</span> <span class="n">helper</span>
+<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="k">import</span> <span class="n">pm3argparse</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">pm3argparse</span><span class="o">.</span><span class="n">PM3ArgumentParser</span><span class="p">(</span><span class="n">__doc__</span><span class="p">)</span>
-<span class="n">p</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s">'file'</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+<span class="n">p</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'file'</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
<span class="n">opts</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">Parse</span><span class="p">()</span>
-<span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s">'Test file'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">opts</span><span class="o">.</span><span class="n">file</span><span class="p">)</span>
+<span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s1">'Test file'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">opts</span><span class="o">.</span><span class="n">file</span><span class="p">)</span>
-<span class="n">opts</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">opts</span><span class="o">.</span><span class="n">ext</span><span class="p">,</span> <span class="n">opts</span><span class="o">.</span><span class="n">gz</span> <span class="o">=</span> <span class="n">helper</span><span class="o">.</span><span class="n">FileExtension</span><span class="p">(</span><span class="s">'Test file'</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span>
+<span class="n">opts</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">opts</span><span class="o">.</span><span class="n">ext</span><span class="p">,</span> <span class="n">opts</span><span class="o">.</span><span class="n">gz</span> <span class="o">=</span> <span class="n">helper</span><span class="o">.</span><span class="n">FileExtension</span><span class="p">(</span><span class="s1">'Test file'</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span>
<span class="n">opts</span><span class="o">.</span><span class="n">file</span><span class="p">,</span>
- <span class="p">(</span><span class="s">'pdb'</span><span class="p">,</span> <span class="s">'mmcif'</span><span class="p">),</span>
- <span class="n">gzip</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+ <span class="p">(</span><span class="s1">'pdb'</span><span class="p">,</span> <span class="s1">'mmcif'</span><span class="p">),</span>
+ <span class="n">gzip</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
</pre></div>
</div>
<dl class="function">
@@ -237,9 +239,6 @@ script will terminate if a gzip file is found.</li>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -247,11 +246,11 @@ script will terminate if a gzip file is found.</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/core/helper.txt"
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index af6c850eff696102202c58faeb9a58eb77c6a922..774d53ed424cd8915182a7f8216297a4fe85bde9 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>core - ProMod3 Core Functionality — ProMod3 1.1.0 documentation</title>
+ <title>core - ProMod3 Core Functionality — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
<link rel="prev" title="Loading Precomputed Objects" href="../loop/load_loop_objects.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -59,6 +61,7 @@ modeling per se but cover standard programming issues.</p>
</li>
<li class="toctree-l1"><a class="reference internal" href="geometry.html">Geometry functions</a></li>
<li class="toctree-l1"><a class="reference internal" href="runtime_profiling.html">Runtime profiling</a></li>
+<li class="toctree-l1"><a class="reference internal" href="graph_minimizer.html">Graph Minimizer</a></li>
</ul>
</div>
</div>
@@ -94,9 +97,6 @@ modeling per se but cover standard programming issues.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -104,11 +104,11 @@ modeling per se but cover standard programming issues.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/core/index.txt"
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index 6f049e99f43e4b5e6051f44e039b68398b84ddcb..c92c89603a57ec80a32e2435a5661d076d14f31a 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>pm3argparse - Parsing Command Lines — ProMod3 1.1.0 documentation</title>
+ <title>pm3argparse - Parsing Command Lines — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="helper - Shared Functionality For the Everything" href="helper.html" />
<link rel="prev" title="core - ProMod3 Core Functionality" href="index.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -52,14 +54,14 @@ There <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentP
simplification. It provides a set of standard arguments you just need to
activate for your action plus it comes with some verification functionality for
input.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="sd">"""</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="sd">"""</span>
<span class="sd">Place the description of your script right in the file and import</span>
<span class="sd">it via '__doc__' as description to the parser ('-h', '--help').</span>
<span class="sd">"""</span>
-<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">pm3argparse</span>
+<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="k">import</span> <span class="n">pm3argparse</span>
-<span class="c"># make sure we see output when passing '-h'</span>
+<span class="c1"># make sure we see output when passing '-h'</span>
<span class="kn">import</span> <span class="nn">ost</span>
<span class="n">ost</span><span class="o">.</span><span class="n">PushVerbosityLevel</span><span class="p">(</span><span class="mi">2</span><span class="p">)</span>
@@ -154,7 +156,7 @@ sequence is used. File can be plain or gzipped.</li>
<li><code class="docutils literal"><span class="pre">-j/--json</span> <span class="pre"><OBJECT>|<FILE></span></code> - Alignments provided as JSON
file/object. File can be plain or gzipped.</li>
</ul>
-<p>See <a class="reference internal" href="../actions/index.html#promod-build-model"><span>here</span></a> for details on the file formats.</p>
+<p>See <a class="reference internal" href="../actions/index.html#promod-build-model"><span class="std std-ref">here</span></a> for details on the file formats.</p>
<p>Attributes added to the namespace returned by <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.Parse" title="promod3.core.pm3argparse.PM3ArgumentParser.Parse"><code class="xref py py-meth docutils literal"><span class="pre">Parse()</span></code></a>:</p>
<ul class="simple">
<li><code class="xref py py-attr docutils literal"><span class="pre">fasta</span></code> - filled with the input of the <code class="docutils literal"><span class="pre">--fasta</span></code> option, a
@@ -211,7 +213,7 @@ input is post processed and checked in <a class="reference internal" href="#prom
to <a class="reference internal" href="#promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment" title="promod3.core.pm3argparse.PM3ArgumentParser.AddAlignment"><code class="xref py py-meth docutils literal"><span class="pre">AddAlignment()</span></code></a>. Chains for each sequence
are identified based on the sequence name of the
templates in the alignments (see
-<a class="reference internal" href="../actions/index.html#promod-build-model"><span>here</span></a> for details).</td>
+<a class="reference internal" href="../actions/index.html#promod-build-model"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -334,9 +336,6 @@ and with the right constraints.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -344,11 +343,11 @@ and with the right constraints.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/core/pm3argparse.txt"
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index c0b3d5d6181ec1cbe5963d9be53733855a330d43..2466ad9d3f6e6d8de264e1874c43332677a3a97a 100644
--- a/doc/html/core/runtime_profiling.html
+++ b/doc/html/core/runtime_profiling.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Runtime profiling — ProMod3 1.1.0 documentation</title>
+ <title>Runtime profiling — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
- <link rel="next" title="SetCompoundsChemlib()" href="setcompoundschemlib.html" />
+ <link rel="next" title="Graph Minimizer" href="graph_minimizer.html" />
<link rel="prev" title="Geometry functions" href="geometry.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -170,7 +172,7 @@ will fail miserably if timers are currently running.</p>
<li><a href="../users.html">Documentation For Users</a><ul>
<li><a href="index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
<li>Previous: <a href="geometry.html" title="previous chapter">Geometry functions</a></li>
- <li>Next: <a href="setcompoundschemlib.html" title="next chapter"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
+ <li>Next: <a href="graph_minimizer.html" title="next chapter">Graph Minimizer</a></li>
</ul></li>
</ul></li>
</ul></li>
@@ -191,9 +193,6 @@ will fail miserably if timers are currently running.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -201,11 +200,11 @@ will fail miserably if timers are currently running.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/core/runtime_profiling.txt"
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index 1d400cd0581fb53191bd47ace59e84b0d5bb8f75..e0e9cb4d4256b35a60b91b487c28cbea9efd04cf 100644
--- a/doc/html/core/setcompoundschemlib.html
+++ b/doc/html/core/setcompoundschemlib.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>SetCompoundsChemlib() — ProMod3 1.1.0 documentation</title>
+ <title>SetCompoundsChemlib() — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Documentation For Developers" href="../developers.html" />
- <link rel="prev" title="Runtime profiling" href="runtime_profiling.html" />
+ <link rel="prev" title="Graph Minimizer" href="graph_minimizer.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -75,7 +77,7 @@ enabled globally.</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li>Previous: <a href="runtime_profiling.html" title="previous chapter">Runtime profiling</a></li>
+ <li>Previous: <a href="graph_minimizer.html" title="previous chapter">Graph Minimizer</a></li>
<li>Next: <a href="../developers.html" title="next chapter">Documentation For Developers</a></li>
</ul></li>
</ul></li>
@@ -96,9 +98,6 @@ enabled globally.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -106,11 +105,11 @@ enabled globally.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/core/setcompoundschemlib.txt"
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index 3ff8fe004347ca275dbef3cb11121d983eb8b853..f58b1ee6ad20de2cf87c9fc6bf8c81d1ba15d6b5 100644
--- a/doc/html/dev_setup.html
+++ b/doc/html/dev_setup.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3 Setup — ProMod3 1.1.0 documentation</title>
+ <title>ProMod3 Setup — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="Contributing" href="contributing.html" />
<link rel="prev" title="Documentation For Developers" href="developers.html" />
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -85,9 +87,9 @@ created something that could go into a release, tidy things up according to the
rules from above and merge it into <code class="docutils literal"><span class="pre">develop</span></code>. From there it will
automatically find its way into the next release.</p>
<p>To set up your own branch, start from a current <code class="docutils literal"><span class="pre">develop</span></code> branch:</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git checkout develop <span class="c"># switch to branch develop</span>
-<span class="gp">$</span> git pull --rebase <span class="c"># update branch develop</span>
-<span class="gp">$</span> git checkout -b <BRANCHNAME> <span class="c"># create branch <BRANCHNAME> and switch to it</span>
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout develop <span class="c1"># switch to branch develop</span>
+<span class="gp">$</span> git pull --rebase <span class="c1"># update branch develop</span>
+<span class="gp">$</span> git checkout -b <BRANCHNAME> <span class="c1"># create branch <BRANCHNAME> and switch to it</span>
</pre></div>
</div>
<p>Over time, <code class="docutils literal"><span class="pre">develop</span></code> may recognise some changes, e.g. new features, which you
@@ -95,7 +97,7 @@ want to make use of in your project. Keeping your branch up to date is a three
step process. Git does not allow updates on top of changed code, so either
changes have to be committed, or if in the middle of implementing something,
stored away temporarily. Making commits is straight forward:</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git commit -m <span class="s1">'<DESCRIPTION>'</span> <span class="c"># commit changes including a comment</span>
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git commit -m <span class="s1">'<DESCRIPTION>'</span> <span class="c1"># commit changes including a comment</span>
</pre></div>
</div>
<p>Hiding your changes away from Git just for updating files is a bit more
@@ -106,15 +108,15 @@ you have changed, too, and stashed away, this may end up in a non-resolvable
merge conflict and your changes are lost. Usually the log tells you, which
files were recently modified. Moving all current changes to the stack is
achieved by:</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git stash save
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git stash save
</pre></div>
</div>
<p>To revive them, use:</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git stash pop
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git stash pop
</pre></div>
</div>
<p>After cleaning up your branch, switch to <code class="docutils literal"><span class="pre">develop</span></code>, update it and switch back:</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git checkout develop
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git checkout develop
<span class="gp">$</span> git pull --rebase
<span class="gp">$</span> git checkout <BRANCHNAME>
</pre></div>
@@ -123,11 +125,11 @@ achieved by:</p>
and rebasing. A rebase may only be done, if you <strong>never</strong> pushed your branch to
the origin of the repository (otherwise you will mess up history, in the worst
case <code class="docutils literal"><span class="pre">develop</span></code> may be unusable once you merge):</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git rebase develop
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git rebase develop
</pre></div>
</div>
<p>For branches which are available to others, do a proper merge:</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git merge develop
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git merge develop
</pre></div>
</div>
<p>This may require some manual conflict solving and will end up in a merge commit.</p>
@@ -136,17 +138,17 @@ case <code class="docutils literal"><span class="pre">develop</span></code> may
<h2>Git Hooks<a class="headerlink" href="#git-hooks" title="Permalink to this headline">¶</a></h2>
<p>Git hooks are scripts invoked by Git in connection to certain commands.
ProMod3 currently provides one for <strong class="command">commit</strong>. It is installed by</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> cp extras/pre_commit/pre-commit .git/hooks/
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> cp extras/pre_commit/pre-commit .git/hooks/
</pre></div>
</div>
<p>Its task is applying coding standards and doing a bunch of other checks on the
files involved in a commit. Everything around the script is hosted in
<code class="file docutils literal"><span class="pre">extras/pre_commit/</span></code>. The checks can be manually executed with</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> python .git/hooks/pre-commit
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> python .git/hooks/pre-commit
</pre></div>
</div>
<p>If you ever have to skip the hook,</p>
-<div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> git commit --no-verify
+<div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> git commit --no-verify
</pre></div>
</div>
<p>does the trick. <strong>But</strong> checks are always run on the complete file containing
@@ -172,7 +174,7 @@ is invoked on unit test code, where we may go a little bit less restrictive.</p>
everything together that belongs together’. That is, code, documentation and
extra data should be gathered on a per-module basis immediately in the
repository root. The directory structure of your module should look like this:</p>
-<div class="highlight-text"><div class="highlight"><pre>promod3.git/ Project folder
+<div class="highlight-text"><div class="highlight"><pre><span></span>promod3.git/ Project folder
your_module/ Module directory
CMakeLists.txt CMake configuration
data/ Extra data (if needed)
@@ -204,13 +206,13 @@ repository root. The directory structure of your module should look like this:</
<p>Additionally to the module directories there are a few extra folders:</p>
<ul class="simple">
<li><code class="file docutils literal"><span class="pre">actions</span></code>: Scripts callable as <code class="docutils literal"><span class="pre">pm</span> <span class="pre"><ACTION_NAME></span></code>.
-See <a class="reference internal" href="contributing.html#how-to-start-your-own-action"><span>here</span></a> for details.</li>
+See <a class="reference internal" href="contributing.html#how-to-start-your-own-action"><span class="std std-ref">here</span></a> for details.</li>
<li><code class="file docutils literal"><span class="pre">cmake_support</span></code>: Helper functions for CMake.
-See <a class="reference internal" href="cmake/index.html#pm3-cmake-doc"><span>here</span></a> for details.</li>
+See <a class="reference internal" href="cmake/index.html#pm3-cmake-doc"><span class="std std-ref">here</span></a> for details.</li>
<li><code class="file docutils literal"><span class="pre">doc</span></code>: High-level documentation, test scripts (<code class="file docutils literal"><span class="pre">doc/tests</span></code>) and a
copy of the generated html documentation (<code class="file docutils literal"><span class="pre">doc/html</span></code>). The latter must
be kept up-to-date at least on the <code class="docutils literal"><span class="pre">master</span></code> branch.
-See <a class="reference internal" href="contributing.html#writing-documentation"><span>here</span></a> for details.</li>
+See <a class="reference internal" href="contributing.html#writing-documentation"><span class="std std-ref">here</span></a> for details.</li>
<li><code class="file docutils literal"><span class="pre">extras</span></code>: Extra data and information that doesn’t fit anywhere
else (e.g. Git hooks or scripts to recreate the binary files).</li>
<li><code class="file docutils literal"><span class="pre">scripts</span></code>: Input for scripts that end up in <code class="file docutils literal"><span class="pre">stage/bin</span></code></li>
@@ -225,7 +227,7 @@ Python modules are declared there as well as which files belong to the
documentation. CMake is a rather complex topic (unfortunately all usable
build systems seem to be) so we skip a detailed view, here, and just advice you
to go by example. There is a tiny bit of documentation on our additions to
-CMake <a class="reference internal" href="cmake/index.html#pm3-cmake-doc"><span>here</span></a>. If you really need to make changes to the
+CMake <a class="reference internal" href="cmake/index.html#pm3-cmake-doc"><span class="std std-ref">here</span></a>. If you really need to make changes to the
build system, other than adding new files and modules, you have to dive into
CMake documentation all by yourself and on your own responsibility. You have
been warned.</p>
@@ -283,9 +285,6 @@ modules from there, use the binaries from <code class="file docutils literal"><s
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -293,11 +292,11 @@ modules from there, use the binaries from <code class="file docutils literal"><s
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/dev_setup.txt"
diff --git a/doc/html/developers.html b/doc/html/developers.html
index b0e89ed94976d7191cf20e01038ccd570dec8c19..89882a9474b79f60d2d36dbbc47bec5394e3ccc3 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Documentation For Developers — ProMod3 1.1.0 documentation</title>
+ <title>Documentation For Developers — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,15 +23,17 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
<link rel="next" title="ProMod3 Setup" href="dev_setup.html" />
<link rel="prev" title="SetCompoundsChemlib()" href="core/setcompoundschemlib.html" />
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -114,9 +116,6 @@ new features.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -124,11 +123,11 @@ new features.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/developers.txt"
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index a4b8a6fb84b1412936a635669decd771273df8ab..4e5da3b46b5ba10cbb6458cf8b9eee2e6aeedac4 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -7,7 +7,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Index — ProMod3 1.1.0 documentation</title>
+ <title>Index — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -15,7 +15,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,13 +24,15 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -230,6 +232,10 @@
</dt>
+ <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.AddEdge">AddEdge() (promod3.core.GraphMinimizer method)</a>
+ </dt>
+
+
<dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.AddFragmentInfo">AddFragmentInfo() (promod3.modelling.LoopCandidates method)</a>
</dt>
@@ -260,6 +266,10 @@
</dt>
+ <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.AddNode">AddNode() (promod3.core.GraphMinimizer method)</a>
+ </dt>
+
+
<dt><a href="modelling/loop_closing.html#promod3.modelling.BackboneRelaxer.AddNRestraint">AddNRestraint() (promod3.modelling.BackboneRelaxer method)</a>
</dt>
@@ -329,12 +339,12 @@
<dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_sidechain_env">all_atom_sidechain_env (promod3.modelling.ModellingHandle attribute)</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/all_atom.html#promod3.loop.AllAtomEnvPositions.all_pos">all_pos (promod3.loop.AllAtomEnvPositions attribute)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer">AllAtomClashScorer (class in promod3.scoring)</a>
</dt>
@@ -430,11 +440,11 @@
</dt>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.ApplyDEE">ApplyDEE() (promod3.sidechain.RotamerGraph method)</a>
+ <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.ApplyDEE">ApplyDEE() (promod3.core.GraphMinimizer method)</a>
</dt>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.ApplyEdgeDecomposition">ApplyEdgeDecomposition() (promod3.sidechain.RotamerGraph method)</a>
+ <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.ApplyEdgeDecomposition">ApplyEdgeDecomposition() (promod3.core.GraphMinimizer method)</a>
</dt>
@@ -486,7 +496,7 @@
</dt>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.AStarSolve">AStarSolve() (promod3.sidechain.RotamerGraph method)</a>
+ <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.AStarSolve">AStarSolve() (promod3.core.GraphMinimizer method)</a>
</dt>
@@ -682,6 +692,10 @@
</dt>
+ <dt><a href="loop/structure_db.html#promod3.loop.CoordInfo.chain_name">chain_name (promod3.loop.CoordInfo attribute)</a>
+ </dt>
+
+
<dt><a href="modelling/pipeline.html#promod3.modelling.CheckFinalModel">CheckFinalModel() (in module promod3.modelling)</a>
</dt>
@@ -815,7 +829,7 @@
</dt>
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructBackboneFrameResidue">ConstructBackboneFrameResidue() (promod3.sidechain.SCWRLRotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructBackboneFrameResidue">[1]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructBackboneFrameResidue">[2]</a>
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructBackboneFrameResidue">ConstructBackboneFrameResidue() (promod3.sidechain.SCWRLRotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructBackboneFrameResidue">[1]</a>
</dt>
@@ -835,7 +849,7 @@
</dt>
- <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">ConstructRRMRotamerGroup() (promod3.sidechain.SCWRLRotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">[1]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">[2]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">[3]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">[4]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">[5]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">[6]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">[7]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">[8]</a>
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">ConstructRRMRotamerGroup() (promod3.sidechain.SCWRLRotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">[1]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">[2]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">[3]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">[4]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">[5]</a>
</dt>
@@ -932,10 +946,6 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.DensityScorer">DensityScorer (class in promod3.scoring)</a>
- </dt>
-
-
<dt><a href="modelling/monte_carlo.html#promod3.modelling.DirtyCCDCloser">DirtyCCDCloser (class in promod3.modelling)</a>
</dt>
@@ -955,20 +965,122 @@
<dt><a href="core/geometry.html#promod3.core.StemPairOrientation.distance">distance (promod3.core.StemPairOrientation attribute)</a>
</dt>
+
+ <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.disulfid_bridges">disulfid_bridges (promod3.modelling.SidechainReconstructionData attribute)</a>
+ </dt>
+
+
+ <dt><a href="sidechain/disulfid.html#promod3.sidechain.DisulfidScore">DisulfidScore() (in module promod3.sidechain)</a>
+ </dt>
+
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.disulfid_bridges">disulfid_bridges (promod3.modelling.SidechainReconstructionData attribute)</a>
+ <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer.DoExternalScores">DoExternalScores() (promod3.scoring.AllAtomClashScorer method)</a>
</dt>
+ <dd><dl>
+
+ <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.DoExternalScores">(promod3.scoring.AllAtomInteractionScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.DoExternalScores">(promod3.scoring.CBetaScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ClashScorer.DoExternalScores">(promod3.scoring.ClashScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.DoExternalScores">(promod3.scoring.HBondScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer.DoExternalScores">(promod3.scoring.PairwiseScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.DoExternalScores">(promod3.scoring.ReducedScorer method)</a>
+ </dt>
+
+ </dl></dd>
- <dt><a href="sidechain/disulfid.html#promod3.sidechain.DisulfidRawScore">DisulfidRawScore() (in module promod3.sidechain)</a>
+ <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer.DoInternalScores">DoInternalScores() (promod3.scoring.AllAtomClashScorer method)</a>
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.DoInternalScores">(promod3.scoring.AllAtomInteractionScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.DoInternalScores">(promod3.scoring.CBetaScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ClashScorer.DoInternalScores">(promod3.scoring.ClashScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.DoInternalScores">(promod3.scoring.HBondScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer.DoInternalScores">(promod3.scoring.PairwiseScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.DoInternalScores">(promod3.scoring.ReducedScorer method)</a>
</dt>
+ </dl></dd>
- <dt><a href="sidechain/disulfid.html#promod3.sidechain.DisulfidScore">DisulfidScore() (in module promod3.sidechain)</a>
+ <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomClashScorer.DoNormalize">DoNormalize() (promod3.scoring.AllAtomClashScorer method)</a>
+ </dt>
+
+ <dd><dl>
+
+ <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.DoNormalize">(promod3.scoring.AllAtomInteractionScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomPackingScorer.DoNormalize">(promod3.scoring.AllAtomPackingScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.DoNormalize">(promod3.scoring.CBPackingScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBetaScorer.DoNormalize">(promod3.scoring.CBetaScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ClashScorer.DoNormalize">(promod3.scoring.ClashScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.HBondScorer.DoNormalize">(promod3.scoring.HBondScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer.DoNormalize">(promod3.scoring.PairwiseScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.ReducedScorer.DoNormalize">(promod3.scoring.ReducedScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer.DoNormalize">(promod3.scoring.SSAgreementScorer method)</a>
+ </dt>
+
+
+ <dt><a href="scoring/backbone_scorers.html#promod3.scoring.TorsionScorer.DoNormalize">(promod3.scoring.TorsionScorer method)</a>
</dt>
+ </dl></dd>
<dt><a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.Draw">Draw() (promod3.loop.TorsionSampler method)</a>, <a href="loop/torsion_sampler.html#promod3.loop.TorsionSampler.Draw">[1]</a>
</dt>
@@ -1302,14 +1414,6 @@
</dt>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.GetActiveEdges">GetActiveEdges() (promod3.sidechain.RotamerGraph method)</a>
- </dt>
-
-
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.GetActiveRotamers">GetActiveRotamers() (promod3.sidechain.RotamerGraph method)</a>
- </dt>
-
-
<dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetActiveSubrotamer">GetActiveSubrotamer() (promod3.sidechain.FRMRotamer method)</a>
</dt>
@@ -1418,7 +1522,7 @@
</dt>
- <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetCoordIndex">GetCoordIndex() (promod3.loop.StructureDB method)</a>
+ <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.GetCoordIdx">GetCoordIdx() (promod3.loop.StructureDB method)</a>
</dt>
@@ -1454,10 +1558,6 @@
</dt>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.GetEdges">GetEdges() (promod3.sidechain.RotamerGraph method)</a>
- </dt>
-
-
<dt><a href="loop/all_atom.html#promod3.loop.AminoAcidLookup.GetElement">GetElement() (promod3.loop.AminoAcidLookup static method)</a>
</dt>
@@ -1553,6 +1653,8 @@
</dt>
</dl></dd>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/mm_system_creation.html#promod3.loop.MmSystemCreator.GetIndexing">GetIndexing() (promod3.loop.MmSystemCreator method)</a>
</dt>
@@ -1561,8 +1663,6 @@
<dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.GetInternalConnectivity">GetInternalConnectivity() (promod3.loop.ForcefieldLookup method)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetInternalEnergy">GetInternalEnergy() (promod3.sidechain.FRMRotamer method)</a>
</dt>
@@ -1632,18 +1732,6 @@
</dt>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.GetNumActiveEdges">GetNumActiveEdges() (promod3.sidechain.RotamerGraph method)</a>
- </dt>
-
-
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.GetNumActiveNodes">GetNumActiveNodes() (promod3.sidechain.RotamerGraph method)</a>
- </dt>
-
-
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.GetNumActiveRotamers">GetNumActiveRotamers() (promod3.sidechain.RotamerGraph method)</a>
- </dt>
-
-
<dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetNumAtoms">GetNumAtoms() (promod3.loop.AllAtomPositions method)</a>
</dt>
@@ -1666,10 +1754,6 @@
</dt>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.GetNumEdges">GetNumEdges() (promod3.sidechain.RotamerGraph method)</a>
- </dt>
-
-
<dt><a href="loop/structure_db.html#promod3.loop.FragDB.GetNumFragments">GetNumFragments() (promod3.loop.FragDB method)</a>
</dt>
@@ -1682,10 +1766,6 @@
</dt>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.GetNumNodes">GetNumNodes() (promod3.sidechain.RotamerGraph method)</a>
- </dt>
-
-
<dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetNumResidues">GetNumResidues() (promod3.loop.AllAtomPositions method)</a>
</dt>
@@ -1696,10 +1776,6 @@
</dl></dd>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.GetNumRotamers">GetNumRotamers() (promod3.sidechain.RotamerGraph method)</a>
- </dt>
-
-
<dt><a href="loop/structure_db.html#promod3.loop.FragDB.GetNumStemPairs">GetNumStemPairs() (promod3.loop.FragDB method)</a>
</dt>
@@ -1736,10 +1812,6 @@
</dt>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.GetPairwiseEnergies">GetPairwiseEnergies() (promod3.sidechain.RotamerGraph method)</a>
- </dt>
-
-
<dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetParticleType">GetParticleType() (promod3.sidechain.Particle method)</a>
</dt>
@@ -1820,20 +1892,16 @@
</dt>
- <dt><a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">GetScore() (promod3.loop.Fragger method)</a>, <a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">[1]</a>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.GetScore">GetScore() (in module promod3.modelling)</a>
</dt>
<dd><dl>
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.LinearScorer.GetScore">(promod3.modelling.LinearScorer method)</a>
+ <dt><a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">(promod3.loop.Fragger method)</a>, <a href="loop/structure_db.html#promod3.loop.Fragger.GetScore">[1]</a>
</dt>
</dl></dd>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.GetSelfEnergies">GetSelfEnergies() (promod3.sidechain.RotamerGraph method)</a>
- </dt>
-
-
<dt><a href="sidechain/rotamer.html#promod3.sidechain.FRMRotamer.GetSelfEnergy">GetSelfEnergy() (promod3.sidechain.FRMRotamer method)</a>
</dt>
@@ -1933,6 +2001,10 @@
<dt><a href="modelling/loop_candidates.html#promod3.modelling.ScoringWeights.GetWeights">GetWeights() (promod3.modelling.ScoringWeights static method)</a>
</dt>
+
+ <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer">GraphMinimizer (class in promod3.core)</a>
+ </dt>
+
</dl></td>
</tr></table>
@@ -1952,12 +2024,16 @@
</dt>
- <dt><a href="loop/structure_db.html#promod3.loop.FragDB.HasFragLength">HasFragLength() (promod3.loop.FragDB method)</a>
+ <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.HasData">HasData() (promod3.loop.StructureDB method)</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
+ <dt><a href="loop/structure_db.html#promod3.loop.FragDB.HasFragLength">HasFragLength() (promod3.loop.FragDB method)</a>
+ </dt>
+
+
<dt><a href="modelling/loop_candidates.html#promod3.modelling.LoopCandidates.HasFragmentInfos">HasFragmentInfos() (promod3.modelling.LoopCandidates method)</a>
</dt>
@@ -1976,6 +2052,10 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
+ <dt><a href="loop/structure_db.html#promod3.loop.CoordInfo.id">id (promod3.loop.CoordInfo attribute)</a>
+ </dt>
+
+
<dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldHarmonicImproperInfo.index_four">index_four (promod3.loop.ForcefieldHarmonicImproperInfo attribute)</a>
</dt>
@@ -2099,12 +2179,12 @@
<dt><a href="modelling/pipeline.html#promod3.modelling.IsAllAtomScoringSetUp">IsAllAtomScoringSetUp() (in module promod3.modelling)</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.IsAllSet">IsAllSet() (promod3.loop.AllAtomPositions method)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.IsAnySet">IsAnySet() (promod3.loop.AllAtomPositions method)</a>
</dt>
@@ -2190,10 +2270,6 @@
</dt>
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.LinearScorer">LinearScorer (class in promod3.modelling)</a>
- </dt>
-
-
<dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.lj_pairs">lj_pairs (promod3.loop.ForcefieldConnectivity attribute)</a>
</dt>
@@ -2299,12 +2375,12 @@
<dt><a href="sidechain/loading.html#promod3.sidechain.LoadDunbrackLib">LoadDunbrackLib() (in module promod3.sidechain)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/load_loop_objects.html#promod3.loop.LoadFragDB">LoadFragDB() (in module promod3.loop)</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="scoring/backbone_scorers.html#promod3.scoring.LoadHBondScorer">LoadHBondScorer() (in module promod3.scoring)</a>
</dt>
@@ -2460,7 +2536,7 @@
</dt>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.MCSolve">MCSolve() (promod3.sidechain.RotamerGraph method)</a>
+ <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.MCSolve">MCSolve() (promod3.core.GraphMinimizer method)</a>
</dt>
@@ -2540,6 +2616,10 @@
<dt><a href="core/geometry.html#promod3.core.StemCoords.n_coord">n_coord (promod3.core.StemCoords attribute)</a>
</dt>
+
+ <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.NaiveSolve">NaiveSolve() (promod3.core.GraphMinimizer method)</a>
+ </dt>
+
</dl></td>
<td style="width: 33%" valign="top"><dl>
@@ -2593,10 +2673,6 @@
</dt>
- <dt><a href="loop/structure_db.html#promod3.loop.CoordInfo.pdb_id">pdb_id (promod3.loop.CoordInfo attribute)</a>
- </dt>
-
-
<dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.periodic_dihedrals">periodic_dihedrals (promod3.loop.ForcefieldConnectivity attribute)</a>
</dt>
@@ -2636,6 +2712,10 @@
</dt>
+ <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.Pop">Pop() (promod3.scoring.BackboneScoreEnv method)</a>
+ </dt>
+
+
<dt><a href="loop/structure_db.html#promod3.loop.FragDB.PrintStatistics">PrintStatistics() (promod3.loop.FragDB method)</a>
</dt>
@@ -2713,7 +2793,7 @@
</dl></dd>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.Prune">Prune() (promod3.sidechain.RotamerGraph method)</a>
+ <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.Prune">Prune() (promod3.core.GraphMinimizer method)</a>
</dt>
@@ -2794,6 +2874,10 @@
</dt>
+ <dt><a href="loop/structure_db.html#promod3.loop.StructureDB.RemoveCoordinates">RemoveCoordinates() (promod3.loop.StructureDB method)</a>
+ </dt>
+
+
<dt><a href="modelling/pipeline.html#promod3.modelling.RemoveTerminalGaps">RemoveTerminalGaps() (in module promod3.modelling)</a>
</dt>
@@ -2814,12 +2898,12 @@
</dt>
- <dt><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler.Reset">Reset() (promod3.modelling.ExponentialCooler method)</a>
+ <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.Reset">Reset() (promod3.core.GraphMinimizer method)</a>
</dt>
<dd><dl>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.Reset">(promod3.sidechain.RotamerGraph method)</a>
+ <dt><a href="modelling/monte_carlo.html#promod3.modelling.ExponentialCooler.Reset">(promod3.modelling.ExponentialCooler method)</a>
</dt>
</dl></dd>
@@ -2835,12 +2919,12 @@
<dt><a href="modelling/algorithms.html#promod3.modelling.RigidBlocks">RigidBlocks() (in module promod3.modelling)</a>, <a href="modelling/algorithms.html#promod3.modelling.RigidBlocks">[1]</a>, <a href="modelling/algorithms.html#promod3.modelling.RigidBlocks">[2]</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/backbone.html#promod3.loop.BackboneList.RMSD">RMSD() (promod3.loop.BackboneList method)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="modelling/sidechain_reconstruction.html#promod3.modelling.SidechainReconstructionData.rotamer_res_indices">rotamer_res_indices (promod3.modelling.SidechainReconstructionData attribute)</a>
</dt>
@@ -3070,6 +3154,14 @@
</dt>
+ <dt><a href="scoring/other_scoring_functions.html#promod3.scoring.SCWRL3DisulfidScore">SCWRL3DisulfidScore() (in module promod3.scoring)</a>
+ </dt>
+
+
+ <dt><a href="scoring/other_scoring_functions.html#promod3.scoring.SCWRL3PairwiseScore">SCWRL3PairwiseScore() (in module promod3.scoring)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRLRotamerConstructor">SCWRLRotamerConstructor (class in promod3.sidechain)</a>
</dt>
@@ -3272,10 +3364,6 @@
</dt>
- <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.SetMap">SetMap() (promod3.scoring.BackboneScoreEnv method)</a>
- </dt>
-
-
<dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetMasses">SetMasses() (promod3.loop.ForcefieldLookup method)</a>
</dt>
@@ -3291,8 +3379,6 @@
<dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetO">SetO() (promod3.loop.BackboneList method)</a>
</dt>
- </dl></td>
- <td style="width: 33%" valign="top"><dl>
<dt><a href="loop/backbone.html#promod3.loop.BackboneList.SetOLC">SetOLC() (promod3.loop.BackboneList method)</a>
</dt>
@@ -3301,6 +3387,8 @@
<dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldLookup.SetPeptideBoundConnectivity">SetPeptideBoundConnectivity() (promod3.loop.ForcefieldLookup method)</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.SetPolarDirection">SetPolarDirection() (promod3.sidechain.Particle method)</a>
</dt>
@@ -3384,6 +3472,10 @@
</dt>
+ <dt><a href="loop/structure_db.html#promod3.loop.CoordInfo.shift">shift (promod3.loop.CoordInfo attribute)</a>
+ </dt>
+
+
<dt><a href="modelling/gap_handling.html#promod3.modelling.StructuralGap.ShiftCTerminal">ShiftCTerminal() (promod3.modelling.StructuralGap method)</a>
</dt>
@@ -3448,10 +3540,18 @@
</dt>
+ <dt><a href="loop/structure_db.html#promod3.loop.CoordInfo.start_resnum">start_resnum (promod3.loop.CoordInfo attribute)</a>
+ </dt>
+
+
<dt><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler.StartScoped">StartScoped() (promod3.core.StaticRuntimeProfiler static method)</a>
</dt>
+ <dt><a href="scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv.Stash">Stash() (promod3.scoring.BackboneScoreEnv method)</a>
+ </dt>
+
+
<dt><a href="core/runtime_profiling.html#promod3.core.StaticRuntimeProfiler">StaticRuntimeProfiler (class in promod3.core)</a>
</dt>
@@ -3480,6 +3580,10 @@
</dt>
+ <dt><a href="loop/structure_db.html#promod3.loop.StructureDBDataType">StructureDBDataType (class in promod3.loop)</a>
+ </dt>
+
+
<dt><a href="sidechain/subrotamer_optimizer.html#promod3.sidechain.SubrotamerOptimizer">SubrotamerOptimizer() (in module promod3.sidechain)</a>
</dt>
@@ -3548,7 +3652,7 @@
</dt>
- <dt><a href="sidechain/graph.html#promod3.sidechain.RotamerGraph.TreeSolve">TreeSolve() (promod3.sidechain.RotamerGraph method)</a>
+ <dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.TreeSolve">TreeSolve() (promod3.core.GraphMinimizer method)</a>
</dt>
</dl></td>
@@ -3571,18 +3675,10 @@
</dt>
</dl></dd>
-
- <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.urey_bradley_angles">urey_bradley_angles (promod3.loop.ForcefieldConnectivity attribute)</a>
- </dt>
-
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.UseClassicMode">UseClassicMode() (promod3.scoring.CBPackingScorer method)</a>
- </dt>
-
-
- <dt><a href="scoring/backbone_scorers.html#promod3.scoring.CBPackingScorer.UseIncludeEnvMode">UseIncludeEnvMode() (promod3.scoring.CBPackingScorer method)</a>
+ <dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldConnectivity.urey_bradley_angles">urey_bradley_angles (promod3.loop.ForcefieldConnectivity attribute)</a>
</dt>
</dl></td>
@@ -3612,9 +3708,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -3622,11 +3715,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index 58aa46d167e2e9cdf9ec4730f9396b637b60f214..f984958d7fd43ff0e604a8031e37bb8b44e74eec 100644
--- a/doc/html/gettingstarted.html
+++ b/doc/html/gettingstarted.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Getting Started — ProMod3 1.1.0 documentation</title>
+ <title>Getting Started — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Users" href="users.html" />
<link rel="next" title="ProMod3 Actions" href="actions/index.html" />
<link rel="prev" title="Documentation For Users" href="users.html" />
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -46,27 +48,27 @@
<p>First steps to get ProMod3 up and running:</p>
<ol class="arabic simple">
<li>Obtain all dependencies and compile ProMod3 with <code class="docutils literal"><span class="pre">cmake</span></code> and <code class="docutils literal"><span class="pre">make</span></code>
-(see <a class="reference internal" href="buildsystem.html#building-promod"><span>here</span></a>).</li>
+(see <a class="reference internal" href="buildsystem.html#building-promod"><span class="std std-ref">here</span></a>).</li>
<li>Ensure that you have a <code class="docutils literal"><span class="pre">stage/bin</span></code> folder which includes a <code class="docutils literal"><span class="pre">pm</span></code> executable.
For convenience, add the folder to your <code class="docutils literal"><span class="pre">PATH</span></code> env. variable.</li>
<li>You can now execute ProMod3 by running the following in your terminal:</li>
</ol>
<blockquote>
-<div><div class="highlight-console"><div class="highlight"><pre><span class="gp">$</span> pm <COMMAND>
+<div><div class="highlight-console"><div class="highlight"><pre><span></span><span class="gp">$</span> pm <COMMAND>
</pre></div>
</div>
<p>Here <code class="docutils literal"><span class="pre"><COMMAND></span></code> can be:</p>
<ul>
-<li><p class="first">a predefined “action” (see <a class="reference internal" href="actions/index.html#promod-actions"><span>here</span></a>)</p>
+<li><p class="first">a predefined “action” (see <a class="reference internal" href="actions/index.html#promod-actions"><span class="std std-ref">here</span></a>)</p>
</li>
<li><p class="first">the path to a python script, such as the following example:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
-<span class="c"># generate backbone with dihedrals of a helix and store it</span>
-<span class="n">sequence</span> <span class="o">=</span> <span class="s">"HELLYEAH"</span>
+<span class="c1"># generate backbone with dihedrals of a helix and store it</span>
+<span class="n">sequence</span> <span class="o">=</span> <span class="s2">"HELLYEAH"</span>
<span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s">"test.pdb"</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s2">"test.pdb"</span><span class="p">)</span>
</pre></div>
</div>
<p>The execution of this script should generate a <code class="docutils literal"><span class="pre">test.pdb</span></code> file, which you
@@ -86,7 +88,7 @@ is conserved</li>
<li>Perform loop modelling to close all gaps (see <a class="reference internal" href="loop/index.html#module-promod3.loop" title="promod3.loop: Loop Handling"><code class="xref py py-mod docutils literal"><span class="pre">loop</span></code></a> module)</li>
<li>Reconstruct sidechains (using <a class="reference internal" href="sidechain/index.html#module-promod3.sidechain" title="promod3.sidechain: Sidechain Modelling"><code class="xref py py-mod docutils literal"><span class="pre">sidechain</span></code></a> module)</li>
<li>Minimize energy of final model using molecular mechanics
-(using <code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code> from OST)</li>
+(using <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
</ul>
<p>Since a good amount of time is spent in OpenMM routines to minimize energy, we
try to use the fast and multi-threaded “CPU” platform of OpenMM (should be
@@ -138,9 +140,6 @@ not set, 1 thread will be used by default.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -148,11 +147,11 @@ not set, 1 thread will be used by default.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/gettingstarted.txt"
diff --git a/doc/html/index.html b/doc/html/index.html
index 99a24e3a4490f694d3d4e4ddca49fb7b85a122c8..9a9a20281972b758a64c9e1976765ce31fd410cc 100644
--- a/doc/html/index.html
+++ b/doc/html/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Welcome To ProMod3’s Documentation! — ProMod3 1.1.0 documentation</title>
+ <title>Welcome To ProMod3’s Documentation! — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,14 +23,16 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="#" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="#" />
<link rel="next" title="Documentation For Users" href="users.html" />
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -73,9 +75,9 @@
<div class="section" id="indices-and-tables">
<h1>Indices And Tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
<ul class="simple">
-<li><a class="reference internal" href="genindex.html"><span>Index</span></a></li>
-<li><a class="reference internal" href="py-modindex.html"><span>Module Index</span></a></li>
-<li><a class="reference internal" href="search.html"><span>Search Page</span></a></li>
+<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li>
+<li><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></li>
+<li><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></li>
</ul>
</div>
@@ -115,9 +117,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -125,11 +124,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/index.txt"
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index 88e7357757fc1066ae4c7d8287ae90582124e50b..df65f9c542ab9108208ba0e8740ebb02e80413e0 100644
--- a/doc/html/loop/all_atom.html
+++ b/doc/html/loop/all_atom.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Handling All Atom Positions — ProMod3 1.1.0 documentation</title>
+ <title>Handling All Atom Positions — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
<link rel="prev" title="Structural Data" href="structure_db.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -46,32 +48,32 @@
positions of all their heavy atoms and an environment (<a class="reference internal" href="#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a>) to
handle changes during loop modelling.</p>
<p>The example below showcases some operations on the two classes:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">geom</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">geom</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
-<span class="c"># load example (has res. numbering starting at 1)</span>
-<span class="n">ent</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">"data/1CRN.pdb"</span><span class="p">)</span>
+<span class="c1"># load example (has res. numbering starting at 1)</span>
+<span class="n">ent</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s2">"data/1CRN.pdb"</span><span class="p">)</span>
<span class="n">res_list</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">residues</span>
-<span class="n">seqres_str</span> <span class="o">=</span> <span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res_list</span><span class="p">])</span>
+<span class="n">seqres_str</span> <span class="o">=</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res_list</span><span class="p">])</span>
-<span class="c"># initialize an environment</span>
+<span class="c1"># initialize an environment</span>
<span class="n">env</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">AllAtomEnv</span><span class="p">(</span><span class="n">seqres_str</span><span class="p">)</span>
<span class="n">env</span><span class="o">.</span><span class="n">SetInitialEnvironment</span><span class="p">(</span><span class="n">ent</span><span class="p">)</span>
-<span class="c"># get all atom position for part of it</span>
+<span class="c1"># get all atom position for part of it</span>
<span class="n">all_atoms</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">AllAtomPositions</span><span class="p">(</span><span class="n">res_list</span><span class="p">[</span><span class="mi">35</span><span class="p">:</span><span class="mi">44</span><span class="p">])</span>
-<span class="c"># change pos. at res. index 1 (= res. number 37)</span>
-<span class="n">idx_ca_res_37</span> <span class="o">=</span> <span class="n">all_atoms</span><span class="o">.</span><span class="n">GetIndex</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="s">"CA"</span><span class="p">)</span>
+<span class="c1"># change pos. at res. index 1 (= res. number 37)</span>
+<span class="n">idx_ca_res_37</span> <span class="o">=</span> <span class="n">all_atoms</span><span class="o">.</span><span class="n">GetIndex</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="s2">"CA"</span><span class="p">)</span>
<span class="n">new_pos</span> <span class="o">=</span> <span class="n">all_atoms</span><span class="o">.</span><span class="n">GetPos</span><span class="p">(</span><span class="n">idx_ca_res_37</span><span class="p">)</span> <span class="o">+</span> <span class="n">geom</span><span class="o">.</span><span class="n">Vec3</span><span class="p">(</span><span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.2</span><span class="p">)</span>
<span class="n">all_atoms</span><span class="o">.</span><span class="n">SetPos</span><span class="p">(</span><span class="n">idx_ca_res_37</span><span class="p">,</span> <span class="n">new_pos</span><span class="p">)</span>
-<span class="c"># insert into ent and store updated entity</span>
+<span class="c1"># insert into ent and store updated entity</span>
<span class="n">all_atoms</span><span class="o">.</span><span class="n">InsertInto</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">ent</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="mi">37</span><span class="p">)</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">ent</span><span class="p">,</span> <span class="s">"all_atom_pos.pdb"</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">ent</span><span class="p">,</span> <span class="s2">"all_atom_pos.pdb"</span><span class="p">)</span>
-<span class="c"># update environment with new positions</span>
+<span class="c1"># update environment with new positions</span>
<span class="n">env</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span><span class="n">all_atoms</span><span class="p">,</span> <span class="mi">36</span><span class="p">)</span>
-<span class="c"># store all positions of environment</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">env</span><span class="o">.</span><span class="n">GetAllAtomPositions</span><span class="p">()</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s">"all_atom_env.pdb"</span><span class="p">)</span>
+<span class="c1"># store all positions of environment</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">env</span><span class="o">.</span><span class="n">GetAllAtomPositions</span><span class="p">()</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s2">"all_atom_env.pdb"</span><span class="p">)</span>
</pre></div>
</div>
<div class="section" id="the-allatomenv-class">
@@ -88,8 +90,8 @@ new loop is being added.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
</tr>
</tbody>
@@ -111,7 +113,7 @@ concatenated one after each other (indexing starts at 0)</li>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</td>
</tr>
@@ -141,7 +143,7 @@ means, that positions in the env. may be reset, newly set or cleared.</p>
<li><strong>new_env_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomEnvPositions" title="promod3.loop.AllAtomEnvPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnvPositions</span></code></a>) – Structural data to be set as environment.</li>
<li><strong>new_pos</strong> (<a class="reference internal" href="#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPositions</span></code></a>) – Structural data to be set as environment.</li>
<li><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Backbone data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the start position in the SEQRES.</li>
<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</li>
</ul>
</td>
@@ -218,7 +220,7 @@ a loop to reset later with <a class="reference internal" href="#promod3.loop.All
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -352,7 +354,7 @@ and if found set the corresponding position, otherwise we unset it.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</li>
</ul>
</td>
</tr>
@@ -398,7 +400,7 @@ out of bounds or if residues in the two containers are inconsistent
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Set position at that index.</li>
-<li><strong>pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</li>
</ul>
</td>
</tr>
@@ -448,7 +450,7 @@ out of bounds or if residues in the two containers are inconsistent
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position at given index.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom position index.</td>
</tr>
@@ -552,7 +554,7 @@ if <em>atom_name</em> is not one of that residue’s heavy atoms.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of residue at index <em>res_index</em>.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</td>
</tr>
@@ -831,9 +833,9 @@ atom (N, CA, C, O).</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">All residues packed in a single chain as an OST entity.
-Connectivity resolved with <code class="xref py py-class docutils literal"><span class="pre">ost.conop.HeuristicProcessor</span></code>.</td>
+Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -853,8 +855,8 @@ function efficient, we require the backbone atoms (N, C, CA) to be set.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>res_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index</li>
-<li><strong>chain</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – Chain into which we insert</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</li>
</ul>
</td>
</tr>
@@ -947,7 +949,7 @@ integer in the range [0, <em>XXX_NUM_HYDROGENS</em>-1].</p>
<dt id="promod3.loop.AminoAcidLookup">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">AminoAcidLookup</code><a class="headerlink" href="#promod3.loop.AminoAcidLookup" title="Permalink to this definition">¶</a></dt>
<dd><p>Collection of static methods to lookup properties of amino acid types
-(<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) and
+(<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>), heavy atom types (<a class="reference internal" href="#promod3.loop.AminoAcidAtom" title="promod3.loop.AminoAcidAtom"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidAtom</span></code></a>) and
hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydrogen" title="promod3.loop.AminoAcidHydrogen"><code class="xref py py-class docutils literal"><span class="pre">AminoAcidHydrogen</span></code></a>).</p>
<dl class="staticmethod">
<dt id="promod3.loop.AminoAcidLookup.GetOLC">
@@ -960,7 +962,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -982,7 +984,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumAtoms(aa)-1])</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
@@ -1012,7 +1014,7 @@ hydrogen types (<a class="reference internal" href="#promod3.loop.AminoAcidHydro
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Atom index (in [0, GetNumHydrogens(aa)-1])</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
@@ -1041,7 +1043,7 @@ atom.</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
</td>
@@ -1069,7 +1071,7 @@ and atom.</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</li>
<li><strong>atom_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Atom name</li>
</ul>
</td>
@@ -1093,7 +1095,7 @@ hydrogens of <em>aa</em>.</p>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -1125,7 +1127,7 @@ hydrogens of <em>aa</em>.</p>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -1158,7 +1160,7 @@ hydrogens of <em>aa</em>.</p>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Amino acid type of the given heavy atom type</p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a></p>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a></p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
@@ -1252,7 +1254,7 @@ when residue is peptide bound.</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if no such atom (i.e. PRO)</td>
</tr>
@@ -1276,7 +1278,7 @@ when residue is N terminal.</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if no such atom (i.e. H3 for PRO)</td>
</tr>
@@ -1333,9 +1335,6 @@ when residue is N terminal.</td>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -1343,11 +1342,11 @@ when residue is N terminal.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/loop/all_atom.txt"
diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index 6bad77d4feef8e70af8d8177c659f86e348f5206..096e988e0855d432d670e2d868e5e9d6da9309ab 100644
--- a/doc/html/loop/backbone.html
+++ b/doc/html/loop/backbone.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Representing Loops — ProMod3 1.1.0 documentation</title>
+ <title>Representing Loops — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
<link rel="prev" title="loop - Loop Handling" href="index.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -44,27 +46,27 @@
<p>The most simple representation of structural information in ProMod3 is the
<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>. It provides a way to store the backbone positions of
residues. They provide structural manipulations, they can be manipulated and
-converted from, to, or inserted to a <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">conop</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">conop</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
-<span class="n">sequence</span> <span class="o">=</span> <span class="s">"AAAAAAAA"</span>
+<span class="n">sequence</span> <span class="o">=</span> <span class="s2">"AAAAAAAA"</span>
-<span class="c"># the backbone gets initially constructed with backbone dihedrals</span>
-<span class="c"># typical for helices</span>
+<span class="c1"># the backbone gets initially constructed with backbone dihedrals</span>
+<span class="c1"># typical for helices</span>
<span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">sequence</span><span class="p">)</span>
-<span class="c"># let's have a look at the set dihedral angles</span>
+<span class="c1"># let's have a look at the set dihedral angles</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">bb_list</span><span class="p">)):</span>
- <span class="k">print</span> <span class="s">"Looking at position </span><span class="si">%d</span><span class="s">"</span> <span class="o">%</span> <span class="n">i</span>
+ <span class="nb">print</span> <span class="s2">"Looking at position </span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="n">i</span>
<span class="k">if</span> <span class="n">i</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
- <span class="k">print</span> <span class="s">"phi: </span><span class="si">%.4f</span><span class="s">"</span> <span class="o">%</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">GetPhiTorsion</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+ <span class="nb">print</span> <span class="s2">"phi: </span><span class="si">%.4f</span><span class="s2">"</span> <span class="o">%</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">GetPhiTorsion</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
<span class="k">if</span> <span class="n">i</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">bb_list</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">:</span>
- <span class="k">print</span> <span class="s">"psi: </span><span class="si">%.4f</span><span class="s">"</span> <span class="o">%</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">GetPsiTorsion</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+ <span class="nb">print</span> <span class="s2">"psi: </span><span class="si">%.4f</span><span class="s2">"</span> <span class="o">%</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">GetPsiTorsion</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
-<span class="c"># we now use a TorsionSampler to set random dihedral angles</span>
+<span class="c1"># we now use a TorsionSampler to set random dihedral angles</span>
<span class="n">torsion_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSampler</span><span class="p">()</span>
<span class="n">idx</span> <span class="o">=</span> <span class="n">torsion_sampler</span><span class="o">.</span><span class="n">GetHistogramIndex</span><span class="p">(</span><span class="n">conop</span><span class="o">.</span><span class="n">ALA</span><span class="p">,</span>
<span class="n">conop</span><span class="o">.</span><span class="n">ALA</span><span class="p">,</span>
@@ -76,8 +78,8 @@ converted from, to, or inserted to a <a class="reference external" href="http://
<span class="k">if</span> <span class="n">i</span> <span class="o"><</span> <span class="nb">len</span><span class="p">(</span><span class="n">bb_list</span><span class="p">)</span><span class="o">-</span><span class="mi">1</span><span class="p">:</span>
<span class="n">bb_list</span><span class="o">.</span><span class="n">SetPsiTorsion</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">dihedrals</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-<span class="c"># let's save down the randomized fragment</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s">"randomized_fragment.pdb"</span><span class="p">)</span>
+<span class="c1"># let's save down the randomized fragment</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s2">"randomized_fragment.pdb"</span><span class="p">)</span>
</pre></div>
</div>
<div class="section" id="the-backbonelist-class">
@@ -158,7 +160,7 @@ code which is not one of the 20 default amino acids or if
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of created BackboneList</li>
-<li><strong>residues</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) – List of <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+<li><strong>residues</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) – List of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
which the backbone positions are extracted.</li>
</ul>
</td>
@@ -182,7 +184,7 @@ a residue not providing all necessary positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to a density map.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -192,7 +194,7 @@ a residue not providing all necessary positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>padding</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – </li>
-<li><strong>sampling</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – </li>
+<li><strong>sampling</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – </li>
<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – </li>
<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – </li>
</ul>
@@ -211,7 +213,7 @@ a residue not providing all necessary positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The whole backbone list converted to an OST entity.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -228,8 +230,8 @@ be replaced, otherwise they will be added to the entity.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>chain</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</li>
+<li><strong>chain</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a>) – The chain</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number defining the start location of insertion</li>
</ul>
</td>
</tr>
@@ -245,7 +247,7 @@ be replaced, otherwise they will be added to the entity.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>map</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a>) – </li>
+<li><strong>map</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a>) – </li>
<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – </li>
<li><strong>high_resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – </li>
</ul>
@@ -264,7 +266,7 @@ be replaced, otherwise they will be added to the entity.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"></td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.AlignedCuboid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>all_atom</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – </td>
</tr>
@@ -367,7 +369,7 @@ actual fragment at specified <em>index</em></p>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Position of nitrogen / alpha carbon / beta carbon / carbon / oxygen
atom for residue at given index.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</td>
</tr>
@@ -392,7 +394,7 @@ atom for residue at given index.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
/ oxygen atom to this.</li>
</ul>
</td>
@@ -444,7 +446,7 @@ atom for residue at given index.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type of the residue at given index.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</td>
</tr>
@@ -461,7 +463,7 @@ atom for residue at given index.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>aa</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Set amino acid type of the residue to this.</li>
</ul>
</td>
</tr>
@@ -487,12 +489,12 @@ and set the amino acid type according to the given one letter code.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
-<li><strong>o_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
<li><strong>olc</strong> (<code class="xref py py-class docutils literal"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
</ul>
</td>
@@ -562,12 +564,12 @@ to the given one letter code.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
-<li><strong>o_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) – Residue from which to extract backbone atom positions</li>
+<li><strong>n_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen atom to this.</li>
+<li><strong>ca_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of alpha carbon atom to this.</li>
+<li><strong>cb_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of beta carbon atom to this.</li>
+<li><strong>c_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of carbon atom to this.</li>
+<li><strong>o_pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of oxygen atom to this.</li>
<li><strong>olc</strong> (<code class="xref py py-class docutils literal"><span class="pre">char</span></code>) – Set one letter code of the residue to this.</li>
</ul>
</td>
@@ -631,7 +633,7 @@ reconstructed if the residue handle is valid.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>after_c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue following the C stem (C stem residue is last
element of this backbone list)</td>
</tr>
</tbody>
@@ -648,7 +650,7 @@ element of this backbone list)</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>transform</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
</ul>
</td>
</tr>
@@ -668,7 +670,7 @@ element of this backbone list)</td>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>from</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Start index.</li>
<li><strong>to</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – End index (one past last residue to transform).</li>
-<li><strong>transform</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
</ul>
</td>
</tr>
@@ -684,7 +686,7 @@ element of this backbone list)</td>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="http://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>transform</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Transform</span></code> / <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td>
</tr>
</tbody>
</table>
@@ -704,12 +706,12 @@ residue <em>other_index</em> of <em>other</em> backbone list considering the
positions of the N, CA and C atoms.</p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="http://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></p>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index.</li>
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The other residue.</li>
<li><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</li>
<li><strong>other_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Residue index in <em>other</em> backbone list.</li>
</ul>
@@ -729,7 +731,7 @@ positions of the N, CA and C atoms.</p>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Get minimum RMSD transformation of CA positions of this backbone
list onto CA positions of <em>other</em> backbone list.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>other</strong> (<a class="reference internal" href="#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The other backbone list.</td>
</tr>
@@ -994,9 +996,6 @@ backbone list.</td>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -1004,11 +1003,11 @@ backbone list.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/loop/backbone.txt"
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index 26fc9a364cac64b1de012f48f2c7f886312da19b..4ceff047a047b214b7ec544b3426b6026963b818 100644
--- a/doc/html/loop/index.html
+++ b/doc/html/loop/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>loop - Loop Handling — ProMod3 1.1.0 documentation</title>
+ <title>loop - Loop Handling — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Representing Loops" href="backbone.html" />
- <link rel="prev" title="All Atom Scorers" href="../scoring/all_atom_scorers.html" />
+ <link rel="prev" title="Other Scoring Functions" href="../scoring/other_scoring_functions.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -44,14 +46,14 @@
<p>Tools and algorithms for loop handling. This module provides ways for
representation of peptides and to obtain fragments to potentially use as
loops. The following example should give you an idea of what can be done:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
-<span class="c"># load an example structure</span>
-<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1CRN.pdb'</span><span class="p">)</span>
+<span class="c1"># load an example structure</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
-<span class="c"># extract some additional information</span>
-<span class="n">seqres</span> <span class="o">=</span> <span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
+<span class="c1"># extract some additional information</span>
+<span class="n">seqres</span> <span class="o">=</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
<span class="n">frag_pos</span> <span class="o">=</span> <span class="mi">35</span>
<span class="n">frag_length</span> <span class="o">=</span> <span class="mi">9</span>
<span class="n">frag_seq</span> <span class="o">=</span> <span class="n">seqres</span><span class="p">[</span><span class="n">frag_pos</span><span class="p">:</span><span class="n">frag_pos</span><span class="o">+</span><span class="n">frag_length</span><span class="p">]</span>
@@ -60,29 +62,29 @@ loops. The following example should give you an idea of what can be done:</p>
<span class="n">n_stem</span> <span class="o">=</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">frag_pos</span><span class="p">]</span>
<span class="n">c_stem</span> <span class="o">=</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">frag_pos</span><span class="o">+</span><span class="n">frag_length</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
-<span class="c"># extract potential loops from fragment database based on geometry</span>
+<span class="c1"># extract potential loops from fragment database based on geometry</span>
<span class="n">frag_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">()</span>
<span class="n">fragments</span> <span class="o">=</span> <span class="n">frag_db</span><span class="o">.</span><span class="n">SearchDB</span><span class="p">(</span><span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">,</span> <span class="n">frag_length</span><span class="p">)</span>
-<span class="k">print</span> <span class="s">"Num. fragments found in FragDB: </span><span class="si">%d</span><span class="s">"</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">fragments</span><span class="p">)</span>
-<span class="c"># compare with reference</span>
+<span class="nb">print</span> <span class="s2">"Num. fragments found in FragDB: </span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">fragments</span><span class="p">)</span>
+<span class="c1"># compare with reference</span>
<span class="n">struct_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fragments</span><span class="p">)):</span>
- <span class="c"># get structure from structural database</span>
+ <span class="c1"># get structure from structural database</span>
<span class="n">bb_list</span> <span class="o">=</span> <span class="n">struct_db</span><span class="o">.</span><span class="n">GetBackboneList</span><span class="p">(</span><span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">,</span>
<span class="n">fragments</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">frag_seq</span><span class="p">)</span>
- <span class="n">ca_rmsd</span> <span class="o">=</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">CARMSD</span><span class="p">(</span><span class="n">ref_backbone</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
- <span class="k">print</span> <span class="s">"-> fragment </span><span class="si">%d</span><span class="s"> has CA RMSD of </span><span class="si">%.3f</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">ca_rmsd</span><span class="p">)</span>
+ <span class="n">ca_rmsd</span> <span class="o">=</span> <span class="n">bb_list</span><span class="o">.</span><span class="n">CARMSD</span><span class="p">(</span><span class="n">ref_backbone</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
+ <span class="nb">print</span> <span class="s2">"-> fragment </span><span class="si">%d</span><span class="s2"> has CA RMSD of </span><span class="si">%.3f</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">ca_rmsd</span><span class="p">)</span>
-<span class="c"># extract potential loops from fragment database based on sequence</span>
+<span class="c1"># extract potential loops from fragment database based on sequence</span>
<span class="n">fragger</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">Fragger</span><span class="p">(</span><span class="n">frag_seq</span><span class="p">)</span>
-<span class="c"># for simplicity we just use a sequence similarity score</span>
+<span class="c1"># for simplicity we just use a sequence similarity score</span>
<span class="n">fragger</span><span class="o">.</span><span class="n">AddSeqSimParameters</span><span class="p">(</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">seq</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">BLOSUM62</span><span class="p">)</span>
<span class="n">fragger</span><span class="o">.</span><span class="n">Fill</span><span class="p">(</span><span class="n">struct_db</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
-<span class="k">print</span> <span class="s">"Num. fragments found in Fragger: </span><span class="si">%d</span><span class="s">"</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">fragger</span><span class="p">)</span>
-<span class="c"># compare fraggers with reference</span>
+<span class="nb">print</span> <span class="s2">"Num. fragments found in Fragger: </span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">fragger</span><span class="p">)</span>
+<span class="c1"># compare fraggers with reference</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fragger</span><span class="p">)):</span>
- <span class="n">ca_rmsd</span> <span class="o">=</span> <span class="n">fragger</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">CARMSD</span><span class="p">(</span><span class="n">ref_backbone</span><span class="p">,</span> <span class="bp">True</span><span class="p">)</span>
- <span class="k">print</span> <span class="s">"-> fragment </span><span class="si">%d</span><span class="s"> has CA RMSD of </span><span class="si">%.3f</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">ca_rmsd</span><span class="p">)</span>
+ <span class="n">ca_rmsd</span> <span class="o">=</span> <span class="n">fragger</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">CARMSD</span><span class="p">(</span><span class="n">ref_backbone</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
+ <span class="nb">print</span> <span class="s2">"-> fragment </span><span class="si">%d</span><span class="s2"> has CA RMSD of </span><span class="si">%.3f</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">ca_rmsd</span><span class="p">)</span>
</pre></div>
</div>
<p>Contents:</p>
@@ -132,7 +134,7 @@ loops. The following example should give you an idea of what can be done:</p>
<ul>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
- <li>Previous: <a href="../scoring/all_atom_scorers.html" title="previous chapter">All Atom Scorers</a></li>
+ <li>Previous: <a href="../scoring/other_scoring_functions.html" title="previous chapter">Other Scoring Functions</a></li>
<li>Next: <a href="backbone.html" title="next chapter">Representing Loops</a></li>
</ul></li>
</ul></li>
@@ -153,9 +155,6 @@ loops. The following example should give you an idea of what can be done:</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -163,11 +162,11 @@ loops. The following example should give you an idea of what can be done:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/loop/index.txt"
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index 56f91dea84cc704904c77f5eb31e1cdb7f96a875..8425953c8165937468f1c690d1e44d38250cfe99 100644
--- a/doc/html/loop/load_loop_objects.html
+++ b/doc/html/loop/load_loop_objects.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Loading Precomputed Objects — ProMod3 1.1.0 documentation</title>
+ <title>Loading Precomputed Objects — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="core - ProMod3 Core Functionality" href="../core/index.html" />
<link rel="prev" title="Generate ost.mol.mm systems" href="mm_system_creation.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -201,9 +203,6 @@ Proteins, 62(4):892–908, Mar 2006.</dd>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -211,11 +210,11 @@ Proteins, 62(4):892–908, Mar 2006.</dd>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/loop/load_loop_objects.txt"
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index 0c214fb25876f02900cc6f80891671864c4882a5..38cdf31e4748d13ed4624067799504894827ea98 100644
--- a/doc/html/loop/mm_system_creation.html
+++ b/doc/html/loop/mm_system_creation.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Generate ost.mol.mm systems — ProMod3 1.1.0 documentation</title>
+ <title>Generate ost.mol.mm systems — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Loading Precomputed Objects" href="load_loop_objects.html" />
<link rel="prev" title="Handling All Atom Positions" href="all_atom.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -40,49 +42,49 @@
<div class="body" role="main">
<div class="section" id="generate-ost-mol-mm-systems">
-<h1>Generate <code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
-<p>To simplify the creation of <code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code> / OpenMM simulations for loops in
+<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> systems<a class="headerlink" href="#generate-ost-mol-mm-systems" title="Permalink to this headline">¶</a></h1>
+<p>To simplify the creation of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
proteins, we define a system creator for loops (<a class="reference internal" href="#promod3.loop.MmSystemCreator" title="promod3.loop.MmSystemCreator"><code class="xref py py-class docutils literal"><span class="pre">MmSystemCreator</span></code></a>) and a
specialized forcefield lookup for amino acids (<a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a>).</p>
<p>The example below showcases the creation and use of an MM system:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">geom</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">geom</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
-<span class="c"># setup system creator</span>
+<span class="c1"># setup system creator</span>
<span class="n">ff_lookup</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">ForcefieldLookup</span><span class="o">.</span><span class="n">GetDefault</span><span class="p">()</span>
<span class="n">mm_sys</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">MmSystemCreator</span><span class="p">(</span><span class="n">ff_lookup</span><span class="p">)</span>
-<span class="c"># load example (has res. numbering starting at 1)</span>
-<span class="n">ent</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">"data/1CRN.pdb"</span><span class="p">)</span>
+<span class="c1"># load example (has res. numbering starting at 1)</span>
+<span class="n">ent</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s2">"data/1CRN.pdb"</span><span class="p">)</span>
<span class="n">res_list</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">residues</span>
<span class="n">num_residues</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">res_list</span><span class="p">)</span>
-<span class="c"># get all atom positions for full protein</span>
+<span class="c1"># get all atom positions for full protein</span>
<span class="n">all_atoms</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">AllAtomPositions</span><span class="p">(</span><span class="n">res_list</span><span class="p">)</span>
-<span class="c"># here full structure in res_indices but in practice this could</span>
-<span class="c"># be just a subset of residues relevant to the loop of interest</span>
+<span class="c1"># here full structure in res_indices but in practice this could</span>
+<span class="c1"># be just a subset of residues relevant to the loop of interest</span>
<span class="n">res_indices</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="n">num_residues</span><span class="p">)</span>
-<span class="c"># define two loops (indices into res_indices list)</span>
+<span class="c1"># define two loops (indices into res_indices list)</span>
<span class="n">loop_start_indices</span> <span class="o">=</span> <span class="p">[</span><span class="mi">10</span><span class="p">,</span> <span class="mi">20</span><span class="p">]</span>
<span class="n">loop_lengths</span> <span class="o">=</span> <span class="p">[</span><span class="mi">6</span><span class="p">,</span> <span class="mi">4</span><span class="p">]</span>
-<span class="c"># define which of the res_indices is terminal</span>
-<span class="n">is_n_ter</span> <span class="o">=</span> <span class="p">[</span><span class="bp">True</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="bp">False</span><span class="p">]</span> <span class="o">*</span> <span class="p">(</span><span class="n">num_residues</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span>
-<span class="n">is_c_ter</span> <span class="o">=</span> <span class="p">[</span><span class="bp">False</span><span class="p">]</span> <span class="o">*</span> <span class="p">(</span><span class="n">num_residues</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="p">[</span><span class="bp">True</span><span class="p">]</span>
-<span class="c"># get disulfid bridges</span>
+<span class="c1"># define which of the res_indices is terminal</span>
+<span class="n">is_n_ter</span> <span class="o">=</span> <span class="p">[</span><span class="kc">True</span><span class="p">]</span> <span class="o">+</span> <span class="p">[</span><span class="kc">False</span><span class="p">]</span> <span class="o">*</span> <span class="p">(</span><span class="n">num_residues</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span>
+<span class="n">is_c_ter</span> <span class="o">=</span> <span class="p">[</span><span class="kc">False</span><span class="p">]</span> <span class="o">*</span> <span class="p">(</span><span class="n">num_residues</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="o">+</span> <span class="p">[</span><span class="kc">True</span><span class="p">]</span>
+<span class="c1"># get disulfid bridges</span>
<span class="n">disulfid_bridges</span> <span class="o">=</span> <span class="n">mm_sys</span><span class="o">.</span><span class="n">GetDisulfidBridges</span><span class="p">(</span><span class="n">all_atoms</span><span class="p">,</span> <span class="n">res_indices</span><span class="p">)</span>
-<span class="c"># setup MM system</span>
+<span class="c1"># setup MM system</span>
<span class="n">mm_sys</span><span class="o">.</span><span class="n">SetupSystem</span><span class="p">(</span><span class="n">all_atoms</span><span class="p">,</span> <span class="n">res_indices</span><span class="p">,</span> <span class="n">loop_start_indices</span><span class="p">,</span>
<span class="n">loop_lengths</span><span class="p">,</span> <span class="n">is_n_ter</span><span class="p">,</span> <span class="n">is_c_ter</span><span class="p">,</span> <span class="n">disulfid_bridges</span><span class="p">)</span>
-<span class="c"># run simulation</span>
+<span class="c1"># run simulation</span>
<span class="n">sim</span> <span class="o">=</span> <span class="n">mm_sys</span><span class="o">.</span><span class="n">GetSimulation</span><span class="p">()</span>
-<span class="k">print</span> <span class="s">"Potential energy before: </span><span class="si">%g</span><span class="s">"</span> <span class="o">%</span> <span class="n">sim</span><span class="o">.</span><span class="n">GetPotentialEnergy</span><span class="p">()</span>
+<span class="nb">print</span> <span class="s2">"Potential energy before: </span><span class="si">%g</span><span class="s2">"</span> <span class="o">%</span> <span class="n">sim</span><span class="o">.</span><span class="n">GetPotentialEnergy</span><span class="p">()</span>
<span class="n">sim</span><span class="o">.</span><span class="n">ApplySD</span><span class="p">(</span><span class="mf">0.01</span><span class="p">,</span> <span class="mi">100</span><span class="p">)</span>
-<span class="k">print</span> <span class="s">"Potential energy after: </span><span class="si">%g</span><span class="s">"</span> <span class="o">%</span> <span class="n">sim</span><span class="o">.</span><span class="n">GetPotentialEnergy</span><span class="p">()</span>
+<span class="nb">print</span> <span class="s2">"Potential energy after: </span><span class="si">%g</span><span class="s2">"</span> <span class="o">%</span> <span class="n">sim</span><span class="o">.</span><span class="n">GetPotentialEnergy</span><span class="p">()</span>
-<span class="c"># extract new loop positions and store it</span>
+<span class="c1"># extract new loop positions and store it</span>
<span class="n">mm_sys</span><span class="o">.</span><span class="n">ExtractLoopPositions</span><span class="p">(</span><span class="n">all_atoms</span><span class="p">,</span> <span class="n">res_indices</span><span class="p">)</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">all_atoms</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s">"mm_sys_output.pdb"</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">all_atoms</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s2">"mm_sys_output.pdb"</span><span class="p">)</span>
</pre></div>
</div>
<div class="admonition note">
@@ -286,7 +288,7 @@ acid types for <em>out_pos[res_indices[i]]</em> and <em>all_pos[res_indices[i]]<
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Simulation object setup by <a class="reference internal" href="#promod3.loop.MmSystemCreator.SetupSystem" title="promod3.loop.MmSystemCreator.SetupSystem"><code class="xref py py-meth docutils literal"><span class="pre">SetupSystem()</span></code></a>. Use this to run
MM simulations.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
</tr>
</tbody>
</table>
@@ -433,7 +435,7 @@ FF specific data for amino acids in a protein. We distinguish amino acid types
<dl class="class">
<dt id="promod3.loop.ForcefieldLookup">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLookup</code><a class="headerlink" href="#promod3.loop.ForcefieldLookup" title="Permalink to this definition">¶</a></dt>
-<dd><p>This class provides all functionality to generate <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
+<dd><p>This class provides all functionality to generate <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a> objects. Specifically, we can:</p>
<ul class="simple">
<li>get a consistent indexing of each atom of each residue in [<em>0, N-1</em>], where
<em>N</em> = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a> (note that only OXT indexing depends on whether a
@@ -511,7 +513,7 @@ less machine-dependent).</p>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.ForcefieldLookup" title="promod3.loop.ForcefieldLookup"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldLookup</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -523,7 +525,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.loop.ForcefieldLookup.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.ForcefieldLookup.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -546,7 +548,7 @@ for details.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Amino acid type for given <em>ff_aa</em></td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ff_aa</strong> (<a class="reference internal" href="#promod3.loop.ForcefieldAminoAcid" title="promod3.loop.ForcefieldAminoAcid"><code class="xref py py-class docutils literal"><span class="pre">ForcefieldAminoAcid</span></code></a>) – Forcefield-specific amino acid type</td>
</tr>
@@ -662,7 +664,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for LJ 1,4 interactions (see
-<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeLJ()</span></code></a>)</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
</tr>
@@ -678,7 +680,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Dampening factor for electrostatic 1,4 interactions (see
-<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetFudgeQQ()</span></code></a>)</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></td>
</tr>
@@ -693,7 +695,7 @@ for details.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Mass for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetMasses()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -717,7 +719,7 @@ for details.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Charge for each atom (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetCharges()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -742,7 +744,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Sigma in nm for each atom
-(see <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetSigmas()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -767,7 +769,7 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Epsilon in kJ/mol for each atom
-(see <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.SetEpsilons()</span></code></a>)</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> (length = <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">GetNumAtoms()</span></code></a>)</p>
@@ -913,7 +915,7 @@ for details.</p>
<dt id="promod3.loop.ForcefieldAminoAcid">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldAminoAcid</code><a class="headerlink" href="#promod3.loop.ForcefieldAminoAcid" title="Permalink to this definition">¶</a></dt>
<dd><p>Enumerates the amino acid types for forcefields. The first 20 values
-correspond to the 20 values of <a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
+correspond to the 20 values of <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>. Additionally,
there are values for disulfid bridges (<em>FF_CYS2</em>), d-protonated histidine
(<em>FF_HISD</em>, default for <em>ost.conop.HIS</em> is <em>FF_HISE</em>) and <em>FF_XXX</em> for unknown
types. The full list of values is:</p>
@@ -930,7 +932,7 @@ types. The full list of values is:</p>
<dd><p>Contains lists of bonds, angles, dihedrals, impropers and LJ pairs (exclusions
are the combination of all bonds and 1,3 pairs of angles and are not stored
separately). Each type of connectivity has it’s own class (see below) storing
-indices and parameters to be used for methods of <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Topology</span></code></a>.
+indices and parameters to be used for methods of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Topology</span></code></a>.
The indexing of atoms for internal connectivities is in [<em>0, N-1</em>], where <em>N</em>
= <a class="reference internal" href="#promod3.loop.ForcefieldLookup.GetNumAtoms" title="promod3.loop.ForcefieldLookup.GetNumAtoms"><code class="xref py py-meth docutils literal"><span class="pre">ForcefieldLookup.GetNumAtoms()</span></code></a>. For connectivities of pairs of
residues, atoms of the first residue are in [<em>0, N1-1</em>] and atoms of the
@@ -1040,7 +1042,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldBondInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldBondInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic bond (see <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
+<dd><p>Define harmonic bond (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicBond()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldBondInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldBondInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1102,7 +1104,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic angle (see <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
+<dd><p>Define harmonic angle (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicAngleInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1179,7 +1181,7 @@ False, False)</em>.</p>
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldUreyBradleyAngleInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define Urey-Bradley angle
-(see <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
+(see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddUreyBradleyAngle()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldUreyBradleyAngleInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1284,8 +1286,8 @@ False, False)</em>.</p>
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldPeriodicDihedralInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>Define periodic dihedral or improper (see
-<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
-<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicDihedral()</span></code></a> and
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddPeriodicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldPeriodicDihedralInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldPeriodicDihedralInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1389,7 +1391,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldHarmonicImproperInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define harmonic improper (see <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
+<dd><p>Define harmonic improper (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddHarmonicImproper()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldHarmonicImproperInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldHarmonicImproperInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1479,7 +1481,7 @@ False, False)</em>.</p>
<dl class="class">
<dt id="promod3.loop.ForcefieldLJPairInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">ForcefieldLJPairInfo</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>Define LJ pair (see <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
+<dd><p>Define LJ pair (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.mm.Topology.AddLJPair()</span></code></a>)</p>
<dl class="attribute">
<dt id="promod3.loop.ForcefieldLJPairInfo.index_one">
<code class="descname">index_one</code><a class="headerlink" href="#promod3.loop.ForcefieldLJPairInfo.index_one" title="Permalink to this definition">¶</a></dt>
@@ -1583,9 +1585,6 @@ False, False)</em>.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -1593,11 +1592,11 @@ False, False)</em>.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/loop/mm_system_creation.txt"
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 3cd58befeece6c7b0a2c8e9667378dd6f46fb7ba..9e2c5705f18ee62396096e5fb1a4622a9ff814dc 100644
--- a/doc/html/loop/structure_db.html
+++ b/doc/html/loop/structure_db.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Structural Data — ProMod3 1.1.0 documentation</title>
+ <title>Structural Data — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Handling All Atom Positions" href="all_atom.html" />
<link rel="prev" title="Sampling Dihedral Angles" href="torsion_sampler.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -41,57 +43,89 @@
<div class="section" id="structural-data">
<h1>Structural Data<a class="headerlink" href="#structural-data" title="Permalink to this headline">¶</a></h1>
-<p>The structural database serves as a container for structural backbone
-and profile data. It can be filled with chains of pdb structures with their
-corresponding profiles as they are produced by the HHSuite tools <a class="reference internal" href="#soding2005" id="id1">[soding2005]</a>.
-Structural and profile data get complemented by with additional information.
-Following features get stored on a per residue basis:</p>
-<ul class="simple">
-<li>The amino acid one letter code</li>
-<li>The coordinates of the backbone atoms (N,CA,C,O)</li>
+<p>The structural database serves as a container for structural backbone and
+sequence data. Custom accessor objects can be implemented that relate
+arbitrary features to structural data. Examples provided by ProMod3 include
+accession using matching stem geometry (see: <a class="reference internal" href="#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) or sequence
+features (see: <a class="reference internal" href="#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a>).
+Besides backbone and sequence data, derived features can
+optionally be stored. E.g. sequence profiles or secondary structure information.
+Optional data includes:</p>
+<blockquote>
+<div><ul class="simple">
<li>The phi/psi dihedral angles</li>
<li>The secondary structure state as defined by dssp</li>
<li>The solvent accessibility in square Angstrom</li>
-<li>The residue depth defined as the average distance from all atoms of a
-residue to the closest surface vertex as calculated by msms <a class="reference internal" href="#sanner1996" id="id2">[sanner1996]</a>.
-This is a simplified version of the residue depth as discussed in
-<a class="reference internal" href="#chakravarty1999" id="id3">[chakravarty1999]</a> and gets directly calculated when structural information
-gets added to the StructureDB.</li>
<li>The amino acid frequencies as given by an input sequence profile</li>
+<li>The residue depth - The residue depth is defined as the minimum distance of
+a residue towards any of the exposed residues.
+Distances are calculated using CB positions (artificially constructed in case
+of glycine) and exposed is defined as:
+relative solvent accessibility > 25% and at least one atom being exposed
+to the OUTER surface. To determine whether an atom is part of that outer
+surface, the full structure is placed into a 3D grid and a flood fill
+algorithm is used to determine the atoms of interest.
+Internal cavities are excluded by using this approach. This is a simplified
+version of the residue depth as discussed in <a class="reference internal" href="#chakravarty1999" id="id1">[chakravarty1999]</a> and gets
+directly calculated when structural information is added to the StructureDB.</li>
<li>The amino acid frequency derived from structural alignments as described
-in <a class="reference internal" href="#zhou2005" id="id4">[zhou2005]</a> - Since the calculation of such a profile already requires a
+in <a class="reference internal" href="#zhou2005" id="id2">[zhou2005]</a> - Since the calculation of such a profile already requires a
StructureDB, we end up in a hen and egg problem here... When adding
structural information to the StructureDB, the according memory gets
just allocated and set to zero. The usage of this information
is therefore only meaningful if you calculate these profiles
and manually set them (or load the provided default database).</li>
</ul>
+</div></blockquote>
<div class="section" id="defining-chains-and-fragments">
<h2>Defining Chains and Fragments<a class="headerlink" href="#defining-chains-and-fragments" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.loop.CoordInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">CoordInfo</code><a class="headerlink" href="#promod3.loop.CoordInfo" title="Permalink to this definition">¶</a></dt>
<dd><p>The CoordInfo gets automatically generated when new chains are added to
-the structural database. It contains internal information of how
-the according chain is stored in the database.</p>
+the structural database. It contains internal information of how a
+connected stretch of residues is stored in the database.</p>
+<dl class="attribute">
+<dt id="promod3.loop.CoordInfo.id">
+<code class="descname">id</code><a class="headerlink" href="#promod3.loop.CoordInfo.id" title="Permalink to this definition">¶</a></dt>
+<dd><p>An id string specified when adding the corresponding stretch to the
+structure db</p>
+</dd></dl>
+
<dl class="attribute">
-<dt id="promod3.loop.CoordInfo.pdb_id">
-<code class="descname">pdb_id</code><a class="headerlink" href="#promod3.loop.CoordInfo.pdb_id" title="Permalink to this definition">¶</a></dt>
-<dd><p>A character residue string containing the 4 character pdb_id and the
-1 character chain_id. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>)</p>
+<dt id="promod3.loop.CoordInfo.chain_name">
+<code class="descname">chain_name</code><a class="headerlink" href="#promod3.loop.CoordInfo.chain_name" title="Permalink to this definition">¶</a></dt>
+<dd><p>A chain name string specified when adding the corresponding stretch to the
+structure db</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.offset">
<code class="descname">offset</code><a class="headerlink" href="#promod3.loop.CoordInfo.offset" title="Permalink to this definition">¶</a></dt>
-<dd><p>All residues of the added structures are stored in a linear memory layout.
-The offset parameter tells us where it exactly starts. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+<dd><p>All residues of the added stretch are stored in a linear memory layout.
+The offset parameter tells us where it exactly starts in the global data
+structure. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.CoordInfo.size">
<code class="descname">size</code><a class="headerlink" href="#promod3.loop.CoordInfo.size" title="Permalink to this definition">¶</a></dt>
-<dd><p>The length of the stretch of residues. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+<dd><p>The number of residues in that stretch (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.loop.CoordInfo.start_resnum">
+<code class="descname">start_resnum</code><a class="headerlink" href="#promod3.loop.CoordInfo.start_resnum" title="Permalink to this definition">¶</a></dt>
+<dd><p>Residue number of first residue in the added stretch. The residue number
+is relative to the SEQRES provided in the input profile when adding the
+stuff to the structure db.</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.loop.CoordInfo.shift">
+<code class="descname">shift</code><a class="headerlink" href="#promod3.loop.CoordInfo.shift" title="Permalink to this definition">¶</a></dt>
+<dd><p>Translation from original coordinates that has been applied before storing
+structural information in db.</p>
</dd></dl>
</dd></dl>
@@ -99,7 +133,8 @@ The offset parameter tells us where it exactly starts. (<a class="reference exte
<dl class="class">
<dt id="promod3.loop.FragmentInfo">
<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">FragmentInfo</code><span class="sig-paren">(</span><em>chain_index</em>, <em>offset</em>, <em>length</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragmentInfo" title="Permalink to this definition">¶</a></dt>
-<dd><p>The FragmentInfo defines a fragment in the structural database.</p>
+<dd><p>The FragmentInfo defines any fragment in the structural database. If you
+implement your own accessor object, thats the information you want to store.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -116,13 +151,14 @@ The offset parameter tells us where it exactly starts. (<a class="reference exte
<dl class="attribute">
<dt id="promod3.loop.FragmentInfo.chain_index">
<code class="descname">chain_index</code><a class="headerlink" href="#promod3.loop.FragmentInfo.chain_index" title="Permalink to this definition">¶</a></dt>
-<dd><p>The index of the chain (defined by <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a>) in the structure db this particle belongs to. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+<dd><p>The index of the chain (defined by <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a>) in the structure db
+this particle belongs to. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.loop.FragmentInfo.offset">
<code class="descname">offset</code><a class="headerlink" href="#promod3.loop.FragmentInfo.offset" title="Permalink to this definition">¶</a></dt>
-<dd><p>Index of residue in <strong>chain</strong> the fragment starts. (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
+<dd><p>Index of residue in <strong>chain</strong> the fragment starts. (0-based, <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
@@ -138,97 +174,141 @@ The offset parameter tells us where it exactly starts. (<a class="reference exte
<h2>The Structure Database<a class="headerlink" href="#the-structure-database" title="Permalink to this headline">¶</a></h2>
<p>The following code example demonstrates how to create a structural database
and fill it with content.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
<span class="kn">import</span> <span class="nn">os</span>
-<span class="c"># we also need the external tools dssp and msms, you have to make</span>
-<span class="c"># sure that they are somewhere in your PATH</span>
-<span class="kn">from</span> <span class="nn">ost.bindings</span> <span class="kn">import</span> <span class="n">dssp</span>
-<span class="kn">from</span> <span class="nn">ost.bindings</span> <span class="kn">import</span> <span class="n">msms</span>
-
-<span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">StructureDB</span><span class="p">()</span>
+<span class="c1"># StructureDB where all data get extracted</span>
+<span class="n">structure_db_one</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">StructureDB</span><span class="p">(</span><span class="n">loop</span><span class="o">.</span><span class="n">StructureDBDataType</span><span class="o">.</span><span class="n">All</span><span class="p">)</span>
-<span class="c"># lets fill in some structures. It gets assumed, that all required</span>
-<span class="c"># data lies in the following directories</span>
-<span class="n">structure_dir</span> <span class="o">=</span> <span class="s">"data"</span>
-<span class="n">prof_dir</span> <span class="o">=</span> <span class="s">"data"</span>
+<span class="c1"># StructureDB where we only have the default data </span>
+<span class="c1"># (positions and sequence) plus residue depths and dihedrals.</span>
+<span class="c1"># In order to pass the required flags, we use a bitwise or.</span>
+<span class="n">structure_db_two</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">StructureDB</span><span class="p">(</span>
+ <span class="n">loop</span><span class="o">.</span><span class="n">StructureDBDataType</span><span class="o">.</span><span class="n">ResidueDepths</span> <span class="o">|</span>
+ <span class="n">loop</span><span class="o">.</span><span class="n">StructureDBDataType</span><span class="o">.</span><span class="n">Dihedrals</span><span class="p">)</span>
-<span class="c"># the first 4 letters are suposed to be the pdb id, and the last one</span>
-<span class="c"># the corresponding chain name. The naming of the files in the</span>
-<span class="c"># directories is e.g. 1CRN.pdb for the structure and 1CRNA.hhm for</span>
-<span class="c"># the profile. Please note, that the structure can contain several</span>
-<span class="c"># chains, whereas the hhm file is only for that specific chain.</span>
-<span class="n">ids</span> <span class="o">=</span> <span class="p">[</span><span class="s">"1CRNA"</span><span class="p">,</span> <span class="s">"1AKIA"</span><span class="p">]</span>
+<span class="c1"># Lets fill in some structures. It gets assumed, that all required</span>
+<span class="c1"># data lies in the following directories.</span>
+<span class="n">structure_dir</span> <span class="o">=</span> <span class="s2">"data"</span>
+<span class="n">prof_dir</span> <span class="o">=</span> <span class="s2">"data"</span>
-<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">ids</span><span class="p">:</span>
+<span class="c1"># The naming of the files in the directories is e.g. 1CRN.pdb for </span>
+<span class="c1"># the structure and 1CRNA.hhm for the profile. Please note, </span>
+<span class="c1"># that the structure can contain several chains, whereas the hhm </span>
+<span class="c1"># file is only for that specific chain.</span>
+<span class="n">structure_ids</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"1CRN"</span><span class="p">,</span> <span class="s2">"1AKI"</span><span class="p">]</span>
+<span class="n">chain_names</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"A"</span><span class="p">,</span> <span class="s2">"A"</span><span class="p">]</span>
- <span class="n">pdb_id</span> <span class="o">=</span> <span class="n">i</span><span class="p">[:</span><span class="mi">4</span><span class="p">]</span>
- <span class="n">chain_id</span> <span class="o">=</span> <span class="n">i</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
+<span class="k">for</span> <span class="n">s_id</span><span class="p">,</span> <span class="n">ch_name</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">structure_ids</span><span class="p">,</span> <span class="n">chain_names</span><span class="p">):</span>
- <span class="c"># join together the data paths</span>
- <span class="n">structure_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">structure_dir</span><span class="p">,</span> <span class="n">pdb_id</span> <span class="o">+</span> <span class="s">".pdb"</span><span class="p">)</span>
- <span class="n">prof_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">prof_dir</span><span class="p">,</span> <span class="n">pdb_id</span> <span class="o">+</span> <span class="n">chain_id</span> <span class="o">+</span> <span class="s">".hhm"</span><span class="p">)</span>
+ <span class="c1"># Join together the data paths.</span>
+ <span class="n">structure_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">structure_dir</span><span class="p">,</span> <span class="n">s_id</span> <span class="o">+</span> <span class="s2">".pdb"</span><span class="p">)</span>
+ <span class="n">prof_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">prof_dir</span><span class="p">,</span> <span class="n">s_id</span> <span class="o">+</span> <span class="n">ch_name</span> <span class="o">+</span> <span class="s2">".hhm"</span><span class="p">)</span>
- <span class="c"># let's load the structure</span>
- <span class="n">structure</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="n">structure_path</span><span class="p">)</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"peptide=True"</span><span class="p">)</span>
- <span class="n">single_chain_structure</span> <span class="o">=</span> <span class="n">structure</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"cname="</span> <span class="o">+</span> <span class="n">chain_id</span><span class="p">)</span>
+ <span class="c1"># Let's load the structure.</span>
+ <span class="n">structure</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="n">structure_path</span><span class="p">)</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"peptide=True"</span><span class="p">)</span>
- <span class="c"># and the according profile in hhm format</span>
+ <span class="c1"># And the according profile in hhm format.</span>
<span class="n">prof</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadSequenceProfile</span><span class="p">(</span><span class="n">prof_path</span><span class="p">)</span>
- <span class="c"># we run dssp in a way, that the secondary structure, as well as</span>
- <span class="c"># the solvent accessibily gets assigned</span>
- <span class="n">dssp</span><span class="o">.</span><span class="n">AssignDSSP</span><span class="p">(</span><span class="n">structure</span><span class="p">,</span> <span class="n">extract_burial_status</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
-
- <span class="c"># as a final step we need the surface as calculated by msms</span>
- <span class="n">surf</span> <span class="o">=</span> <span class="n">msms</span><span class="o">.</span><span class="n">CalculateSurface</span><span class="p">(</span><span class="n">structure</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
-
- <span class="c"># let's add it! Please note, that we calculated solvent </span>
- <span class="c"># accessiblity / secondary structure and surface on the full</span>
- <span class="c"># structure but only add one of the chains.</span>
- <span class="n">structure_db</span><span class="o">.</span><span class="n">AddCoordinates</span><span class="p">(</span><span class="n">pdb_id</span><span class="p">,</span> <span class="n">chain_id</span><span class="p">,</span>
- <span class="n">single_chain_structure</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span>
- <span class="n">surf</span><span class="p">,</span> <span class="n">prof</span><span class="p">)</span>
-
-<span class="c"># we now have two structures in the database...</span>
-
-<span class="c"># Please note, that there is no profile derived from structures</span>
-<span class="c"># assigned yet. To demonstrate, we use our small db to derive</span>
-<span class="c"># profiles.</span>
-<span class="n">src_db</span> <span class="o">=</span> <span class="n">structure_db</span>
-<span class="c"># In practice you might want to use the default StructureDB instead:</span>
-<span class="c"># src_db = loop.LoadStructureDB()</span>
-
-<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">structure_db</span><span class="o">.</span><span class="n">GetNumCoords</span><span class="p">()):</span>
- <span class="c"># get the CoordInfo for chain with index i </span>
- <span class="n">coord_info</span> <span class="o">=</span> <span class="n">structure_db</span><span class="o">.</span><span class="n">GetCoordInfo</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
- <span class="c"># define a fragment, that covers the full length</span>
+ <span class="c1"># For simplicity we use as SEQRES the sequence from the profile.</span>
+ <span class="c1"># In this case the numbering of the structures already matches.</span>
+ <span class="n">seqres</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="n">ch_name</span><span class="p">,</span> <span class="n">prof</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span>
+
+ <span class="c1"># Add the stuff to the first StructureDB</span>
+ <span class="n">structure_db_one</span><span class="o">.</span><span class="n">AddCoordinates</span><span class="p">(</span><span class="n">s_id</span><span class="p">,</span> <span class="n">ch_name</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span>
+ <span class="n">seqres</span><span class="p">,</span> <span class="n">prof</span><span class="p">)</span>
+
+ <span class="c1"># Add the stuff to the second StructureDB, </span>
+ <span class="c1"># No profile required here...</span>
+ <span class="n">structure_db_two</span><span class="o">.</span><span class="n">AddCoordinates</span><span class="p">(</span><span class="n">s_id</span><span class="p">,</span> <span class="n">ch_name</span><span class="p">,</span> <span class="n">structure</span><span class="p">,</span>
+ <span class="n">seqres</span><span class="p">)</span>
+
+
+<span class="c1"># We now have two structures in both databases...</span>
+
+<span class="c1"># Please note, that there is no profile derived from structures</span>
+<span class="c1"># assigned yet to structure_db_one, the memory is only allocated</span>
+<span class="c1"># and set to zero. In structure_db_two, there'll never be stored a </span>
+<span class="c1"># structure profile as we did not initialize it accordingly. </span>
+<span class="c1"># However, we can still use its coordinates and residue depths to</span>
+<span class="c1"># generate profiles! </span>
+<span class="c1"># To demonstrate, we use our structure_db_two to derive profiles </span>
+<span class="c1"># and set them in structure_db_one.</span>
+
+<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">structure_db_one</span><span class="o">.</span><span class="n">GetNumCoords</span><span class="p">()):</span>
+
+ <span class="c1"># get the CoordInfo for chain with index i </span>
+ <span class="n">coord_info</span> <span class="o">=</span> <span class="n">structure_db_one</span><span class="o">.</span><span class="n">GetCoordInfo</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
+
+ <span class="c1"># define a fragment, that covers the full length</span>
<span class="n">frag_info</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">FragmentInfo</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">coord_info</span><span class="o">.</span><span class="n">size</span><span class="p">)</span>
- <span class="c"># generate a profile based on the structural data in the src_db</span>
- <span class="n">prof</span> <span class="o">=</span> <span class="n">src_db</span><span class="o">.</span><span class="n">GenerateStructureProfile</span><span class="p">(</span><span class="n">structure_db</span><span class="p">,</span> <span class="n">frag_info</span><span class="p">)</span>
- <span class="c"># and add it to the previously created structure_db</span>
- <span class="n">structure_db</span><span class="o">.</span><span class="n">SetStructureProfile</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">prof</span><span class="p">)</span>
-<span class="c"># That's it! Let's save it down...</span>
-<span class="n">structure_db</span><span class="o">.</span><span class="n">Save</span><span class="p">(</span><span class="s">"my_db.dat"</span><span class="p">)</span>
+ <span class="c1"># extract all required information</span>
+ <span class="n">sequence</span> <span class="o">=</span> <span class="n">structure_db_one</span><span class="o">.</span><span class="n">GetSequence</span><span class="p">(</span><span class="n">frag_info</span><span class="p">)</span>
+ <span class="n">bb_list</span> <span class="o">=</span> <span class="n">structure_db_one</span><span class="o">.</span><span class="n">GetBackboneList</span><span class="p">(</span><span class="n">frag_info</span><span class="p">,</span> <span class="n">sequence</span><span class="p">)</span>
+ <span class="n">res_depths</span> <span class="o">=</span> <span class="n">structure_db_one</span><span class="o">.</span><span class="n">GetResidueDepths</span><span class="p">(</span><span class="n">frag_info</span><span class="p">)</span>
+
+ <span class="c1"># generate structure profiles based on structure_db_two</span>
+ <span class="n">prof</span> <span class="o">=</span> <span class="n">structure_db_two</span><span class="o">.</span><span class="n">GenerateStructureProfile</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span>
+ <span class="n">res_depths</span><span class="p">)</span>
+ <span class="c1"># and add it to the previously created structure_db</span>
+ <span class="n">structure_db_one</span><span class="o">.</span><span class="n">SetStructureProfile</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">prof</span><span class="p">)</span>
+
+<span class="c1"># That's it! Let's save both databases down.</span>
+<span class="c1"># structure_db_two will use much less memory, as it contains less data. </span>
+<span class="c1"># Sidenote: We're saving the portable version. If you intent to use </span>
+<span class="c1"># your database only on one system, the Save / Load functions should</span>
+<span class="c1"># be preferred, as the loading will be much faster.</span>
+<span class="n">structure_db_one</span><span class="o">.</span><span class="n">SavePortable</span><span class="p">(</span><span class="s2">"my_db_one.dat"</span><span class="p">)</span>
+<span class="n">structure_db_two</span><span class="o">.</span><span class="n">SavePortable</span><span class="p">(</span><span class="s2">"my_db_two.dat"</span><span class="p">)</span>
</pre></div>
</div>
-<p>Calculating the structural profiles is highly expensive and heavily depends on
+<p>Calculating the structural profiles is expensive and heavily depends on
the size of the database used as source. If you want to do this for a larger
database, you might want to consider two things:</p>
<ol class="arabic simple">
-<li>Use a database of limited size as structural source (something
+<li>Use a database of limited size to generate the actual profiles (something
in between 5000 and 10000 nonredundant chains is enough)</li>
-<li>Use the <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
+<li>Use the <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileDB</span></code></a> to gather profiles produced from jobs
running in parallel</li>
</ol>
+<dl class="class">
+<dt id="promod3.loop.StructureDBDataType">
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">StructureDBDataType</code><a class="headerlink" href="#promod3.loop.StructureDBDataType" title="Permalink to this definition">¶</a></dt>
+<dd><p>The StructureDBDataType enum has to be passed at initialization of a
+StructureDB in order to define what data you want to store additionally
+to backbone coordinates and sequence.
+If you want to store all data possible, use All. If you only want a subset,
+you can combine some of the datatypes with a bitwise or operation
+(see example script for StructureDB). One important note:
+If you enable AAFrequenciesStruct, the actual information is not automatically
+assigned. Only the according memory is allocated and set to zero, the actual
+information must be assigned manually (see example script again...).</p>
+<p>All, Dihedrals, SolventAccessibilities, ResidueDepths, DSSP, AAFrequencies,
+AAFrequenciesStruct</p>
+</dd></dl>
+
<dl class="class">
<dt id="promod3.loop.StructureDB">
-<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">StructureDB</code><a class="headerlink" href="#promod3.loop.StructureDB" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="staticmethod">
+<em class="property">class </em><code class="descclassname">promod3.loop.</code><code class="descname">StructureDB</code><span class="sig-paren">(</span><em>data_to_store</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB" title="Permalink to this definition">¶</a></dt>
+<dd><p>Generates an empty StructureDB that can be filled with content through
+<a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-func docutils literal"><span class="pre">AddCoordinates()</span></code></a>. The information extracted there is defined by
+<em>data_to_store</em>. Have a look at the <a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal"><span class="pre">StructureDBDataType</span></code></a>
+documentation and at the example script...</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data_to_store</strong> (<a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal"><span class="pre">StructureDBDataType</span></code></a>) – Specifies what data to store in the database, several
+flags can be combined with a bitwise or operator.</td>
+</tr>
+</tbody>
+</table>
+<dl class="staticmethod">
<dt id="promod3.loop.StructureDB.Load">
-<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em>, <em>load_frequencies=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.Load" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">Load</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.Load" title="Permalink to this definition">¶</a></dt>
<dt id="promod3.loop.StructureDB.LoadPortable">
<em class="property">static </em><code class="descname">LoadPortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.LoadPortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Loads raw binary file generated with <a class="reference internal" href="#promod3.loop.StructureDB.Save" title="promod3.loop.StructureDB.Save"><code class="xref py py-meth docutils literal"><span class="pre">Save()</span></code></a> (optimized for fast
@@ -238,26 +318,14 @@ less machine-dependent).</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load the database.</li>
-<li><strong>load_frequencies</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If True, the full database including profile
-information for every position gets loaded.
-A database without profiles loads faster and
-requires less memory. But it’s not possible
-to add new coordinates or call one of the
-profile dependent functions.</li>
-</ul>
-</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file from which to load the database.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The loaded data base</p>
-</td>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">The loaded data base</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a></p>
-</td>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a></td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</p>
-</td>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -269,7 +337,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.loop.StructureDB.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -277,9 +345,25 @@ for details.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path to the file where the database will be saved</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-db has been loaded with load_frequencies=False (enforces only
-complete databases to be saved down)</td>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.loop.StructureDB.HasData">
+<code class="descname">HasData</code><span class="sig-paren">(</span><em>data_type</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.HasData" title="Permalink to this definition">¶</a></dt>
+<dd><p>Checks, whether requested data type is available in the current database.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data_type</strong> (<a class="reference internal" href="#promod3.loop.StructureDBDataType" title="promod3.loop.StructureDBDataType"><code class="xref py py-class docutils literal"><span class="pre">StructureDBDataType</span></code></a>) – Data type to check</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Whether the requested datatype is available</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a></td>
</tr>
</tbody>
</table>
@@ -287,47 +371,62 @@ complete databases to be saved down)</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.AddCoordinates">
-<code class="descname">AddCoordinates</code><span class="sig-paren">(</span><em>pdb_id</em>, <em>chain_name</em>, <em>chain</em>, <em>surf</em>, <em>prof</em>, <em>solvent_accessibility_string="solvent_accessibility"</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.AddCoordinates" title="Permalink to this definition">¶</a></dt>
-<dd><p>This method takes a structural chain and searches the longest stretch of
-connected residues containing all necessary backbone atoms. This stretch
-gets then added to the database. Due to technical reasons, The maximal
-extent along one of the base axis cannot exceed 650 A.
-Following features are expected to be set on a per residue level in <em>chain</em>:
-The secondary structure (e.g. call <code class="xref py py-meth docutils literal"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code> on the
-full <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a> the <em>chain</em> belongs to) and
-the solvent accessibility assigned using a float property with name
-<em>solvent_accessibility_string</em> as name on a per residue level (e.g. call
-<code class="xref py py-meth docutils literal"><span class="pre">ost.mol.alg.Accessibility()</span></code> on the full <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>
-the chain belongs to and take care to pass the appropriate
-<em>solvent_accessibility_string</em>).</p>
+<code class="descname">AddCoordinates</code><span class="sig-paren">(</span><em>id</em>, <em>chain_name</em>, <em>ent</em>, <em>seqres</em>, <em>prof=None</em>, <em>only_longest_stretch=True</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.AddCoordinates" title="Permalink to this definition">¶</a></dt>
+<dd><p>This method takes an entity and adds coordinates and the sequence
+of one of its chains to the structural database. Additionally, all
+data as specified at the initialization of the database is extracted
+fully automatically by considering the full <em>ent</em> (e.g. when
+calculating solvent accessibilities etc.).
+The only exception is AAFrequencies, where a valid sequence profile
+is expected in <em>prof</em> that has matching sequence with <em>seqres</em>
+All residues in chain with name <em>chain_name</em> must have residue numbers
+that directly relate them to the <em>seqres</em> with an indexing scheme
+starting from one.
+If this is not the case, an error gets thrown. You might want to
+consider to use <code class="xref py py-meth docutils literal"><span class="pre">ost.seq.Renumber()</span></code> for proper numbering.
+Based on consecutive numbering and additionally checking for valid
+peptide bonds, connected stretches are identified
+and every added connected stretch gets its own entry with
+<a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a> as a descriptor.
+To avoid cluttering the database with many small fragments, the flag:
+<em>only_longest_stretch</em> can be used. Set it to False if all
+connected stretches of chain with name <em>chain_name</em> should be added.
+There is one final catch you have to consider: Due to the internal
+lossy data compression for the positions, the extent in x, y and
+z - direction for every connected stretch is limited to 655A. This should
+be sufficient for most structures, but stretches exceeding this maximum
+are discarded. For storing the structural data given these restraints,
+a translation is applied that gets stored as the <em>shift</em> attribute
+in the according <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a> object.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>pdb_id</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – 4-letter code of the structure the chain belongs to</li>
-<li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of the chain consisting of one letter</li>
-<li><strong>chain</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainView" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainView</span></code></a>) – The actual chain</li>
-<li><strong>surf</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/surface/#ost.mol.SurfaceHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.SurfaceHandle</span></code></a>) – A surface describing the solvent accessible surface
-(we advise you to provide a surface estimated with the
-full <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a> the <em>chain</em> belongs to)</li>
-<li><strong>prof</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for this <em>chain</em>.</li>
-<li><strong>solvent_accessibility_string</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of float property where the
-solvent accessibilities are stored
-on a per residue basis in <em>chain</em></li>
+<li><strong>id</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – identifier of the added structure (e.g. pdb id)</li>
+<li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of the chain in <em>ent</em> you want to add</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) – The full entity that must contain a chain named
+as specified by <em>chain_name</em>.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The reference sequence of chain with name <em>chain_name</em></li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
+<em>chain_name</em>. The profile sequence must match <em>seqres</em>.</li>
+<li><strong>only_longest_stretch</strong> – Flag whether you want to add only the longest
+connected stretch of residues are all connected
+stretches of residues</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">DB index of added chain.</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">indices of added stretches in db</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <cite>int</cite></p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if size of chain is too large,
-when db has been loaded with load_frequencies=False or when the
-ATOMSEQ form the <em>chain</em> can’t be aligned with the SEQRES from
-the <em>prof</em>.</p>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if the residues in chain with
+name <em>chain_name</em> do not match <em>seqres</em> given the
+residue numbers, when AAFrequencies have to to be extracted and
+the sequence in <em>prof</em> does not match the <em>seqres</em> or <em>prof</em> is
+invalid.</p>
</td>
</tr>
</tbody>
@@ -335,22 +434,43 @@ the <em>prof</em>.</p>
</dd></dl>
<dl class="method">
-<dt id="promod3.loop.StructureDB.GetCoordIndex">
-<code class="descname">GetCoordIndex</code><span class="sig-paren">(</span><em>pdb_id</em>, <em>chain_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetCoordIndex" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.loop.StructureDB.RemoveCoordinates">
+<code class="descname">RemoveCoordinates</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.RemoveCoordinates" title="Permalink to this definition">¶</a></dt>
+<dd><p>Removes coordinates at specified location and all its associated data. This
+has an impact on the offset values of all <a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a> objects
+that are internally stored afterwards and on the actual coord indices
+(all shifted by one). So make sure that you adapt your data access
+accordingly!</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Specifies coordinates to be removed</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>coord_idx</em> is invalid</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.loop.StructureDB.GetCoordIdx">
+<code class="descname">GetCoordIdx</code><span class="sig-paren">(</span><em>id</em>, <em>chain_name</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetCoordIdx" title="Permalink to this definition">¶</a></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The StructureDB index (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1]) of the
-chain of interest, -1 if it cannot be found.</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The StructureDB indices (in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1]) of
+of all coords (connected stretches) with matching
+<em>id</em> / <em>chain_name</em>.</p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>pdb_id</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – 4-letter code of the structure the chain belongs to</li>
-<li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of the chain consisting of one letter</li>
+<li><strong>id</strong> – Identifier given when calling <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-meth docutils literal"><span class="pre">AddCoordinates()</span></code></a></li>
+<li><strong>chain_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of chain given when calling <a class="reference internal" href="#promod3.loop.StructureDB.AddCoordinates" title="promod3.loop.StructureDB.AddCoordinates"><code class="xref py py-meth docutils literal"><span class="pre">AddCoordinates()</span></code></a></li>
</ul>
</td>
</tr>
@@ -365,7 +485,8 @@ chain of interest, -1 if it cannot be found.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Object describing the chain with index <em>idx</em>.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Object describing the stretch of connected residues with
+index <em>idx</em>.</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.CoordInfo" title="promod3.loop.CoordInfo"><code class="xref py py-class docutils literal"><span class="pre">CoordInfo</span></code></a></td>
</tr>
@@ -375,6 +496,28 @@ chain of interest, -1 if it cannot be found.</p>
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.loop.StructureDB.GetNumCoords">
+<code class="descname">GetNumCoords</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetNumCoords" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of connected stretches of residues that have been added to
+the database.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.loop.StructureDB.PrintStatistics">
+<code class="descname">PrintStatistics</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.PrintStatistics" title="Permalink to this definition">¶</a></dt>
+<dd><p>Prints out some information about the db.</p>
+</dd></dl>
+
<dl class="method">
<dt id="promod3.loop.StructureDB.GetBackboneList">
<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>fragment</em>, <em>sequence</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetBackboneList" title="Permalink to this definition">¶</a></dt>
@@ -393,44 +536,23 @@ chain of interest, -1 if it cannot be found.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract positions.</li>
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence to set for the returned backbone list.</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s N-terminus should be
superposed onto.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Positions on which the backbone list’s C-terminus should be
superposed onto.</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if fragment is invalid (happens
-if the fragment does not fully fit into one of the chains in the
-database) or if <em>sequence</em> contains a one letter code which is not
-one of the 20 default amino acids.</p>
+if the fragment does not fully fit into one of the connected
+stretches in the database) or if <em>sequence</em> contains a one letter
+code which is not one of the 20 default amino acids.</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>
-<dl class="method">
-<dt id="promod3.loop.StructureDB.GetNumCoords">
-<code class="descname">GetNumCoords</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetNumCoords" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Number of chains that have been added to the database.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.loop.StructureDB.PrintStatistics">
-<code class="descname">PrintStatistics</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.PrintStatistics" title="Permalink to this definition">¶</a></dt>
-<dd><p>Prints out some information about the db.</p>
-</dd></dl>
-
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSequence">
<code class="descname">GetSequence</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSequence" title="Permalink to this definition">¶</a></dt>
@@ -446,7 +568,7 @@ one of the 20 default amino acids.</p>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
-chains in the database.</td>
+connected stretches of residues in the database.</td>
</tr>
</tbody>
</table>
@@ -465,9 +587,10 @@ chains in the database.</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the states.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if fragment is invalid. This is
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain dssp
+data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
-chains in the database.</td>
+connected stretches of residues in the database.</td>
</tr>
</tbody>
</table>
@@ -486,9 +609,10 @@ chains in the database.</td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the dihedrals.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if fragment is invalid. This is
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+dihedral angle data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
-chains in the database.</td>
+connected stretches of residues in the database.</td>
</tr>
</tbody>
</table>
@@ -508,9 +632,10 @@ chains in the database.</td>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the residue
depths</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if fragment is invalid. This is
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+residue depth data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
-chains in the database.</td>
+connected stretches of residues in the database.</td>
</tr>
</tbody>
</table>
@@ -531,9 +656,10 @@ as calculated by dssp.</td>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the solvent
accessibilities</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if fragment is invalid. This is
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+solvent accessibility data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
-chains in the database.</td>
+connected stretches of residues in the database.</td>
</tr>
</tbody>
</table>
@@ -549,14 +675,15 @@ chains in the database.</td>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The sequence profile for the residues defined by <em>fragment</em> with
the BLOSUM62 probabilities as NULL model.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the sequence
profile</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if fragment is invalid. This is
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not cotain
+aa frequency data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
-chains in the database.</td>
+connected stretches of residues in the database.</td>
</tr>
</tbody>
</table>
@@ -572,14 +699,15 @@ chains in the database.</td>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The structure profile for the residues defined by <em>fragment</em> with
the BLOSUM62 probabilities as NULL model.</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
</tr>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from which to extract the structure
profile</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if fragment is invalid. This is
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if database does not contain
+aa frequencies struct data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
-chains in the database.</td>
+connected stretches of residues in the database.</td>
</tr>
</tbody>
</table>
@@ -587,18 +715,18 @@ chains in the database.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.GenerateStructureProfile">
-<code class="descname">GenerateStructureProfile</code><span class="sig-paren">(</span><em>other_db</em>, <em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GenerateStructureProfile" title="Permalink to this definition">¶</a></dt>
-<dd><p>Takes the CA positions and residue depths for <em>fragment</em> defined from
-<em>other_db</em> to calculate a structure profile using the full internal
-structural data of this database with their corresponding residue depths.</p>
+<code class="descname">GenerateStructureProfile</code><span class="sig-paren">(</span><em>bb_list</em>, <em>residue_depths</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GenerateStructureProfile" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculates a structure profile for <em>bb_list</em> with given <em>residue_depths</em>
+using the full internal data of this StructureDB.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>fragment</strong> (<a class="reference internal" href="#promod3.loop.FragmentInfo" title="promod3.loop.FragmentInfo"><code class="xref py py-class docutils literal"><span class="pre">FragmentInfo</span></code></a>) – Fragment definition from <em>other_db</em>.</li>
-<li><strong>other_db</strong> (<a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – Structural database from which we extract CA positions and
-residue depths for <em>fragment</em>.</li>
+<li><strong>bb_list</strong> (<a class="reference internal" href="backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Positions for which to calculate the structural profile</li>
+<li><strong>residue_depths</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The residue depth for each residue in <em>bb_list</em>
+as you would extract it from any StructureDB
+containing that data.</li>
</ul>
</td>
</tr>
@@ -606,11 +734,12 @@ residue depths for <em>fragment</em>.</li>
probabilities as NULL model.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>bb_list</em> and
-<em>residue_depths</em> differ in size or when their size is 0</p>
+<em>residue_depths</em> differ in size, when their size is 0
+or when database does not contain aa frequencies struct data.</p>
</td>
</tr>
</tbody>
@@ -619,23 +748,24 @@ probabilities as NULL model.</p>
<dl class="method">
<dt id="promod3.loop.StructureDB.SetStructureProfile">
-<code class="descname">SetStructureProfile</code><span class="sig-paren">(</span><em>chain_idx</em>, <em>prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.SetStructureProfile" title="Permalink to this definition">¶</a></dt>
+<code class="descname">SetStructureProfile</code><span class="sig-paren">(</span><em>coord_idx</em>, <em>prof</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.SetStructureProfile" title="Permalink to this definition">¶</a></dt>
<dd><p>Takes the <em>prof</em> and sets the corresponding StructureProfile
-frequencies in entry with <em>chain_idx</em></p>
+frequencies in entry with <em>coord_idx</em></p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>prof</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – StructureDB index of entry for which to set frequencies
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li>
+<li><strong>coord_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – StructureDB index of entry for which to set frequencies
(in [0, <a class="reference internal" href="#promod3.loop.StructureDB.GetNumCoords" title="promod3.loop.StructureDB.GetNumCoords"><code class="xref py py-meth docutils literal"><span class="pre">GetNumCoords()</span></code></a>-1])</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>chain_idx</em> does not match
-any entry in the db or when the size of the <em>prof</em> does not
-exactly match the size of entry at <em>chain_idx</em></p>
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>coord_idx</em> does not match
+any entry in the db, when the size of the <em>prof</em> does not
+exactly match the size of entry at <em>coord_idx</em> or when database
+does not contain aa frequency struct data.</p>
</td>
</tr>
</tbody>
@@ -677,40 +807,40 @@ between the N-stem C atom and the C-stem N atom). It can therefore be searched
for fragments matching a certain geometry of N and C stems. The bins are
accessed through a hash table, making searching the database ultra fast.</p>
<p>This example illustrates how to create a custom FragDB based on a StructureDB:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
-<span class="c"># let's load the default structure_db </span>
-<span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">StructureDB</span><span class="o">.</span><span class="n">LoadPortable</span><span class="p">(</span><span class="s">"data/port_str_db.dat"</span><span class="p">)</span>
-<span class="c"># in practice you might want to use the default StructureDB instead:</span>
-<span class="c"># structure_db = loop.LoadStructureDB()</span>
+<span class="c1"># let's load the default structure_db </span>
+<span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">StructureDB</span><span class="o">.</span><span class="n">LoadPortable</span><span class="p">(</span><span class="s2">"data/port_str_db.dat"</span><span class="p">)</span>
+<span class="c1"># in practice you might want to use the default StructureDB instead:</span>
+<span class="c1"># structure_db = loop.LoadStructureDB()</span>
-<span class="c"># and our beloved crambin...</span>
-<span class="n">structure</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1CRN.pdb'</span><span class="p">)</span>
+<span class="c1"># and our beloved crambin...</span>
+<span class="n">structure</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
-<span class="c"># we now want to connect the residue with index 17 and 21</span>
+<span class="c1"># we now want to connect the residue with index 17 and 21</span>
<span class="n">sub_res_list</span> <span class="o">=</span> <span class="n">structure</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">17</span><span class="p">:</span><span class="mi">22</span><span class="p">]</span>
<span class="n">n_stem</span> <span class="o">=</span> <span class="n">sub_res_list</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
<span class="n">c_stem</span> <span class="o">=</span> <span class="n">sub_res_list</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
-<span class="n">frag_seq</span> <span class="o">=</span> <span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">sub_res_list</span><span class="p">])</span>
+<span class="n">frag_seq</span> <span class="o">=</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">sub_res_list</span><span class="p">])</span>
-<span class="c"># a custom FragDB can be built to identify fragments</span>
-<span class="c"># fulfilling these particular geometric constraints</span>
+<span class="c1"># a custom FragDB can be built to identify fragments</span>
+<span class="c1"># fulfilling these particular geometric constraints</span>
<span class="n">frag_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">FragDB</span><span class="p">(</span><span class="mf">1.0</span><span class="p">,</span> <span class="mi">20</span><span class="p">)</span>
-<span class="c"># at this point we add all possible fragments of length 5 </span>
-<span class="c"># with an RMSD threshold of 0.5</span>
+<span class="c1"># at this point we add all possible fragments of length 5 </span>
+<span class="c1"># with an RMSD threshold of 0.5</span>
<span class="n">frag_db</span><span class="o">.</span><span class="n">AddFragments</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">)</span>
-<span class="c"># the FragDB can now be used to extract FragmentInfo objects to</span>
-<span class="c"># finally query the StructureDB</span>
+<span class="c1"># the FragDB can now be used to extract FragmentInfo objects to</span>
+<span class="c1"># finally query the StructureDB</span>
<span class="n">fragment_infos</span> <span class="o">=</span> <span class="n">frag_db</span><span class="o">.</span><span class="n">SearchDB</span><span class="p">(</span><span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
-<span class="c"># get the fragments in form of BackboneList objects and store them</span>
+<span class="c1"># get the fragments in form of BackboneList objects and store them</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">f_i</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">fragment_infos</span><span class="p">):</span>
<span class="n">bb_list</span> <span class="o">=</span> <span class="n">structure_db</span><span class="o">.</span><span class="n">GetBackboneList</span><span class="p">(</span><span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">,</span>
<span class="n">f_i</span><span class="p">,</span> <span class="n">frag_seq</span><span class="p">)</span>
- <span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s">".pdb"</span><span class="p">)</span>
+ <span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">+</span> <span class="s2">".pdb"</span><span class="p">)</span>
</pre></div>
</div>
<dl class="class">
@@ -747,7 +877,7 @@ less machine-dependent).</p>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -759,7 +889,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.loop.FragDB.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.FragDB.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -922,8 +1052,8 @@ and <strong>c_stem</strong> and of the same length as the <strong>frag_size</str
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The N-stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The C-stem</li>
<li><strong>frag_size</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues of the fragment</li>
<li><strong>extra_bins</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Whether to extend the search to include fragments from
<em>extra_bins</em> additional bins surrounding the bin given by
@@ -963,9 +1093,9 @@ Calculates the avg. substitution matrix based sequence similarity of amino acids
when comparing a potential fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> and the target
sequence</li>
<li><strong>SSAgree</strong>:
-Calculates the avg. agreement of the predicted secondary structure by PSIPRED <a class="reference internal" href="#jones1999" id="id5">[Jones1999]</a>
-and the dssp <a class="reference internal" href="#kabsch1983" id="id6">[kabsch1983]</a> assignment stored in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>.
-The Agreement term is based on a probabilistic approach also used in HHSearch <a class="reference internal" href="#soding2005" id="id7">[soding2005]</a>.</li>
+Calculates the avg. agreement of the predicted secondary structure by PSIPRED <a class="reference internal" href="#jones1999" id="id3">[Jones1999]</a>
+and the dssp <a class="reference internal" href="#kabsch1983" id="id4">[kabsch1983]</a> assignment stored in the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>.
+The Agreement term is based on a probabilistic approach also used in HHSearch <a class="reference internal" href="#soding2005" id="id5">[soding2005]</a>.</li>
<li><strong>TorsionProbability</strong>:
Calculates the avg. probability of observing the phi/psi dihedral angles of a potential
fragment from the <a class="reference internal" href="#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a> given the target sequence. The probabilities are
@@ -980,51 +1110,51 @@ fragment from the <a class="reference internal" href="#promod3.loop.StructureDB"
in between them. The scores are calculated as L1 distances between the profile columns.
In this case, the amino acid frequencies extracted from structural alignments are used.</li>
</ul>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
-<span class="c"># load an example structure</span>
-<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1CRN.pdb'</span><span class="p">)</span>
+<span class="c1"># load an example structure</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
-<span class="c"># extract some additional information</span>
-<span class="n">seqres</span> <span class="o">=</span> <span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
+<span class="c1"># extract some additional information</span>
+<span class="n">seqres</span> <span class="o">=</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
<span class="n">frag_pos</span> <span class="o">=</span> <span class="mi">35</span>
<span class="n">frag_length</span> <span class="o">=</span> <span class="mi">9</span>
<span class="n">frag_seq</span> <span class="o">=</span> <span class="n">seqres</span><span class="p">[</span><span class="n">frag_pos</span><span class="p">:</span><span class="n">frag_pos</span><span class="o">+</span><span class="n">frag_length</span><span class="p">]</span>
<span class="n">frag_residues</span> <span class="o">=</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">frag_pos</span><span class="p">:</span><span class="n">frag_pos</span><span class="o">+</span><span class="n">frag_length</span><span class="p">]</span>
<span class="n">ref_backbone</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">frag_seq</span><span class="p">,</span> <span class="n">frag_residues</span><span class="p">)</span>
-<span class="c"># let's load the StructureDB and a substitution matrix</span>
+<span class="c1"># let's load the StructureDB and a substitution matrix</span>
<span class="n">db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
<span class="n">subst_matrix</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">alg</span><span class="o">.</span><span class="n">BLOSUM62</span>
-<span class="c"># the fragger object needs to be initialized with its target sequence</span>
+<span class="c1"># the fragger object needs to be initialized with its target sequence</span>
<span class="n">fragger</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">Fragger</span><span class="p">(</span><span class="n">frag_seq</span><span class="p">)</span>
-<span class="c"># we could now add an arbitrary number of parameters from different</span>
-<span class="c"># features for now we only go for the sequence similarity score</span>
+<span class="c1"># we could now add an arbitrary number of parameters from different</span>
+<span class="c1"># features for now we only go for the sequence similarity score</span>
<span class="n">fragger</span><span class="o">.</span><span class="n">AddSeqSimParameters</span><span class="p">(</span><span class="mf">1.0</span><span class="p">,</span> <span class="n">subst_matrix</span><span class="p">)</span>
-<span class="c"># the Fragger can finally be filled by providing a StructureDB</span>
+<span class="c1"># the Fragger can finally be filled by providing a StructureDB</span>
<span class="n">fragger</span><span class="o">.</span><span class="n">Fill</span><span class="p">(</span><span class="n">db</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="mi">100</span><span class="p">)</span>
-<span class="c"># let's see how good the fragments are...</span>
+<span class="c1"># let's see how good the fragments are...</span>
<span class="n">below_three</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">fragger</span><span class="p">)):</span>
- <span class="n">ca_rmsd</span> <span class="o">=</span> <span class="n">fragger</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">CARMSD</span><span class="p">(</span><span class="n">ref_backbone</span><span class="p">,</span><span class="bp">True</span><span class="p">)</span>
- <span class="k">print</span> <span class="s">"Fragment </span><span class="si">%d</span><span class="s"> has CA RMSD of </span><span class="si">%.3f</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">ca_rmsd</span><span class="p">)</span>
+ <span class="n">ca_rmsd</span> <span class="o">=</span> <span class="n">fragger</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">CARMSD</span><span class="p">(</span><span class="n">ref_backbone</span><span class="p">,</span><span class="kc">True</span><span class="p">)</span>
+ <span class="nb">print</span> <span class="s2">"Fragment </span><span class="si">%d</span><span class="s2"> has CA RMSD of </span><span class="si">%.3f</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">ca_rmsd</span><span class="p">)</span>
<span class="k">if</span> <span class="n">ca_rmsd</span> <span class="o"><</span> <span class="mf">3.0</span><span class="p">:</span>
<span class="n">below_three</span> <span class="o">+=</span> <span class="mi">1</span>
<span class="n">fraction</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">below_three</span><span class="p">)</span><span class="o">/</span><span class="nb">len</span><span class="p">(</span><span class="n">fragger</span><span class="p">)</span>
-<span class="k">print</span> <span class="s">"Fraction of fragments below 3A: </span><span class="si">%.2f</span><span class="s">"</span> <span class="o">%</span> <span class="n">fraction</span>
+<span class="nb">print</span> <span class="s2">"Fraction of fragments below 3A: </span><span class="si">%.2f</span><span class="s2">"</span> <span class="o">%</span> <span class="n">fraction</span>
-<span class="c"># add into a cached map with ID based on frag_pos</span>
+<span class="c1"># add into a cached map with ID based on frag_pos</span>
<span class="n">fragger_map</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">FraggerMap</span><span class="p">()</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">fragger_map</span><span class="o">.</span><span class="n">Contains</span><span class="p">(</span><span class="n">frag_pos</span><span class="p">):</span>
<span class="n">fragger_map</span><span class="p">[</span><span class="n">frag_pos</span><span class="p">]</span> <span class="o">=</span> <span class="n">fragger</span>
-<span class="c"># store it for future use</span>
-<span class="n">fragger_map</span><span class="o">.</span><span class="n">SaveBB</span><span class="p">(</span><span class="s">"frag_map.dat"</span><span class="p">)</span>
+<span class="c1"># store it for future use</span>
+<span class="n">fragger_map</span><span class="o">.</span><span class="n">SaveBB</span><span class="p">(</span><span class="s2">"frag_map.dat"</span><span class="p">)</span>
</pre></div>
</div>
<dl class="class">
@@ -1147,7 +1277,7 @@ linked to this object.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</li>
-<li><strong>prof</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
</ul>
</td>
</tr>
@@ -1165,7 +1295,7 @@ linked to this object.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>w</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – linear weight</li>
-<li><strong>prof</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
</ul>
</td>
</tr>
@@ -1567,37 +1697,31 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
<table class="docutils citation" frame="void" id="soding2005" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
-<tr><td class="label">[soding2005]</td><td><em>(<a class="fn-backref" href="#id1">1</a>, <a class="fn-backref" href="#id7">2</a>)</em> Söding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.</td></tr>
-</tbody>
-</table>
-<table class="docutils citation" frame="void" id="sanner1996" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id2">[sanner1996]</a></td><td>Sanner M, Olson AJ, Spehner JC (1996). Reduced Surface: an Efficient Way to Compute Molecular Surfaces. Biopolymers 38 (3): 305-320.</td></tr>
+<tr><td class="label"><a class="fn-backref" href="#id5">[soding2005]</a></td><td>Söding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.</td></tr>
</tbody>
</table>
<table class="docutils citation" frame="void" id="chakravarty1999" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id3">[chakravarty1999]</a></td><td>Chakravarty S, Varadarajan R (1999). Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7 (7): 723–732.</td></tr>
+<tr><td class="label"><a class="fn-backref" href="#id1">[chakravarty1999]</a></td><td>Chakravarty S, Varadarajan R (1999). Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7 (7): 723–732.</td></tr>
</tbody>
</table>
<table class="docutils citation" frame="void" id="zhou2005" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id4">[zhou2005]</a></td><td>Zhou H, Zhou Y (2005). Fold Recognition by Combining Sequence Profiles Derived From Evolution and From Depth-Dependent Structural Alignment of Fragments. Proteins 58 (2): 321–328.</td></tr>
+<tr><td class="label"><a class="fn-backref" href="#id2">[zhou2005]</a></td><td>Zhou H, Zhou Y (2005). Fold Recognition by Combining Sequence Profiles Derived From Evolution and From Depth-Dependent Structural Alignment of Fragments. Proteins 58 (2): 321–328.</td></tr>
</tbody>
</table>
<table class="docutils citation" frame="void" id="jones1999" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id5">[Jones1999]</a></td><td>Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.</td></tr>
+<tr><td class="label"><a class="fn-backref" href="#id3">[Jones1999]</a></td><td>Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.</td></tr>
</tbody>
</table>
<table class="docutils citation" frame="void" id="kabsch1983" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id6">[kabsch1983]</a></td><td>Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 2577-2637.</td></tr>
+<tr><td class="label"><a class="fn-backref" href="#id4">[kabsch1983]</a></td><td>Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 2577-2637.</td></tr>
</tbody>
</table>
</div>
@@ -1648,9 +1772,6 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -1658,11 +1779,11 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/loop/structure_db.txt"
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index b74d69f2abcffb9915d106d749bc10a39a861a27..c9d75287ca27196ad6349d2f16c1aeb7a3c7df34 100644
--- a/doc/html/loop/torsion_sampler.html
+++ b/doc/html/loop/torsion_sampler.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Sampling Dihedral Angles — ProMod3 1.1.0 documentation</title>
+ <title>Sampling Dihedral Angles — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
<link rel="next" title="Structural Data" href="structure_db.html" />
<link rel="prev" title="Representing Loops" href="backbone.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -54,23 +56,23 @@ most methods which need to access a specific distribution can either take 3
residue names or an index as input.</p>
<p>As a showcase example, we randomly sample from a given torsion sample and
store the resulting samples as a scatter plot:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span>
-<span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">conop</span>
-<span class="c"># this requires matplotlib and numpy</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span>
+<span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">conop</span>
+<span class="c1"># this requires matplotlib and numpy</span>
<span class="kn">import</span> <span class="nn">matplotlib</span>
-<span class="c"># change next line, if you wish to use a GUI-based plot-output</span>
-<span class="n">matplotlib</span><span class="o">.</span><span class="n">use</span><span class="p">(</span><span class="s">"Agg"</span><span class="p">)</span>
-<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="kn">as</span> <span class="nn">plt</span>
-<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
+<span class="c1"># change next line, if you wish to use a GUI-based plot-output</span>
+<span class="n">matplotlib</span><span class="o">.</span><span class="n">use</span><span class="p">(</span><span class="s2">"Agg"</span><span class="p">)</span>
+<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
-<span class="c"># load a default sampler</span>
+<span class="c1"># load a default sampler</span>
<span class="n">t_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSampler</span><span class="p">()</span>
-<span class="c"># dihedral angles will be stored in here</span>
+<span class="c1"># dihedral angles will be stored in here</span>
<span class="n">phi</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="n">psi</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
-<span class="c"># draw from a random distribution</span>
+<span class="c1"># draw from a random distribution</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1000</span><span class="p">):</span>
<span class="n">dihedral_pair</span> <span class="o">=</span> <span class="n">t_sampler</span><span class="o">.</span><span class="n">Draw</span><span class="p">(</span><span class="n">conop</span><span class="o">.</span><span class="n">ALA</span><span class="p">,</span>
<span class="n">conop</span><span class="o">.</span><span class="n">PRO</span><span class="p">,</span>
@@ -78,16 +80,16 @@ store the resulting samples as a scatter plot:</p>
<span class="n">phi</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dihedral_pair</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
<span class="n">psi</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">dihedral_pair</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-<span class="c"># and plot it</span>
+<span class="c1"># and plot it</span>
<span class="n">plt</span><span class="o">.</span><span class="n">xlim</span><span class="p">(</span><span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">)</span>
<span class="n">plt</span><span class="o">.</span><span class="n">ylim</span><span class="p">(</span><span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">)</span>
-<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">phi</span><span class="p">,</span> <span class="n">psi</span><span class="p">,</span> <span class="s">'.'</span><span class="p">)</span>
-<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s">"phi"</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="s">'large'</span><span class="p">)</span>
-<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s">"psi"</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="s">'large'</span><span class="p">)</span>
-<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s">"ALA-PRO-ALA"</span><span class="p">)</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">phi</span><span class="p">,</span> <span class="n">psi</span><span class="p">,</span> <span class="s1">'.'</span><span class="p">)</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">xlabel</span><span class="p">(</span><span class="s2">"phi"</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="s1">'large'</span><span class="p">)</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">"psi"</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="s1">'large'</span><span class="p">)</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">title</span><span class="p">(</span><span class="s2">"ALA-PRO-ALA"</span><span class="p">)</span>
-<span class="c"># store plot as png file</span>
-<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s">"torsion_plot.png"</span><span class="p">)</span>
+<span class="c1"># store plot as png file</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s2">"torsion_plot.png"</span><span class="p">)</span>
</pre></div>
</div>
<div class="section" id="defining-amino-acid-triplets">
@@ -136,7 +138,7 @@ acids not matching any of the group definitions.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>view</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>) – structure from which parameters will be extracted</td>
</tr>
</tbody>
</table>
@@ -173,7 +175,7 @@ less machine-dependent).</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</p>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</p>
</td>
</tr>
</tbody>
@@ -186,7 +188,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.loop.TorsionSampler.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.TorsionSampler.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -208,9 +210,9 @@ for details.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</li>
-<li><strong>after</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for the central residue</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
</ul>
</td>
</tr>
@@ -250,9 +252,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which torsion angles will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
</ul>
</td>
</tr>
@@ -288,9 +290,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>phi</em> will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – <em>psi</em> angle</li>
</ul>
</td>
@@ -332,9 +334,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</li>
-<li><strong>after</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the <em>psi</em> angle will be drawn</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – <em>phi</em> angle</li>
</ul>
</td>
@@ -376,9 +378,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
@@ -422,9 +424,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
@@ -446,9 +448,9 @@ standard amino acid</td>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
-<li><strong>central</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
-<li><strong>after</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue before <em>central</em></li>
+<li><strong>central</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue for which the probability is calculated.</li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – id of the residue after <em>central</em></li>
<li><strong>psi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – phi angle</li>
<li><strong>phi</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – psi angle</li>
</ul>
@@ -580,9 +582,6 @@ standard amino acid</td>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -590,11 +589,11 @@ standard amino acid</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/loop/torsion_sampler.txt"
diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index 38468c44ec13aa3c4aa4dbcb41263e7bda7d9045..0cd8be8702bde9b8f390725a811a36e6c272ea21 100644
--- a/doc/html/modelling/algorithms.html
+++ b/doc/html/modelling/algorithms.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Modelling Algorithms — ProMod3 1.1.0 documentation</title>
+ <title>Modelling Algorithms — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="sidechain - Sidechain Modelling" href="../sidechain/index.html" />
<link rel="prev" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -59,11 +61,9 @@ iterative superposition multiple times by using a sliding window to select the
initial subset and gathers all unique results. These results can be very
similar and only differ by single positions. The algorithm therefore reduces
the amount of solutions by merging them based on a threshold of similarity.
-If the sum of matching positions within the distance threshold divided by
-the maximum length of the two solutions is above a cluster thresh, the two
-solutions get merged by producing a common solution containing the shared
-positions. As a final result, the algorithm therefore detects common rigid
-subsets of positions.</p>
+The similarity is defined by the fraction of positions in solution A that are
+also present in solution B. As a final result, the algorithm therefore detects
+common rigid subsets of positions.</p>
<dl class="method">
<dt id="promod3.modelling.RigidBlocks">
<code class="descclassname">promod3.modelling.</code><code class="descname">RigidBlocks</code><span class="sig-paren">(</span><em>bb_list_one</em>, <em>bb_list_two</em><span class="optional">[</span>, <em>window_length = 12</em>, <em>max_iterations=20</em>, <em>distance_thresh=3.0</em>, <em>cluster_thresh=0.9</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.RigidBlocks" title="Permalink to this definition">¶</a></dt>
@@ -94,7 +94,7 @@ of the solutions</li>
indices of the common subsets (rigid blocks) relative
to the input <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> objects
and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>bb_list_one</strong>
onto <strong>bb_list_two</strong></p>
</td>
@@ -112,7 +112,7 @@ onto <strong>bb_list_two</strong></p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aln</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – An alignment with attached <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityView</span></code></a>
objects from which the positions are extracted</li>
<li><strong>seq_idx_one</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The idx of the first sequence from which the CA
positions will be extracted</li>
@@ -133,9 +133,9 @@ of the solutions</li>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> with the first element being a
<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <code class="xref py py-class docutils literal"><span class="pre">list</span></code> defining the
column indices of the common subsets (rigid blocks)
-relative to the input <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
+relative to the input <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>
and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions from the first
sequence onto the second sequence.</p>
</td>
@@ -172,7 +172,7 @@ of the solutions</li>
indices of the common subsets (rigid blocks) relative
to the input <code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code> objects
and the second element being a <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
+<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a> defining the transformations to
superpose the according positions in <strong>pos_one</strong>
onto <strong>pos_two</strong></p>
</td>
@@ -235,8 +235,8 @@ Weird things are happening otherwise.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>/<a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</li>
-<li><strong>profile</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</li>
+<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>/<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – SEQRES for this chain</li>
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Sequence profile for this chain.</li>
<li><strong>psipred_pred</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – Psipred prediction for this chain.</li>
<li><strong>fragment_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length (num. residues) of fragments to be extracted.</li>
<li><strong>fragments_per_position</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of fragments to be extracted at each
@@ -313,7 +313,7 @@ used when <cite>filename</cite> was saved.</p>
<dl class="function">
<dt id="promod3.modelling.GenerateDeNovoTrajectories">
-<code class="descclassname">promod3.modelling.</code><code class="descname">GenerateDeNovoTrajectories</code><span class="sig-paren">(</span><em>sequence</em>, <em>num_trajectories=200</em>, <em>avg_sampling_per_position=600</em>, <em>profile=None</em>, <em>psipred_prediction=None</em>, <em>fragment_handler=None</em>, <em>scorer=None</em>, <em>scoring_weights=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_denovo.html#GenerateDeNovoTrajectories"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.GenerateDeNovoTrajectories" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">GenerateDeNovoTrajectories</code><span class="sig-paren">(</span><em>sequence</em>, <em>num_trajectories=200</em>, <em>avg_sampling_per_position=600</em>, <em>profile=None</em>, <em>psipred_prediction=None</em>, <em>fragment_handler=None</em>, <em>scorer=None</em>, <em>scorer_env=None</em>, <em>scoring_weights=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_denovo.html#GenerateDeNovoTrajectories"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.GenerateDeNovoTrajectories" title="Permalink to this definition">¶</a></dt>
<dd><p>Example de novo modelling pipeline based on Fragment sampling and
backbone scoring. Take this as a starting point for more advanced
de novo procedures.</p>
@@ -328,7 +328,7 @@ want to generate</li>
<li><strong>avg_sampling_per_position</strong> – Number of Monte Carlo sampling steps
the total number is:
len(<strong>sequence</strong>) * <strong>avg_sampling_per_position</strong></li>
-<li><strong>profile</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
+<li><strong>profile</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profile for <strong>sequence</strong>. This increases the
fragment search performance.</li>
<li><strong>psipred_prediction</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.PsipredPrediction" title="promod3.loop.PsipredPrediction"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.PsipredPrediction</span></code></a>) – The psipred prediction for <strong>sequence</strong>. This
increases the fragment search performance</li>
@@ -342,6 +342,8 @@ get used instead.</li>
default one gets loaded with default objects with
following keys: clash, reduced, cb_packing, hbond, cbeta,
torsion and pairwise</li>
+<li><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">promod3.scoring.BackboneScoreEnv</span></code></a>) – The scoring env that relates to <strong>scorer</strong>
+This environment will be changed!</li>
<li><strong>scoring_weights</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a>) – Linear weights for different scores. If not provided,
the output of ScoringWeights.GetWeights() is used.
Please note, that the weights must be consistent
@@ -402,9 +404,6 @@ with the keys of the scores in <strong>scorer</strong></li>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -412,11 +411,11 @@ with the keys of the scores in <strong>scorer</strong></li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/algorithms.txt"
diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index 916d24a1617cf48a310fc932dd1a2904acf28c82..032f3350c35708976935479acb04659939e587f6 100644
--- a/doc/html/modelling/gap_handling.html
+++ b/doc/html/modelling/gap_handling.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Handling Gaps — ProMod3 1.1.0 documentation</title>
+ <title>Handling Gaps — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Handling Loop Candidates" href="loop_candidates.html" />
<link rel="prev" title="Model Checking" href="model_checking.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -58,8 +60,8 @@ invalid residue handles to <cite>before</cite> or <cite>after</cite>.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>before</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal"><span class="pre">before</span></code></a></li>
-<li><strong>after</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal"><span class="pre">after</span></code></a></li>
+<li><strong>before</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.before" title="promod3.modelling.StructuralGap.before"><code class="xref py py-attr docutils literal"><span class="pre">before</span></code></a></li>
+<li><strong>after</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.after" title="promod3.modelling.StructuralGap.after"><code class="xref py py-attr docutils literal"><span class="pre">after</span></code></a></li>
<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Fills <a class="reference internal" href="#promod3.modelling.StructuralGap.seq" title="promod3.modelling.StructuralGap.seq"><code class="xref py py-attr docutils literal"><span class="pre">seq</span></code></a></li>
</ul>
</td>
@@ -114,7 +116,7 @@ are valid and:</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Chain, the gap is belonging to</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -265,13 +267,13 @@ extend the gap past another gap.</p>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.before">
<code class="descname">before</code><a class="headerlink" href="#promod3.modelling.StructuralGap.before" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue before the gap (read-only, <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue before the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
<dt id="promod3.modelling.StructuralGap.after">
<code class="descname">after</code><a class="headerlink" href="#promod3.modelling.StructuralGap.after" title="Permalink to this definition">¶</a></dt>
-<dd><p>Residue after the gap (read-only, <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
+<dd><p>Residue after the gap (read-only, <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
@@ -298,7 +300,7 @@ False if no new extension possible.</p>
<dt id="promod3.modelling.GapExtender">
<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">GapExtender</code><span class="sig-paren">(</span><em>gap</em>, <em>seqres</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GapExtender" title="Permalink to this definition">¶</a></dt>
<dd><p>The extender cycles through the following steps:</p>
-<div class="highlight-none"><div class="highlight"><pre> -
+<div class="highlight-none"><div class="highlight"><pre><span></span> -
--
--
---
@@ -316,7 +318,7 @@ False if no new extension possible.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.GapExtender.Extend" title="promod3.modelling.GapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
</ul>
</td>
</tr>
@@ -357,7 +359,7 @@ valid termini.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.FullGapExtender.Extend" title="promod3.modelling.FullGapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
<li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – <ul>
<li>If -1, all possible non-terminal gaps are returned.</li>
<li>If >= 0, this restricts the max. gap-length
@@ -410,7 +412,7 @@ score = num_gap_extensions * <cite>extension_penalty</cite> + sum( <cite>penalti
<li><strong>gap</strong> (<a class="reference internal" href="#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>) – The gap which will be extended by <a class="reference internal" href="#promod3.modelling.ScoringGapExtender.Extend" title="promod3.modelling.ScoringGapExtender.Extend"><code class="xref py py-meth docutils literal"><span class="pre">Extend()</span></code></a>.</li>
<li><strong>extension_penalty</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Penalty for length of gap.</li>
<li><strong>penalties</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Penalty for each residue added to gap.</li>
-<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The full sequence of the chain, the gap is associated with.</li>
<li><strong>max_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – <ul>
<li>If -2, <a class="reference internal" href="#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a> is used instead of <a class="reference internal" href="#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal"><span class="pre">FullGapExtender</span></code></a>
(i.e. it stops at gaps and termini).</li>
@@ -643,9 +645,6 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -653,11 +652,11 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/gap_handling.txt"
diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html
index 6760e8c8f9de9611a3f6c785bf48e46c6aac9f9d..79fbb0d1cc6ff30dd9e85dc0aebdb05f2097a5e4 100644
--- a/doc/html/modelling/index.html
+++ b/doc/html/modelling/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>modelling - Protein Modelling — ProMod3 1.1.0 documentation</title>
+ <title>modelling - Protein Modelling — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Modelling Pipeline" href="pipeline.html" />
<link rel="prev" title="Building ProMod3" href="../buildsystem.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -48,18 +50,18 @@ capabilities to extract useful template data for the target and to fill the
remaining structural data to create a full model of the target. In its simplest
form, you can use a target-template alignment and a template structure to create
a model fully automatically as follows:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
-<span class="c"># get raw model</span>
-<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1crn_cut.pdb'</span><span class="p">)</span>
-<span class="n">aln</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadAlignment</span><span class="p">(</span><span class="s">'data/1crn.fasta'</span><span class="p">)</span>
+<span class="c1"># get raw model</span>
+<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1crn_cut.pdb'</span><span class="p">)</span>
+<span class="n">aln</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadAlignment</span><span class="p">(</span><span class="s1">'data/1crn.fasta'</span><span class="p">)</span>
<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
<span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
-<span class="c"># build final model</span>
+<span class="c1"># build final model</span>
<span class="n">final_model</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildFromRawModel</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">final_model</span><span class="p">,</span> <span class="s">'model.pdb'</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">final_model</span><span class="p">,</span> <span class="s1">'model.pdb'</span><span class="p">)</span>
</pre></div>
</div>
<p>The various steps involved in protein modelling are described here:</p>
@@ -148,9 +150,6 @@ a model fully automatically as follows:</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -158,11 +157,11 @@ a model fully automatically as follows:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/index.txt"
diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index 411f6291eb8c6e3e75449d21e66646eb648fb8b2..b1803ae6baaba3a96330a07192ae2987307a9f9b 100644
--- a/doc/html/modelling/loop_candidates.html
+++ b/doc/html/modelling/loop_candidates.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Handling Loop Candidates — ProMod3 1.1.0 documentation</title>
+ <title>Handling Loop Candidates — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Fitting Loops Into Gaps" href="loop_closing.html" />
<link rel="prev" title="Handling Gaps" href="gap_handling.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -47,59 +49,59 @@ filled manually or generated using static filling functions using the
functionality from the <a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a> or Monte Carlo algorithms.
Once it contains candidates you can apply closing, scoring or clustering
algorithms on all loop candidates. Example:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">modelling</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">modelling</span>
-<span class="c"># let's load a crambin structure from the pdb</span>
-<span class="n">crambin</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1CRN.pdb'</span><span class="p">)</span>
-<span class="n">SEQRES</span> <span class="o">=</span> <span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">crambin</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
+<span class="c1"># let's load a crambin structure from the pdb</span>
+<span class="n">crambin</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
+<span class="n">SEQRES</span> <span class="o">=</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">crambin</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
-<span class="c"># this is the sequence we want to remodel</span>
+<span class="c1"># this is the sequence we want to remodel</span>
<span class="n">loop_seq</span> <span class="o">=</span> <span class="n">SEQRES</span><span class="p">[</span><span class="mi">23</span><span class="p">:</span><span class="mi">31</span><span class="p">]</span>
-<span class="c"># let's define the stem residues</span>
+<span class="c1"># let's define the stem residues</span>
<span class="n">n_stem</span> <span class="o">=</span> <span class="n">crambin</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">23</span><span class="p">]</span>
<span class="n">c_stem</span> <span class="o">=</span> <span class="n">crambin</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="mi">30</span><span class="p">]</span>
-<span class="c"># we use the StructureDB as source for structural information</span>
+<span class="c1"># we use the StructureDB as source for structural information</span>
<span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
-<span class="c"># the FragDB allows to access the StructureDB based on geometric </span>
-<span class="c"># features of the loop stem residue</span>
+<span class="c1"># the FragDB allows to access the StructureDB based on geometric </span>
+<span class="c1"># features of the loop stem residue</span>
<span class="n">frag_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">()</span>
-<span class="c"># the LoopCandidates allow to handle several loops at once</span>
-<span class="c"># we directly want to find potential loop candidates from the</span>
-<span class="c"># previously loaded databases</span>
+<span class="c1"># the LoopCandidates allow to handle several loops at once</span>
+<span class="c1"># we directly want to find potential loop candidates from the</span>
+<span class="c1"># previously loaded databases</span>
<span class="n">loop_candidates</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">LoopCandidates</span><span class="o">.</span><span class="n">FillFromDatabase</span><span class="p">(</span>\
<span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">,</span> <span class="n">loop_seq</span><span class="p">,</span> <span class="n">frag_db</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">)</span>
-<span class="c"># candidates usually don't match exactly the required stem coords.</span>
-<span class="c"># CCD (Cyclic Coordinate Descent) is one way to enforce this match.</span>
+<span class="c1"># candidates usually don't match exactly the required stem coords.</span>
+<span class="c1"># CCD (Cyclic Coordinate Descent) is one way to enforce this match.</span>
<span class="n">loop_candidates</span><span class="o">.</span><span class="n">ApplyCCD</span><span class="p">(</span><span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">)</span>
-<span class="c"># setup backbone scorer with clash and cbeta scoring</span>
+<span class="c1"># setup backbone scorer with clash and cbeta scoring</span>
<span class="n">score_env</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">BackboneScoreEnv</span><span class="p">(</span><span class="n">SEQRES</span><span class="p">)</span>
<span class="n">score_env</span><span class="o">.</span><span class="n">SetInitialEnvironment</span><span class="p">(</span><span class="n">crambin</span><span class="p">)</span>
<span class="n">scorer</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">BackboneOverallScorer</span><span class="p">()</span>
-<span class="n">scorer</span><span class="p">[</span><span class="s">"cbeta"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadCBetaScorer</span><span class="p">()</span>
-<span class="n">scorer</span><span class="p">[</span><span class="s">"clash"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">ClashScorer</span><span class="p">()</span>
+<span class="n">scorer</span><span class="p">[</span><span class="s2">"cbeta"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadCBetaScorer</span><span class="p">()</span>
+<span class="n">scorer</span><span class="p">[</span><span class="s2">"clash"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">ClashScorer</span><span class="p">()</span>
<span class="n">scorer</span><span class="o">.</span><span class="n">AttachEnvironment</span><span class="p">(</span><span class="n">score_env</span><span class="p">)</span>
-<span class="c"># the scorer can then be used on the LoopCandidates object to</span>
-<span class="c"># calculate desired scores (here: cbeta & clash, start resnum = 24)</span>
+<span class="c1"># the scorer can then be used on the LoopCandidates object to</span>
+<span class="c1"># calculate desired scores (here: cbeta & clash, start resnum = 24)</span>
<span class="n">bb_scores</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">ScoreContainer</span><span class="p">()</span>
-<span class="n">loop_candidates</span><span class="o">.</span><span class="n">CalculateBackboneScores</span><span class="p">(</span><span class="n">bb_scores</span><span class="p">,</span> <span class="n">scorer</span><span class="p">,</span>
- <span class="p">[</span><span class="s">"cbeta"</span><span class="p">,</span> <span class="s">"clash"</span><span class="p">],</span> <span class="mi">24</span><span class="p">)</span>
-<span class="c"># we finally perform a weighted linear combination of the scores,</span>
-<span class="c"># pick the best one, insert it into our structure and save it</span>
-<span class="n">weights</span> <span class="o">=</span> <span class="p">{</span><span class="s">"cbeta"</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s">"clash"</span><span class="p">:</span> <span class="mi">1</span><span class="p">}</span>
+<span class="n">loop_candidates</span><span class="o">.</span><span class="n">CalculateBackboneScores</span><span class="p">(</span><span class="n">bb_scores</span><span class="p">,</span> <span class="n">scorer</span><span class="p">,</span> <span class="n">score_env</span><span class="p">,</span>
+ <span class="p">[</span><span class="s2">"cbeta"</span><span class="p">,</span> <span class="s2">"clash"</span><span class="p">],</span> <span class="mi">24</span><span class="p">)</span>
+<span class="c1"># we finally perform a weighted linear combination of the scores,</span>
+<span class="c1"># pick the best one, insert it into our structure and save it</span>
+<span class="n">weights</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"cbeta"</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s2">"clash"</span><span class="p">:</span> <span class="mi">1</span><span class="p">}</span>
<span class="n">scores</span> <span class="o">=</span> <span class="n">bb_scores</span><span class="o">.</span><span class="n">LinearCombine</span><span class="p">(</span><span class="n">weights</span><span class="p">)</span>
<span class="n">min_score</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="n">scores</span><span class="p">)</span>
<span class="n">min_candidate</span> <span class="o">=</span> <span class="n">scores</span><span class="o">.</span><span class="n">index</span><span class="p">(</span><span class="n">min_score</span><span class="p">)</span>
<span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop_candidates</span><span class="p">[</span><span class="n">min_candidate</span><span class="p">]</span>
<span class="n">bb_list</span><span class="o">.</span><span class="n">InsertInto</span><span class="p">(</span><span class="n">crambin</span><span class="o">.</span><span class="n">chains</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">n_stem</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">())</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">crambin</span><span class="p">,</span> <span class="s">"modified_crambin.pdb"</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">crambin</span><span class="p">,</span> <span class="s2">"modified_crambin.pdb"</span><span class="p">)</span>
</pre></div>
</div>
<div class="section" id="the-loopcandidates-class">
@@ -130,8 +132,8 @@ a fragment database.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop</li>
<li><strong>seq</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – The sequence of residues to be added including the
<em>n_stem</em> and <em>c_stem</em></li>
<li><strong>frag_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.FragDB" title="promod3.loop.FragDB"><code class="xref py py-class docutils literal"><span class="pre">FragDB</span></code></a>) – The fragment database</li>
@@ -163,6 +165,14 @@ atoms.</p>
<em class="property">static </em><code class="descname">FillFromMonteCarloSampler</code><span class="sig-paren">(</span><em>initial_bb</em>, <em>seq</em>, <em>num_loops</em>, <em>steps</em>, <em>sampler</em>, <em>closer</em>, <em>scorer</em>, <em>cooler</em>, <em>random_seed=0</em><span class="sig-paren">)</span></dt>
<dd><p>Uses Monte Carlo simulated annealing to sample the loop to be modelled.
If <em>initial_bb</em> is given, every Monte Carlo run starts from that configuration.</p>
+<div class="admonition warning">
+<p class="first admonition-title">Warning</p>
+<p class="last">The <a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a>
+attached to <em>scorer</em> will be altered in the specified stretch.
+You might consider the Stash / Pop mechanism of the
+<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> to restore to the
+original state once the sampling is done.</p>
+</div>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -173,10 +183,10 @@ If <em>initial_bb</em> is given, every Monte Carlo run starts from that configur
<li><strong>num_loops</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of loop candidates to return</li>
<li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of MC steps to perform for each loop candidate
generated</li>
-<li><strong>sampler</strong> (<a class="reference internal" href="monte_carlo.html#mc-sampler-object"><span>Sampler Object</span></a>) – Used to generate a new configuration at each MC step</li>
-<li><strong>closer</strong> (<a class="reference internal" href="monte_carlo.html#mc-closer-object"><span>Closer Object</span></a>) – Used to close the loop after each MC step</li>
-<li><strong>scorer</strong> (<a class="reference internal" href="monte_carlo.html#mc-scorer-object"><span>Scorer Object</span></a>) – Used to score the generated configurations at each MC step</li>
-<li><strong>cooler</strong> (<a class="reference internal" href="monte_carlo.html#mc-cooler-object"><span>Cooler Object</span></a>) – Controls the temperature profile of the simulated annealing</li>
+<li><strong>sampler</strong> (<a class="reference internal" href="monte_carlo.html#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>) – Used to generate a new configuration at each MC step</li>
+<li><strong>closer</strong> (<a class="reference internal" href="monte_carlo.html#mc-closer-object"><span class="std std-ref">Closer Object</span></a>) – Used to close the loop after each MC step</li>
+<li><strong>scorer</strong> (<a class="reference internal" href="monte_carlo.html#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>) – Used to score the generated configurations at each MC step</li>
+<li><strong>cooler</strong> (<a class="reference internal" href="monte_carlo.html#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) – Controls the temperature profile of the simulated annealing</li>
<li><strong>random_seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Seed to feed the random number generator for
accepting/rejecting proposed monte carlo steps.
For every monte carlo run, the random number generator
@@ -234,9 +244,9 @@ not depending on a metropolis criterium.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
should match. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code>
of <a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a>) – A torsion sampler (used for all residues) or a list
@@ -278,9 +288,9 @@ candidate. This leads to an increase in number of loops.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n-stem positions every candidate
should match</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c-stem positions every candidate
should match</li>
<li><strong>pivot_one</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – First pivot residue</li>
<li><strong>pivot_two</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Second pivot residue</li>
@@ -303,9 +313,13 @@ useful to keep track of scores and other data extracted before.</p>
<dl class="method">
<dt id="promod3.modelling.LoopCandidates.CalculateBackboneScores">
-<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>scorer</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateBackboneScores" title="Permalink to this definition">¶</a></dt>
+<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>scorer</em>, <em>scorer_env</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateBackboneScores" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>scorer</em>, <em>scorer_env</em>, <em>keys</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
<dt>
-<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>scorer</em>, <em>keys</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
+<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>mhandle</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
+<dt>
+<code class="descname">CalculateBackboneScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>mhandle</em>, <em>keys</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span></dt>
<dt id="promod3.modelling.LoopCandidates.CalculateAllAtomScores">
<code class="descname">CalculateAllAtomScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>mhandle</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateAllAtomScores" title="Permalink to this definition">¶</a></dt>
<dt>
@@ -322,7 +336,9 @@ Note that (unless otherwise noted) a lower “score” is better!</p>
key names (or the ones from <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a>)</li>
<li><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneOverallScorer</span></code></a>) – Backbone scoring object with set environment for the
particular loop modelling problem.</li>
-<li><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle set up for all atom scoring (see
+<li><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a>) – The scoring environment attached to <em>scorer</em></li>
+<li><strong>mhandle</strong> (<a class="reference internal" href="pipeline.html#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Modelling handle set up scoring (see
+<a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultBackboneScoring()</span></code></a>
<a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a>).</li>
<li><strong>keys</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Keys of the desired scorers. If not given, we use the set of
keys given by <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetBackboneScoringKeys" title="promod3.modelling.ScoringWeights.GetBackboneScoringKeys"><code class="xref py py-meth docutils literal"><span class="pre">ScoringWeights.GetBackboneScoringKeys()</span></code></a> /
@@ -348,7 +364,7 @@ anything is raised when calculating the scores.</p>
<code class="descname">CalculateStructureProfileScores</code><span class="sig-paren">(</span><em>score_container</em>, <em>structure_db</em>, <em>prof</em>, <em>offset=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LoopCandidates.CalculateStructureProfileScores" title="Permalink to this definition">¶</a></dt>
<dd><p>Calculates a score comparing the given profile <em>prof</em> starting at <em>offset</em>
with the sequence / structure profile of each candidate as extracted from
-<em>structure_db</em> (see <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
+<em>structure_db</em> (see <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.seq.ProfileHandle.GetAverageScore()</span></code></a> for
details, <em>prof.null_model</em> is used for weighting).</p>
<p>Note that for profile scores a higher “score” is better! So take care when
combining this to other scores, where it is commonly the other way around.</p>
@@ -364,7 +380,7 @@ with this DB).</p>
<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a></li>
<li><strong>structural_db</strong> (<a class="reference internal" href="../loop/structure_db.html#promod3.loop.StructureDB" title="promod3.loop.StructureDB"><code class="xref py py-class docutils literal"><span class="pre">StructureDB</span></code></a>) – Structural database used in <a class="reference internal" href="#promod3.modelling.LoopCandidates.FillFromDatabase" title="promod3.modelling.LoopCandidates.FillFromDatabase"><code class="xref py py-meth docutils literal"><span class="pre">FillFromDatabase()</span></code></a></li>
-<li><strong>prof</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</li>
<li><strong>offset</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Loop starts at index <em>offset</em> in <em>prof</em>.</li>
</ul>
</td>
@@ -396,8 +412,8 @@ positions and the corresponding atoms in <em>c_stem</em>.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>score_container</strong> (<a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a>) – Add scores to this score container using the default
key name defined in <a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a></li>
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the N-terminal end of the loop.</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – The residue at the C-terminal end of the loop.</li>
</ul>
</td>
</tr>
@@ -801,11 +817,17 @@ matching keys).</p>
<dd><p>Globally accessible set of weights to be used in scoring. This also defines
a consistent naming of keys used for backbone and all atom scorers as set up
by <a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultBackboneScoring" title="promod3.modelling.SetupDefaultBackboneScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultBackboneScoring()</span></code></a> and <a class="reference internal" href="pipeline.html#promod3.modelling.SetupDefaultAllAtomScoring" title="promod3.modelling.SetupDefaultAllAtomScoring"><code class="xref py py-func docutils literal"><span class="pre">SetupDefaultAllAtomScoring()</span></code></a>.</p>
+<p>Different sets of weights are available. You can get general weights
+that have been optimized for a non redundant set of loops with lengths [3,14]
+(including stem residues). The alternative is to get weights that have only
+been optimized on a length specific subset of loops. By default you get
+different weights for following lengths: [0,1,2,3,4], [5,6], [7,8], [9,10],
+[11,12], [13,14].</p>
<p>If you choose to modify the weights, please ensure to set consistently named
keys in here and to use consistently named scorers and scoring computations!</p>
<dl class="staticmethod">
<dt id="promod3.modelling.ScoringWeights.GetWeights">
-<em class="property">static </em><code class="descname">GetWeights</code><span class="sig-paren">(</span><em>with_db=False</em>, <em>with_aa=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetWeights" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetWeights</code><span class="sig-paren">(</span><em>with_db=False</em>, <em>with_aa=False</em>, <em>length_dependent=False</em>, <em>loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetWeights" title="Permalink to this definition">¶</a></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -813,7 +835,9 @@ keys in here and to use consistently named scorers and scoring computations!</p>
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Named weights to be used when scoring loop candidates. The default
weights were optimized to give the best performance when choosing
the loop candidate with the lowest combined score. Each set of
-weights includes (different) backbone scoring weights.</p>
+weights includes (different) backbone scoring weights, that are
+optionally only trained on a subset of loops with corresponding
+loop length.</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)</p>
@@ -823,6 +847,11 @@ weights includes (different) backbone scoring weights.</p>
<li><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True to choose a set of weights including DB specific scores
(stem RMSD and profile scores)</li>
<li><strong>with_aa</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True to choose a set of weights including all atom scores</li>
+<li><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to use general weights or their length
+length dependent counterparts.</li>
+<li><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of full loop. If no weights are available for
+this length or when <em>loop_length</em> is -1, the general
+weights are returned.</li>
</ul>
</td>
</tr>
@@ -832,13 +861,13 @@ weights includes (different) backbone scoring weights.</p>
<dl class="staticmethod">
<dt id="promod3.modelling.ScoringWeights.SetWeights">
-<em class="property">static </em><code class="descname">SetWeights</code><span class="sig-paren">(</span><em>with_db</em>, <em>with_aa</em>, <em>weights</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetWeights" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">SetWeights</code><span class="sig-paren">(</span><em>with_db</em>, <em>with_aa</em>, <em>weights</em>, <em>length_dependent=False</em>, <em>loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.SetWeights" title="Permalink to this definition">¶</a></dt>
<dd><p>Overwrite a set of weights as returned by <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a>.</p>
</dd></dl>
<dl class="staticmethod">
<dt id="promod3.modelling.ScoringWeights.GetBackboneWeights">
-<em class="property">static </em><code class="descname">GetBackboneWeights</code><span class="sig-paren">(</span><em>with_db=False</em>, <em>with_aa=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetBackboneWeights" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetBackboneWeights</code><span class="sig-paren">(</span><em>with_db=False</em>, <em>with_aa=False</em>, <em>length_dependent=False</em>, <em>loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetBackboneWeights" title="Permalink to this definition">¶</a></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -853,6 +882,8 @@ weights includes (different) backbone scoring weights.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
<li><strong>with_aa</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
+<li><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
+<li><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
</ul>
</td>
</tr>
@@ -862,17 +893,24 @@ weights includes (different) backbone scoring weights.</p>
<dl class="staticmethod">
<dt id="promod3.modelling.ScoringWeights.GetAllAtomWeights">
-<em class="property">static </em><code class="descname">GetAllAtomWeights</code><span class="sig-paren">(</span><em>with_db=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetAllAtomWeights" title="Permalink to this definition">¶</a></dt>
+<em class="property">static </em><code class="descname">GetAllAtomWeights</code><span class="sig-paren">(</span><em>with_db=False</em>, <em>length_dependent=False</em>, <em>loop_length=-1</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.ScoringWeights.GetAllAtomWeights" title="Permalink to this definition">¶</a></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Subset of <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a> for all atom scoring as in
-<code class="xref py py-meth docutils literal"><span class="pre">scoring.AllAtomOverallScorer.CalculateLinearCombination()</span></code>.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Subset of <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a> for all atom scoring as in
+<code class="xref py py-meth docutils literal"><span class="pre">scoring.AllAtomOverallScorer.CalculateLinearCombination()</span></code>.</p>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)</td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>, values: <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)</p>
+</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>with_db</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
+<li><strong>length_dependent</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
+<li><strong>loop_length</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – As in <a class="reference internal" href="#promod3.modelling.ScoringWeights.GetWeights" title="promod3.modelling.ScoringWeights.GetWeights"><code class="xref py py-meth docutils literal"><span class="pre">GetWeights()</span></code></a></li>
+</ul>
+</td>
</tr>
</tbody>
</table>
@@ -960,93 +998,92 @@ gap for a model. This shows the combined usage of <a class="reference internal"
keep a consistent modelling environment, <a class="reference internal" href="#promod3.modelling.LoopCandidates" title="promod3.modelling.LoopCandidates"><code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code></a> with its
scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreContainer" title="promod3.modelling.ScoreContainer"><code class="xref py py-class docutils literal"><span class="pre">ScoreContainer</span></code></a> for keeping track of scores and
<a class="reference internal" href="#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a> to combine scores:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
-
-<span class="c"># setup raw model</span>
-<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1crn_cut.pdb'</span><span class="p">)</span>
-<span class="n">seq_trg</span> <span class="o">=</span> <span class="s">'TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN'</span>
-<span class="n">seq_tpl</span> <span class="o">=</span> <span class="s">'TTCCPSIVARSNFNVCRLPGTPEA------GCIIIPGATCPGDYAN'</span>
-<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s">'trg'</span><span class="p">,</span> <span class="n">seq_trg</span><span class="p">),</span>
- <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s">'tpl'</span><span class="p">,</span> <span class="n">seq_tpl</span><span class="p">))</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+
+<span class="c1"># setup raw model</span>
+<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1crn_cut.pdb'</span><span class="p">)</span>
+<span class="n">seq_trg</span> <span class="o">=</span> <span class="s1">'TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN'</span>
+<span class="n">seq_tpl</span> <span class="o">=</span> <span class="s1">'TTCCPSIVARSNFNVCRLPGTPEA------GCIIIPGATCPGDYAN'</span>
+<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'trg'</span><span class="p">,</span> <span class="n">seq_trg</span><span class="p">),</span>
+ <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'tpl'</span><span class="p">,</span> <span class="n">seq_tpl</span><span class="p">))</span>
<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
<span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
-<span class="k">print</span><span class="p">(</span><span class="s">"Number of gaps in raw model: </span><span class="si">%d</span><span class="s">"</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
+<span class="nb">print</span><span class="p">(</span><span class="s2">"Number of gaps in raw model: </span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
-<span class="c"># setup default scorers for modelling handle</span>
+<span class="c1"># setup default scorers for modelling handle</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">SetupDefaultBackboneScoring</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">SetupDefaultAllAtomScoring</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
-<span class="c"># setup databases</span>
+<span class="c1"># setup databases</span>
<span class="n">frag_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">()</span>
<span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
<span class="n">torsion_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">()</span>
-<span class="c"># get data for gap to close</span>
+<span class="c1"># get data for gap to close</span>
<span class="n">gap</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
-<span class="k">print</span><span class="p">(</span><span class="s">"Gap to close: </span><span class="si">%s</span><span class="s">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">gap</span><span class="p">))</span>
+<span class="nb">print</span><span class="p">(</span><span class="s2">"Gap to close: </span><span class="si">%s</span><span class="s2">"</span> <span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">gap</span><span class="p">))</span>
<span class="n">n_stem</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">before</span>
<span class="n">c_stem</span> <span class="o">=</span> <span class="n">gap</span><span class="o">.</span><span class="n">after</span>
<span class="n">start_resnum</span> <span class="o">=</span> <span class="n">n_stem</span><span class="o">.</span><span class="n">GetNumber</span><span class="p">()</span><span class="o">.</span><span class="n">GetNum</span><span class="p">()</span>
-<span class="n">start_idx</span> <span class="o">=</span> <span class="n">start_resnum</span> <span class="o">-</span> <span class="mi">1</span> <span class="c"># res. num. starts at 1</span>
+<span class="n">start_idx</span> <span class="o">=</span> <span class="n">start_resnum</span> <span class="o">-</span> <span class="mi">1</span> <span class="c1"># res. num. starts at 1</span>
-<span class="c"># get loop candidates from FragDB</span>
+<span class="c1"># get loop candidates from FragDB</span>
<span class="n">candidates</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">LoopCandidates</span><span class="o">.</span><span class="n">FillFromDatabase</span><span class="p">(</span>\
<span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">,</span> <span class="n">gap</span><span class="o">.</span><span class="n">full_seq</span><span class="p">,</span> <span class="n">frag_db</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">)</span>
-<span class="k">print</span><span class="p">(</span><span class="s">"Number of loop candidates: </span><span class="si">%d</span><span class="s">"</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">))</span>
+<span class="nb">print</span><span class="p">(</span><span class="s2">"Number of loop candidates: </span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">))</span>
-<span class="c"># all scores will be kept in a score container which we update</span>
+<span class="c1"># all scores will be kept in a score container which we update</span>
<span class="n">all_scores</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">ScoreContainer</span><span class="p">()</span>
-<span class="c"># the keys used to identify scores are globally defined</span>
-<span class="k">print</span><span class="p">(</span><span class="s">"Stem RMSD key = '</span><span class="si">%s</span><span class="s">'"</span> \
+<span class="c1"># the keys used to identify scores are globally defined</span>
+<span class="nb">print</span><span class="p">(</span><span class="s2">"Stem RMSD key = '</span><span class="si">%s</span><span class="s2">'"</span> \
<span class="o">%</span> <span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetStemRMSDsKey</span><span class="p">())</span>
-<span class="k">print</span><span class="p">(</span><span class="s">"Profile keys = ['</span><span class="si">%s</span><span class="s">', '</span><span class="si">%s</span><span class="s">']"</span> \
+<span class="nb">print</span><span class="p">(</span><span class="s2">"Profile keys = ['</span><span class="si">%s</span><span class="s2">', '</span><span class="si">%s</span><span class="s2">']"</span> \
<span class="o">%</span> <span class="p">(</span><span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetSequenceProfileScoresKey</span><span class="p">(),</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetStructureProfileScoresKey</span><span class="p">()))</span>
-<span class="k">print</span><span class="p">(</span><span class="s">"Backbone scoring keys = </span><span class="si">%s</span><span class="s">"</span> \
+<span class="nb">print</span><span class="p">(</span><span class="s2">"Backbone scoring keys = </span><span class="si">%s</span><span class="s2">"</span> \
<span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetBackboneScoringKeys</span><span class="p">()))</span>
-<span class="k">print</span><span class="p">(</span><span class="s">"All atom scoring keys = </span><span class="si">%s</span><span class="s">"</span> \
+<span class="nb">print</span><span class="p">(</span><span class="s2">"All atom scoring keys = </span><span class="si">%s</span><span class="s2">"</span> \
<span class="o">%</span> <span class="nb">str</span><span class="p">(</span><span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetAllAtomScoringKeys</span><span class="p">()))</span>
-<span class="c"># get stem RMSDs for each candidate (i.e. how well does it fit?)</span>
-<span class="c"># -> this must be done before CCD to be meaningful</span>
+<span class="c1"># get stem RMSDs for each candidate (i.e. how well does it fit?)</span>
+<span class="c1"># -> this must be done before CCD to be meaningful</span>
<span class="n">candidates</span><span class="o">.</span><span class="n">CalculateStemRMSDs</span><span class="p">(</span><span class="n">all_scores</span><span class="p">,</span> <span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">)</span>
-<span class="c"># close the candidates with CCD</span>
+<span class="c1"># close the candidates with CCD</span>
<span class="n">orig_indices</span> <span class="o">=</span> <span class="n">candidates</span><span class="o">.</span><span class="n">ApplyCCD</span><span class="p">(</span><span class="n">n_stem</span><span class="p">,</span> <span class="n">c_stem</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="p">)</span>
-<span class="k">print</span><span class="p">(</span><span class="s">"Number of closed loop candidates: </span><span class="si">%d</span><span class="s">"</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">))</span>
+<span class="nb">print</span><span class="p">(</span><span class="s2">"Number of closed loop candidates: </span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">candidates</span><span class="p">))</span>
-<span class="c"># get subset of previously computed scores</span>
+<span class="c1"># get subset of previously computed scores</span>
<span class="n">all_scores</span> <span class="o">=</span> <span class="n">all_scores</span><span class="o">.</span><span class="n">Extract</span><span class="p">(</span><span class="n">orig_indices</span><span class="p">)</span>
-<span class="c"># add profile scores (needs profile for target sequence)</span>
-<span class="n">prof</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadSequenceProfile</span><span class="p">(</span><span class="s">"data/1CRNA.hhm"</span><span class="p">)</span>
+<span class="c1"># add profile scores (needs profile for target sequence)</span>
+<span class="n">prof</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadSequenceProfile</span><span class="p">(</span><span class="s2">"data/1CRNA.hhm"</span><span class="p">)</span>
<span class="n">candidates</span><span class="o">.</span><span class="n">CalculateSequenceProfileScores</span><span class="p">(</span><span class="n">all_scores</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">,</span>
<span class="n">prof</span><span class="p">,</span> <span class="n">start_idx</span><span class="p">)</span>
<span class="n">candidates</span><span class="o">.</span><span class="n">CalculateStructureProfileScores</span><span class="p">(</span><span class="n">all_scores</span><span class="p">,</span> <span class="n">structure_db</span><span class="p">,</span>
<span class="n">prof</span><span class="p">,</span> <span class="n">start_idx</span><span class="p">)</span>
-<span class="c"># add backbone scores</span>
-<span class="n">scorer</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">backbone_scorer</span>
-<span class="n">candidates</span><span class="o">.</span><span class="n">CalculateBackboneScores</span><span class="p">(</span><span class="n">all_scores</span><span class="p">,</span> <span class="n">scorer</span><span class="p">,</span> <span class="n">start_resnum</span><span class="p">)</span>
-<span class="c"># add all atom scores</span>
+<span class="c1"># add backbone scores</span>
+<span class="n">candidates</span><span class="o">.</span><span class="n">CalculateBackboneScores</span><span class="p">(</span><span class="n">all_scores</span><span class="p">,</span> <span class="n">mhandle</span><span class="p">,</span> <span class="n">start_resnum</span><span class="p">)</span>
+<span class="c1"># add all atom scores</span>
<span class="n">candidates</span><span class="o">.</span><span class="n">CalculateAllAtomScores</span><span class="p">(</span><span class="n">all_scores</span><span class="p">,</span> <span class="n">mhandle</span><span class="p">,</span> <span class="n">start_resnum</span><span class="p">)</span>
-<span class="c"># use default weights to combine scores</span>
-<span class="n">weights</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetWeights</span><span class="p">(</span><span class="n">with_db</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span>
- <span class="n">with_aa</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+<span class="c1"># use default weights to combine scores</span>
+<span class="n">weights</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">ScoringWeights</span><span class="o">.</span><span class="n">GetWeights</span><span class="p">(</span><span class="n">with_db</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+ <span class="n">with_aa</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">scores</span> <span class="o">=</span> <span class="n">all_scores</span><span class="o">.</span><span class="n">LinearCombine</span><span class="p">(</span><span class="n">weights</span><span class="p">)</span>
-<span class="c"># rank them (best = lowest "score")</span>
+<span class="c1"># rank them (best = lowest "score")</span>
<span class="n">arg_sorted_scores</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">([(</span><span class="n">v</span><span class="p">,</span><span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">v</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">scores</span><span class="p">)])</span>
-<span class="k">print</span><span class="p">(</span><span class="s">"Ranked candidates: score, index"</span><span class="p">)</span>
+<span class="nb">print</span><span class="p">(</span><span class="s2">"Ranked candidates: score, index"</span><span class="p">)</span>
<span class="k">for</span> <span class="n">v</span><span class="p">,</span><span class="n">i</span> <span class="ow">in</span> <span class="n">arg_sorted_scores</span><span class="p">:</span>
- <span class="k">print</span><span class="p">(</span><span class="s">"</span><span class="si">%g</span><span class="s">, </span><span class="si">%d</span><span class="s">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">v</span><span class="p">,</span><span class="n">i</span><span class="p">))</span>
+ <span class="nb">print</span><span class="p">(</span><span class="s2">"</span><span class="si">%g</span><span class="s2">, </span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="p">(</span><span class="n">v</span><span class="p">,</span><span class="n">i</span><span class="p">))</span>
-<span class="c"># insert best into model, update scorers and clear gaps</span>
+<span class="c1"># insert best into model, update scorers and clear gaps</span>
<span class="n">best_candidate</span> <span class="o">=</span> <span class="n">candidates</span><span class="p">[</span><span class="n">arg_sorted_scores</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]]</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">InsertLoopClearGaps</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">best_candidate</span><span class="p">,</span> <span class="n">gap</span><span class="p">)</span>
-<span class="k">print</span><span class="p">(</span><span class="s">"Number of gaps in closed model: </span><span class="si">%d</span><span class="s">"</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="s">"model.pdb"</span><span class="p">)</span>
+<span class="nb">print</span><span class="p">(</span><span class="s2">"Number of gaps in closed model: </span><span class="si">%d</span><span class="s2">"</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">))</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">model</span><span class="p">,</span> <span class="s2">"model.pdb"</span><span class="p">)</span>
</pre></div>
</div>
</div>
@@ -1095,9 +1132,6 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -1105,11 +1139,11 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/loop_candidates.txt"
diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index 6c740a42b4a178d4631dec8b11877fdf935647b4..d6e5827539347b83e178f2de00f6fbfc0a8fd73c 100644
--- a/doc/html/modelling/loop_closing.html
+++ b/doc/html/modelling/loop_closing.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Fitting Loops Into Gaps — ProMod3 1.1.0 documentation</title>
+ <title>Fitting Loops Into Gaps — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Generating Loops De Novo" href="monte_carlo.html" />
<link rel="prev" title="Handling Loop Candidates" href="loop_candidates.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -81,11 +83,11 @@ to avoid moving into unfavourable regions of the backbone dihedrals.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of the backbones to be closed</li>
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem.
If the residue before <em>n_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
and phi angle (-1.0472) to evaluate the first angle.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem.
If the residue after <em>c_stem</em> doesn’t exist, the
torsion sampler will use a default residue (ALA) and
psi angle (-0.7854) to evaluate the last angle.</li>
@@ -122,8 +124,8 @@ This is faster but might lead to weird backbone dihedral pairs.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the n_stem</li>
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue defining the c_stem</li>
<li><strong>max_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Maximal number of iterations</li>
<li><strong>rmsd_cutoff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The algorithm stops as soon as the c_stem of the loop to
be closed has RMSD below the given <em>c_stem</em></li>
@@ -282,7 +284,11 @@ should be kept rigid during relaxation.</li>
<dl class="method">
<dt id="promod3.modelling.BackboneRelaxer.Run">
<code class="descname">Run</code><span class="sig-paren">(</span><em>bb_list</em>, <em>steps=100</em>, <em>stop_criterion=0.01</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.BackboneRelaxer.Run" title="Permalink to this definition">¶</a></dt>
-<dd><p>Performs steepest descent on given BackboneList.</p>
+<dd><p>Performs steepest descent on given BackboneList. The function possibly fails
+if there are particles (almost) on top of each other, resulting in NaN
+positions in the OpenMM system. The positions of <strong>bb_list</strong> are not touched
+in this case and the function returns an infinit potential energy.
+In Python you can check for that with float(“inf”).</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -296,7 +302,7 @@ relaxation aborts.</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Forcefield energy upon relaxation</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Forcefield energy upon relaxation, infinity in case of OpenMM Error</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
@@ -320,7 +326,7 @@ size or sequence as the initial one.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -342,7 +348,7 @@ size or sequence as the initial one.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -365,7 +371,7 @@ doesn’t do anything if specified residue is a glycine</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -387,7 +393,7 @@ doesn’t do anything if specified residue is a glycine</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -409,7 +415,7 @@ doesn’t do anything if specified residue is a glycine</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Idx of residue</li>
-<li><strong>pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>force_constant</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Force constant in kJ/mol/nm^2</li>
</ul>
</td>
@@ -464,33 +470,33 @@ means no cutoff.</td>
<a class="reference internal" href="sidechain_reconstruction.html#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal"><span class="pre">SidechainReconstructor</span></code></a>, it may be desired to
quickly relax the loop. The <a class="reference internal" href="#promod3.modelling.AllAtomRelaxer" title="promod3.modelling.AllAtomRelaxer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomRelaxer</span></code></a> class takes care of that.</p>
<p>Example usage:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
-<span class="c"># load example (has res. numbering starting at 1)</span>
-<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1CRN.pdb'</span><span class="p">)</span>
+<span class="c1"># load example (has res. numbering starting at 1)</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
<span class="n">res_list</span> <span class="o">=</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span>
-<span class="n">seqres_str</span> <span class="o">=</span> <span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res_list</span><span class="p">])</span>
+<span class="n">seqres_str</span> <span class="o">=</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res_list</span><span class="p">])</span>
-<span class="c"># initialize AllAtom environment and sidechain reconstructor</span>
+<span class="c1"># initialize AllAtom environment and sidechain reconstructor</span>
<span class="n">env</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">AllAtomEnv</span><span class="p">(</span><span class="n">seqres_str</span><span class="p">)</span>
<span class="n">env</span><span class="o">.</span><span class="n">SetInitialEnvironment</span><span class="p">(</span><span class="n">prot</span><span class="p">)</span>
<span class="n">sc_rec</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">SidechainReconstructor</span><span class="p">()</span>
<span class="n">sc_rec</span><span class="o">.</span><span class="n">AttachEnvironment</span><span class="p">(</span><span class="n">env</span><span class="p">)</span>
-<span class="c"># "reconstruct" subset (res. num. 6..10) -> sidechains kept here</span>
+<span class="c1"># "reconstruct" subset (res. num. 6..10) -> sidechains kept here</span>
<span class="n">sc_result</span> <span class="o">=</span> <span class="n">sc_rec</span><span class="o">.</span><span class="n">Reconstruct</span><span class="p">(</span><span class="mi">6</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
-<span class="c"># setup sys creator</span>
+<span class="c1"># setup sys creator</span>
<span class="n">ff_lookup</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">ForcefieldLookup</span><span class="o">.</span><span class="n">GetDefault</span><span class="p">()</span>
<span class="n">mm_sys</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">MmSystemCreator</span><span class="p">(</span><span class="n">ff_lookup</span><span class="p">)</span>
<span class="n">relaxer</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">AllAtomRelaxer</span><span class="p">(</span><span class="n">sc_result</span><span class="p">,</span> <span class="n">mm_sys</span><span class="p">)</span>
-<span class="c"># relax loop</span>
+<span class="c1"># relax loop</span>
<span class="n">pot_e</span> <span class="o">=</span> <span class="n">relaxer</span><span class="o">.</span><span class="n">Run</span><span class="p">(</span><span class="n">sc_result</span><span class="p">,</span> <span class="mi">300</span><span class="p">,</span> <span class="mf">0.1</span><span class="p">)</span>
-<span class="k">print</span> <span class="s">"Potential energy after: </span><span class="si">%g</span><span class="s">"</span> <span class="o">%</span> <span class="n">pot_e</span>
-<span class="c"># update environment with solution</span>
+<span class="nb">print</span> <span class="s2">"Potential energy after: </span><span class="si">%g</span><span class="s2">"</span> <span class="o">%</span> <span class="n">pot_e</span>
+<span class="c1"># update environment with solution</span>
<span class="n">env</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span><span class="n">sc_result</span><span class="o">.</span><span class="n">env_pos</span><span class="p">)</span>
-<span class="c"># store all positions of environment</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">env</span><span class="o">.</span><span class="n">GetAllAtomPositions</span><span class="p">()</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s">'aa_relax_test.pdb'</span><span class="p">)</span>
+<span class="c1"># store all positions of environment</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">env</span><span class="o">.</span><span class="n">GetAllAtomPositions</span><span class="p">()</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s1">'aa_relax_test.pdb'</span><span class="p">)</span>
</pre></div>
</div>
<dl class="class">
@@ -515,7 +521,11 @@ system creator, which takes care of generating a simulation object.</p>
<dt id="promod3.modelling.AllAtomRelaxer.Run">
<code class="descname">Run</code><span class="sig-paren">(</span><em>sc_data</em>, <em>steps=100</em>, <em>stop_criterion=0.01</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.AllAtomRelaxer.Run" title="Permalink to this definition">¶</a></dt>
<dd><p>Performs steepest descent for this system and writes updated positions into
-<em>sc_data.env_pos.all_pos</em>.</p>
+<em>sc_data.env_pos.all_pos</em>. The function possibly fails
+if there are particles (almost) on top of each other, resulting in NaN
+positions in the OpenMM system. The positions of <em>sc_data.env_pos.all_pos</em>
+are not touched in this case and the function returns an infinit potential
+energy. In Python you can check for that with float(“inf”).</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -528,7 +538,7 @@ that threshold, the relaxation aborts.</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Potential energy after relaxation</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Potential energy after relaxation, infinity in case of OpenMM Error</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
@@ -638,9 +648,6 @@ the one given in the constructor.</td>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -648,11 +655,11 @@ the one given in the constructor.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/loop_closing.txt"
diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index ef3d3396534f0b22419b019bf9cb10aee814dc23..914620c01d9b7ab91692936ea61927682e9a7a87 100644
--- a/doc/html/modelling/model_checking.html
+++ b/doc/html/modelling/model_checking.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Model Checking — ProMod3 1.1.0 documentation</title>
+ <title>Model Checking — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Handling Gaps" href="gap_handling.html" />
<link rel="prev" title="Modelling Pipeline" href="pipeline.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -55,14 +57,14 @@ three of the atoms exist (center and radii are estimated then).</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect rings.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of rings to perform ring checks. Each ring is a named
tuple with:
-center (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>),
-plane (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/composite/#ost.geom.Plane" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Plane</span></code></a>),
+center (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>),
+plane (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/composite/#ost.geom.Plane" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Plane</span></code></a>),
radius (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>),
-residue (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>).</td>
+residue (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>).</td>
</tr>
</tbody>
</table>
@@ -78,11 +80,11 @@ residue (<a class="reference external" href="http://www.openstructure.org/docs/d
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal"><span class="pre">GetRings()</span></code></a>.</li>
-<li><strong>ent</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of residues (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) which
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of residues (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) which
have a punched ring.</p>
</td>
</tr>
@@ -101,7 +103,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rings</strong> – List of rings as provided by <a class="reference internal" href="#promod3.modelling.GetRings" title="promod3.modelling.GetRings"><code class="xref py py-func docutils literal"><span class="pre">GetRings()</span></code></a>.</li>
-<li><strong>ent</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a> or <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a>) – Structure for which to detect punches.</li>
</ul>
</td>
</tr>
@@ -126,7 +128,7 @@ This check is faster than using <a class="reference internal" href="#promod3.mod
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>candidates</strong> (<code class="xref py py-class docutils literal"><span class="pre">LoopCandidates</span></code>) – Loop candidates meant to fill <em>gap</em> within <em>model</em>.
Offending candidates are removed from this list.</li>
-<li><strong>model</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</li>
+<li><strong>model</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a>) – Model for which loop is to be filled.</li>
<li><strong>gap</strong> (<a class="reference internal" href="gap_handling.html#promod3.modelling.StructuralGap" title="promod3.modelling.StructuralGap"><code class="xref py py-class docutils literal"><span class="pre">StructuralGap</span></code></a>.) – Gap for which loop is to be filled.</li>
<li><strong>orig_indices</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code>) – Mapping to old indexing of candidates. If given, it
must have as many elements as <em>candidates</em>.</li>
@@ -152,9 +154,9 @@ See <a class="reference internal" href="#promod3.modelling.FilterCandidates" tit
<code class="descclassname">promod3.modelling.</code><code class="descname">RunMolProbity</code><span class="sig-paren">(</span><em>target_pdb</em>, <em>molprobity_bin=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_molprobity.html#RunMolProbity"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.RunMolProbity" title="Permalink to this definition">¶</a></dt>
<dd><p>Run <code class="docutils literal"><span class="pre">MolProbity</span></code> from <code class="docutils literal"><span class="pre">Phenix</span></code> on a given PDB file.</p>
<p>MolProbity score computation: (formula from molprobity source code)</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="n">clashscore</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s">"Clashscore"</span><span class="p">]</span>
-<span class="n">rota_out</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s">"Rotamer outliers"</span><span class="p">]</span>
-<span class="n">rama_iffy</span> <span class="o">=</span> <span class="mf">100.</span> <span class="o">-</span> <span class="n">result</span><span class="p">[</span><span class="s">"Ramachandran favored"</span><span class="p">]</span>
+<div class="highlight-python"><div class="highlight"><pre><span></span><span class="n">clashscore</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s2">"Clashscore"</span><span class="p">]</span>
+<span class="n">rota_out</span> <span class="o">=</span> <span class="n">result</span><span class="p">[</span><span class="s2">"Rotamer outliers"</span><span class="p">]</span>
+<span class="n">rama_iffy</span> <span class="o">=</span> <span class="mf">100.</span> <span class="o">-</span> <span class="n">result</span><span class="p">[</span><span class="s2">"Ramachandran favored"</span><span class="p">]</span>
<span class="n">mpscore</span> <span class="o">=</span> <span class="p">((</span> <span class="mf">0.426</span> <span class="o">*</span> <span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">clashscore</span><span class="p">)</span> <span class="p">)</span> <span class="o">+</span>
<span class="p">(</span> <span class="mf">0.33</span> <span class="o">*</span> <span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="nb">max</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">rota_out</span> <span class="o">-</span> <span class="mi">1</span><span class="p">))</span> <span class="p">)</span> <span class="o">+</span>
<span class="p">(</span> <span class="mf">0.25</span> <span class="o">*</span> <span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="nb">max</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">rama_iffy</span> <span class="o">-</span> <span class="mi">2</span><span class="p">))</span> <span class="p">))</span> <span class="o">+</span> <span class="mf">0.5</span>
@@ -191,7 +193,7 @@ with <code class="docutils literal"><span class="pre">MolProbity</span> <span cl
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a></p>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://www.openstructure.org/docs/dev/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
+<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">FileNotFound</span></code></a> if the “phenix.molprobity”
executable is not found.</p>
</td>
</tr>
@@ -208,7 +210,7 @@ executable is not found.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ost_ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</td>
</tr>
</tbody>
</table>
@@ -273,9 +275,6 @@ executable is not found.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -283,11 +282,11 @@ executable is not found.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/model_checking.txt"
diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index c3239cb82b334f9c53cda4c07dfd39faff17e065..6732e2a0fa011a0b43ada5c9968d35caabf3e393 100644
--- a/doc/html/modelling/monte_carlo.html
+++ b/doc/html/modelling/monte_carlo.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Generating Loops De Novo — ProMod3 1.1.0 documentation</title>
+ <title>Generating Loops De Novo — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Sidechain Reconstruction" href="sidechain_reconstruction.html" />
<link rel="prev" title="Fitting Loops Into Gaps" href="loop_closing.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -46,66 +48,67 @@ novo structure candidates for loops or N-/C-Termini. Every iteration of the
sampling process consists basically of four steps and we define objects for
each step:</p>
<ul class="simple">
-<li><a class="reference internal" href="#mc-sampler-object"><span>Sampler Object</span></a>: Propose new conformation</li>
-<li><a class="reference internal" href="#mc-closer-object"><span>Closer Object</span></a>: Adapt new conformation to the environment</li>
-<li><a class="reference internal" href="#mc-scorer-object"><span>Scorer Object</span></a>: Score the new conformation</li>
-<li><a class="reference internal" href="#mc-cooler-object"><span>Cooler Object</span></a>: Accept/Reject new conformation based on the score and
+<li><a class="reference internal" href="#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>: Propose new conformation</li>
+<li><a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>: Adapt new conformation to the environment</li>
+<li><a class="reference internal" href="#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>: Score the new conformation</li>
+<li><a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>: Accept/Reject new conformation based on the score and
a temperature controlled Metropolis criterion</li>
</ul>
<p>These steps can be arbitrarily combined to generate custom Monte Carlo sampling
pipelines. This combination either happens manually or by using the convenient
<a class="reference internal" href="#promod3.modelling.SampleMonteCarlo" title="promod3.modelling.SampleMonteCarlo"><code class="xref py py-func docutils literal"><span class="pre">SampleMonteCarlo()</span></code></a> function. For example, here we show how to apply Monte
Carlo sampling to the N-terminal part of crambin:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">modelling</span>
-<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span><span class="p">,</span> <span class="n">modelling</span>
+<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
-<span class="c"># setup protein</span>
-<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1CRN.pdb'</span><span class="p">)</span>
+<span class="c1"># setup protein</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
<span class="n">chain_index</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">start_resnum</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">terminal_len</span> <span class="o">=</span> <span class="mi">8</span>
-<span class="n">seqres</span> <span class="o">=</span> <span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
+<span class="n">seqres</span> <span class="o">=</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
<span class="n">terminal_seqres</span> <span class="o">=</span> <span class="n">seqres</span><span class="p">[:</span><span class="n">terminal_len</span><span class="p">]</span>
-<span class="c"># setup mc_sampler</span>
+<span class="c1"># setup mc_sampler</span>
<span class="n">torsion_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSampler</span><span class="p">()</span>
<span class="n">mc_sampler</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">SoftSampler</span><span class="p">(</span><span class="n">terminal_seqres</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="p">,</span>
<span class="mf">10.0</span> <span class="o">/</span> <span class="mi">180</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">)</span>
-<span class="c"># setup mc_closer</span>
+<span class="c1"># setup mc_closer</span>
<span class="n">mc_closer</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">NTerminalCloser</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">terminal_len</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
-<span class="c"># setup backbone scorer with clash and cbeta scoring</span>
+<span class="c1"># setup backbone scorer with clash and cbeta scoring</span>
<span class="n">score_env</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">BackboneScoreEnv</span><span class="p">(</span><span class="n">seqres</span><span class="p">)</span>
<span class="n">score_env</span><span class="o">.</span><span class="n">SetInitialEnvironment</span><span class="p">(</span><span class="n">prot</span><span class="p">)</span>
<span class="n">scorer</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">BackboneOverallScorer</span><span class="p">()</span>
-<span class="n">scorer</span><span class="p">[</span><span class="s">"cbeta"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadCBetaScorer</span><span class="p">()</span>
-<span class="n">scorer</span><span class="p">[</span><span class="s">"clash"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">ClashScorer</span><span class="p">()</span>
+<span class="n">scorer</span><span class="p">[</span><span class="s2">"cbeta"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadCBetaScorer</span><span class="p">()</span>
+<span class="n">scorer</span><span class="p">[</span><span class="s2">"clash"</span><span class="p">]</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">ClashScorer</span><span class="p">()</span>
<span class="n">scorer</span><span class="o">.</span><span class="n">AttachEnvironment</span><span class="p">(</span><span class="n">score_env</span><span class="p">)</span>
-<span class="c"># set up mc_scorer</span>
+<span class="c1"># set up mc_scorer</span>
<span class="n">weights</span> <span class="o">=</span> <span class="nb">dict</span><span class="p">()</span>
-<span class="n">weights</span><span class="p">[</span><span class="s">"cbeta"</span><span class="p">]</span> <span class="o">=</span> <span class="mf">10.0</span>
-<span class="n">weights</span><span class="p">[</span><span class="s">"clash"</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.1</span>
-<span class="n">mc_scorer</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">LinearScorer</span><span class="p">(</span><span class="n">scorer</span><span class="p">,</span> <span class="n">start_resnum</span><span class="p">,</span>
+<span class="n">weights</span><span class="p">[</span><span class="s2">"cbeta"</span><span class="p">]</span> <span class="o">=</span> <span class="mf">10.0</span>
+<span class="n">weights</span><span class="p">[</span><span class="s2">"clash"</span><span class="p">]</span> <span class="o">=</span> <span class="mf">0.1</span>
+<span class="n">mc_scorer</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">LinearScorer</span><span class="p">(</span><span class="n">scorer</span><span class="p">,</span> <span class="n">score_env</span><span class="p">,</span>
+ <span class="n">start_resnum</span><span class="p">,</span> <span class="n">terminal_len</span><span class="p">,</span>
<span class="n">chain_index</span><span class="p">,</span> <span class="n">weights</span><span class="p">)</span>
-<span class="c"># setup mc_cooler</span>
+<span class="c1"># setup mc_cooler</span>
<span class="n">mc_cooler</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">ExponentialCooler</span><span class="p">(</span><span class="mi">100</span><span class="p">,</span> <span class="mi">100</span><span class="p">,</span> <span class="mf">0.9</span><span class="p">)</span>
-<span class="c"># create BackboneList from n-terminus</span>
+<span class="c1"># create BackboneList from n-terminus</span>
<span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">terminal_seqres</span><span class="p">,</span>
<span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[:</span><span class="n">terminal_len</span><span class="p">])</span>
-<span class="c"># shake it!</span>
+<span class="c1"># shake it!</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">SampleMonteCarlo</span><span class="p">(</span><span class="n">mc_sampler</span><span class="p">,</span> <span class="n">mc_closer</span><span class="p">,</span> <span class="n">mc_scorer</span><span class="p">,</span>
- <span class="n">mc_cooler</span><span class="p">,</span> <span class="mi">10000</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">,</span> <span class="bp">False</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
+ <span class="n">mc_cooler</span><span class="p">,</span> <span class="mi">10000</span><span class="p">,</span> <span class="n">bb_list</span><span class="p">,</span> <span class="kc">False</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
-<span class="c"># save down the result</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s">"sampled_frag.pdb"</span><span class="p">)</span>
+<span class="c1"># save down the result</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">bb_list</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s2">"sampled_frag.pdb"</span><span class="p">)</span>
</pre></div>
</div>
<dl class="method">
@@ -124,12 +127,12 @@ ever encountered or the last accepted proposal.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sampler</strong> (<a class="reference internal" href="#mc-sampler-object"><span>Sampler Object</span></a>) – Sampler object capable of initializing and altering
+<li><strong>sampler</strong> (<a class="reference internal" href="#mc-sampler-object"><span class="std std-ref">Sampler Object</span></a>) – Sampler object capable of initializing and altering
conformations.</li>
-<li><strong>closer</strong> (<a class="reference internal" href="#mc-closer-object"><span>Closer Object</span></a>) – Closer object to adapt a new conformation to
+<li><strong>closer</strong> (<a class="reference internal" href="#mc-closer-object"><span class="std std-ref">Closer Object</span></a>) – Closer object to adapt a new conformation to
the environment.</li>
-<li><strong>scorer</strong> (<a class="reference internal" href="#mc-scorer-object"><span>Scorer Object</span></a>) – Scorer object to score new loop conformations.</li>
-<li><strong>cooler</strong> (<a class="reference internal" href="#mc-cooler-object"><span>Cooler Object</span></a>) – Cooler object to control the temperature of the
+<li><strong>scorer</strong> (<a class="reference internal" href="#mc-scorer-object"><span class="std std-ref">Scorer Object</span></a>) – Scorer object to score new loop conformations.</li>
+<li><strong>cooler</strong> (<a class="reference internal" href="#mc-cooler-object"><span class="std std-ref">Cooler Object</span></a>) – Cooler object to control the temperature of the
Monte Carlo trajectory.</li>
<li><strong>steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of Monte Carlo iterations to be performed.</li>
<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – The chosen conformation gets stored here.</li>
@@ -410,9 +413,9 @@ avoid moving into unfavourable phi/psi ranges.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt. See <a class="reference internal" href="loop_closing.html#promod3.modelling.CCD.CCD" title="promod3.modelling.CCD.CCD"><code class="xref py py-meth docutils literal"><span class="pre">CCD()</span></code></a>.</li>
<li><strong>sequence</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Sequence of the conformation to be closed.</li>
<li><strong>torsion_sampler</strong> (<a class="reference internal" href="../loop/torsion_sampler.html#promod3.loop.TorsionSampler" title="promod3.loop.TorsionSampler"><code class="xref py py-class docutils literal"><span class="pre">TorsionSampler</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code>
@@ -459,9 +462,9 @@ the stems given by the closer.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
+<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</li>
</ul>
</td>
@@ -501,7 +504,7 @@ solutions. The KICCloser simply picks the first one.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</li>
<li><strong>c_stem</strong> – Defining stem positions the closed conformation should
adapt.</li>
@@ -542,7 +545,7 @@ the c_stem with the desired positions.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Whether closing was successful</td>
@@ -560,7 +563,7 @@ the n_stem with the desired positions.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">Whether closing was successful</td>
@@ -575,12 +578,22 @@ adapt.</td>
<p>The scorer asses a proposed conformation and are intended to return a pseudo
energy, the lower the better.</p>
<dl class="class">
-<dt id="promod3.modelling.LinearScorer">
-<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">LinearScorer</code><span class="sig-paren">(</span><em>scorer</em>, <em>start_resnum</em>, <em>chain_idx</em>, <em>linear_weights</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">LinearScorer(scorer, scorer_env, start_resnum, num_residues,</code></dt>
+<dt>
+<code class="descname">chain_idx, linear_weights)</code></dt>
<dd><p>The LinearScorer allows to combine the scores available from
<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneOverallScorer</span></code></a> in a linear manner. See
<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination" title="promod3.scoring.BackboneOverallScorer.CalculateLinearCombination"><code class="xref py py-meth docutils literal"><span class="pre">CalculateLinearCombination()</span></code></a> for a
detailed description of the arguments.</p>
+<div class="admonition warning">
+<p class="first admonition-title">Warning</p>
+<p class="last">The provided <em>scorer_env</em> will be altered in every
+<a class="reference internal" href="#promod3.modelling.GetScore" title="promod3.modelling.GetScore"><code class="xref py py-func docutils literal"><span class="pre">GetScore()</span></code></a> call.
+You might consider the Stash / Pop mechanism of the
+<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> to restore to the
+original state once the sampling is done.</p>
+</div>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -588,7 +601,9 @@ detailed description of the arguments.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>scorer</strong> (<a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneOverallScorer</span></code></a>) – Scorer Object with set environment for the particular loop
modelling problem.</li>
+<li><strong>scorer_env</strong> (<a class="reference internal" href="../scoring/backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a>) – The environment that is linked to the <em>scorer</em></li>
<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES.</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues to score</li>
<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belong to.</li>
<li><strong>linear_weights</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">dict</span></code></a> (keys: <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>,
values: <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)) – Weights for each desired scorer.</li>
@@ -602,8 +617,8 @@ which no scorer exists</p>
</tbody>
</table>
<dl class="method">
-<dt id="promod3.modelling.LinearScorer.GetScore">
-<code class="descname">GetScore</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.LinearScorer.GetScore" title="Permalink to this definition">¶</a></dt>
+<dt id="promod3.modelling.GetScore">
+<code class="descclassname">promod3.modelling.</code><code class="descname">GetScore</code><span class="sig-paren">(</span><em>bb_list</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.GetScore" title="Permalink to this definition">¶</a></dt>
<dd><table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -713,9 +728,6 @@ the returned temperature gets multiplied by the <em>cooling_factor</em>.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -723,11 +735,11 @@ the returned temperature gets multiplied by the <em>cooling_factor</em>.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/monte_carlo.txt"
diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
index fdf455dc507efbf870475eb13814ee084bf355c3..9973f610b7e21bd5badbd8e66be478d0bc0272bd 100644
--- a/doc/html/modelling/pipeline.html
+++ b/doc/html/modelling/pipeline.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Modelling Pipeline — ProMod3 1.1.0 documentation</title>
+ <title>Modelling Pipeline — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Model Checking" href="model_checking.html" />
<link rel="prev" title="modelling - Protein Modelling" href="index.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -58,41 +60,41 @@ heuristics)</li>
with the <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildFromRawModel()</span></code></a> function. If you want to run and tweak the
internal steps, you can start with the following code and adapt it to your
purposes:</p>
-<div class="highlight-python" id="modelling-steps-example"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<div class="highlight-default" id="modelling-steps-example"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
-<span class="c"># setup</span>
+<span class="c1"># setup</span>
<span class="n">merge_distance</span> <span class="o">=</span> <span class="mi">4</span>
<span class="n">fragment_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">()</span>
<span class="n">structure_db</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">()</span>
<span class="n">torsion_sampler</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">()</span>
-<span class="c"># get raw model</span>
-<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1crn_cut.pdb'</span><span class="p">)</span>
-<span class="n">aln</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadAlignment</span><span class="p">(</span><span class="s">'data/1crn.fasta'</span><span class="p">)</span>
+<span class="c1"># get raw model</span>
+<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1crn_cut.pdb'</span><span class="p">)</span>
+<span class="n">aln</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadAlignment</span><span class="p">(</span><span class="s1">'data/1crn.fasta'</span><span class="p">)</span>
<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
<span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
-<span class="c"># we're not modelling termini</span>
+<span class="c1"># we're not modelling termini</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">RemoveTerminalGaps</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
-<span class="c"># perform loop modelling to close all gaps</span>
+<span class="c1"># perform loop modelling to close all gaps</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">CloseGaps</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">merge_distance</span><span class="p">,</span> <span class="n">fragment_db</span><span class="p">,</span>
<span class="n">structure_db</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="p">)</span>
-<span class="c"># build sidechains</span>
+<span class="c1"># build sidechains</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">BuildSidechains</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">merge_distance</span><span class="p">,</span> <span class="n">fragment_db</span><span class="p">,</span>
<span class="n">structure_db</span><span class="p">,</span> <span class="n">torsion_sampler</span><span class="p">)</span>
-<span class="c"># minimize energy of final model using molecular mechanics</span>
+<span class="c1"># minimize energy of final model using molecular mechanics</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">MinimizeModelEnergy</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
-<span class="c"># check final model and report issues</span>
+<span class="c1"># check final model and report issues</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">CheckFinalModel</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
-<span class="c"># extract final model</span>
+<span class="c1"># extract final model</span>
<span class="n">final_model</span> <span class="o">=</span> <span class="n">mhandle</span><span class="o">.</span><span class="n">model</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">final_model</span><span class="p">,</span> <span class="s">'model.pdb'</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">final_model</span><span class="p">,</span> <span class="s1">'model.pdb'</span><span class="p">)</span>
</pre></div>
</div>
<div class="section" id="build-raw-modelling-handle">
@@ -115,7 +117,7 @@ chain follows afterwards.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -141,13 +143,13 @@ Gaps of different chains are appended one after another.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.seqres">
<code class="descname">seqres</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.seqres" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of sequences with one <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceHandle</span></code></a> for each chain
+<dd><p>List of sequences with one <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">SequenceHandle</span></code></a> for each chain
of the target protein.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceList</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -156,7 +158,7 @@ of the target protein.</p>
<dl class="attribute">
<dt id="promod3.modelling.ModellingHandle.profiles">
<code class="descname">profiles</code><a class="headerlink" href="#promod3.modelling.ModellingHandle.profiles" title="Permalink to this definition">¶</a></dt>
-<dd><p>List of profiles with one <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
+<dd><p>List of profiles with one <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a> for each chain of
the target protein (same order as in <a class="reference internal" href="#promod3.modelling.ModellingHandle.seqres" title="promod3.modelling.ModellingHandle.seqres"><code class="xref py py-attr docutils literal"><span class="pre">seqres</span></code></a>). Please note, that this
attribute won’t be set by simply calling <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>. You have
to fill it manually or even better by the convenient function
@@ -165,7 +167,7 @@ to fill it manually or even better by the convenient function
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
+<tr class="field-odd field"><th class="field-name">Type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -319,7 +321,7 @@ alignment handle or an alignment handle list. Every list item is treated as a
single chain in the final raw model.</p>
<p>Each alignment handle must contain exactly two sequences and the second
sequence is considered the template sequence, which must have a
-<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a> attached.</p>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityView</span></code></a> attached.</p>
<p>This is a basic protein core modelling algorithm that copies backbone
coordinates based on the sequence alignment. For matching residues, the
side chain coordinates are also copied. Gaps are ignored. Hydrogen an
@@ -347,7 +349,7 @@ as information about insertions and deletions in the gaps list.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aln</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
+<li><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">AlignmentHandle</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">AlignmentList</span></code>) – Single alignment handle for raw model with single chain or
list of alignment handles for raw model with multiple chains.</li>
<li><strong>include_ligands</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True, if we wish to include ligands in the model. This
searches for ligands in all OST handles of the views
@@ -373,7 +375,7 @@ in SMTL). All ligands are added to a new chain named
<li>the second sequence does not have an attached structure</li>
<li>the residues of the template structure do not match with the
alignment sequence (note that you can set an “offset” (see
-<a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v1.6.0)"><code class="xref py py-meth docutils literal"><span class="pre">SetSequenceOffset()</span></code></a>) for the
+<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">SetSequenceOffset()</span></code></a>) for the
template sequence (but not for the target))</li>
<li>the target sequence has a non-zero offset (cannot be honored as
the resulting model will always start its residue numbering at 1)</li>
@@ -393,7 +395,7 @@ the resulting model will always start its residue numbering at 1)</li>
<dd><p>Build a model starting with a raw model (see <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildRawModel()</span></code></a>).</p>
<p>This function implements a recommended pipeline to generate complete models
from a raw model. The steps are shown in detail in the code example
-<a class="reference internal" href="#modelling-steps-example"><span>above</span></a>. If you wish to use your own
+<a class="reference internal" href="#modelling-steps-example"><span class="std std-ref">above</span></a>. If you wish to use your own
pipeline, you can use that code as a starting point for your own custom
modelling pipeline. For reproducibility, we recommend that you keep copies
of custom pipelines.</p>
@@ -411,12 +413,12 @@ return an incomplete model.</p>
<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – The prepared template coordinates loaded with the input
alignment.</li>
<li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
-CHARMM one (see <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v1.6.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
-and <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v1.6.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
+CHARMM one (see <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v1.7.1)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
+and <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v1.7.1)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadCHARMMForcefield()</span></code></a>).
Both do a similarly good job without ligands (CHARMM
slightly better), but you will want to be consistent
with the optional force fields in <cite>extra_force_fields</cite>.</li>
-<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
+<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use if a
(ligand) residue cannot be parametrized with the
default force field. The force fields are tried
in the order as given and ligands without an
@@ -427,7 +429,7 @@ existing parametrization are skipped.</li>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Delivers the model as an OST entity.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
</td>
</tr>
</tbody>
@@ -449,10 +451,8 @@ The scorers added (with their respective keys) are:</p>
<li>“reduced”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal"><span class="pre">ReducedScorer</span></code></a></li>
<li>“clash”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.ClashScorer" title="promod3.scoring.ClashScorer"><code class="xref py py-class docutils literal"><span class="pre">ClashScorer</span></code></a></li>
<li>“hbond”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal"><span class="pre">HBondScorer</span></code></a></li>
-<li>“ss_agreement”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal"><span class="pre">SSAgreementScorer</span></code></a></li>
<li>“torsion”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal"><span class="pre">TorsionScorer</span></code></a></li>
<li>“pairwise”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.PairwiseScorer" title="promod3.scoring.PairwiseScorer"><code class="xref py py-class docutils literal"><span class="pre">PairwiseScorer</span></code></a></li>
-<li>“density”: <a class="reference internal" href="../scoring/backbone_scorers.html#promod3.scoring.DensityScorer" title="promod3.scoring.DensityScorer"><code class="xref py py-class docutils literal"><span class="pre">DensityScorer</span></code></a></li>
</ul>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -604,7 +604,7 @@ environments get updated in <strong>target_mhandle</strong>.</p>
<li><strong>target_chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – This is the chain where the info goes to</li>
<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – First residue of the copied stretch</li>
<li><strong>end_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Last residue of the copied stretch</li>
-<li><strong>transform</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
+<li><strong>transform</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – Transformation to be applied to all atom positions when
they’re copied over</li>
</ul>
</td>
@@ -635,7 +635,7 @@ while ensuring consistency with the <a class="reference internal" href="#promod3
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>mhandle</strong> (<a class="reference internal" href="#promod3.modelling.ModellingHandle" title="promod3.modelling.ModellingHandle"><code class="xref py py-class docutils literal"><span class="pre">ModellingHandle</span></code></a>) – Will have the profiles attached afterwards</li>
-<li><strong>profiles</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</li>
+<li><strong>profiles</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – The sequence profiles to attach</li>
</ul>
</td>
</tr>
@@ -673,7 +673,7 @@ with seqres in <strong>mhandle</strong></p>
<dl class="function">
<dt id="promod3.modelling.CloseGaps">
-<code class="descclassname">promod3.modelling.</code><code class="descname">CloseGaps</code><span class="sig-paren">(</span><em>mhandle</em>, <em>merge_distance=4</em>, <em>fragment_db=None</em>, <em>structure_db=None</em>, <em>torsion_sampler=None</em>, <em>fragger_handles=None</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_closegaps.html#CloseGaps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.CloseGaps" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">CloseGaps</code><span class="sig-paren">(</span><em>mhandle</em>, <em>merge_distance=4</em>, <em>fragment_db=None</em>, <em>structure_db=None</em>, <em>torsion_sampler=None</em>, <em>fragger_handles=None</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_closegaps.html#CloseGaps"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.CloseGaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Tries to close all gaps in a model, except termini. It will go through
following steps:</p>
<ul class="simple">
@@ -713,6 +713,11 @@ gets executed.</li>
processed</li>
<li><strong>resnum_range</strong> (<code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> containing two <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
processed.</li>
+<li><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a> provides different sets
+of weights that have been trained on different
+loop subsets. If this flag is true, the length
+dependent weights are used to close loops with
+database / Monte Carlo.</li>
</ul>
</td>
</tr>
@@ -730,19 +735,19 @@ Before diving into the more demanding tasks in modeling, those may be closed
already in the raw-model. After closure some checks are done to see if the
solution is stereochemically sensible.</p>
<p>Closed gaps are removed from <code class="xref py py-attr docutils literal"><span class="pre">mhandle.gaps</span></code>.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
-<span class="c"># setup</span>
-<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/gly.pdb'</span><span class="p">)</span>
-<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s">'trg'</span><span class="p">,</span> <span class="s">'GGG-GGG'</span><span class="p">),</span>
- <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s">'tpl'</span><span class="p">,</span> <span class="s">'GGGAGGG'</span><span class="p">))</span>
+<span class="c1"># setup</span>
+<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/gly.pdb'</span><span class="p">)</span>
+<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'trg'</span><span class="p">,</span> <span class="s1">'GGG-GGG'</span><span class="p">),</span>
+ <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'tpl'</span><span class="p">,</span> <span class="s1">'GGGAGGG'</span><span class="p">))</span>
<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
<span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
-<span class="c"># close small deletion</span>
-<span class="k">print</span> <span class="s">'Number of gaps before: </span><span class="si">%d</span><span class="s">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="c1"># close small deletion</span>
+<span class="nb">print</span> <span class="s1">'Number of gaps before: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">CloseSmallDeletions</span><span class="p">(</span><span class="n">mhandle</span><span class="p">)</span>
-<span class="k">print</span> <span class="s">'Number of gaps after: </span><span class="si">%d</span><span class="s">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="nb">print</span> <span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
</pre></div>
</div>
<table class="docutils field-list" frame="void" rules="none">
@@ -763,7 +768,8 @@ The gap is penalized according as
For the scondary-structure-penalty to work,
the model-template must have the appropriate
information before <a class="reference internal" href="#promod3.modelling.BuildRawModel" title="promod3.modelling.BuildRawModel"><code class="xref py py-func docutils literal"><span class="pre">BuildRawModel()</span></code></a> is
-called (e.g. with <a class="reference external" href="http://www.openstructure.org/docs/dev/bindings/dssp/#module-ost.bindings.dssp" title="(in OpenStructure v1.6.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.bindings.dssp</span></code></a>).</li>
+called (e.g. with
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v1.7.1)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li>
<li><strong>use_full_extender</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – True = use <a class="reference internal" href="gap_handling.html#promod3.modelling.FullGapExtender" title="promod3.modelling.FullGapExtender"><code class="xref py py-class docutils literal"><span class="pre">FullGapExtender</span></code></a> instead of
of <a class="reference internal" href="gap_handling.html#promod3.modelling.GapExtender" title="promod3.modelling.GapExtender"><code class="xref py py-class docutils literal"><span class="pre">GapExtender</span></code></a>. Also works in combination
with <cite>use_scoring_extender</cite>. This allows the gap
@@ -796,21 +802,21 @@ stretch of original gaps and the deleted region. Original gaps will be
removed. Stem residues count to the gap, so <strong>A-A-A</strong> has a distance of 0.</p>
<p>IMPORTANT: we assume here that <em>mhandle</em> stores gaps sequentially.
Non-sequential gaps are ignored!</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
-<span class="c"># setup</span>
-<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1crn_cut.pdb'</span><span class="p">)</span>
-<span class="n">seq_trg</span> <span class="o">=</span> <span class="s">'TTCCPSIVARSNFNVCRLPGTPEAICATGYTCIIIPGATCPGDYAN'</span>
-<span class="n">seq_tpl</span> <span class="o">=</span> <span class="s">'TTCCPSIVARSNFNVCRLPGTPEA----G--CIIIPGATCPGDYAN'</span>
-<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s">'trg'</span><span class="p">,</span> <span class="n">seq_trg</span><span class="p">),</span>
- <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s">'tpl'</span><span class="p">,</span> <span class="n">seq_tpl</span><span class="p">))</span>
+<span class="c1"># setup</span>
+<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1crn_cut.pdb'</span><span class="p">)</span>
+<span class="n">seq_trg</span> <span class="o">=</span> <span class="s1">'TTCCPSIVARSNFNVCRLPGTPEAICATGYTCIIIPGATCPGDYAN'</span>
+<span class="n">seq_tpl</span> <span class="o">=</span> <span class="s1">'TTCCPSIVARSNFNVCRLPGTPEA----G--CIIIPGATCPGDYAN'</span>
+<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'trg'</span><span class="p">,</span> <span class="n">seq_trg</span><span class="p">),</span>
+ <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'tpl'</span><span class="p">,</span> <span class="n">seq_tpl</span><span class="p">))</span>
<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
<span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
-<span class="c"># merge gaps</span>
-<span class="k">print</span> <span class="s">'Number of gaps before: </span><span class="si">%d</span><span class="s">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="c1"># merge gaps</span>
+<span class="nb">print</span> <span class="s1">'Number of gaps before: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">MergeGapsByDistance</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
-<span class="k">print</span> <span class="s">'Number of gaps after: </span><span class="si">%d</span><span class="s">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="nb">print</span> <span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
</pre></div>
</div>
<table class="docutils field-list" frame="void" rules="none">
@@ -834,29 +840,29 @@ both in this resnum range.</li>
<dl class="function">
<dt id="promod3.modelling.FillLoopsByDatabase">
-<code class="descclassname">promod3.modelling.</code><code class="descname">FillLoopsByDatabase</code><span class="sig-paren">(</span><em>mhandle</em>, <em>fragment_db</em>, <em>structure_db</em>, <em>torsion_sampler</em>, <em>max_loops_to_search=40</em>, <em>min_loops_required=4</em>, <em>max_res_extension=-1</em>, <em>extended_search=True</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>score_variant=0</em>, <em>ring_punch_detection=1</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>max_num_all_atom=0</em>, <em>clash_thresh=-1</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_closegaps.html#FillLoopsByDatabase"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.FillLoopsByDatabase" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">FillLoopsByDatabase</code><span class="sig-paren">(</span><em>mhandle</em>, <em>fragment_db</em>, <em>structure_db</em>, <em>torsion_sampler</em>, <em>max_loops_to_search=40</em>, <em>min_loops_required=4</em>, <em>max_res_extension=-1</em>, <em>extended_search=True</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>score_variant=0</em>, <em>ring_punch_detection=1</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>max_num_all_atom=0</em>, <em>clash_thresh=-1</em>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_closegaps.html#FillLoopsByDatabase"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.FillLoopsByDatabase" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to fill up loops from a structural database.</p>
<p>Usually this will extend the gaps a bit to match candidates from the
database. Do not expect a gap being filled in between its actual stem
residues.
This function cannot fill gaps at C- or N-terminal.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
-<span class="c"># setup</span>
-<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1crn_cut.pdb'</span><span class="p">)</span>
-<span class="n">seq_trg</span> <span class="o">=</span> <span class="s">'TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN'</span>
-<span class="n">seq_tpl</span> <span class="o">=</span> <span class="s">'TTCCPSIVARSNFNVCRLPGTPEA------GCIIIPGATCPGDYAN'</span>
-<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s">'trg'</span><span class="p">,</span> <span class="n">seq_trg</span><span class="p">),</span>
- <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s">'tpl'</span><span class="p">,</span> <span class="n">seq_tpl</span><span class="p">))</span>
+<span class="c1"># setup</span>
+<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1crn_cut.pdb'</span><span class="p">)</span>
+<span class="n">seq_trg</span> <span class="o">=</span> <span class="s1">'TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN'</span>
+<span class="n">seq_tpl</span> <span class="o">=</span> <span class="s1">'TTCCPSIVARSNFNVCRLPGTPEA------GCIIIPGATCPGDYAN'</span>
+<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'trg'</span><span class="p">,</span> <span class="n">seq_trg</span><span class="p">),</span>
+ <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'tpl'</span><span class="p">,</span> <span class="n">seq_tpl</span><span class="p">))</span>
<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
<span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
-<span class="c"># close gaps</span>
-<span class="k">print</span> <span class="s">'Number of gaps before: </span><span class="si">%d</span><span class="s">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="c1"># close gaps</span>
+<span class="nb">print</span> <span class="s1">'Number of gaps before: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">FillLoopsByDatabase</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span> <span class="n">loop</span><span class="o">.</span><span class="n">LoadFragDB</span><span class="p">(),</span>
<span class="n">loop</span><span class="o">.</span><span class="n">LoadStructureDB</span><span class="p">(),</span>
<span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">())</span>
-<span class="k">print</span> <span class="s">'Number of gaps after: </span><span class="si">%d</span><span class="s">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="nb">print</span> <span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
</pre></div>
</div>
<table class="docutils field-list" frame="void" rules="none">
@@ -922,6 +928,11 @@ approx. 2x slower than without and will give a
slight improvement in loop selection.</li>
<li><strong>clash_thresh</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – If > 0, we only keep loop candidates which have a
backbone clash score lower than this.</li>
+<li><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a> provides different sets
+of weights that have been trained on different
+loop subsets. If this flag is true, the length
+dependent weights are used to select the final
+loops.</li>
</ul>
</td>
</tr>
@@ -931,7 +942,7 @@ backbone clash score lower than this.</li>
<dl class="function">
<dt id="promod3.modelling.FillLoopsByMonteCarlo">
-<code class="descclassname">promod3.modelling.</code><code class="descname">FillLoopsByMonteCarlo</code><span class="sig-paren">(</span><em>mhandle</em>, <em>torsion_sampler</em>, <em>max_loops_to_search=6</em>, <em>max_extension=30</em>, <em>mc_num_loops=2</em>, <em>mc_steps=5000</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>score_variant=0</em>, <em>ring_punch_detection=1</em>, <em>fragger_handles=None</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_closegaps.html#FillLoopsByMonteCarlo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.FillLoopsByMonteCarlo" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">promod3.modelling.</code><code class="descname">FillLoopsByMonteCarlo</code><span class="sig-paren">(</span><em>mhandle</em>, <em>torsion_sampler</em>, <em>max_loops_to_search=6</em>, <em>max_extension=30</em>, <em>mc_num_loops=2</em>, <em>mc_steps=5000</em>, <em>use_scoring_extender=True</em>, <em>use_full_extender=True</em>, <em>score_variant=0</em>, <em>ring_punch_detection=1</em>, <em>fragger_handles=None</em>, <em>chain_idx=None</em>, <em>resnum_range=None</em>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_closegaps.html#FillLoopsByMonteCarlo"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.FillLoopsByMonteCarlo" title="Permalink to this definition">¶</a></dt>
<dd><p>Try to fill up loops with Monte Carlo sampling.</p>
<p>This is meant as a “last-resort” approach when it is not possible to fill
the loops from the database with <a class="reference internal" href="#promod3.modelling.FillLoopsByDatabase" title="promod3.modelling.FillLoopsByDatabase"><code class="xref py py-func docutils literal"><span class="pre">FillLoopsByDatabase()</span></code></a>.
@@ -941,22 +952,22 @@ more loop candidates to be found.</p>
<em>fragger_handles</em> is given) <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> lists. The latter
is only used if the gap length is >= the length of fragments stored.</p>
<p>This function cannot fill gaps at C- or N-terminal.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
-<span class="c"># setup</span>
-<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1crn_cut.pdb'</span><span class="p">)</span>
-<span class="n">seq_trg</span> <span class="o">=</span> <span class="s">'TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN'</span>
-<span class="n">seq_tpl</span> <span class="o">=</span> <span class="s">'TTCCPSIVARSNFNVCRLPGTPEA------GCIIIPGATCPGDYAN'</span>
-<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s">'trg'</span><span class="p">,</span> <span class="n">seq_trg</span><span class="p">),</span>
- <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s">'tpl'</span><span class="p">,</span> <span class="n">seq_tpl</span><span class="p">))</span>
+<span class="c1"># setup</span>
+<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1crn_cut.pdb'</span><span class="p">)</span>
+<span class="n">seq_trg</span> <span class="o">=</span> <span class="s1">'TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN'</span>
+<span class="n">seq_tpl</span> <span class="o">=</span> <span class="s1">'TTCCPSIVARSNFNVCRLPGTPEA------GCIIIPGATCPGDYAN'</span>
+<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'trg'</span><span class="p">,</span> <span class="n">seq_trg</span><span class="p">),</span>
+ <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'tpl'</span><span class="p">,</span> <span class="n">seq_tpl</span><span class="p">))</span>
<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
<span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
-<span class="c"># close gaps</span>
-<span class="k">print</span> <span class="s">'Number of gaps before: </span><span class="si">%d</span><span class="s">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="c1"># close gaps</span>
+<span class="nb">print</span> <span class="s1">'Number of gaps before: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">FillLoopsByMonteCarlo</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span>
<span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">())</span>
-<span class="k">print</span> <span class="s">'Number of gaps after: </span><span class="si">%d</span><span class="s">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="nb">print</span> <span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
</pre></div>
</div>
<table class="docutils field-list" frame="void" rules="none">
@@ -990,6 +1001,11 @@ fragger handle for each chain in <em>mhandle</em>.</li>
processed</li>
<li><strong>resnum_range</strong> (<code class="xref py py-class docutils literal"><span class="pre">tuple</span></code> containing two <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – If not None, only gaps within this resnum range get
processed</li>
+<li><strong>length_dep_weights</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – <a class="reference internal" href="loop_candidates.html#promod3.modelling.ScoringWeights" title="promod3.modelling.ScoringWeights"><code class="xref py py-class docutils literal"><span class="pre">ScoringWeights</span></code></a> provides different sets
+of weights that have been trained on different
+loop subsets. If this flag is true, the length
+dependent weights are used to select the final
+loops.</li>
</ul>
</td>
</tr>
@@ -1044,22 +1060,22 @@ but we do not assume that the resulting termini are of high quality!</p>
<em>fragger_handles</em> is given) <a class="reference internal" href="../loop/structure_db.html#promod3.loop.Fragger" title="promod3.loop.Fragger"><code class="xref py py-class docutils literal"><span class="pre">Fragger</span></code></a> lists. The latter
is only used if the gap length is >= the length of fragments stored.</p>
<p>Terminal gaps of length 1 are ignored by this function!</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span><span class="p">,</span> <span class="n">loop</span>
-<span class="c"># setup</span>
-<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/gly.pdb'</span><span class="p">)</span>
-<span class="n">seq_trg</span> <span class="o">=</span> <span class="s">'AAAAGGGGGGGGGGGGGGGGGGGGAAAAAA'</span>
-<span class="n">seq_tpl</span> <span class="o">=</span> <span class="s">'----GGGGGGGGGGGGGGGGGGGG------'</span>
-<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s">'trg'</span><span class="p">,</span> <span class="n">seq_trg</span><span class="p">),</span>
- <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s">'tpl'</span><span class="p">,</span> <span class="n">seq_tpl</span><span class="p">))</span>
+<span class="c1"># setup</span>
+<span class="n">tpl</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/gly.pdb'</span><span class="p">)</span>
+<span class="n">seq_trg</span> <span class="o">=</span> <span class="s1">'AAAAGGGGGGGGGGGGGGGGGGGGAAAAAA'</span>
+<span class="n">seq_tpl</span> <span class="o">=</span> <span class="s1">'----GGGGGGGGGGGGGGGGGGGG------'</span>
+<span class="n">aln</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">CreateAlignment</span><span class="p">(</span><span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'trg'</span><span class="p">,</span> <span class="n">seq_trg</span><span class="p">),</span>
+ <span class="n">seq</span><span class="o">.</span><span class="n">CreateSequence</span><span class="p">(</span><span class="s1">'tpl'</span><span class="p">,</span> <span class="n">seq_tpl</span><span class="p">))</span>
<span class="n">aln</span><span class="o">.</span><span class="n">AttachView</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">tpl</span><span class="o">.</span><span class="n">CreateFullView</span><span class="p">())</span>
<span class="n">mhandle</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">BuildRawModel</span><span class="p">(</span><span class="n">aln</span><span class="p">)</span>
-<span class="c"># close gaps</span>
-<span class="k">print</span> <span class="s">'Number of gaps before: </span><span class="si">%d</span><span class="s">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="c1"># close gaps</span>
+<span class="nb">print</span> <span class="s1">'Number of gaps before: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
<span class="n">modelling</span><span class="o">.</span><span class="n">ModelTermini</span><span class="p">(</span><span class="n">mhandle</span><span class="p">,</span>
<span class="n">loop</span><span class="o">.</span><span class="n">LoadTorsionSamplerCoil</span><span class="p">())</span>
-<span class="k">print</span> <span class="s">'Number of gaps after: </span><span class="si">%d</span><span class="s">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
+<span class="nb">print</span> <span class="s1">'Number of gaps after: </span><span class="si">%d</span><span class="s1">'</span> <span class="o">%</span> <span class="nb">len</span><span class="p">(</span><span class="n">mhandle</span><span class="o">.</span><span class="n">gaps</span><span class="p">)</span>
</pre></div>
</div>
<table class="docutils field-list" frame="void" rules="none">
@@ -1118,7 +1134,7 @@ if None.</li>
<dt id="promod3.modelling.MinimizeModelEnergy">
<code class="descclassname">promod3.modelling.</code><code class="descname">MinimizeModelEnergy</code><span class="sig-paren">(</span><em>mhandle</em>, <em>max_iterations=12</em>, <em>max_iter_sd=20</em>, <em>max_iter_lbfgs=10</em>, <em>use_amber_ff=False</em>, <em>extra_force_fields=[]</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/modelling/_pipeline.html#MinimizeModelEnergy"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.modelling.MinimizeModelEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Minimize energy of final model using molecular mechanics.</p>
-<p>Uses <code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code> to perform energy minimization.
+<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.7.1)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
It will iteratively (at most <em>max_iterations</em> times):</p>
<ul class="simple">
<li>run up to <em>max_iter_sd</em> minimization iter. of a steepest descend method</li>
@@ -1142,7 +1158,7 @@ If the variable is not set, 1 thread will be used by default.</p>
<li><strong>max_iter_lbfgs</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max. number of iterations within LBFGS method</li>
<li><strong>use_amber_ff</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – if True, use the AMBER force field instead of the def.
CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
-<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
+<li><strong>extra_force_fields</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Forcefield</span></code></a>) – Additional list of force fields to use (see
<a class="reference internal" href="#promod3.modelling.BuildFromRawModel" title="promod3.modelling.BuildFromRawModel"><code class="xref py py-meth docutils literal"><span class="pre">BuildFromRawModel()</span></code></a>).</li>
</ul>
</td>
@@ -1150,7 +1166,7 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The model including all oxygens as used in the minimizer.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
</td>
</tr>
</tbody>
@@ -1217,9 +1233,6 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -1227,11 +1240,11 @@ CHARMM one (see <a class="reference internal" href="#promod3.modelling.BuildFrom
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/pipeline.txt"
diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
index e5940d829e08a43dfb35a33ca4a8b2867f4ca481..85e5fae720597dac6cad027ccab4fa3d2bf0d636 100644
--- a/doc/html/modelling/sidechain_reconstruction.html
+++ b/doc/html/modelling/sidechain_reconstruction.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Sidechain Reconstruction — ProMod3 1.1.0 documentation</title>
+ <title>Sidechain Reconstruction — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="modelling - Protein Modelling" href="index.html" />
<link rel="next" title="Modelling Algorithms" href="algorithms.html" />
<link rel="prev" title="Generating Loops De Novo" href="monte_carlo.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -44,48 +46,48 @@
<p>Two methods are provided to fully reconstruct sidechains of residues:</p>
<ul class="simple">
<li>the <a class="reference internal" href="#promod3.modelling.ReconstructSidechains" title="promod3.modelling.ReconstructSidechains"><code class="xref py py-func docutils literal"><span class="pre">ReconstructSidechains()</span></code></a> function handles a full OST
-<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></li>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></li>
<li>the <a class="reference internal" href="#promod3.modelling.SidechainReconstructor" title="promod3.modelling.SidechainReconstructor"><code class="xref py py-class docutils literal"><span class="pre">SidechainReconstructor</span></code></a> is linked to an all atom environment
and used to reconstruct sidechains of single loops</li>
</ul>
<p>Example usage:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">mol</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">modelling</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">mol</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">modelling</span>
-<span class="c"># load a protein </span>
-<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1CRN.pdb'</span><span class="p">)</span>
-<span class="c"># get only amino acids</span>
-<span class="n">prot</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"peptide=true"</span><span class="p">),</span> <span class="bp">True</span><span class="p">)</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="s">'sidechain_test_orig.pdb'</span><span class="p">)</span>
-<span class="c"># reconstruct sidechains</span>
-<span class="n">modelling</span><span class="o">.</span><span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="s">'sidechain_test_rec.pdb'</span><span class="p">)</span>
+<span class="c1"># load a protein </span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
+<span class="c1"># get only amino acids</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"peptide=true"</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="s1">'sidechain_test_orig.pdb'</span><span class="p">)</span>
+<span class="c1"># reconstruct sidechains</span>
+<span class="n">modelling</span><span class="o">.</span><span class="n">ReconstructSidechains</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="n">keep_sidechains</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="s1">'sidechain_test_rec.pdb'</span><span class="p">)</span>
</pre></div>
</div>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">modelling</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">modelling</span>
-<span class="c"># load example (has res. numbering starting at 1)</span>
-<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1CRN.pdb'</span><span class="p">)</span>
+<span class="c1"># load example (has res. numbering starting at 1)</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
<span class="n">res_list</span> <span class="o">=</span> <span class="n">prot</span><span class="o">.</span><span class="n">residues</span>
-<span class="n">seqres_str</span> <span class="o">=</span> <span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res_list</span><span class="p">])</span>
+<span class="n">seqres_str</span> <span class="o">=</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">res_list</span><span class="p">])</span>
-<span class="c"># initialize AllAtom environment and sidechain reconstructor</span>
+<span class="c1"># initialize AllAtom environment and sidechain reconstructor</span>
<span class="n">env</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">AllAtomEnv</span><span class="p">(</span><span class="n">seqres_str</span><span class="p">)</span>
<span class="n">env</span><span class="o">.</span><span class="n">SetInitialEnvironment</span><span class="p">(</span><span class="n">prot</span><span class="p">)</span>
-<span class="n">sc_rec</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">SidechainReconstructor</span><span class="p">(</span><span class="n">keep_sidechains</span><span class="o">=</span><span class="bp">False</span><span class="p">)</span>
+<span class="n">sc_rec</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">SidechainReconstructor</span><span class="p">(</span><span class="n">keep_sidechains</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
<span class="n">sc_rec</span><span class="o">.</span><span class="n">AttachEnvironment</span><span class="p">(</span><span class="n">env</span><span class="p">)</span>
-<span class="c"># reconstruct subset (res. num. 6..10)</span>
+<span class="c1"># reconstruct subset (res. num. 6..10)</span>
<span class="n">res</span> <span class="o">=</span> <span class="n">sc_rec</span><span class="o">.</span><span class="n">Reconstruct</span><span class="p">(</span><span class="mi">6</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
-<span class="c"># reconstruct two loops (6..10 and 20..25)</span>
+<span class="c1"># reconstruct two loops (6..10 and 20..25)</span>
<span class="n">res</span> <span class="o">=</span> <span class="n">sc_rec</span><span class="o">.</span><span class="n">Reconstruct</span><span class="p">(</span><span class="n">start_resnum_list</span><span class="o">=</span><span class="p">[</span><span class="mi">6</span><span class="p">,</span> <span class="mi">20</span><span class="p">],</span>
<span class="n">num_residues_list</span><span class="o">=</span><span class="p">[</span><span class="mi">5</span><span class="p">,</span> <span class="mi">6</span><span class="p">],</span>
<span class="n">chain_idx_list</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">])</span>
-<span class="c"># update environment with solution</span>
+<span class="c1"># update environment with solution</span>
<span class="n">env</span><span class="o">.</span><span class="n">SetEnvironment</span><span class="p">(</span><span class="n">res</span><span class="o">.</span><span class="n">env_pos</span><span class="p">)</span>
-<span class="c"># store all positions of environment</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">env</span><span class="o">.</span><span class="n">GetAllAtomPositions</span><span class="p">()</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s">'sc_rec_test.pdb'</span><span class="p">)</span>
+<span class="c1"># store all positions of environment</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">env</span><span class="o">.</span><span class="n">GetAllAtomPositions</span><span class="p">()</span><span class="o">.</span><span class="n">ToEntity</span><span class="p">(),</span> <span class="s1">'sc_rec_test.pdb'</span><span class="p">)</span>
</pre></div>
</div>
<div class="section" id="reconstruct-function">
@@ -99,7 +101,7 @@ and used to reconstruct sidechains of single loops</li>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>ent</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structure for sidechain reconstruction. Note, that the sidechain
reconstruction gets directly applied on the structure itself.</li>
<li><strong>keep_sidechains</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether complete sidechains in <em>ent</em> (i.e.
containing all required atoms) should be kept rigid
@@ -180,9 +182,9 @@ residues within <em>remodel_cutoff</em> already have a
sidechain, the <em>rigid_frame_cutoff</em> won’t have any
effect.</li>
<li><strong>graph_max_complexity</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max. complexity for
-<a class="reference internal" href="../sidechain/graph.html#promod3.sidechain.RotamerGraph.TreeSolve" title="promod3.sidechain.RotamerGraph.TreeSolve"><code class="xref py py-meth docutils literal"><span class="pre">promod3.sidechain.RotamerGraph.TreeSolve()</span></code></a>.</li>
+<code class="xref py py-meth docutils literal"><span class="pre">promod3.sidechain.RotamerGraph.TreeSolve()</span></code>.</li>
<li><strong>graph_intial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Initial epsilon for
-<a class="reference internal" href="../sidechain/graph.html#promod3.sidechain.RotamerGraph.TreeSolve" title="promod3.sidechain.RotamerGraph.TreeSolve"><code class="xref py py-meth docutils literal"><span class="pre">promod3.sidechain.RotamerGraph.TreeSolve()</span></code></a>.</li>
+<code class="xref py py-meth docutils literal"><span class="pre">promod3.sidechain.RotamerGraph.TreeSolve()</span></code>.</li>
<li><strong>disulfid_score_thresh</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – If <code class="xref py py-meth docutils literal"><span class="pre">DisulfidScore()</span></code> between two CYS is
below this threshold, we consider them to be
disulfid-bonded.</li>
@@ -210,7 +212,7 @@ environment before calling this!</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Start of loop.</li>
<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of loop.</li>
<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Chain the loop belongs to.</li>
<li><strong>start_resnum_list</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Starts of loops.</li>
@@ -430,9 +432,6 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -440,11 +439,11 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/modelling/sidechain_reconstruction.txt"
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 81a8d72de97fcc038be6300b37887a25fa9ac54c..c7226c83d6d29c07ee6392a031ad29887d8c9f0f 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/portableIO.html b/doc/html/portableIO.html
index 74404d4b6a833266bab8ea6dc38f97bf5f7be463..ce9c3bed25946e90ca661dc414a86805a914c840 100644
--- a/doc/html/portableIO.html
+++ b/doc/html/portableIO.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Using Binary Files In ProMod3 — ProMod3 1.1.0 documentation</title>
+ <title>Using Binary Files In ProMod3 — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="Changelog" href="changelog.html" />
<link rel="prev" title="ProMod3‘s Share Of CMake" href="cmake/index.html" />
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -108,7 +110,7 @@ Generally, we store any data-structure value-by-value as fixed-width types!</p>
</ul>
<p>Each serializable class must define a <code class="docutils literal"><span class="pre">Serialize</span></code> function that accepts sinks
and sources, such as:</p>
-<div class="highlight-cpp"><div class="highlight"><pre><span class="k">template</span> <span class="o"><</span><span class="k">typename</span> <span class="n">DS</span><span class="o">></span>
+<div class="highlight-cpp"><div class="highlight"><pre><span></span><span class="k">template</span> <span class="o"><</span><span class="k">typename</span> <span class="n">DS</span><span class="o">></span>
<span class="kt">void</span> <span class="n">Serialize</span><span class="p">(</span><span class="n">DS</span><span class="o">&</span> <span class="n">ds</span><span class="p">)</span> <span class="p">{</span>
<span class="c1">// serialize element-by-element</span>
<span class="p">}</span>
@@ -116,7 +118,7 @@ and sources, such as:</p>
</div>
<p>Or if this is not possible for an object of type <code class="docutils literal"><span class="pre">T</span></code>, we need to define
global functions such as:</p>
-<div class="highlight-cpp"><div class="highlight"><pre><span class="kr">inline</span> <span class="kt">void</span> <span class="nf">Serialize</span><span class="p">(</span><span class="n">core</span><span class="o">::</span><span class="n">PortableBinaryDataSource</span><span class="o">&</span> <span class="n">ds</span><span class="p">,</span> <span class="n">T</span><span class="o">&</span> <span class="n">t</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span>
+<div class="highlight-cpp"><div class="highlight"><pre><span></span><span class="kr">inline</span> <span class="kt">void</span> <span class="nf">Serialize</span><span class="p">(</span><span class="n">core</span><span class="o">::</span><span class="n">PortableBinaryDataSource</span><span class="o">&</span> <span class="n">ds</span><span class="p">,</span> <span class="n">T</span><span class="o">&</span> <span class="n">t</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span>
<span class="kr">inline</span> <span class="kt">void</span> <span class="nf">Serialize</span><span class="p">(</span><span class="n">core</span><span class="o">::</span><span class="n">PortableBinaryDataSink</span><span class="o">&</span> <span class="n">ds</span><span class="p">,</span> <span class="n">T</span> <span class="n">t</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span>
</pre></div>
</div>
@@ -143,17 +145,17 @@ serialize the values manually and convert each element appropriately.</li>
<h2>Code Example<a class="headerlink" href="#code-example" title="Permalink to this headline">¶</a></h2>
<p>Here is an example of a class which provides functionality for portable
and non-portable I/O:</p>
-<div class="highlight-cpp"><div class="highlight"><pre><span class="c1">// includes for this class</span>
-<span class="cp">#include <boost/shared_ptr.hpp></span>
-<span class="cp">#include <iostream></span>
-<span class="cp">#include <fstream></span>
-<span class="cp">#include <sstream></span>
-<span class="cp">#include <vector></span>
+<div class="highlight-cpp"><div class="highlight"><pre><span></span><span class="c1">// includes for this class</span>
+<span class="cp">#include</span> <span class="cpf"><boost/shared_ptr.hpp></span><span class="cp"></span>
+<span class="cp">#include</span> <span class="cpf"><iostream></span><span class="cp"></span>
+<span class="cp">#include</span> <span class="cpf"><fstream></span><span class="cp"></span>
+<span class="cp">#include</span> <span class="cpf"><sstream></span><span class="cp"></span>
+<span class="cp">#include</span> <span class="cpf"><vector></span><span class="cp"></span>
<span class="c1">// includes for I/O</span>
-<span class="cp">#include <promod3/core/message.hh></span>
-<span class="cp">#include <promod3/core/portable_binary_serializer.hh></span>
-<span class="cp">#include <promod3/core/check_io.hh></span>
+<span class="cp">#include</span> <span class="cpf"><promod3/core/message.hh></span><span class="cp"></span>
+<span class="cp">#include</span> <span class="cpf"><promod3/core/portable_binary_serializer.hh></span><span class="cp"></span>
+<span class="cp">#include</span> <span class="cpf"><promod3/core/check_io.hh></span><span class="cp"></span>
<span class="k">using</span> <span class="k">namespace</span> <span class="n">promod3</span><span class="p">;</span>
@@ -468,9 +470,6 @@ in the <code class="file docutils literal"><span class="pre">extras/data_generat
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -478,11 +477,11 @@ in the <code class="file docutils literal"><span class="pre">extras/data_generat
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/portableIO.txt"
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 71f4bc4ddf7474eec8f663839da66c0d80c4b9f4..94cc934014dc70ed49d89fbccbc9117b373ad337 100644
--- a/doc/html/py-modindex.html
+++ b/doc/html/py-modindex.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Python Module Index — ProMod3 1.1.0 documentation</title>
+ <title>Python Module Index — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -122,9 +124,6 @@
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -132,11 +131,11 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index 8927ea93c0fbfb5b887ce479eeb401617d21b90f..983fd1a43688c709ba13f6608a27e1cbd61780b1 100644
--- a/doc/html/scoring/all_atom_scorers.html
+++ b/doc/html/scoring/all_atom_scorers.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>All Atom Scorers — ProMod3 1.1.0 documentation</title>
+ <title>All Atom Scorers — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="scoring - Loop Scoring" href="index.html" />
- <link rel="next" title="loop - Loop Handling" href="../loop/index.html" />
+ <link rel="next" title="Other Scoring Functions" href="other_scoring_functions.html" />
<link rel="prev" title="Backbone Scorers" href="backbone_scorers.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -102,9 +104,9 @@
<dl class="method">
<dt id="promod3.scoring.AllAtomOverallScorer.CalculateLinearCombination">
-<code class="descname">CalculateLinearCombination</code><span class="sig-paren">(</span><em>linear_weights</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.CalculateLinearCombination" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculate linear combination of scores for the desired loop (extracted from
-environment) against the set environment (see
+<code class="descname">CalculateLinearCombination</code><span class="sig-paren">(</span><em>linear_weights</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomOverallScorer.CalculateLinearCombination" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculate linear combination of scores for the desired loop(s) (extracted
+from environment) against the set environment (see
<a class="reference internal" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="promod3.scoring.AllAtomScorer.CalculateScore"><code class="xref py py-meth docutils literal"><span class="pre">AllAtomScorer.CalculateScore()</span></code></a>).</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -115,10 +117,10 @@ environment) against the set environment (see
values: <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)) – Weights for each desired scorer. You can add a
constant value to each score by defining a weight
with key “intercept”.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of loop.</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop belongs to
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of loop(s).</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
</ul>
</td>
@@ -195,23 +197,19 @@ following keys:
<dl class="method">
<dt id="promod3.scoring.AllAtomScorer.CalculateScore">
-<code class="descname">CalculateScore</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculates score for the desired loop (extracted from environment) against
+<code class="descname">CalculateScore</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculates score for the desired loop(s) (extracted from environment) against
the set environment. Unless otherwise noted in the scorer, a lower “score”
is better!</p>
-<p>Note that the structural data of the loop is expected to be in the linked
-environment before calling this! This behavior is different from the
-corresponding function in <a class="reference internal" href="backbone_scorers.html#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a> as, for performance
-reasons, we require all the comparisons to be done against the environment.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of loop.</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop belongs to
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of loop(s).</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
</ul>
</td>
@@ -235,29 +233,26 @@ invalid positions.</p>
<dl class="method">
<dt id="promod3.scoring.AllAtomScorer.CalculateScoreProfile">
<code class="descname">CalculateScoreProfile</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomScorer.CalculateScoreProfile" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculates per residue scores for the desired loop (extracted from
+<dd><p>Calculates per residue scores for the desired loop(s) (extracted from
environment) against the set environment.</p>
-<p>Note that the structural data of the loop is expected to be in the linked
-environment before calling this! This behavior is different from the
-corresponding function in <a class="reference internal" href="backbone_scorers.html#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a> as, for performance
-reasons, we require all the comparisons to be done against the environment.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number(s) defining the position(s) in the SEQRES
(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
-<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of loop.</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop belongs to
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Length of loop(s).</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belongs to
(see <a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomEnv" title="promod3.loop.AllAtomEnv"><code class="xref py py-class docutils literal"><span class="pre">AllAtomEnv</span></code></a> for indexing)</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Scores for the given loop, one for each residue.</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Scores for the given loop(s), one for each residue.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <code class="xref py py-class docutils literal"><span class="pre">list</span></code>
+of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">same <a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> as <a class="reference internal" href="#promod3.scoring.AllAtomScorer.CalculateScore" title="promod3.scoring.AllAtomScorer.CalculateScore"><code class="xref py py-meth docutils literal"><span class="pre">CalculateScore()</span></code></a>.</p>
@@ -280,8 +275,11 @@ pseudo interaction energy between all atoms which are located within a
<em>cutoff</em> and which are at least <em>seq_sep</em> residues apart. An energy is
assigned to each distance using equally sized bins and distinguishing all
possible pairs of atoms (usually the energy only differs for chemically
-distinguishable heavy atoms). The calculated score is normalized by the number
-of interacting atom pairs.</p>
+distinguishable heavy atoms).
+By default, the scorer calculates the scores by
+including everything, the stuff set in the environment and the coordinates
+in the input loops. You can change this behaviour with the according
+functions.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadAllAtomInteractionScorer" title="promod3.scoring.LoadAllAtomInteractionScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadAllAtomInteractionScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer.SetEnergy" title="promod3.scoring.AllAtomInteractionScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>).</p>
<table class="docutils field-list" frame="void" rules="none">
@@ -322,7 +320,7 @@ less machine-dependent).</p>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomInteractionScorer" title="promod3.scoring.AllAtomInteractionScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomInteractionScorer</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -334,7 +332,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.scoring.AllAtomInteractionScorer.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -352,7 +350,10 @@ for details.</p>
<dt id="promod3.scoring.AllAtomInteractionScorer.SetEnergy">
<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>aaa1</em>, <em>aaa2</em>, <em>bin</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
-called for every pair of heavy atom types and for every <em>bin</em> < <em>bins</em>.</p>
+called for every pair of heavy atom types and for every <em>bin</em> < <em>bins</em>.
+Internal symmetry is enforced => Calling SetEnergy(aaa1, aaa2, bin, energy) is
+equivalent to calling SetEnergy(aaa1, aaa2, bin, energy) AND
+SetEnergy(aaa2, aaa1, bin, energy).</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -372,6 +373,48 @@ called for every pair of heavy atom types and for every <em>bin</em> < <em>bi
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.scoring.AllAtomInteractionScorer.DoInternalScores">
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions within the
+loop. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.AllAtomInteractionScorer.DoExternalScores">
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions towards the
+environment. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.AllAtomInteractionScorer.DoNormalize">
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomInteractionScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues in the input loop. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
<dl class="function">
@@ -397,8 +440,7 @@ called for every pair of heavy atom types and for every <em>bin</em> < <em>bi
<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">AllAtomPackingScorer</code><span class="sig-paren">(</span><em>cutoff</em>, <em>max_count</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomScorer</span></code></a>. Evaluates pseudo
energies by counting surrounding atoms within a certain <em>cutoff</em> radius around
-all heavy atoms not belonging to the assessed residue itself. The calculated
-score is normalized by the number of atoms being assessed.</p>
+all heavy atoms not belonging to the assessed residue itself.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadAllAtomPackingScorer" title="promod3.scoring.LoadAllAtomPackingScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadAllAtomPackingScorer()</span></code></a>) or by setting all energies (see
<a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer.SetEnergy" title="promod3.scoring.AllAtomPackingScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>).</p>
@@ -437,7 +479,7 @@ less machine-dependent).</p>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.AllAtomPackingScorer" title="promod3.scoring.AllAtomPackingScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomPackingScorer</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -449,7 +491,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.scoring.AllAtomPackingScorer.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -486,6 +528,20 @@ called for every heavy atom type and for every <em>count</em> <= <em>max_coun
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.scoring.AllAtomPackingScorer.DoNormalize">
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomPackingScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues in the input loop. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
<dl class="function">
@@ -512,8 +568,52 @@ called for every heavy atom type and for every <em>count</em> <= <em>max_coun
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.AllAtomScorer" title="promod3.scoring.AllAtomScorer"><code class="xref py py-class docutils literal"><span class="pre">AllAtomScorer</span></code></a>. Calculates a simple
clash score of all atoms against the environment. There is no need to define
any parameters here as all interaction energies are fixed (see Eq. (11) in
-<a class="reference internal" href="../sidechain/disulfid.html#canutescu2003b" id="id1">[canutescu2003b]</a>). The calculated score is normalized by the number of atoms
-being assessed.</p>
+<a class="reference internal" href="other_scoring_functions.html#canutescu2003b" id="id1">[canutescu2003b]</a>). By default, the scorer calculates the scores by
+including everything, the stuff set in the environment and the coordinates
+in the input loops. You can change this behaviour with the according
+functions.</p>
+<dl class="method">
+<dt id="promod3.scoring.AllAtomClashScorer.DoInternalScores">
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions within the
+loop. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.AllAtomClashScorer.DoExternalScores">
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions towards the
+environment. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.AllAtomClashScorer.DoNormalize">
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.AllAtomClashScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues in the input loop. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
</div>
@@ -543,7 +643,7 @@ being assessed.</p>
<li><a href="../users.html">Documentation For Users</a><ul>
<li><a href="index.html"><code class="docutils literal"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
<li>Previous: <a href="backbone_scorers.html" title="previous chapter">Backbone Scorers</a></li>
- <li>Next: <a href="../loop/index.html" title="next chapter"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a></li>
+ <li>Next: <a href="other_scoring_functions.html" title="next chapter">Other Scoring Functions</a></li>
</ul></li>
</ul></li>
</ul></li>
@@ -564,9 +664,6 @@ being assessed.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -574,11 +671,11 @@ being assessed.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/scoring/all_atom_scorers.txt"
diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index 68882801ba831d30ef8131e11bf36ff921a7e56f..e1b57c32a98e58a6133441cde6027450387db6b9 100644
--- a/doc/html/scoring/backbone_score_env.html
+++ b/doc/html/scoring/backbone_score_env.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Backbone Score Environment — ProMod3 1.1.0 documentation</title>
+ <title>Backbone Score Environment — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="Backbone Scorers" href="backbone_scorers.html" />
<link rel="prev" title="scoring - Loop Scoring" href="index.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -50,16 +52,24 @@
used by the scorers. It is linked to a (list of) seqres (one per chain) at
construction. The idea is to initialize it at the beginning of the modelling
process with all known data (positions extracted from template, psipred
-prediction, density map, etc) and then update the environment whenever a new
-loop is being added. Note that, depending on the used scorers, some
-information must be provided for the score to make sense and any env. data can
-be set at any time before actually calculating a score.</p>
+prediction, etc). All scorers attached to that environment will see that data
+and can calculate scores accordingly.
+Scoring with this setup is a two step process:</p>
+<ul class="simple">
+<li>Set the positions you want to score in the environment to make it available
+to all attached scorers</li>
+<li>Call the scorers to get the desired scores</li>
+</ul>
+<p>One problem that might occur is that you mess around with the environment and
+at some point you want to restore the original state. The
+<a class="reference internal" href="#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> provides a Stash / Pop mechanism to perform this
+task.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
-<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>seqres</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a> /
+<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a>) – Internal SEQRES to be set (single chain or list with one per
chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
</tr>
</tbody>
@@ -96,7 +106,7 @@ structural data was already set, all the existing data gets cleared first.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>env_structure</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>) – Structral data to be set as environment. The chains
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</td>
</tr>
@@ -120,7 +130,7 @@ positions.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Structural data to be set as environment.</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</li>
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Res. number defining the position in the SEQRES.</li>
<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the structural data belongs to.</li>
</ul>
</td>
@@ -178,25 +188,6 @@ predictions’ sizes is inconsistent with the internal SEQRES size.</td>
</table>
</dd></dl>
-<dl class="method">
-<dt id="promod3.scoring.BackboneScoreEnv.SetMap">
-<code class="descname">SetMap</code><span class="sig-paren">(</span><em>map</em>, <em>resolution</em>, <em>all_atom=False</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.SetMap" title="Permalink to this definition">¶</a></dt>
-<dd><p>Sets an internal density map, which is necessary to calculate some scores.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>map</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a>) – The density map</li>
-<li><strong>resolution</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Expected resolution of the density map.</li>
-<li><strong>all_atom</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether the map is accurate enough to resolve all atoms.</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.AddPairwiseFunction">
<code class="descname">AddPairwiseFunction</code><span class="sig-paren">(</span><em>function</em>, <em>function_type</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.AddPairwiseFunction" title="Permalink to this definition">¶</a></dt>
@@ -250,6 +241,35 @@ residue or when <em>f_idx</em> is an invalid index.</p>
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.scoring.BackboneScoreEnv.Stash">
+<code class="descname">Stash</code><span class="sig-paren">(</span><em>start_rnum</em>, <em>num_residues</em>, <em>chain_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Stash" title="Permalink to this definition">¶</a></dt>
+<dd><p>FILO style stashing. You can perform up to 100 stash operations to save
+the current state of certain stretches in the environment. This state can
+be restored by calling <a class="reference internal" href="#promod3.scoring.BackboneScoreEnv.Pop" title="promod3.scoring.BackboneScoreEnv.Pop"><code class="xref py py-func docutils literal"><span class="pre">Pop()</span></code></a>. In one stash operation you can either
+stash one stretch by providing integers as input or several stretches by
+providing lists of integers.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>start_rnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – start rnum of stretch to stash</li>
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – length of stretch to stash</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – chain idx of stretch to stash</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.BackboneScoreEnv.Pop">
+<code class="descname">Pop</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.Pop" title="Permalink to this definition">¶</a></dt>
+<dd><p>Remove and apply the the last stash operation.</p>
+</dd></dl>
+
<dl class="method">
<dt id="promod3.scoring.BackboneScoreEnv.GetSeqres">
<code class="descname">GetSeqres</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScoreEnv.GetSeqres" title="Permalink to this definition">¶</a></dt>
@@ -259,7 +279,7 @@ residue or when <em>f_idx</em> is an invalid index.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">SEQRES that was set in constructor (one sequence per chain).</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -369,7 +389,7 @@ The constraint functions are built after the principle of QMEANDisCo.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>seqres</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</li>
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceHandle</span></code></a>) – The sequence with which all added structures must match</li>
<li><strong>function_type</strong> (<a class="reference internal" href="#promod3.scoring.PairwiseFunctionType" title="promod3.scoring.PairwiseFunctionType"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunctionType</span></code></a>) – Whether you want to assess pairwise distances between CA
or CB atoms</li>
</ul>
@@ -384,7 +404,7 @@ or CB atoms</li>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aln</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
SEQRES and the second sequence the actual structural
info. The second sequence must have a view attached.</td>
</tr>
@@ -483,9 +503,6 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -493,11 +510,11 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/scoring/backbone_score_env.txt"
diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
index dec79f579c701f4453884c1ed2f4be565d356be5..71276424ad8d5762fa2f4f87b16a5e46d6c22fa1 100644
--- a/doc/html/scoring/backbone_scorers.html
+++ b/doc/html/scoring/backbone_scorers.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Backbone Scorers — ProMod3 1.1.0 documentation</title>
+ <title>Backbone Scorers — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="All Atom Scorers" href="all_atom_scorers.html" />
<link rel="prev" title="Backbone Score Environment" href="backbone_score_env.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -102,30 +104,27 @@
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.Calculate">
-<code class="descname">Calculate</code><span class="sig-paren">(</span><em>key</em>, <em>bb_list</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Calculate" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculate score(s) for one or many loop(s) with
-<a class="reference internal" href="#promod3.scoring.BackboneScorer.CalculateScore" title="promod3.scoring.BackboneScorer.CalculateScore"><code class="xref py py-meth docutils literal"><span class="pre">BackboneScorer.CalculateScore()</span></code></a>.</p>
+<code class="descname">Calculate</code><span class="sig-paren">(</span><em>key</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.Calculate" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculate score for one or several stretches of amino acids given the
+current scoring environment.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>key</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Key for desired scorer.</li>
-<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Loop(s) for which to calculate the given score</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belong to
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Score(s) calculated with the desired scorer for the given loop(s).
-In the case of multiple loops, the returned list has the same
-order as the input.</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Score calculated with the desired scorer for the given stretch(es).</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if there is no scorer with that
@@ -138,8 +137,9 @@ order as the input.</p>
<dl class="method">
<dt id="promod3.scoring.BackboneOverallScorer.CalculateLinearCombination">
-<code class="descname">CalculateLinearCombination</code><span class="sig-paren">(</span><em>linear_weights</em>, <em>bb_list</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculate linear combination(s) of scores for one or many loop(s).</p>
+<code class="descname">CalculateLinearCombination</code><span class="sig-paren">(</span><em>linear_weights</em>, <em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneOverallScorer.CalculateLinearCombination" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculate linear combination of scores for one or several stretches of
+amino acids given the current scoring environment.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -149,21 +149,19 @@ order as the input.</p>
values: <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>)) – Weights for each desired scorer. You can add a
constant value to each score by defining a weight
with key “intercept”.</li>
-<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
-<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Loop(s) for which to calculate the given score</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop(s) belong to
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Linear combination(s) of the scores calculated with the desired
-scorers for the given loop(s). In the case of multiple loops, the
-returned list has the same order as the input.</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Linear combination of the scores calculated with the desired
+scorers for the given stretch(es)</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if <em>linear_weights</em> has a <em>key</em> for
@@ -202,7 +200,7 @@ which no scorer exists or anything raised in
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">Loads or creates the default scorers accessible through
following keys:
-“cb_packing”, “cbeta”, “reduced”, “clash”, “hbond”, “ss_agreement”,”torsion”, “pairwise”, “density”</td>
+“cb_packing”, “cbeta”, “reduced”, “clash”, “hbond”, “ss_agreement”,”torsion”, “pairwise”</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneOverallScorer</span></code></a></td>
</tr>
@@ -232,25 +230,24 @@ following keys:
<dl class="method">
<dt id="promod3.scoring.BackboneScorer.CalculateScore">
-<code class="descname">CalculateScore</code><span class="sig-paren">(</span><em>bb_list</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.CalculateScore" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculates score for the given loop internally and against the set
-environment. Data in the environment, which overlaps with the given
-<em>bb_list</em> is ignored. Unless otherwise noted in the scorer, a lower “score”
-is better!</p>
+<code class="descname">CalculateScore</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.CalculateScore" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculates score for one or several stretches given the structural
+information in the attached environment. Unless otherwise noted in the
+scorer, a lower “score” is better!</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Loop for which to calculate the given score</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop belongs to
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Score for the given loop.</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Score for the given stretch(es).</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
@@ -258,8 +255,8 @@ is better!</p>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">(for most scorers) <a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if scorer was
never attached to a score environment, if scorer has never been
-properly initialized or if <em>chain_index</em> / <em>start_resnum</em> lead to
-invalid positions.</p>
+properly initialized or if <em>start_resnum</em> / <em>num_residues</em> /
+<em>chain_idx</em> lead to invalid positions.</p>
</td>
</tr>
</tbody>
@@ -268,27 +265,27 @@ invalid positions.</p>
<dl class="method">
<dt id="promod3.scoring.BackboneScorer.CalculateScoreProfile">
-<code class="descname">CalculateScoreProfile</code><span class="sig-paren">(</span><em>bb_list</em>, <em>start_resnum</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.CalculateScoreProfile" title="Permalink to this definition">¶</a></dt>
-<dd><p>Calculates per residue scores for the given loop internally and against the
-set environment. Data in the environment, which overlaps with the given
-<em>bb_list</em> is ignored.</p>
+<code class="descname">CalculateScoreProfile</code><span class="sig-paren">(</span><em>start_resnum</em>, <em>num_residues</em>, <em>chain_idx=0</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.BackboneScorer.CalculateScoreProfile" title="Permalink to this definition">¶</a></dt>
+<dd><p>Calculates per residue scores for one or several stretches given the
+structural information in the attached environment.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>bb_list</strong> (<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a>) – Loop for which to calculate the given scores</li>
-<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
+<li><strong>start_resnum</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Res. number defining the position in the SEQRES
(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
-<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the loop belongs to
+<li><strong>num_residues</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of residues in the stretch(es) to score</li>
+<li><strong>chain_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a> / <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of chain the stretch(es) belongs to
(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv" title="promod3.scoring.BackboneScoreEnv"><code class="xref py py-class docutils literal"><span class="pre">BackboneScoreEnv</span></code></a> for indexing)</li>
</ul>
</td>
</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Scores for the given loop, one for each residue.</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Scores for the given stretch(es), one for each residue.</p>
</td>
</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a> or <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <code class="xref py py-class docutils literal"><span class="pre">list</span></code>
+of <a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last">same <a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> as <a class="reference internal" href="#promod3.scoring.BackboneScorer.CalculateScore" title="promod3.scoring.BackboneScorer.CalculateScore"><code class="xref py py-meth docutils literal"><span class="pre">CalculateScore()</span></code></a>.</p>
@@ -308,25 +305,7 @@ set environment. Data in the environment, which overlaps with the given
<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">CBPackingScorer</code><span class="sig-paren">(</span><em>cutoff</em>, <em>max_count</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Evaluates pseudo
energies by counting the number of other CB positions within a certain
-<em>cutoff</em> radius of the CB position of the residue to be evaluated. The
-calculated score is normalized by the number of residues in the loop.
-In the default mode, the scorer scores a <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>
-given the defined environment. By placing this
-<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>, the score of the residues in the
-environment also change. It is possible to honour this effect by using the
-“IncludeEnv” mode. In this alternative mode, every environment residue close
-to the input <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a> also contributes
-to the final score by adding the difference in score when the environment
-residue sees the original environment and the score when the environment would
-be modified by the <a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.BackboneList</span></code></a>. You choose the mode
-by specifically calling the according CalculateEnergy functions.
-If you call the CalculateScore function from the parent class
-(e.g. when the scorer is part of the <a class="reference internal" href="#promod3.scoring.BackboneOverallScorer" title="promod3.scoring.BackboneOverallScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneOverallScorer</span></code></a>), it
-gets checked what mode is currently active. You can toggle the mode by calling
-the appropriate functions in this class. By default (when you load a scorer or
-when you create a new scorer) the classic version gets called. If you want to
-get per residue scores, the “IncludeEnv” mode makes not much sense and the
-scorer throws an error if a profile is requeset in this mode.</p>
+<em>cutoff</em> radius of the CB position of the residue to be evaluated.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadCBPackingScorer" title="promod3.scoring.LoadCBPackingScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadCBPackingScorer()</span></code></a>) or by setting all energies (see
<a class="reference internal" href="#promod3.scoring.CBPackingScorer.SetEnergy" title="promod3.scoring.CBPackingScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>).</p>
@@ -365,7 +344,7 @@ less machine-dependent).</p>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.CBPackingScorer" title="promod3.scoring.CBPackingScorer"><code class="xref py py-class docutils literal"><span class="pre">CBPackingScorer</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -377,7 +356,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.scoring.CBPackingScorer.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -401,7 +380,7 @@ called for every type of amino acids and for every <em>count</em> <= <em>max_
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</li>
+<li><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for which to set energy.</li>
<li><strong>count</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of surrounding CB positions for which to set energy.</li>
<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
</ul>
@@ -415,18 +394,17 @@ called for every type of amino acids and for every <em>count</em> <= <em>max_
</dd></dl>
<dl class="method">
-<dt id="promod3.scoring.CBPackingScorer.UseClassicMode">
-<code class="descname">UseClassicMode</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.UseClassicMode" title="Permalink to this definition">¶</a></dt>
-<dd><p>If you call this function, the default mode is set to classic if the
-CalculateScore function from the parent class gets called.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.scoring.CBPackingScorer.UseIncludeEnvMode">
-<code class="descname">UseIncludeEnvMode</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.UseIncludeEnvMode" title="Permalink to this definition">¶</a></dt>
-<dd><p>If you call this function, the default mode is set to the
-described alternative mode if the CalculateScore function from the parent
-class gets called.</p>
+<dt id="promod3.scoring.CBPackingScorer.DoNormalize">
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBPackingScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
</dd></dl>
@@ -455,9 +433,8 @@ class gets called.</p>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Evaluates a pairwise
pseudo interaction energy between CB atoms which are located within a <em>cutoff</em>
and which are at least <em>seq_sep</em> residues apart. An energy is assigned to each
-distance using <em>bins</em> equally sized bins and distinguishing all possible pairs
-of amino acids. The calculated score is normalized by the number of
-interacting CB pairs.</p>
+distance using equally sized bins and distinguishing all possible pairs
+of amino acids.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadCBetaScorer" title="promod3.scoring.LoadCBetaScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadCBetaScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.CBetaScorer.SetEnergy" title="promod3.scoring.CBetaScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>).</p>
<table class="docutils field-list" frame="void" rules="none">
@@ -498,7 +475,7 @@ less machine-dependent).</p>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.CBetaScorer" title="promod3.scoring.CBetaScorer"><code class="xref py py-class docutils literal"><span class="pre">CBetaScorer</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -510,7 +487,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.scoring.CBetaScorer.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -528,14 +505,17 @@ for details.</p>
<dt id="promod3.scoring.CBetaScorer.SetEnergy">
<code class="descname">SetEnergy</code><span class="sig-paren">(</span><em>aa1</em>, <em>aa2</em>, <em>bin</em>, <em>energy</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.SetEnergy" title="Permalink to this definition">¶</a></dt>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
-called for every pair of amino acids and for every <em>bin</em> < <em>bins</em>.</p>
+called for every pair of amino acids and for every <em>bin</em> < <em>bins</em>.
+Internal symmetry is enforced => Calling SetEnergy(aa1, aa2, bin, energy) is
+equivalent to calling SetEnergy(aa1, aa2, bin, energy) AND
+SetEnergy(aa2, aa1, bin, energy).</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa1</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
-<li><strong>aa2</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
<li><strong>bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
<li><strong>energy</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Energy to set for those parameters.</li>
</ul>
@@ -548,6 +528,49 @@ called for every pair of amino acids and for every <em>bin</em> < <em>bins</e
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.scoring.CBetaScorer.DoInternalScores">
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.CBetaScorer.DoExternalScores">
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
+residues towards the surrounding environment.
+True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.CBetaScorer.DoNormalize">
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.CBetaScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
<dl class="function">
@@ -574,7 +597,7 @@ called for every pair of amino acids and for every <em>bin</em> < <em>bins</e
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Evaluates a pairwise
pseudo interaction energy between the reduced representation of residues.
Every residue gets represented by its CA position p and a directional
-component <code class="docutils literal"><span class="pre">v</span> <span class="pre">=</span> <span class="pre">norm(ca_pos-n_pos)</span> <span class="pre">+</span> <span class="pre">norm</span> <span class="pre">(ca_pos-c_pos)</span></code>. Residues with CA
+component <code class="docutils literal"><span class="pre">v</span> <span class="pre">=</span> <span class="pre">norm(p-n_pos)</span> <span class="pre">+</span> <span class="pre">norm(p-c_pos)</span></code>. Residues with CA
distance < <em>cutoff</em> and which are at least <em>seq_sep</em> residues apart are
considered to be interacting. For interacting residues r1 and r2, we can
define a line l between p1 and p2. The potential then considers:</p>
@@ -584,9 +607,6 @@ define a line l between p1 and p2. The potential then considers:</p>
<li>beta => angle between v2 and l</li>
<li>gamma => dihedral between (p1+v1,p1,p2,p2+v2)</li>
</ul>
-<p>Every pairwise interaction within the loop and to the environment gets
-evaluated according to the given parametrization, summed up and finally
-normalized by the number of total interactions.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadReducedScorer" title="promod3.scoring.LoadReducedScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadReducedScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.ReducedScorer.SetEnergy" title="promod3.scoring.ReducedScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>).</p>
<table class="docutils field-list" frame="void" rules="none">
@@ -631,7 +651,7 @@ less machine-dependent).</p>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.ReducedScorer" title="promod3.scoring.ReducedScorer"><code class="xref py py-class docutils literal"><span class="pre">ReducedScorer</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -643,7 +663,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.scoring.ReducedScorer.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -663,14 +683,19 @@ for details.</p>
<dd><p>Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every pair of amino acids, every <em>dist_bin</em> < <em>dist_bins</em>, every
<em>alpha_bin</em> < <em>angle_bins</em>, every <em>beta_bin</em> < <em>angle_bins</em> and every
-<em>gamma_bin</em> < <em>dihedral_bins</em>.</p>
+<em>gamma_bin</em> < <em>dihedral_bins</em>.
+Internal symmetry is enforced => Calling
+SetEnergy(aa1, aa2, dist_bin, alpha_bin, beta_bin, energy) is
+equivalent to calling
+SetEnergy(aa1, aa2, dist_bin, alpha_bin, beta_bin, energy) AND
+SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>aa1</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
-<li><strong>aa2</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
+<li><strong>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for first interaction partner.</li>
+<li><strong>aa2</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – Amino acid for second interaction partner.</li>
<li><strong>dist_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the interaction distance.</li>
<li><strong>alpha_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the alpha angle.</li>
<li><strong>beta_bin</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Discrete bin describing the beta angle.</li>
@@ -686,6 +711,49 @@ called for every pair of amino acids, every <em>dist_bin</em> < <em>dist_bins
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.scoring.ReducedScorer.DoInternalScores">
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.ReducedScorer.DoExternalScores">
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
+residues towards the surrounding environment.
+True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.ReducedScorer.DoNormalize">
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ReducedScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
<dl class="function">
@@ -711,28 +779,51 @@ called for every pair of amino acids, every <em>dist_bin</em> < <em>dist_bins
<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">ClashScorer</code><a class="headerlink" href="#promod3.scoring.ClashScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Calculates a simple
clash score of a loop itself and with the set environment. There is no need to
-define any parameters here as all interaction energies are fixed. The
-calculated score is normalized by the number of residues in the loop.</p>
+define any parameters here as all interaction energies are fixed (see Eq. (11)
+in <a class="reference internal" href="other_scoring_functions.html#canutescu2003b" id="id1">[canutescu2003b]</a>).</p>
+<dl class="method">
+<dt id="promod3.scoring.ClashScorer.DoInternalScores">
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.ClashScorer.DoExternalScores">
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
+residues towards the surrounding environment.
+True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.ClashScorer.DoNormalize">
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.ClashScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
</dd></dl>
-</div>
-<div class="section" id="densityscorer-class">
-<h2>DensityScorer class<a class="headerlink" href="#densityscorer-class" title="Permalink to this headline">¶</a></h2>
-<dl class="class">
-<dt id="promod3.scoring.DensityScorer">
-<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">DensityScorer</code><a class="headerlink" href="#promod3.scoring.DensityScorer" title="Permalink to this definition">¶</a></dt>
-<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Calculates the
-normalized cross correlation between a density generated from the input
-<a class="reference internal" href="../loop/backbone.html#promod3.loop.BackboneList" title="promod3.loop.BackboneList"><code class="xref py py-class docutils literal"><span class="pre">BackboneList</span></code></a> and a set map.</p>
-<p>This scorer requires that the attached environment has a density map defined
-(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv.SetMap" title="promod3.scoring.BackboneScoreEnv.SetMap"><code class="xref py py-meth docutils literal"><span class="pre">BackboneScoreEnv.SetMap()</span></code></a>) as soon as a score is to be calculated.
-The <em>resolution</em> and <em>all_atom</em> flags that were specified in SetMap determine
-how the backbone list is translated into an artificial density map. If
-<em>all_atom</em> is set to False (which is recommended for low resolution maps), the
-artificial map gets constructed by only using CA positions instead of all
-atoms.</p>
-<p>Note that for this scorer a higher “score” is better! So take care when
-combining this to other scores, where it is commonly the other way around.</p>
</dd></dl>
</div>
@@ -757,9 +848,6 @@ states. State 1 for helical residues, state 2 for extended residues and state
0 for other residues. If the state of two interacting particles is the same,
thats the one from which the energy is extracted. In all other cases, the
energy is extracted from the 0 state.</p>
-<p>Every pairwise interaction within the loop and to the environment gets
-evaluated according to the given parametrization, summed up and finally
-normalized by the number of residues in the loop.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadHBondScorer" title="promod3.scoring.LoadHBondScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadHBondScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.HBondScorer.SetEnergy" title="promod3.scoring.HBondScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>).</p>
<table class="docutils field-list" frame="void" rules="none">
@@ -811,7 +899,7 @@ less machine-dependent).</p>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.HBondScorer" title="promod3.scoring.HBondScorer"><code class="xref py py-class docutils literal"><span class="pre">HBondScorer</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -823,7 +911,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.scoring.HBondScorer.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -866,6 +954,49 @@ called for every state ([0, 1, 2]), every <em>d_bin</em> < <em>d_bins</em>, e
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.scoring.HBondScorer.DoInternalScores">
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.HBondScorer.DoExternalScores">
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions of the scored
+residues towards the surrounding environment.
+True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.HBondScorer.DoNormalize">
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.HBondScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
<dl class="function">
@@ -895,8 +1026,7 @@ psipred prediction, its confidence and the actually occurring secondary
structure in the model. In every score evaluation, the secondary structure of
the loop is estimated by searching for hydrogen bonds leading to a secondary
structure as defined by dssp. The hbonds are searched internally in the loop
-as well as in the environment. The final score gets summed up over all
-residues in the loop and normalized by the number of residues.</p>
+as well as in the environment.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadSSAgreementScorer" title="promod3.scoring.LoadSSAgreementScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadSSAgreementScorer()</span></code></a>) or by setting scores for all possible states
(see <a class="reference internal" href="#promod3.scoring.SSAgreementScorer.SetScore" title="promod3.scoring.SSAgreementScorer.SetScore"><code class="xref py py-meth docutils literal"><span class="pre">SetScore()</span></code></a>).</p>
@@ -924,7 +1054,7 @@ less machine-dependent).</p>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.SSAgreementScorer" title="promod3.scoring.SSAgreementScorer"><code class="xref py py-class docutils literal"><span class="pre">SSAgreementScorer</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -936,7 +1066,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.scoring.SSAgreementScorer.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -974,6 +1104,20 @@ is loaded, this must be called for every combination of states.</p>
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.scoring.SSAgreementScorer.DoNormalize">
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SSAgreementScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
<dl class="function">
@@ -999,9 +1143,7 @@ is loaded, this must be called for every combination of states.</p>
<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">TorsionScorer</code><span class="sig-paren">(</span><em>group_definitions</em>, <em>torsion_bins</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Evaluates pseudo
energies based on the identity of three consecutive residues and the phi/psi
-dihedral angles of the central residue. Every residue gets evaluated according
-to the set parametrization and the final score gets normalized by the total
-number of summed pseudo energies. The first phi and last psi angle get
+dihedral angles of the central residue. The first phi and last psi angle get
determined with the help of the environment if set.</p>
<p>The scorer needs to be initialized either by loading a predefined scorer (e.g.
<a class="reference internal" href="#promod3.scoring.LoadTorsionScorer" title="promod3.scoring.LoadTorsionScorer"><code class="xref py py-func docutils literal"><span class="pre">LoadTorsionScorer()</span></code></a>) or by setting all energies (see <a class="reference internal" href="#promod3.scoring.TorsionScorer.SetEnergy" title="promod3.scoring.TorsionScorer.SetEnergy"><code class="xref py py-meth docutils literal"><span class="pre">SetEnergy()</span></code></a>)
@@ -1045,7 +1187,7 @@ less machine-dependent).</p>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.scoring.TorsionScorer" title="promod3.scoring.TorsionScorer"><code class="xref py py-class docutils literal"><span class="pre">TorsionScorer</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -1057,7 +1199,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.scoring.TorsionScorer.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -1097,6 +1239,20 @@ numbering starting at 0.</li>
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.scoring.TorsionScorer.DoNormalize">
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.TorsionScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
<dl class="function">
@@ -1121,15 +1277,54 @@ numbering starting at 0.</li>
<dt id="promod3.scoring.PairwiseScorer">
<em class="property">class </em><code class="descclassname">promod3.scoring.</code><code class="descname">PairwiseScorer</code><a class="headerlink" href="#promod3.scoring.PairwiseScorer" title="Permalink to this definition">¶</a></dt>
<dd><p>Inherits all functionality of <a class="reference internal" href="#promod3.scoring.BackboneScorer" title="promod3.scoring.BackboneScorer"><code class="xref py py-class docutils literal"><span class="pre">BackboneScorer</span></code></a>. Evaluates a list of
-generic pairwise functions (see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunction</span></code></a>). When evaluating a
-loop, the scores of all pairwise functions which involve a residue in the loop
-are summed up (the other residue can be either in the loop or in the env.) and
-normalized by the number of residues in the loop.</p>
-<p>This scorer assumes that the attached environment has pairwise functions
-defined (see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction"><code class="xref py py-meth docutils literal"><span class="pre">BackboneScoreEnv.ApplyPairwiseFunction()</span></code></a>) as soon as a
-score is to be calculated.</p>
+generic pairwise functions (see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.PairwiseFunction" title="promod3.scoring.PairwiseFunction"><code class="xref py py-class docutils literal"><span class="pre">PairwiseFunction</span></code></a>).
+That are set in the attached scoring environment
+(see <a class="reference internal" href="backbone_score_env.html#promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction" title="promod3.scoring.BackboneScoreEnv.ApplyPairwiseFunction"><code class="xref py py-meth docutils literal"><span class="pre">BackboneScoreEnv.ApplyPairwiseFunction()</span></code></a>).</p>
<p>Note that for this scorer a higher “score” is better! So take care when
combining this to other scores, where it is commonly the other way around.</p>
+<dl class="method">
+<dt id="promod3.scoring.PairwiseScorer.DoInternalScores">
+<code class="descname">DoInternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoInternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to include pairwise interactions between
+the scored residues. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.PairwiseScorer.DoExternalScores">
+<code class="descname">DoExternalScores</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoExternalScores" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>, true by default.) – Whether to include pairwise interactions of the scored
+residues towards the surrounding environment.
+True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.PairwiseScorer.DoNormalize">
+<code class="descname">DoNormalize</code><span class="sig-paren">(</span><em>do_it</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.PairwiseScorer.DoNormalize" title="Permalink to this definition">¶</a></dt>
+<dd><table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>do_it</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Whether to normalize the calculated scores by the number
+of residues to be scored. True by default.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
</div>
@@ -1150,7 +1345,6 @@ combining this to other scores, where it is commonly the other way around.</p>
<li><a class="reference internal" href="#cbetascorer-class">CBetaScorer class</a></li>
<li><a class="reference internal" href="#reducedscorer-class">ReducedScorer class</a></li>
<li><a class="reference internal" href="#clashscorer-class">ClashScorer class</a></li>
-<li><a class="reference internal" href="#densityscorer-class">DensityScorer class</a></li>
<li><a class="reference internal" href="#hbondscorer-class">HBondScorer class</a></li>
<li><a class="reference internal" href="#ssagreementscorer-class">SSAgreementScorer class</a></li>
<li><a class="reference internal" href="#torsionscorer-class">TorsionScorer class</a></li>
@@ -1186,9 +1380,6 @@ combining this to other scores, where it is commonly the other way around.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -1196,11 +1387,11 @@ combining this to other scores, where it is commonly the other way around.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/scoring/backbone_scorers.txt"
diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
index eeee00139663ac1378844f314705e982f862f19b..e733603063ec5484bad703f5de8006b1f24d4029 100644
--- a/doc/html/scoring/index.html
+++ b/doc/html/scoring/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>scoring - Loop Scoring — ProMod3 1.1.0 documentation</title>
+ <title>scoring - Loop Scoring — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Backbone Score Environment" href="backbone_score_env.html" />
<link rel="prev" title="Subrotamer Optimization" href="../sidechain/subrotamer_optimizer.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -43,35 +45,30 @@
<span id="scoring-loop-scoring"></span><h1><a class="reference internal" href="#module-promod3.scoring" title="promod3.scoring: Loop Scoring"><code class="xref py py-mod docutils literal"><span class="pre">scoring</span></code></a> - Loop Scoring<a class="headerlink" href="#module-promod3.scoring" title="Permalink to this headline">¶</a></h1>
<p>Tools and algorithms to score loops. The scoring system is split between an
environment which contains model-specific data and scorers which evaluate loops.</p>
-<p>In this example, we load a structure, setup a score environment and a few
-scorers and finally score some loops:</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span>
+<p>In this example, we load a structure, setup a score environment, link a few
+scorers to it and finally score some loops:</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span> <span class="n">seq</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">loop</span><span class="p">,</span> <span class="n">scoring</span>
-<span class="c"># load data</span>
-<span class="n">ent</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">"data/1CRN.pdb"</span><span class="p">)</span>
-<span class="n">ent_seq</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">SequenceFromChain</span><span class="p">(</span><span class="s">'A'</span><span class="p">,</span> <span class="n">ent</span><span class="o">.</span><span class="n">FindChain</span><span class="p">(</span><span class="s">'A'</span><span class="p">))</span>
+<span class="c1"># load data</span>
+<span class="n">ent</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s2">"data/1CRN.pdb"</span><span class="p">)</span>
+<span class="n">ent_seq</span> <span class="o">=</span> <span class="n">seq</span><span class="o">.</span><span class="n">SequenceFromChain</span><span class="p">(</span><span class="s1">'A'</span><span class="p">,</span> <span class="n">ent</span><span class="o">.</span><span class="n">FindChain</span><span class="p">(</span><span class="s1">'A'</span><span class="p">))</span>
-<span class="c"># setup score environment linked to entity</span>
+<span class="c1"># setup score environment linked to entity</span>
<span class="n">score_env</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">BackboneScoreEnv</span><span class="p">(</span><span class="n">ent_seq</span><span class="p">)</span>
<span class="n">score_env</span><span class="o">.</span><span class="n">SetInitialEnvironment</span><span class="p">(</span><span class="n">ent</span><span class="p">)</span>
-<span class="c"># setup scorers attached to that env.</span>
+<span class="c1"># setup scorers attached to that env.</span>
<span class="n">clash_scorer</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">ClashScorer</span><span class="p">()</span>
<span class="n">clash_scorer</span><span class="o">.</span><span class="n">AttachEnvironment</span><span class="p">(</span><span class="n">score_env</span><span class="p">)</span>
<span class="n">cbeta_scorer</span> <span class="o">=</span> <span class="n">scoring</span><span class="o">.</span><span class="n">LoadCBetaScorer</span><span class="p">()</span>
<span class="n">cbeta_scorer</span><span class="o">.</span><span class="n">AttachEnvironment</span><span class="p">(</span><span class="n">score_env</span><span class="p">)</span>
-<span class="c"># get backbone list to be scored</span>
-<span class="c"># (here extracted from the structure, but it could be anything)</span>
-<span class="n">ev</span> <span class="o">=</span> <span class="n">ent</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"rnum >= 23 and rnum <= 30"</span><span class="p">)</span>
-<span class="n">bb_seq</span> <span class="o">=</span> <span class="s">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">r</span><span class="o">.</span><span class="n">one_letter_code</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">ev</span><span class="o">.</span><span class="n">residues</span><span class="p">])</span>
-<span class="n">bb_res</span> <span class="o">=</span> <span class="p">[</span><span class="n">r</span><span class="o">.</span><span class="n">handle</span> <span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">ev</span><span class="o">.</span><span class="n">residues</span><span class="p">]</span>
-<span class="n">bb_list</span> <span class="o">=</span> <span class="n">loop</span><span class="o">.</span><span class="n">BackboneList</span><span class="p">(</span><span class="n">bb_seq</span><span class="p">,</span> <span class="n">bb_res</span><span class="p">)</span>
-
-<span class="c"># score it (note that 23 is the starting res. num.)</span>
-<span class="k">print</span> <span class="s">"Clash-Score"</span><span class="p">,</span> <span class="n">clash_scorer</span><span class="o">.</span><span class="n">CalculateScore</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="mi">23</span><span class="p">)</span>
-<span class="k">print</span> <span class="s">"CBeta-Score"</span><span class="p">,</span> <span class="n">cbeta_scorer</span><span class="o">.</span><span class="n">CalculateScore</span><span class="p">(</span><span class="n">bb_list</span><span class="p">,</span> <span class="mi">23</span><span class="p">)</span>
+<span class="c1"># calculate scores for 10 residues starting at residue number 23.</span>
+<span class="c1"># all required structural information comes from the environment</span>
+<span class="c1"># that can evolve as the modelling proceeds.</span>
+<span class="nb">print</span> <span class="s2">"Clash-Score"</span><span class="p">,</span> <span class="n">clash_scorer</span><span class="o">.</span><span class="n">CalculateScore</span><span class="p">(</span><span class="mi">23</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
+<span class="nb">print</span> <span class="s2">"CBeta-Score"</span><span class="p">,</span> <span class="n">cbeta_scorer</span><span class="o">.</span><span class="n">CalculateScore</span><span class="p">(</span><span class="mi">23</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span>
</pre></div>
</div>
<p>Contents:</p>
@@ -90,7 +87,6 @@ scorers and finally score some loops:</p>
<li class="toctree-l2"><a class="reference internal" href="backbone_scorers.html#cbetascorer-class">CBetaScorer class</a></li>
<li class="toctree-l2"><a class="reference internal" href="backbone_scorers.html#reducedscorer-class">ReducedScorer class</a></li>
<li class="toctree-l2"><a class="reference internal" href="backbone_scorers.html#clashscorer-class">ClashScorer class</a></li>
-<li class="toctree-l2"><a class="reference internal" href="backbone_scorers.html#densityscorer-class">DensityScorer class</a></li>
<li class="toctree-l2"><a class="reference internal" href="backbone_scorers.html#hbondscorer-class">HBondScorer class</a></li>
<li class="toctree-l2"><a class="reference internal" href="backbone_scorers.html#ssagreementscorer-class">SSAgreementScorer class</a></li>
<li class="toctree-l2"><a class="reference internal" href="backbone_scorers.html#torsionscorer-class">TorsionScorer class</a></li>
@@ -105,6 +101,10 @@ scorers and finally score some loops:</p>
<li class="toctree-l2"><a class="reference internal" href="all_atom_scorers.html#allatomclashscorer-class">AllAtomClashScorer class</a></li>
</ul>
</li>
+<li class="toctree-l1"><a class="reference internal" href="other_scoring_functions.html">Other Scoring Functions</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="other_scoring_functions.html#scoring-functions-from-scwrl3">Scoring Functions from SCWRL3</a></li>
+</ul>
+</li>
</ul>
</div>
</div>
@@ -140,9 +140,6 @@ scorers and finally score some loops:</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -150,11 +147,11 @@ scorers and finally score some loops:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
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+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/scoring/index.txt"
diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html
new file mode 100644
index 0000000000000000000000000000000000000000..998c0c6c19f3cec55ad955d5c844295d786d62b2
--- /dev/null
+++ b/doc/html/scoring/other_scoring_functions.html
@@ -0,0 +1,182 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<html xmlns="http://www.w3.org/1999/xhtml">
+ <head>
+ <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+
+ <title>Other Scoring Functions — ProMod3 1.2.0 documentation</title>
+
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+ <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
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+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
+ <link rel="up" title="scoring - Loop Scoring" href="index.html" />
+ <link rel="next" title="loop - Loop Handling" href="../loop/index.html" />
+ <link rel="prev" title="All Atom Scorers" href="all_atom_scorers.html" />
+
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
+
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+ </head>
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+ <div class="documentwrapper">
+ <div class="bodywrapper">
+ <div class="body" role="main">
+
+ <div class="section" id="other-scoring-functions">
+<h1>Other Scoring Functions<a class="headerlink" href="#other-scoring-functions" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="scoring-functions-from-scwrl3">
+<h2>Scoring Functions from SCWRL3<a class="headerlink" href="#scoring-functions-from-scwrl3" title="Permalink to this headline">¶</a></h2>
+<dl class="method">
+<dt id="promod3.scoring.SCWRL3PairwiseScore">
+<code class="descclassname">promod3.scoring.</code><code class="descname">SCWRL3PairwiseScore</code><span class="sig-paren">(</span><em>d</em>, <em>Rij</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3PairwiseScore" title="Permalink to this definition">¶</a></dt>
+<dd><p>Pairwise score from the SCWRL3 sidechain construction algorithm
+<a class="reference internal" href="#canutescu2003b" id="id1">[canutescu2003b]</a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>d</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Distance between the two interacting particles</li>
+<li><strong>Rij</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – <p>Summed hard-sphere radii of the interacting particles.
+Suggestions from the paper:</p>
+<ul>
+<li>carbon: 1.6</li>
+<li>oxygen: 1.3</li>
+<li>nitrogen: 1.3</li>
+<li>sulfur: 1.7</li>
+</ul>
+</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The score</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.scoring.SCWRL3DisulfidScore">
+<code class="descclassname">promod3.scoring.</code><code class="descname">SCWRL3DisulfidScore</code><span class="sig-paren">(</span><em>ca_pos_one</em>, <em>cb_pos_one</em>, <em>sg_pos_one ca_pos_two</em>, <em>cb_pos_two</em>, <em>sg_pos_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.scoring.SCWRL3DisulfidScore" title="Permalink to this definition">¶</a></dt>
+<dd><p>Implements the empirically derived disulfid score from the SCWRL3 sidechain
+construction algorithm <a class="reference internal" href="#canutescu2003b" id="id2">[canutescu2003b]</a>.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>ca_pos_one</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geoom.Vec3</span></code>) – CA carbon position of first amino acid</li>
+<li><strong>cb_pos_one</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geoom.Vec3</span></code>) – CB carbon position of first amino acid</li>
+<li><strong>sg_pos_one</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geoom.Vec3</span></code>) – SG sulfur position of first amino acid</li>
+<li><strong>ca_pos_two</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geoom.Vec3</span></code>) – CA carbon position of second amino acid</li>
+<li><strong>cb_pos_two</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geoom.Vec3</span></code>) – CB carbon position of second amino acid</li>
+<li><strong>sg_pos_two</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geoom.Vec3</span></code>) – SG sulfur position of second amino acid</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The score</p>
+</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<table class="docutils citation" frame="void" id="canutescu2003b" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[canutescu2003b]</td><td><em>(<a class="fn-backref" href="#id1">1</a>, <a class="fn-backref" href="#id2">2</a>)</em> Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).</td></tr>
+</tbody>
+</table>
+</div>
+</div>
+
+
+ </div>
+ </div>
+ </div>
+ <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+ <div class="sphinxsidebarwrapper">
+ <h3><a href="../index.html">Table Of Contents</a></h3>
+ <ul>
+<li><a class="reference internal" href="#">Other Scoring Functions</a><ul>
+<li><a class="reference internal" href="#scoring-functions-from-scwrl3">Scoring Functions from SCWRL3</a></li>
+</ul>
+</li>
+</ul>
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+ <li><a href="../index.html">Documentation overview</a><ul>
+ <li><a href="../users.html">Documentation For Users</a><ul>
+ <li><a href="index.html"><code class="docutils literal"><span class="pre">scoring</span></code> - Loop Scoring</a><ul>
+ <li>Previous: <a href="all_atom_scorers.html" title="previous chapter">All Atom Scorers</a></li>
+ <li>Next: <a href="../loop/index.html" title="next chapter"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a></li>
+ </ul></li>
+ </ul></li>
+ </ul></li>
+</ul>
+</div>
+ <div role="note" aria-label="source link">
+ <h3>This Page</h3>
+ <ul class="this-page-menu">
+ <li><a href="../_sources/scoring/other_scoring_functions.txt"
+ rel="nofollow">Show Source</a></li>
+ </ul>
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+<div id="searchbox" style="display: none" role="search">
+ <h3>Quick search</h3>
+ <form class="search" action="../search.html" method="get">
+ <input type="text" name="q" />
+ <input type="submit" value="Go" />
+ <input type="hidden" name="check_keywords" value="yes" />
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+
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+ <a href="../_sources/scoring/other_scoring_functions.txt"
+ rel="nofollow">Page source</a>
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diff --git a/doc/html/search.html b/doc/html/search.html
index 98d9a3d5ad7153ae993b4f5982f6a12181cde6d8..175b5dbecda4fd05bc276408aaeabcf79e257d85 100644
--- a/doc/html/search.html
+++ b/doc/html/search.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Search — ProMod3 1.1.0 documentation</title>
+ <title>Search — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/searchtools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
<script type="text/javascript">
jQuery(function() { Search.loadIndex("searchindex.js"); });
</script>
@@ -32,12 +32,14 @@
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+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
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@@ -84,11 +86,11 @@
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- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
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- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
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+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
</div>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index da50d0e0a294c6e24a3095b14bcb0d8117909f0d..0c62df2650b19609ccc5d2fdf8536279e9693cc2 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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Actions","<code class=\"docutils literal\"><span class=\"pre\">test_actions</span></code> - Testing Actions","Building ProMod3","Changelog","ProMod3‘s Share Of CMake","Contributing","Geometry functions","Graph Minimizer","<code class=\"docutils literal\"><span class=\"pre\">helper</span></code> - Shared Functionality For the Everything","<code class=\"docutils literal\"><span class=\"pre\">core</span></code> - ProMod3 Core Functionality","<code class=\"docutils literal\"><span class=\"pre\">pm3argparse</span></code> - Parsing Command Lines","Runtime profiling","<code class=\"docutils literal\"><span class=\"pre\">SetCompoundsChemlib()</span></code>","ProMod3 Setup","Documentation For Developers","Getting Started","Welcome To ProMod3’s Documentation!","Handling All Atom Positions","Representing Loops","<code class=\"docutils literal\"><span class=\"pre\">loop</span></code> - Loop Handling","Loading Precomputed Objects","Generate <code class=\"docutils literal\"><span class=\"pre\">ost.mol.mm</span></code> systems","Structural Data","Sampling Dihedral Angles","Modelling Algorithms","Handling Gaps","<code class=\"docutils literal\"><span class=\"pre\">modelling</span></code> - Protein Modelling","Handling Loop Candidates","Fitting Loops Into Gaps","Model Checking","Generating Loops De Novo","Modelling Pipeline","Sidechain Reconstruction","Using Binary Files In ProMod3","All Atom Scorers","Backbone Score Environment","Backbone Scorers","<code class=\"docutils literal\"><span class=\"pre\">scoring</span></code> - Loop Scoring","Other Scoring Functions","Disulfid Bond Evaluation","Frame","Rotamer Graph","<code class=\"docutils literal\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Rotamers","Rotamer Constructor","RotamerID","Rotamer Library","Subrotamer Optimization","Documentation For Users"],titleterms:{"class":[17,18,22,23,25,27,32,34,35,36],"default":31,"function":[4,6,8,9,25,32,35,38],acid:[17,21,23],action:[0,1,4,5],actiontestcas:1,algorithm:24,all:[17,28,34],allatomclashscor:34,allatomenv:17,allatomenvposit:17,allatominteractionscor:34,allatomoverallscor:34,allatompackingscor:34,allatomposit:17,allatomscor:34,amino:[17,21,23],angl:23,api:1,argument:10,atom:[17,28,34],backbon:[28,35,36,47],backbonelist:18,backboneoverallscor:36,backbonescor:36,backbonescoreenv:35,base:[22,34,36],binari:33,block:[24,44],bond:39,branch:13,build:[0,2,31,44],can:46,candid:27,cbetascor:36,cbpackingscor:36,ccd:28,chain:22,changelog:3,check:29,clashscor:36,closer:30,cmake:[1,2,4,13],code:33,command:10,construct:[35,45],constructor:45,contribut:5,conveni:35,cooler:30,core:9,creat:[1,21],data:[22,33],databas:22,defin:[22,23],definit:4,depend:[2,47],detect:29,develop:14,dihedr:23,directori:13,distinguish:17,disulfid:39,document:[4,5,14,16,49],entri:47,environ:35,evalu:39,everyth:8,exampl:[27,33],execut:1,exisit:33,extend:25,featur:[5,22],file:[8,33],find:22,fit:28,forcefield:21,fragment:22,frame:[40,45],from:38,gap:[25,28],gener:[21,30],geometr:22,geometri:6,get:[15,46],git:13,graph:[7,41],group:44,handl:[17,19,25,27,31],have:1,hbondscor:36,header:33,helper:8,hook:13,how:[5,46],indic:16,instal:2,integr:1,introduct:[4,8,10],issu:5,keep:27,kic:28,librari:[43,47],licens:5,line:10,load:[20,43],lookup:21,loop:[18,19,21,27,28,30,37],loopcandid:27,mainten:4,make:[1,2],messag:8,minim:7,model:[0,15,24,26,27,29,31,42],modul:[4,5],mol:21,molprob:29,must:1,non:47,novo:[24,30],object:[20,30,40],optim:48,ost:21,other:38,output:1,own:5,pairwis:35,pairwisescor:36,pars:10,parser:10,parti:5,particl:44,pipelin:[15,31],pm3argpars:10,portabl:33,posit:17,precomput:20,profil:11,promod3:[0,2,4,5,9,13,15,16,33],protein:26,psipredpredict:22,punch:29,quick:5,raw:31,reconstruct:32,reducedscor:36,relax:28,releas:3,repres:18,residu:45,rigid:24,ring:29,rotam:[41,43,44,45,47],rotamerid:46,run:[1,2,15],runtim:11,sampl:23,sampler:[23,30],score:[27,35,37,38],scorer:[5,30,34,36],script:1,scwrl3:38,sequenc:22,setcompoundschemlib:12,setup:13,share:[4,8],sidechain:[32,42],sidechainreconstructiondata:32,sidechainreconstructor:32,smallest:44,ssagreementscor:36,stage:13,start:[5,15],step:31,structur:[13,22],subclass:1,subrotam:48,system:21,tabl:16,test:[1,4,5,8],test_act:1,third:5,torsion:23,torsionscor:36,track:27,triplet:23,type:47,unit:[1,4,5],user:49,welcom:16,write:5,your:5}})
\ No newline at end of file
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index 2c3f97b64a970412ba1934625659447d32ef65d5..3724f552e9c88343293899410277feb0d2ee412e 100644
--- a/doc/html/sidechain/disulfid.html
+++ b/doc/html/sidechain/disulfid.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Disulfid Bond Evaluation — ProMod3 1.1.0 documentation</title>
+ <title>Disulfid Bond Evaluation — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Loading Rotamer Libraries" href="loading.html" />
<link rel="prev" title="Rotamer Graph" href="graph.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -45,48 +47,26 @@
a disulfid bond, one would get an unfavourable energy due to “clashes” between
the sulfur atoms. It is possible to improve performance in sidechain
reconstruction regarding cysteins when finding and separately handle
-disulfid bonds. PROMOD3 implements a simple geometrical description
-<a class="reference internal" href="#canutescu2003b" id="id1">[canutescu2003b]</a> . The paper proposes two rotamers to be in a disulfid
+disulfid bonds. The scoring module implements an empirically derived disulfid
+score (<a class="reference internal" href="../scoring/other_scoring_functions.html#promod3.scoring.SCWRL3DisulfidScore" title="promod3.scoring.SCWRL3DisulfidScore"><code class="xref py py-func docutils literal"><span class="pre">promod3.scoring.SCWRL3DisulfidScore()</span></code></a>) as defined in
+<a class="reference internal" href="../scoring/other_scoring_functions.html#canutescu2003b" id="id1">[canutescu2003b]</a>. The paper proposes two rotamers to be in a disulfid
bonded state, if the resulting disulfid score plus the self energies of the
involved rotamers is below 45. If there are several cysteines close together,
this problem gets another layer of complexity. One has to assure, that
every cysteine only participates in one disulfid bond but the network
of disulfid bonds is geometrically optimal. SCWRL4 proposes an approach,
that has also been implemented here.</p>
-<dl class="method">
-<dt id="promod3.sidechain.DisulfidRawScore">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">DisulfidRawScore</code><span class="sig-paren">(</span><em>ca_pos_one</em>, <em>cb_pos_one</em>, <em>sg_pos_one</em>, <em>ca_pos_two</em>, <em>cb_pos_two</em>, <em>sg_pos_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.DisulfidRawScore" title="Permalink to this definition">¶</a></dt>
-<dd><p>Evaluates the geometric expression based on the input positions</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>ca_pos_one</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA position of first rotamer</li>
-<li><strong>cb_pos_one</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB position of first rotamer</li>
-<li><strong>sg_pos_one</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The gamma sulfur position of first rotamer</li>
-<li><strong>ca_pos_two</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA position of second rotamer</li>
-<li><strong>cb_pos_two</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB position of second rotamer</li>
-<li><strong>sg_pos_two</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The gamma sulfur position of second rotamer</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">The result of the raw score</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
<dl class="method">
<dt id="promod3.sidechain.DisulfidScore">
<code class="descclassname">promod3.sidechain.</code><code class="descname">DisulfidScore</code><span class="sig-paren">(</span><em>rotamer_one</em>, <em>rotamer_two</em>, <em>ca_pos_one</em>, <em>cb_pos_one</em>, <em>ca_pos_two</em>, <em>cb_pos_two</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.DisulfidScore" title="Permalink to this definition">¶</a></dt>
<dd><p>Directly extracts the positions of the gamma sulfurs from the rotamers by
-searching for particles with the name “SG”. In case of <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a>
-It expects exactly one gamma sulfur per rotamer. In case of
-<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> there can be an arbitrary number of gamma sulfurs per
-rotamer (at least one), it then evaluates the score for all possible
-combinations of gamma sulfurs and takes the minimum score.
+searching for particles with the name “SG”.
+The found positions are then passed to
+<a class="reference internal" href="../scoring/other_scoring_functions.html#promod3.scoring.SCWRL3DisulfidScore" title="promod3.scoring.SCWRL3DisulfidScore"><code class="xref py py-func docutils literal"><span class="pre">promod3.scoring.SCWRL3DisulfidScore()</span></code></a>.
+In case of <a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> it expects exactly one gamma sulfur per
+rotamer. In case of <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a> there can be an arbitrary number
+of gamma sulfurs per rotamer (at least one), it then evaluates the score
+for all possible combinations of gamma sulfurs and takes the minimum score.
To get a final DisulfidScore, it finally adds the self energies of the
rotamers to the result of the geometric expression.</p>
<table class="docutils field-list" frame="void" rules="none">
@@ -96,10 +76,10 @@ rotamers to the result of the geometric expression.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rotamer_one</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) – First rotamer</li>
<li><strong>rotamer_two</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> , <a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>) – Second rotamer</li>
-<li><strong>ca_pos_one</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</li>
-<li><strong>cb_pos_one</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</li>
-<li><strong>ca_pos_two</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</li>
-<li><strong>cb_pos_two</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li>
+<li><strong>ca_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of first rotamer</li>
+<li><strong>cb_pos_one</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of first rotamer</li>
+<li><strong>ca_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CA position of second rotamer</li>
+<li><strong>cb_pos_two</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – CB position of second rotamer</li>
</ul>
</td>
</tr>
@@ -132,8 +112,8 @@ possible, the one with the optimal sum of scores gets estimated.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>rotamer_groups</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of
<a class="reference internal" href="rotamer.html#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>/<a class="reference internal" href="rotamer.html#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a>) – Every group represents a cysteine</li>
-<li><strong>ca_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</li>
-<li><strong>cb_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</li>
+<li><strong>ca_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CA positions of the according rotamers</li>
+<li><strong>cb_positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The CB positions of the according rotamers</li>
<li><strong>score_threshold</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The score two rotamers must have to be considered
as a disulfid bond</li>
<li><strong>optimize_subrotamers</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If set to true and the input consists of flexible
@@ -157,12 +137,6 @@ describe the optimal rotamers in the according rotamer groups.</p>
</table>
</dd></dl>
-<table class="docutils citation" frame="void" id="canutescu2003b" rules="none">
-<colgroup><col class="label" /><col /></colgroup>
-<tbody valign="top">
-<tr><td class="label"><a class="fn-backref" href="#id1">[canutescu2003b]</a></td><td>Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).</td></tr>
-</tbody>
-</table>
</div>
@@ -198,9 +172,6 @@ describe the optimal rotamers in the according rotamer groups.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -208,11 +179,11 @@ describe the optimal rotamers in the according rotamer groups.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/disulfid.txt"
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index 776c8e4fb4945ec18bc53f5325542164e279f4ef..9230a415148eeae3d628663743913f9c46ab6705 100644
--- a/doc/html/sidechain/frame.html
+++ b/doc/html/sidechain/frame.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Frame — ProMod3 1.1.0 documentation</title>
+ <title>Frame — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Rotamer Library" href="rotamer_lib.html" />
<link rel="prev" title="Rotamers" href="rotamer.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -159,9 +161,6 @@ can be passed to rotamer groups for calculating frame energies.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -169,11 +168,11 @@ can be passed to rotamer groups for calculating frame energies.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/frame.txt"
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index 2a2e6c16b802c1cfb21a264e3725e8d1d46514ee..e547f6f72ad4a595a7f20713cf3469da52324898 100644
--- a/doc/html/sidechain/graph.html
+++ b/doc/html/sidechain/graph.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamer Graph — ProMod3 1.1.0 documentation</title>
+ <title>Rotamer Graph — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Disulfid Bond Evaluation" href="disulfid.html" />
<link rel="prev" title="Rotamer Constructor" href="rotamer_constructor.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -44,15 +46,15 @@
<p>Once having a frame representing the rigid parts, the internal energies in
rotamer groups can be calculated. To come to a final solution of the sidechain
modelling problem, the pairwise energies also have to be evaluated and an
-overall solution has to be found. PROMOD3 implements an interaction graph that
-takes a list of rotamer groups, calculates the pairwise energies, does edge
-decomposition and dead end elimination. Solutions can finally be found
-using Tree decomposition, AStar or Monte Carlo approaches.</p>
+overall solution has to be found. PROMOD3 implements a
+<a class="reference internal" href="../core/graph_minimizer.html#promod3.core.GraphMinimizer" title="promod3.core.GraphMinimizer"><code class="xref py py-class docutils literal"><span class="pre">promod3.core.GraphMinimizer</span></code></a> that allows to find solutions using
+tree decomposition, A* and Monte Carlo algorithms.</p>
<dl class="class">
<dt id="promod3.sidechain.RotamerGraph">
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerGraph</code><a class="headerlink" href="#promod3.sidechain.RotamerGraph" title="Permalink to this definition">¶</a></dt>
-<dd><p>The Graph object has no constructor exported to python. It is meant to be
-constructed using the static create functions.</p>
+<dd><p>The <a class="reference internal" href="#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal"><span class="pre">RotamerGraph</span></code></a> objects inherits from
+<a class="reference internal" href="../core/graph_minimizer.html#promod3.core.GraphMinimizer" title="promod3.core.GraphMinimizer"><code class="xref py py-class docutils literal"><span class="pre">promod3.core.GraphMinimizer</span></code></a> and extends the minimizer by static
+initialization functions.</p>
<dl class="staticmethod">
<dt id="promod3.sidechain.RotamerGraph.CreateFromRRMList">
<em class="property">static </em><code class="descname">CreateFromRRMList</code><span class="sig-paren">(</span><em>rotamer_groups</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.CreateFromRRMList" title="Permalink to this definition">¶</a></dt>
@@ -73,389 +75,6 @@ conformations for every amino acid position.</td>
</table>
</dd></dl>
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.Prune">
-<code class="descname">Prune</code><span class="sig-paren">(</span><em>epsilon</em><span class="optional">[</span>, <em>e_cut=0.0</em>, <em>consider_all_nodes=False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.Prune" title="Permalink to this definition">¶</a></dt>
-<dd><p>Performs edge decomposition followed by dead end elimination in an
-iterative manner until no changes can be observed anymore given
-<strong>epsilon</strong>.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>epsilon</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The energy threshold to perform edge decomposition.</li>
-<li><strong>e_cut</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Parameter to control dead end elimination. If set to
-0.0, the default goldstein criterion is applied =>
-the rotamer gets removed if it’s dominated by all other
-rotamers in the same node. If you increase this value,
-a rotamer must be dominated by at least this <strong>e_cut</strong>.</li>
-<li><strong>consider_all_nodes</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, wether the dead end elimination should be
-applied to all nodes, or only those who are
-connected with an edge removed by edge
-decomposition. This is useful if already a Prune
-operation has been performed => only those nodes
-connected to a removed edge have the chance for
-successful dead end elimination.</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.ApplyDEE">
-<code class="descname">ApplyDEE</code><span class="sig-paren">(</span><em>node_idx</em><span class="optional">[</span>, <em>e_cut=0.0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.ApplyDEE" title="Permalink to this definition">¶</a></dt>
-<dd><p>Applies dead end elimination on one particular node and potentially
-deactivates certain rotamers.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>node_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Node to apply dead end elimination</li>
-<li><strong>e_cut</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – If set to
-0.0, the default goldstein criterion is applied =>
-the rotamer gets removed if it’s dominated by all other
-rotamers in the same node. If you increase this value,
-a rotamer must be dominated by at least this <strong>e_cut</strong>.</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> whether any rotamer has been deactivated.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.ApplyEdgeDecomposition">
-<code class="descname">ApplyEdgeDecomposition</code><span class="sig-paren">(</span><em>edge_idx</em>, <em>epsilon</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.ApplyEdgeDecomposition" title="Permalink to this definition">¶</a></dt>
-<dd><p>Applies edge decomposition on one particular edge and potentially
-deactivates it.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>edge_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Edge to decompose.
-the idx relates to the list you get back
-when calling the <a class="reference internal" href="#promod3.sidechain.RotamerGraph.GetEdges" title="promod3.sidechain.RotamerGraph.GetEdges"><code class="xref py py-meth docutils literal"><span class="pre">GetEdges()</span></code></a> function.</li>
-<li><strong>epsilon</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The energy threshold to perform edge decomposition.</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a> whether the edge has been decomposed and
-deactivated</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.Reset">
-<code class="descname">Reset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.Reset" title="Permalink to this definition">¶</a></dt>
-<dd><p>Resets the graph by undoing any pruning operation (DEE and edge decomposition)</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.TreeSolve">
-<code class="descname">TreeSolve</code><span class="sig-paren">(</span><span class="optional">[</span><em>max_complexity=inf</em>, <em>initial_epsilon=0.02</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.TreeSolve" title="Permalink to this definition">¶</a></dt>
-<dd><p>The method solves a rotamer graph using a minimal width tree decomposition
-approach in an iterative manner. In every iteration, the algorithm performs
-a pruning step (DEE / Edge Decomposition) and subsequently tries to solve
-each connected component in the graph separately.
-If the number of possible enumerations in the tree constructetd from a
-particular connected component is is larger <strong>max_complexity</strong>,
-this component is solved in a later iteration. The algorithm iterates until
-all connected components are solved and steadily increases the epsilon value
-resulting in a more and more agressive edge decomposition. This function
-assumes all self energies of the rotamers to be calculated and properly set!</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>max_complexity</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Max number of possible permutations, that have to
-be enumerated in the resulting tree after tree
-decomposition.</li>
-<li><strong>initial_epsilon</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – The initial energy threshold to perform edge
-decomposition.</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A tuple with the first element being a list of indices
-representing the single rotamers minimizing
-the overall energy functions from every rotamer group.
-The second element is the according energy value.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.AStarSolve">
-<code class="descname">AStarSolve</code><span class="sig-paren">(</span><em>e_thresh</em><span class="optional">[</span>, <em>max_n=100</em>, <em>max_visited_nodes=100000000</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.AStarSolve" title="Permalink to this definition">¶</a></dt>
-<dd><p>The method solves a rotamer graph using the A* algorithm. Besides creating
-minimal energy solution, the function produces a maximum of <strong>max_n</strong>
-solutions sorted by energy. It aborts as soon as it sees the first solution
-with an energy difference of <strong>e_thresh</strong> to the optimal solution or hits
-<strong>max_n</strong>. If you’re only interested in the optimal solution you should use
-the TreeSolve function since it’s much faster and uses less memory.
-There is no automatic pruning of the graph using DEE or edge decomposition,
-so you have to do it by yourself, otherwise you’ll have a looooooong
-runtime or even hit the <strong>max_visited_nodes</strong> parameter that caps the memory
-usage.
-To have a valid solution you have to take care that you set the <strong>e_cut</strong>
-parameter in the pruning function to <strong>e_tresh</strong>.
-This function assumes all self energies of the rotamers to be calculated
-and properly set!</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>e_thresh</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Maximal energy difference of a solution to the
-optimal solution to be considered.</li>
-<li><strong>max_n</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – The maximum number of solutions that will be generated.</li>
-<li><strong>max_visited_nodes</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Caps the memory usage of the algorithm. Besides
-The memory used for pairwise energies and self
-energies, the algorithm uses about
-<strong>max_visited_nodes</strong> * 20 bytes.</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A tuple with the first element being a list of
-solutions with indices representing the single rotamers
-selected for that solution. The second element is a list
-of energies for the according solutions.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.MCSolve">
-<code class="descname">MCSolve</code><span class="sig-paren">(</span><span class="optional">[</span><em>n=100</em>, <em>mc_steps=100000</em>, <em>start_temperature=1000.0</em>, <em>change_frequency=1000</em>, <em>cooling_factor=0.9</em>, <em>seed=0</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.MCSolve" title="Permalink to this definition">¶</a></dt>
-<dd><p>Does a total of <strong>n</strong> Monte Carlo runs to find low energy solutions
-of the RotamerGraph. Each run starts with a random rotamer
-configuration. At each of the <strong>mc_steps</strong> steps, a random location and
-a random rotamer at that location is selected and an energy difference
-of that random selection relative to the current configuration is
-estimated. If the difference in energy is negative, the step is
-accepted. If not, the step is accepted with a probability given by
-the temperature dependent Metropolis criterion (exp(-ediff/T)).
-The temperature for every run starts with <strong>start_temperature</strong>
-and is multiplied every <strong>change_frequency</strong> steps with <strong>cooling_factor</strong>
-to achieve a simulated annealing effect.
-There is no automatic pruning of the graph using DEE or edge decomposition,
-you have to do that by yourself.
-This function assumes all self energies of the rotamers to be calculated
-and properly set!</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>n</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of Monte Carlo runs</li>
-<li><strong>mc_steps</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of Monte Carlo steps per run</li>
-<li><strong>start_temperature</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Start temperature for the temperature dependent
-Metropolis criterion</li>
-<li><strong>change_frequency</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Number of steps the temperature stays the same</li>
-<li><strong>cooling_factor</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Factor to multiply temperature each
-<strong>change_frequency</strong> steps</li>
-<li><strong>seed</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Seed for random number generator</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A tuple with the first element being a list of
-solutions with indices representing the single rotamers
-selected for that solution. The second element is a list
-of energies for the according solutions.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.GetNumNodes">
-<code class="descname">GetNumNodes</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.GetNumNodes" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The number of nodes in the graph
-=> every RotamerGroup is a node</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.GetNumEdges">
-<code class="descname">GetNumEdges</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.GetNumEdges" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The number of edges in the graph, representing
-connections between nodes with at least one
-nonzero interaction</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.GetNumActiveNodes">
-<code class="descname">GetNumActiveNodes</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.GetNumActiveNodes" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The number of nodes having more than one active rotamer,
-even after performing pruning operations</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.GetNumActiveEdges">
-<code class="descname">GetNumActiveEdges</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.GetNumActiveEdges" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The number of edges representing nonzero interactions,
-even after performing pruning operations</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.GetNumRotamers">
-<code class="descname">GetNumRotamers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.GetNumRotamers" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The total number of rotamers in the graph</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.GetNumActiveRotamers">
-<code class="descname">GetNumActiveRotamers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.GetNumActiveRotamers" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The total number of active rotamers (Total number of
-rotamers minus those that have been deactivated by DEE)</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.GetEdges">
-<code class="descname">GetEdges</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.GetEdges" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A list of tuples describing the edges
-connecting nodes with nonzero pairwise interactions</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.GetActiveEdges">
-<code class="descname">GetActiveEdges</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.GetActiveEdges" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">A <code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <code class="xref py py-class docutils literal"><span class="pre">tuples</span></code> describing the edges
-connecting nodes with nonzero pairwise interactions
-(All edges minus those that have been deactived by edge
-decomposition)</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.GetActiveRotamers">
-<code class="descname">GetActiveRotamers</code><span class="sig-paren">(</span><em>node_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.GetActiveRotamers" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>node_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Specifies node from which the active rotamers should be
-extracted</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">list of the rotamers that are active
-in specified node (all rotamers minus those that have
-been deactivated using DEE)</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.GetSelfEnergies">
-<code class="descname">GetSelfEnergies</code><span class="sig-paren">(</span><em>node_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.GetSelfEnergies" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>node_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Specifies node from which the self energies should be
-extracted</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">list of self energies for all rotamers in
-specified node as they are fed into the solving
-algorithms. Note, that they might slightly differ
-from the original self energies in the input rotamers
-because of approximations introduced in edge
-decomposition.</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.RotamerGraph.GetPairwiseEnergies">
-<code class="descname">GetPairwiseEnergies</code><span class="sig-paren">(</span><em>edge_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerGraph.GetPairwiseEnergies" title="Permalink to this definition">¶</a></dt>
-<dd><table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>edge_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Specifies edge from which the pairwise energies should
-be extracted, the idx relates to the list you get back
-when calling the <a class="reference internal" href="#promod3.sidechain.RotamerGraph.GetEdges" title="promod3.sidechain.RotamerGraph.GetEdges"><code class="xref py py-meth docutils literal"><span class="pre">GetEdges()</span></code></a> function.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">list of list where you can extract
-the energy of rotamer i in the first node in the
-edge with rotamer j in the second node in the edge
-with: e = pairwise_energies[i][j]</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
</dd></dl>
</div>
@@ -493,9 +112,6 @@ with: e = pairwise_energies[i][j]</td>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -503,11 +119,11 @@ with: e = pairwise_energies[i][j]</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/graph.txt"
diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index 496c0b28c9766230aee6cad7725ffa469530248b..3af49da0fb86f519b9e07bbc4fd4a050449415a8 100644
--- a/doc/html/sidechain/index.html
+++ b/doc/html/sidechain/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>sidechain - Sidechain Modelling — ProMod3 1.1.0 documentation</title>
+ <title>sidechain - Sidechain Modelling — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="RotamerID" href="rotamer_id.html" />
<link rel="prev" title="Modelling Algorithms" href="../modelling/algorithms.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -51,21 +53,21 @@ algorithm using the functionality in the module. Note, that this code will crash
as soon as you have structures containing all the weirdness the PDB throws at
us. In this case, you should use the full fletched sidechain reconstruction
pipelines available in the modelling module.</p>
-<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">ost</span> <span class="kn">import</span> <span class="n">io</span><span class="p">,</span><span class="n">mol</span>
-<span class="kn">from</span> <span class="nn">promod3</span> <span class="kn">import</span> <span class="n">sidechain</span>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ost</span> <span class="k">import</span> <span class="n">io</span><span class="p">,</span><span class="n">mol</span>
+<span class="kn">from</span> <span class="nn">promod3</span> <span class="k">import</span> <span class="n">sidechain</span>
-<span class="c"># load a protein</span>
-<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s">'data/1CRN.pdb'</span><span class="p">)</span>
-<span class="c"># load rotamer library</span>
+<span class="c1"># load a protein</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">io</span><span class="o">.</span><span class="n">LoadPDB</span><span class="p">(</span><span class="s1">'data/1CRN.pdb'</span><span class="p">)</span>
+<span class="c1"># load rotamer library</span>
<span class="n">library</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">LoadDunbrackLib</span><span class="p">()</span>
-<span class="c"># we need a rotamer constructor to create any rotamers or </span>
-<span class="c"># frame residues</span>
-<span class="n">rot_constructor</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">SCWRLRotamerConstructor</span><span class="p">()</span>
+<span class="c1"># we need a rotamer constructor to create any rotamers or </span>
+<span class="c1"># frame residues </span>
+<span class="n">rot_constructor</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">SCWRLRotamerConstructor</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
-<span class="c"># create new entity from protein only containing the amino acids</span>
-<span class="n">prot</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s">"peptide=true"</span><span class="p">),</span> <span class="bp">True</span><span class="p">)</span>
+<span class="c1"># create new entity from protein only containing the amino acids</span>
+<span class="n">prot</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">Select</span><span class="p">(</span><span class="s2">"peptide=true"</span><span class="p">),</span> <span class="kc">True</span><span class="p">)</span>
-<span class="c"># gather some data, the rotamer ids and backbone torsion angles</span>
+<span class="c1"># gather some data, the rotamer ids and backbone torsion angles</span>
<span class="n">torsion_angles</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="n">rotamer_ids</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
@@ -74,7 +76,7 @@ pipelines available in the modelling module.</p>
<span class="n">phi_handle</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">GetPhiTorsion</span><span class="p">()</span>
<span class="n">psi_handle</span> <span class="o">=</span> <span class="n">r</span><span class="o">.</span><span class="n">GetPsiTorsion</span><span class="p">()</span>
- <span class="c"># set typical default values for an alpha helix...</span>
+ <span class="c1"># set typical default values for an alpha helix...</span>
<span class="n">phi</span> <span class="o">=</span> <span class="o">-</span><span class="mf">1.0472</span>
<span class="n">psi</span> <span class="o">=</span> <span class="o">-</span><span class="mf">0.7854</span>
<span class="k">if</span> <span class="n">phi_handle</span><span class="o">.</span><span class="n">IsValid</span><span class="p">():</span>
@@ -84,8 +86,8 @@ pipelines available in the modelling module.</p>
<span class="n">torsion_angles</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">phi</span><span class="p">,</span><span class="n">psi</span><span class="p">))</span>
-<span class="c"># first build a frame representing the rigid parts including</span>
-<span class="c"># cystein sidechains</span>
+<span class="c1"># first build a frame representing the rigid parts including</span>
+<span class="c1"># cystein sidechains</span>
<span class="n">frame_residues</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">r</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">):</span>
<span class="n">frame_residue</span> <span class="o">=</span> <span class="n">rot_constructor</span><span class="o">.</span><span class="n">ConstructBackboneFrameResidue</span><span class="p">(</span>
@@ -97,12 +99,12 @@ pipelines available in the modelling module.</p>
<span class="n">frame</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">Frame</span><span class="p">(</span><span class="n">frame_residues</span><span class="p">)</span>
-<span class="c"># let's build up rotamer groups</span>
+<span class="c1"># let's build up rotamer groups</span>
<span class="n">rotamer_groups</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="n">aa_with_rotamers</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span><span class="n">r</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">):</span>
- <span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">GetName</span><span class="p">()</span> <span class="o">==</span> <span class="s">"ALA"</span> <span class="ow">or</span> <span class="n">r</span><span class="o">.</span><span class="n">GetName</span><span class="p">()</span> <span class="o">==</span> <span class="s">"GLY"</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">r</span><span class="o">.</span><span class="n">GetName</span><span class="p">()</span> <span class="o">==</span> <span class="s2">"ALA"</span> <span class="ow">or</span> <span class="n">r</span><span class="o">.</span><span class="n">GetName</span><span class="p">()</span> <span class="o">==</span> <span class="s2">"GLY"</span><span class="p">:</span>
<span class="k">continue</span>
<span class="n">rot_group</span> <span class="o">=</span> <span class="n">rot_constructor</span><span class="o">.</span><span class="n">ConstructFRMRotamerGroup</span><span class="p">(</span>
@@ -110,27 +112,27 @@ pipelines available in the modelling module.</p>
<span class="n">torsion_angles</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">0</span><span class="p">],</span> <span class="n">torsion_angles</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">1</span><span class="p">])</span>
<span class="n">rot_group</span><span class="o">.</span><span class="n">SetFrameEnergy</span><span class="p">(</span><span class="n">frame</span><span class="p">)</span>
- <span class="c"># remove super unlikely rotamer in rotamer group </span>
- <span class="c"># e.g. those who clash with the frame</span>
+ <span class="c1"># remove super unlikely rotamer in rotamer group </span>
+ <span class="c1"># e.g. those who clash with the frame</span>
<span class="n">rot_group</span><span class="o">.</span><span class="n">ApplySelfEnergyThresh</span><span class="p">()</span>
- <span class="c"># finally add it and keep track of the indices</span>
+ <span class="c1"># finally add it and keep track of the indices</span>
<span class="n">rotamer_groups</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">rot_group</span><span class="p">)</span>
<span class="n">aa_with_rotamers</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">i</span><span class="p">)</span>
-<span class="c"># buildup a graph given the rotamer groups</span>
+<span class="c1"># buildup a graph given the rotamer groups</span>
<span class="n">graph</span> <span class="o">=</span> <span class="n">sidechain</span><span class="o">.</span><span class="n">RotamerGraph</span><span class="o">.</span><span class="n">CreateFromFRMList</span><span class="p">(</span><span class="n">rotamer_groups</span><span class="p">)</span>
-<span class="c"># and get a solution out of it using a minimal width tree approach</span>
+<span class="c1"># and get a solution out of it using a minimal width tree approach</span>
<span class="n">solution</span> <span class="o">=</span> <span class="n">graph</span><span class="o">.</span><span class="n">TreeSolve</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
-<span class="c"># let's finally apply the solution to the residues</span>
+<span class="c1"># let's finally apply the solution to the residues</span>
<span class="k">for</span> <span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">rot_group</span><span class="p">,</span> <span class="n">sol</span><span class="p">)</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">aa_with_rotamers</span><span class="p">,</span>
<span class="n">rotamer_groups</span><span class="p">,</span>
<span class="n">solution</span><span class="p">):</span>
<span class="n">rot_group</span><span class="p">[</span><span class="n">sol</span><span class="p">]</span><span class="o">.</span><span class="n">ApplyOnResidue</span><span class="p">(</span><span class="n">prot</span><span class="o">.</span><span class="n">residues</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
-<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="s">"example_reconstruction.pdb"</span><span class="p">)</span>
+<span class="n">io</span><span class="o">.</span><span class="n">SavePDB</span><span class="p">(</span><span class="n">prot</span><span class="p">,</span> <span class="s2">"example_reconstruction.pdb"</span><span class="p">)</span>
</pre></div>
</div>
<p>Contents:</p>
@@ -206,9 +208,6 @@ pipelines available in the modelling module.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -216,11 +215,11 @@ pipelines available in the modelling module.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/index.txt"
diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
index 449c456a2d3cd28a1f5db305a69782fb3ea119e6..cca071873f529654b50e681922af16e723f72672 100644
--- a/doc/html/sidechain/loading.html
+++ b/doc/html/sidechain/loading.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Loading Rotamer Libraries — ProMod3 1.1.0 documentation</title>
+ <title>Loading Rotamer Libraries — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Subrotamer Optimization" href="subrotamer_optimizer.html" />
<link rel="prev" title="Disulfid Bond Evaluation" href="disulfid.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -158,9 +160,6 @@ incomplete if the last problem gets triggered.</td>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -168,11 +167,11 @@ incomplete if the last problem gets triggered.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/loading.txt"
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index 1ae73b516dbffd03010d02c937fdc44924db455f..582ce7f7647665d09d4bb7ee052bdda578fd494e 100644
--- a/doc/html/sidechain/rotamer.html
+++ b/doc/html/sidechain/rotamer.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamers — ProMod3 1.1.0 documentation</title>
+ <title>Rotamers — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Frame" href="frame.html" />
<link rel="prev" title="RotamerID" href="rotamer_id.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -84,11 +86,11 @@ has to be defined at initialization.</p>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>type</strong> (<a class="reference internal" href="#promod3.sidechain.SidechainParticle" title="promod3.sidechain.SidechainParticle"><code class="xref py py-class docutils literal"><span class="pre">SidechainParticle</span></code></a>) – Type of particle</li>
-<li><strong>pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Positions of particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Positions of particle</li>
<li><strong>charge</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">float</span></code></a>) – Charge of particle, will be used in case H-Bonds</li>
<li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Name of particle. This name will be given to an actual
-<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.AtomHandle</span></code></a> if a rotamer gets applied
-to a <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a></li>
+<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.AtomHandle</span></code></a> if a rotamer gets applied
+to a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a></li>
</ul>
</td>
</tr>
@@ -196,7 +198,7 @@ to a <a class="reference external" href="http://www.openstructure.org/docs/dev/m
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>lone_pair</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Lone pair direction</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>lone_pair</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Lone pair direction</td>
</tr>
</tbody>
</table>
@@ -211,7 +213,7 @@ hydrogen, this would be the direction of backbone-N to backbone-H.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>polar_direction</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Polar direction of particle</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Polar direction of particle</td>
</tr>
</tbody>
</table>
@@ -281,13 +283,14 @@ particular <a class="reference internal" href="#promod3.sidechain.RRMRotamerGrou
<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>res</em>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Iterates over every particle and searches for the according atom in
<strong>res</strong>. If it’s present, the position gets reset to the particle position.
-If not, a new atom gets added to <strong>res</strong>.</p>
+If not, a new atom gets added to <strong>res</strong>. No atoms are removed from <strong>res</strong>
+in this process.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
<strong>res</strong></li>
<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of <strong>res</strong>. Nothing happens in case of the
@@ -556,13 +559,14 @@ particular <a class="reference internal" href="#promod3.sidechain.FRMRotamerGrou
<code class="descname">ApplyOnResidue</code><span class="sig-paren">(</span><em>res</em>, <em>consider_hydrogens=False</em>, <em>new_res_name=""</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.FRMRotamer.ApplyOnResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Iterates over every particle of the active subrotamer and searches for the
according atom in <strong>res</strong>. If it’s present, the position gets reset to the
-particle position. If not, a new atom gets added to <strong>res</strong>.</p>
+particle position. If not, a new atom gets added to <strong>res</strong>.
+No atoms are removed from <strong>res</strong> in this process.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</li>
<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -962,7 +966,7 @@ particles of the same residue.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</li>
<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -1096,7 +1100,7 @@ particles of the same residue.</li>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Rotamer index</li>
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>consider_hydrogens</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Flag, whether polar hydrogens should be added to
the sidechain</li>
<li><strong>new_res_name</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – New name of residue. Nothing happens in case of the
@@ -1213,9 +1217,6 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -1223,11 +1224,11 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/rotamer.txt"
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index f277f8341490d2efbf65997eec857ada4429787c..0a026c732216121edf1f9e241a6df6442596da23 100644
--- a/doc/html/sidechain/rotamer_constructor.html
+++ b/doc/html/sidechain/rotamer_constructor.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamer Constructor — ProMod3 1.1.0 documentation</title>
+ <title>Rotamer Constructor — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Rotamer Graph" href="graph.html" />
<link rel="prev" title="Rotamer Library" href="rotamer_lib.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -47,12 +49,29 @@ functionality provided by PROMOD3</p>
<h2>Constructing Rotamers and Frame Residues<a class="headerlink" href="#constructing-rotamers-and-frame-residues" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.SCWRLRotamerConstructor">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRLRotamerConstructor</code><a class="headerlink" href="#promod3.sidechain.SCWRLRotamerConstructor" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRLRotamerConstructor</code><span class="sig-paren">(</span><em>cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRLRotamerConstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructing rotamers and frame residues that are parametrized according to
the SCWRL4 method. They contain all heavy atoms, but also the
-polar hydrogens. The rotamers start after the CB atom (typically CG).
+polar hydrogens.
In case of the <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> construction, the
constructor distinguishes between backbone and sidechain frame residues.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>cb_in_sidechain</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – If set to true, all constructed rotamers will contain
+the cb atom. This flag also affects the construction
+of frame residues and controls whether the cb atom
+shows up in the backbone frame residues or sidechain
+frame residues.
+This is useful when you want to represent ALA or
+GLY with actual rotamers, but be aware of increased
+runtime. This flag can be set to False for most
+modeling applications and you just don’t generate
+any rotamers for ALA and GLY.</td>
+</tr>
+</tbody>
+</table>
<dl class="method">
<dt id="promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup">
<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>res</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib</em><span class="optional">[</span>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRLRotamerConstructor.ConstructRRMRotamerGroup" title="Permalink to this definition">¶</a></dt>
@@ -63,11 +82,6 @@ constructor distinguishes between backbone and sidechain frame residues.</p>
<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>all_atom_pos</em>, <em>aa_res_idx</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib</em><span class="optional">[</span>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd></dd></dl>
-<dl class="method">
-<dt>
-<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib</em><span class="optional">[</span>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
-<dd></dd></dl>
-
<dl class="method">
<dt>
<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>res</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
@@ -78,11 +92,6 @@ constructor distinguishes between backbone and sidechain frame residues.</p>
<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>all_atom_pos</em>, <em>aa_res_idx</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd></dd></dl>
-<dl class="method">
-<dt>
-<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
-<dd></dd></dl>
-
<dl class="method">
<dt>
<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>res</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib_entries</em><span class="optional">[</span>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
@@ -91,11 +100,6 @@ constructor distinguishes between backbone and sidechain frame residues.</p>
<dl class="method">
<dt>
<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>all_atom_pos</em>, <em>aa_res_idx</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib_entries</em><span class="optional">[</span>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
-<dd></dd></dl>
-
-<dl class="method">
-<dt>
-<code class="descname">ConstructRRMRotamerGroup</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>cb_pos</em>, <em>id</em>, <em>residue_index</em>, <em>rot_lib_entries</em><span class="optional">[</span>, <em>probability_cutoff = 0.98</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
<dd><p>All functions are also avaible for their flexible rotamer model counterpart.
=>ConstructFRMRotamerGroup(...) with exactly the same parameters.</p>
<table class="docutils field-list" frame="void" rules="none">
@@ -103,13 +107,10 @@ constructor distinguishes between backbone and sidechain frame residues.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the N, CA, CB backbone anchor</li>
-<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the N, CA, CB backbone anchor</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – To extract the required backbone atoms</li>
+<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the required backbone atoms</li>
<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
-extract the backbone anchor</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – To directly feed in the backbone anchor positions</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – To directly feed in the backbone anchor positions</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – To directly feed in the backbone anchor positions</li>
+extract the required backbone atoms</li>
<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain.</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
@@ -139,9 +140,8 @@ probabilities extracted from the rotamer library.</p>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> when not all required backbone
-atoms are present in <strong>residue</strong>, not all required atom
-positions are set in <strong>all_atom_pos</strong> or when the rotamer library
-does not contain any entries for <strong>id</strong></p>
+atoms are present in <strong>residue</strong> or not all required atom
+positions are set in <strong>all_atom_pos</strong></p>
</td>
</tr>
</tbody>
@@ -156,14 +156,8 @@ does not contain any entries for <strong>id</strong></p>
<dl class="method">
<dt>
<code class="descname">ConstructBackboneFrameResidue</code><span class="sig-paren">(</span><em>all_atom_pos</em>, <em>aa_res_idx</em>, <em>id</em>, <em>residue_index</em>, <em>Real phi</em><span class="optional">[</span>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
-<dd></dd></dl>
-
-<dl class="method">
-<dt>
-<code class="descname">ConstructBackboneFrameResidue</code><span class="sig-paren">(</span><em>n_pos</em>, <em>ca_pos</em>, <em>c_pos</em>, <em>o_pos</em>, <em>cb_pos</em>, <em>id</em>, <em>residue_index</em>, <em>Real phi</em><span class="optional">[</span>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span></dt>
-<dd><p>Constructs backbone frame residues for amino acid residues. It extracts
-the n, ca, c, o and cb positions and constructs a frame residue based on
-the parametrizations of SCWRL4. In case of <strong>n_ter</strong>, there are additional
+<dd><p>Constructs backbone frame residues for amino acid residues based on the
+parametrizations of SCWRL4. In case of <strong>n_ter</strong>, there are additional
hydrogens added at the nitrogen to represent a proper n-terminus. The same
is true for <strong>c_ter</strong>, an additional oxygen is built instead. In any case,
a single hydrogen is added to the nitrogen (except proline), this is
@@ -173,15 +167,10 @@ why the phi angle of the residue is required as an input.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the backbone positions</li>
<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the backbone positions</li>
<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the backbone positions</li>
-<li><strong>n_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – To directly feed in the backbone positions</li>
-<li><strong>ca_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – To directly feed in the backbone positions</li>
-<li><strong>c_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – To directly feed in the backbone positions</li>
-<li><strong>o_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – To directly feed in the backbone positions</li>
-<li><strong>cb_pos</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – To directly feed in the backbone positions</li>
<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identifies the sidechain</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Important for the energy calculations towards the
<a class="reference internal" href="frame.html#promod3.sidechain.Frame" title="promod3.sidechain.Frame"><code class="xref py py-class docutils literal"><span class="pre">Frame</span></code></a> you don’t want to calculate a pairwise
@@ -200,7 +189,7 @@ represent a proper c-terminus</li>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Raises:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> when not all required backbone
-atoms are present in <strong>residue</strong>, not all required atom
+atoms are present in <strong>residue</strong> or not all required atom
positions are set in <strong>all_atom_pos</strong>.</p>
</td>
</tr>
@@ -224,7 +213,7 @@ particles for all polar hydrogens.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the sidechain positions</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to extract the sidechain positions</li>
<li><strong>all_atom_pos</strong> (<a class="reference internal" href="../loop/all_atom.html#promod3.loop.AllAtomPositions" title="promod3.loop.AllAtomPositions"><code class="xref py py-class docutils literal"><span class="pre">promod3.loop.AllAtomPositions</span></code></a>) – To extract the sidechain positions</li>
<li><strong>aa_res_idx</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index of residue in <strong>all_atom_pos</strong> from which to
extract the sidechain positions</li>
@@ -248,7 +237,7 @@ atom positions are set in <strong>all_atom_pos</strong>.</p>
<dl class="method">
<dt id="promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidue">
<code class="descname">ConstructFrameResidue</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidue" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>.
This can be useful to mark a region occupied by a ligand. Note, that
there won’t be any parametrization of hbonds in this function. All atoms
of the residue will be represented as carbons and hydrogens are skipped.</p>
@@ -257,7 +246,7 @@ of the residue will be represented as carbons and hydrogens are skipped.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>residue</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>.</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
</ul>
@@ -273,7 +262,7 @@ construct a <a class="reference internal" href="frame.html#promod3.sidechain.Fra
<dl class="method">
<dt id="promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidueHeuristic">
<code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>residue</em>, <em>residue_index</em>, <em>comp_lib</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidueHeuristic" title="Permalink to this definition">¶</a></dt>
-<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+<dd><p>Constructs a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> from a <a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
a heuristic treatment of the atoms based on the passed compounds library.
This is meant to be used as an alternative to <a class="reference internal" href="#promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidue" title="promod3.sidechain.SCWRLRotamerConstructor.ConstructFrameResidue"><code class="xref py py-func docutils literal"><span class="pre">ConstructFrameResidue()</span></code></a>,
which will be called by this function if the residue is not known by the given
@@ -291,10 +280,10 @@ as in the <a class="reference internal" href="rotamer.html#promod3.sidechain.Sid
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>residue</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
+<li><strong>residue</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which all atoms will be taken to
construct a <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a>.</li>
<li><strong>residue_index</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Index this <a class="reference internal" href="frame.html#promod3.sidechain.FrameResidue" title="promod3.sidechain.FrameResidue"><code class="xref py py-class docutils literal"><span class="pre">FrameResidue</span></code></a> belongs to.</li>
-<li><strong>comp_lib</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</li>
+<li><strong>comp_lib</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.CompoundLib</span></code></a>) – OST compound library to use</li>
</ul>
</td>
</tr>
@@ -372,9 +361,6 @@ to be assigned</td>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -382,11 +368,11 @@ to be assigned</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/rotamer_constructor.txt"
diff --git a/doc/html/sidechain/rotamer_id.html b/doc/html/sidechain/rotamer_id.html
index bda098709cdddf59bd795f334d6559be95a71453..e324b292b422c8a57350ef8cfba159adabf832f7 100644
--- a/doc/html/sidechain/rotamer_id.html
+++ b/doc/html/sidechain/rotamer_id.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>RotamerID — ProMod3 1.1.0 documentation</title>
+ <title>RotamerID — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Rotamers" href="rotamer.html" />
<link rel="prev" title="sidechain - Sidechain Modelling" href="index.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -91,7 +93,7 @@ or as <code class="docutils literal"><span class="pre">promod3.sidechain.Rotamer
<div class="section" id="how-can-i-get-an-id">
<h2>How can I get an ID?<a class="headerlink" href="#how-can-i-get-an-id" title="Permalink to this headline">¶</a></h2>
<p>The RotamerID enum can directly be accessed from Python. Two convenient
-functions exist to get RotamerIDs from the <a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
+functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a> enum
or from amino acid three letter codes.</p>
<dl class="method">
<dt id="promod3.sidechain.TLCToRotID">
@@ -116,12 +118,12 @@ exactly the naming convention defined above.</p>
<dd><p>Directly translates <strong>aa</strong> into a RotamerID. Note, that it is not possible
to generate special IDs this way
(e.g. HSD, HSE or the special prolines/cysteins) since they’re simply not
-defined in <a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
+defined in <a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a></p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>aa</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>, XXX if <strong>aa</strong> is invalid.</td>
</tr>
@@ -174,9 +176,6 @@ defined in <a class="reference external" href="http://www.openstructure.org/docs
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -184,11 +183,11 @@ defined in <a class="reference external" href="http://www.openstructure.org/docs
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/rotamer_id.txt"
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index 84f762d5194755fcd32bd35b6e184ba4309fe834..7bfcf345dae719027bd12f4096db2da54f3ca84b 100644
--- a/doc/html/sidechain/rotamer_lib.html
+++ b/doc/html/sidechain/rotamer_lib.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Rotamer Library — ProMod3 1.1.0 documentation</title>
+ <title>Rotamer Library — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="Rotamer Constructor" href="rotamer_constructor.html" />
<link rel="prev" title="Frame" href="frame.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -80,7 +82,7 @@ less machine-dependent).</p>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerLib" title="promod3.sidechain.RotamerLib"><code class="xref py py-class docutils literal"><span class="pre">RotamerLib</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -92,7 +94,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.sidechain.RotamerLib.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLib.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -200,7 +202,7 @@ less machine-dependent).</p>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.BBDepRotamerLib" title="promod3.sidechain.BBDepRotamerLib"><code class="xref py py-class docutils literal"><span class="pre">BBDepRotamerLib</span></code></a></td>
</tr>
<tr class="field-even field"><th class="field-name">Raises:</th><td class="field-body"><a class="reference external" href="https://docs.python.org/2.7/library/exceptions.html#exceptions.RuntimeError" title="(in Python v2.7)"><code class="xref py py-exc docutils literal"><span class="pre">RuntimeError</span></code></a> if file cannot be opened or if
-file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a> for details).</td>
+file cannot be parsed (see <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a> for details).</td>
</tr>
</tbody>
</table>
@@ -212,7 +214,7 @@ file cannot be parsed (see <a class="reference internal" href="../portableIO.htm
<dt id="promod3.sidechain.BBDepRotamerLib.SavePortable">
<code class="descname">SavePortable</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.BBDepRotamerLib.SavePortable" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves a raw / portable binary representation. Use portable files for
-distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span>here</span></a>
+distribution and convert locally to raw files. See <a class="reference internal" href="../portableIO.html#portableio"><span class="std std-ref">here</span></a>
for details.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
@@ -438,7 +440,7 @@ standard deviations are NaN.</p>
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a></td>
</tr>
@@ -462,7 +464,7 @@ are NaN.</p>
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>res</strong> (<a class="reference external" href="http://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.6.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/dev/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.7.1)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li>
<li><strong>id</strong> (<a class="reference internal" href="rotamer_id.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – The identity of the returned <a class="reference internal" href="#promod3.sidechain.RotamerLibEntry" title="promod3.sidechain.RotamerLibEntry"><code class="xref py py-class docutils literal"><span class="pre">RotamerLibEntry</span></code></a></li>
</ul>
</td>
@@ -640,9 +642,6 @@ considered similar</li>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -650,11 +649,11 @@ considered similar</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/rotamer_lib.txt"
diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
index 115320995a81dc0ba9270cb4f10ab83b5c8e2759..569714780b9983a1a1ad56afc95d30978e7b9a21 100644
--- a/doc/html/sidechain/subrotamer_optimizer.html
+++ b/doc/html/sidechain/subrotamer_optimizer.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Subrotamer Optimization — ProMod3 1.1.0 documentation</title>
+ <title>Subrotamer Optimization — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,16 +23,18 @@
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="../index.html" />
<link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="next" title="scoring - Loop Scoring" href="../scoring/index.html" />
<link rel="prev" title="Loading Rotamer Libraries" href="loading.html" />
+ <link rel="stylesheet" href="../_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -116,9 +118,6 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -126,11 +125,11 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="../_sources/sidechain/subrotamer_optimizer.txt"
diff --git a/doc/html/users.html b/doc/html/users.html
index 2a206b56c716fc91b19016a617ef5596bbb76efc..cbda6deb9b452b831f78abc83db49bf749632748 100644
--- a/doc/html/users.html
+++ b/doc/html/users.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Documentation For Users — ProMod3 1.1.0 documentation</title>
+ <title>Documentation For Users — ProMod3 1.2.0 documentation</title>
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '1.1.0',
+ VERSION: '1.2.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -23,15 +23,17 @@
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
- <link rel="top" title="ProMod3 1.1.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 1.2.0 documentation" href="index.html" />
<link rel="next" title="Getting Started" href="gettingstarted.html" />
<link rel="prev" title="Welcome To ProMod3’s Documentation!" href="index.html" />
+ <link rel="stylesheet" href="_static/custom.css" type="text/css" />
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
+ <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
</head>
- <body role="document">
+ <body role="document">
+
<div class="document">
<div class="documentwrapper">
@@ -88,6 +90,7 @@ scripts using the functionality of this library.</p>
<li class="toctree-l2"><a class="reference internal" href="scoring/backbone_score_env.html">Backbone Score Environment</a></li>
<li class="toctree-l2"><a class="reference internal" href="scoring/backbone_scorers.html">Backbone Scorers</a></li>
<li class="toctree-l2"><a class="reference internal" href="scoring/all_atom_scorers.html">All Atom Scorers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="scoring/other_scoring_functions.html">Other Scoring Functions</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="loop/index.html"><code class="docutils literal"><span class="pre">loop</span></code> - Loop Handling</a><ul>
@@ -104,6 +107,7 @@ scripts using the functionality of this library.</p>
<li class="toctree-l2"><a class="reference internal" href="core/helper.html"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/geometry.html">Geometry functions</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/runtime_profiling.html">Runtime profiling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="core/graph_minimizer.html">Graph Minimizer</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
@@ -140,9 +144,6 @@ scripts using the functionality of this library.</p>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
@@ -150,11 +151,11 @@ scripts using the functionality of this library.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2017, ProMod3 authors.
+ ©2018, ProMod3 authors.
|
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.6</a>
+ Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
+ & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.8</a>
|
<a href="_sources/users.txt"
diff --git a/doc/tests/data/port_str_db.dat b/doc/tests/data/port_str_db.dat
index 5c183190ce902c88a35cc99fb5e4fd69a71ef62f..a861977c6a974dd2a15929b9f5c71415d57901d3 100644
Binary files a/doc/tests/data/port_str_db.dat and b/doc/tests/data/port_str_db.dat differ
diff --git a/doc/tests/scripts/loop_frag_db.py b/doc/tests/scripts/loop_frag_db.py
index c1489985dbb9d51bbea02cf9f41ea9075a1f0556..0efd8226859dbfc115f5973d3d456b6e1b88bfed 100644
--- a/doc/tests/scripts/loop_frag_db.py
+++ b/doc/tests/scripts/loop_frag_db.py
@@ -31,4 +31,4 @@ fragment_infos = frag_db.SearchDB(n_stem, c_stem, 5)
for i,f_i in enumerate(fragment_infos):
bb_list = structure_db.GetBackboneList(n_stem, c_stem,
f_i, frag_seq)
- io.SavePDB(bb_list.ToEntity(), str(i) + ".pdb")
\ No newline at end of file
+ io.SavePDB(bb_list.ToEntity(), str(i) + ".pdb")
diff --git a/doc/tests/scripts/loop_structure_db.py b/doc/tests/scripts/loop_structure_db.py
index 65e87c37a572d47a7fc126082f04e07353cf81a6..e8aca38a2d3b101be4a486209203f62116caf01b 100644
--- a/doc/tests/scripts/loop_structure_db.py
+++ b/doc/tests/scripts/loop_structure_db.py
@@ -1,74 +1,89 @@
from promod3 import loop
-from ost import io
+from ost import io, seq
import os
-# we also need the external tools dssp and msms, you have to make
-# sure that they are somewhere in your PATH
-from ost.bindings import dssp
-from ost.bindings import msms
+# StructureDB where all data get extracted
+structure_db_one = loop.StructureDB(loop.StructureDBDataType.All)
-structure_db = loop.StructureDB()
+# StructureDB where we only have the default data
+# (positions and sequence) plus residue depths and dihedrals.
+# In order to pass the required flags, we use a bitwise or.
+structure_db_two = loop.StructureDB(
+ loop.StructureDBDataType.ResidueDepths |
+ loop.StructureDBDataType.Dihedrals)
-# lets fill in some structures. It gets assumed, that all required
-# data lies in the following directories
+# Lets fill in some structures. It gets assumed, that all required
+# data lies in the following directories.
structure_dir = "data"
prof_dir = "data"
-# the first 4 letters are suposed to be the pdb id, and the last one
-# the corresponding chain name. The naming of the files in the
-# directories is e.g. 1CRN.pdb for the structure and 1CRNA.hhm for
-# the profile. Please note, that the structure can contain several
-# chains, whereas the hhm file is only for that specific chain.
-ids = ["1CRNA", "1AKIA"]
+# The naming of the files in the directories is e.g. 1CRN.pdb for
+# the structure and 1CRNA.hhm for the profile. Please note,
+# that the structure can contain several chains, whereas the hhm
+# file is only for that specific chain.
+structure_ids = ["1CRN", "1AKI"]
+chain_names = ["A", "A"]
-for i in ids:
+for s_id, ch_name in zip(structure_ids, chain_names):
- pdb_id = i[:4]
- chain_id = i[4]
+ # Join together the data paths.
+ structure_path = os.path.join(structure_dir, s_id + ".pdb")
+ prof_path = os.path.join(prof_dir, s_id + ch_name + ".hhm")
- # join together the data paths
- structure_path = os.path.join(structure_dir, pdb_id + ".pdb")
- prof_path = os.path.join(prof_dir, pdb_id + chain_id + ".hhm")
-
- # let's load the structure
+ # Let's load the structure.
structure = io.LoadPDB(structure_path).Select("peptide=True")
- single_chain_structure = structure.Select("cname=" + chain_id)
- # and the according profile in hhm format
+ # And the according profile in hhm format.
prof = io.LoadSequenceProfile(prof_path)
- # we run dssp in a way, that the secondary structure, as well as
- # the solvent accessibily gets assigned
- dssp.AssignDSSP(structure, extract_burial_status=True)
+ # For simplicity we use as SEQRES the sequence from the profile.
+ # In this case the numbering of the structures already matches.
+ seqres = seq.CreateSequence(ch_name, prof.sequence)
- # as a final step we need the surface as calculated by msms
- surf = msms.CalculateSurface(structure)[0]
+ # Add the stuff to the first StructureDB
+ structure_db_one.AddCoordinates(s_id, ch_name, structure,
+ seqres, prof)
- # let's add it! Please note, that we calculated solvent
- # accessiblity / secondary structure and surface on the full
- # structure but only add one of the chains.
- structure_db.AddCoordinates(pdb_id, chain_id,
- single_chain_structure.chains[0],
- surf, prof)
+ # Add the stuff to the second StructureDB,
+ # No profile required here...
+ structure_db_two.AddCoordinates(s_id, ch_name, structure,
+ seqres)
-# we now have two structures in the database...
+
+# We now have two structures in both databases...
# Please note, that there is no profile derived from structures
-# assigned yet. To demonstrate, we use our small db to derive
-# profiles.
-src_db = structure_db
-# In practice you might want to use the default StructureDB instead:
-# src_db = loop.LoadStructureDB()
+# assigned yet to structure_db_one, the memory is only allocated
+# and set to zero. In structure_db_two, there'll never be stored a
+# structure profile as we did not initialize it accordingly.
+# However, we can still use its coordinates and residue depths to
+# generate profiles!
+# To demonstrate, we use our structure_db_two to derive profiles
+# and set them in structure_db_one.
+
+for i in range(structure_db_one.GetNumCoords()):
-for i in range(structure_db.GetNumCoords()):
# get the CoordInfo for chain with index i
- coord_info = structure_db.GetCoordInfo(i)
+ coord_info = structure_db_one.GetCoordInfo(i)
+
# define a fragment, that covers the full length
frag_info = loop.FragmentInfo(i, 0, coord_info.size)
- # generate a profile based on the structural data in the src_db
- prof = src_db.GenerateStructureProfile(structure_db, frag_info)
+
+ # extract all required information
+ sequence = structure_db_one.GetSequence(frag_info)
+ bb_list = structure_db_one.GetBackboneList(frag_info, sequence)
+ res_depths = structure_db_one.GetResidueDepths(frag_info)
+
+ # generate structure profiles based on structure_db_two
+ prof = structure_db_two.GenerateStructureProfile(bb_list,
+ res_depths)
# and add it to the previously created structure_db
- structure_db.SetStructureProfile(i, prof)
+ structure_db_one.SetStructureProfile(i, prof)
-# That's it! Let's save it down...
-structure_db.Save("my_db.dat")
+# That's it! Let's save both databases down.
+# structure_db_two will use much less memory, as it contains less data.
+# Sidenote: We're saving the portable version. If you intent to use
+# your database only on one system, the Save / Load functions should
+# be preferred, as the loading will be much faster.
+structure_db_one.SavePortable("my_db_one.dat")
+structure_db_two.SavePortable("my_db_two.dat")
diff --git a/doc/tests/scripts/modelling_loop_candidates.py b/doc/tests/scripts/modelling_loop_candidates.py
index 7c351c224f05541004af964c30cbab8deb99a670..60d4abeb8836fd3e035c877bfe1c09982958fa67 100644
--- a/doc/tests/scripts/modelling_loop_candidates.py
+++ b/doc/tests/scripts/modelling_loop_candidates.py
@@ -40,7 +40,7 @@ scorer.AttachEnvironment(score_env)
# the scorer can then be used on the LoopCandidates object to
# calculate desired scores (here: cbeta & clash, start resnum = 24)
bb_scores = modelling.ScoreContainer()
-loop_candidates.CalculateBackboneScores(bb_scores, scorer,
+loop_candidates.CalculateBackboneScores(bb_scores, scorer, score_env,
["cbeta", "clash"], 24)
# we finally perform a weighted linear combination of the scores,
# pick the best one, insert it into our structure and save it
diff --git a/doc/tests/scripts/modelling_loop_scoring.py b/doc/tests/scripts/modelling_loop_scoring.py
index a3b97a71fa295692176887c0c09d2b26248f2f39..b6456842b3765897d54c6fd9bb5060a142604291 100644
--- a/doc/tests/scripts/modelling_loop_scoring.py
+++ b/doc/tests/scripts/modelling_loop_scoring.py
@@ -64,8 +64,7 @@ candidates.CalculateSequenceProfileScores(all_scores, structure_db,
candidates.CalculateStructureProfileScores(all_scores, structure_db,
prof, start_idx)
# add backbone scores
-scorer = mhandle.backbone_scorer
-candidates.CalculateBackboneScores(all_scores, scorer, start_resnum)
+candidates.CalculateBackboneScores(all_scores, mhandle, start_resnum)
# add all atom scores
candidates.CalculateAllAtomScores(all_scores, mhandle, start_resnum)
diff --git a/doc/tests/scripts/modelling_monte_carlo.py b/doc/tests/scripts/modelling_monte_carlo.py
index 1ba67afd737052b0cfb7becd7b09026cef786f47..b3d7d07b76016f7f9f3746a5ea683a4dd9630165 100644
--- a/doc/tests/scripts/modelling_monte_carlo.py
+++ b/doc/tests/scripts/modelling_monte_carlo.py
@@ -32,7 +32,8 @@ scorer.AttachEnvironment(score_env)
weights = dict()
weights["cbeta"] = 10.0
weights["clash"] = 0.1
-mc_scorer = modelling.LinearScorer(scorer, start_resnum,
+mc_scorer = modelling.LinearScorer(scorer, score_env,
+ start_resnum, terminal_len,
chain_index, weights)
# setup mc_cooler
diff --git a/doc/tests/scripts/scoring_main.py b/doc/tests/scripts/scoring_main.py
index 827ac2908250392428b24bcc50e8a90a680b6e4a..a5bb94771e369e18b2f14720e4c312689386e566 100644
--- a/doc/tests/scripts/scoring_main.py
+++ b/doc/tests/scripts/scoring_main.py
@@ -15,13 +15,8 @@ clash_scorer.AttachEnvironment(score_env)
cbeta_scorer = scoring.LoadCBetaScorer()
cbeta_scorer.AttachEnvironment(score_env)
-# get backbone list to be scored
-# (here extracted from the structure, but it could be anything)
-ev = ent.Select("rnum >= 23 and rnum <= 30")
-bb_seq = ''.join([r.one_letter_code for r in ev.residues])
-bb_res = [r.handle for r in ev.residues]
-bb_list = loop.BackboneList(bb_seq, bb_res)
-
-# score it (note that 23 is the starting res. num.)
-print "Clash-Score", clash_scorer.CalculateScore(bb_list, 23)
-print "CBeta-Score", cbeta_scorer.CalculateScore(bb_list, 23)
+# calculate scores for 10 residues starting at residue number 23.
+# all required structural information comes from the environment
+# that can evolve as the modelling proceeds.
+print "Clash-Score", clash_scorer.CalculateScore(23, 10)
+print "CBeta-Score", cbeta_scorer.CalculateScore(23, 10)
diff --git a/doc/tests/scripts/sidechain_steps.py b/doc/tests/scripts/sidechain_steps.py
index bf1a3866356d84db21819df5fa63218a41575b58..aa903d2477f57fcdaee574060afddb3b6c4a013e 100644
--- a/doc/tests/scripts/sidechain_steps.py
+++ b/doc/tests/scripts/sidechain_steps.py
@@ -6,8 +6,8 @@ prot = io.LoadPDB('data/1CRN.pdb')
# load rotamer library
library = sidechain.LoadDunbrackLib()
# we need a rotamer constructor to create any rotamers or
-# frame residues
-rot_constructor = sidechain.SCWRLRotamerConstructor()
+# frame residues
+rot_constructor = sidechain.SCWRLRotamerConstructor(False)
# create new entity from protein only containing the amino acids
prot = mol.CreateEntityFromView(prot.Select("peptide=true"), True)
diff --git a/doc/tests/test_doctests.py b/doc/tests/test_doctests.py
index 533148559befc5dc1d2fd23e01fcea2c4a2d962d..bd9d89a001f8f883e1804a08bf7dd3d48dbbf009 100644
--- a/doc/tests/test_doctests.py
+++ b/doc/tests/test_doctests.py
@@ -204,31 +204,14 @@ class DocTests(unittest.TestCase):
os.remove('randomized_fragment.pdb')
def testLoopStructureDB(self):
- # check binaries
- binaries_found = True
- try:
- # same check used in OST
- settings.Locate(['dsspcmbi','dssp','mkdssp'],
- env_name='DSSP_EXECUTABLE')
- except settings.FileNotFound:
- print 'dssp binary is missing. Please install it and make it ' + \
- 'available in your PATH to execute test testLoopStructureDB.'
- binaries_found = False
- try:
- # same check used in OST
- settings.Locate('msms')
- except settings.FileNotFound:
- print 'msms binary is missing. Please install it and make it ' + \
- 'available in your PATH to execute test testLoopStructureDB.'
- binaries_found = False
- if not binaries_found:
- return
# run it
self.checkPMRun('loop_structure_db.py', [], 0)
# check that result exists and is readable
- loop.StructureDB.Load('my_db.dat')
+ loop.StructureDB.LoadPortable('my_db_one.dat')
+ loop.StructureDB.LoadPortable('my_db_two.dat')
# clean up
- os.remove('my_db.dat')
+ os.remove('my_db_one.dat')
+ os.remove('my_db_two.dat')
def testLoopFragDB(self):
# run it
@@ -248,7 +231,7 @@ class DocTests(unittest.TestCase):
self.assertEqual(len(out_lines), 101)
# NOTE: this last output depends on the structure-db!
self.assertEqual(out_lines[-1].strip(),
- 'Fraction of fragments below 3A: 0.48')
+ 'Fraction of fragments below 3A: 0.47')
# check that result exists and is readable
loop.FraggerMap.LoadBB('frag_map.dat')
# clean up
diff --git a/extras/data_generation/frag_db/build_frag_db.py b/extras/data_generation/frag_db/build_frag_db.py
index 19602b2f274ac4bd04699dac11c4c89053ceeacf..5faa5ad22d6b209846544ddbc1900aa43e5c7b36 100644
--- a/extras/data_generation/frag_db/build_frag_db.py
+++ b/extras/data_generation/frag_db/build_frag_db.py
@@ -16,5 +16,5 @@ for i in range(3,15):
fragdb.AddFragments(i,max_pairwise_rmsd,structure_db)
fragdb.PrintStatistics()
-fragdb.Save('frag_db.dat')
+fragdb.SavePortable('frag_db.dat')
diff --git a/extras/data_generation/structure_db/README b/extras/data_generation/structure_db/README
index ed5115ddf021c6095061af6b05ae971248816da0..f86fa19e8c37a82083e61ecc780679ff606a4dbb 100644
--- a/extras/data_generation/structure_db/README
+++ b/extras/data_generation/structure_db/README
@@ -9,6 +9,8 @@ Steps to obtain a structural database:
from PISCES: http://dunbrack.fccc.edu/PISCES.php
The get_data_from_smtl.py script directly reads in such a file and produces
the input for the second step in StructureDB generation.
+ BUT: THE CHAIN NAMING WILL BE THE ONE AS IN THE SMTL, IT DOESN'T RELATE
+ ANYMORE TO THE PDB NAMING!
2. Build an initial database: use build_structure_db.py with input generated
in step one.
@@ -20,9 +22,12 @@ BUT BE AWARE, THE ACCORDING FREQUENCIES IN THE DATABASE WILL BE SET TO 0.0!
The script calculates the structure profiles for a subset of the
sequences in the desired StructureDB and is intended for parallelization
-4. Parallelize step 3: use submit_structure_profile_calculations.py
- This script uses the SGE submission on BC2 and you might have to
- adapt for your system
+4. Parallelize step 3: use prepare_slurm_submission_structure_profiles.py
+ This script generates a submission script and a batch command file
+ that you can submit with sbatch structure_profile_generation_array.sh.
+ This is intended to be used with the SLURM submission system.
+ IMPORTANT: there are many paths to adapt on top of
+ prepare_slurm_submission_structure_profiles.py
5. Assign the structure profiles generated in step 3 and 4 to the
initial database generated in step 2:
@@ -31,10 +36,9 @@ BUT BE AWARE, THE ACCORDING FREQUENCIES IN THE DATABASE WILL BE SET TO 0.0!
To qualitatively reproduce the default StructuralDB in ProMod3, you first
perform step 1 and 2 with a non redundant set of protein structures as
-defined by PISCES with around 25000 chains (e.g. seq id threshold: 90,
-resolution threshold: 2.2).
+defined by PISCES with around 20000 chains (e.g. seq id threshold: 60,
+resolution threshold: 2.5).
Repeat step 1 and 2 with a smaller PISCES list (5000-6000 entries,
-e.g. seq id threshold: 25 , resolution threshold: 1.8).
+e.g. seq id threshold: 20 , resolution threshold: 2.0).
The first database serves as default StructureDB and the second db as
the source db for the structural profiles generated in steps 3-5.
-
diff --git a/extras/data_generation/structure_db/assign_structure_profiles.py b/extras/data_generation/structure_db/assign_structure_profiles.py
index 64029be3aedf16222f622dd102fd8c664b5295c5..2c14c44087fbd2a84be740c1f626565cfae81dd4 100644
--- a/extras/data_generation/structure_db/assign_structure_profiles.py
+++ b/extras/data_generation/structure_db/assign_structure_profiles.py
@@ -1,49 +1,50 @@
import os
from promod3 import loop
-
+from ost import seq
# Path to StructureDB to which you want to assign the profile information.
# (relative to current working directory!)
-db_path = "structure_db.dat"
+db_path = "portable_structure_db_60.dat"
# Directory that contains the profile databases (and only profile databases)
# as generated by the create_structure_profiles.py script.
# (relative to current working directory)
-profile_dir = "profile_dbs"
+profile_dir = "structure_profile_dbs"
# path to store the StructureDB with assigned_profiles
# (relative to current working directory!)
-db_out_path = "structure_db_with_structure_profiles.dat"
-
+db_out_path = "portable_structure_db_60_with_structure_profiles.dat"
-structure_db = loop.StructureDB.Load(db_path)
+structure_db = loop.StructureDB.LoadPortable(db_path)
# lets gather all profiles in one ProfileDB
profile_db_files = os.listdir(profile_dir)
-profile_db = ost.seq.ProfileDB()
+profile_db = seq.ProfileDB()
for f in profile_db_files:
db_path = os.path.join(profile_dir, f)
- loaded_db = ost.seq.ProfileDB.Load(db_path)
+ loaded_db = seq.ProfileDB.Load(db_path)
entry_names = loaded_db.GetNames()
for name in entry_names:
profile_db.AddProfile(name, loaded_db.GetProfile(name))
- print name
# Assign the profiles
for coord_idx in range(structure_db.GetNumCoords()):
coord_info = structure_db.GetCoordInfo(coord_idx)
- entry_id = coord_info.pdb_id
+
+ entry_id = coord_info.id
+ entry_chain_name = coord_info.chain_name
+ full_id = '_'.join([entry_id, entry_chain_name])
structure_profile = None
try:
- structure_profile = profile_db.GetProfile(entry_id)
+ structure_profile = profile_db.GetProfile(full_id)
except:
- print "Could not find structure profile for ", entry_id, " skip..."
+ print "Could not find structure profile for ", full_id, " skip..."
continue
structure_db.SetStructureProfile(coord_idx, structure_profile)
# DONE!
-structure_db.Save(db_out_path)
+structure_db.SavePortable(db_out_path)
diff --git a/extras/data_generation/structure_db/build_structure_db.py b/extras/data_generation/structure_db/build_structure_db.py
index 409f67b34a8f775ad00db032a1f963282936e447..450899c4e2d2f9e95ee001cbaf19f6e2032543e5 100644
--- a/extras/data_generation/structure_db/build_structure_db.py
+++ b/extras/data_generation/structure_db/build_structure_db.py
@@ -2,115 +2,14 @@ from promod3 import loop
import os
import traceback
from ost import io
-from ost.bindings import msms
-from ost.mol.alg import AssignSecStruct
-from ost.mol.alg import Accessibility
-
-###############
-# SCROLL DOWN #
-###############
-
-bb_atoms = ["N","CA","C","O","CB"]
-
-parent_residues = dict()
-parent_residues["MSE"] = "MET"
-parent_residues["CSX"] = "CYS"
-parent_residues["FP9"] = "PRO"
-parent_residues["HYP"] = "PRO"
-parent_residues["SEP"] = "SER"
-parent_residues["SAH"] = "CYS"
-parent_residues["MLY"] = "LYS"
-parent_residues["NLE"] = "LEU"
-parent_residues["ABA"] = "ALA"
-parent_residues["SLZ"] = "LYS"
-parent_residues["KCX"] = "LYS"
-parent_residues["OCS"] = "CYS"
-parent_residues["HIC"] = "HIS"
-parent_residues["TPO"] = "THR"
-parent_residues["CME"] = "CYS"
-parent_residues["ALY"] = "LYS"
-parent_residues["SAM"] = "MET"
-parent_residues["MEN"] = "ASN"
-parent_residues["LLP"] = "LYS"
-parent_residues["CSD"] = "ALA"
-parent_residues["PCA"] = "PRO"
-parent_residues["SCY"] = "CYS"
-parent_residues["CSO"] = "CYS"
-parent_residues["PHD"] = "ASP"
-parent_residues["SLZ"] = "LYS"
-parent_residues["TYS"] = "TYR"
-parent_residues["CAS"] = "CYS"
-parent_residues["TRQ"] = "TRP"
-parent_residues["DPR"] = "PRO"
-parent_residues["CSW"] = "CYS"
-parent_residues["CAF"] = "CYS"
-parent_residues["NIY"] = "TYR"
-parent_residues["LYZ"] = "LYS"
-parent_residues["SME"] = "MET"
-parent_residues["CSS"] = "CYS"
-parent_residues["MLZ"] = "LYS"
-parent_residues["DAH"] = "PHE"
-parent_residues["MSO"] = "MET"
-parent_residues["PHI"] = "PHE"
-parent_residues["TYI"] = "TYR"
-parent_residues["GLX"] = "GLU" #could also be GLN
-parent_residues["OMT"] = "MET"
-parent_residues["CSU"] = "CYS"
-parent_residues["HZP"] = "PRO"
-parent_residues["SEC"] = "CYS"
-parent_residues["DPN"] = "PHE"
-parent_residues["NEP"] = "HIS"
-parent_residues["HIP"] = "HIS"
-parent_residues["DGL"] = "GLU"
-
-one_letter_codes = dict()
-one_letter_codes["ALA"] = 'A'
-one_letter_codes["ARG"] = 'R'
-one_letter_codes["HIS"] = 'H'
-one_letter_codes["LYS"] = 'K'
-one_letter_codes["ASP"] = 'D'
-one_letter_codes["GLU"] = 'E'
-one_letter_codes["SER"] = 'S'
-one_letter_codes["THR"] = 'T'
-one_letter_codes["ASN"] = 'N'
-one_letter_codes["GLN"] = 'Q'
-one_letter_codes["CYS"] = 'C'
-one_letter_codes["GLY"] = 'G'
-one_letter_codes["PRO"] = 'P'
-one_letter_codes["VAL"] = 'V'
-one_letter_codes["ILE"] = 'I'
-one_letter_codes["LEU"] = 'L'
-one_letter_codes["MET"] = 'M'
-one_letter_codes["PHE"] = 'F'
-one_letter_codes["TYR"] = 'Y'
-one_letter_codes["TRP"] = 'W'
-
-def Clean(prot):
- ed = prot.handle.EditXCS()
-
- for r_view in prot.residues:
- if r_view.GetName() in parent_residues:
- r = r_view.handle
- ed.RenameResidue(r,parent_residues[r.GetName()])
- r.SetOneLetterCode(one_letter_codes[r.GetName()])
-
- atoms_to_delete = list()
-
- for a in r.atoms:
- if a.GetName() not in bb_atoms:
- atoms_to_delete.append(a)
- else:
- a.is_hetatom=False
-
-
- for a in atoms_to_delete:
- ed.DeleteAtom(a)
-
-
+from ost import seq
+from ost import mol
+from ost import conop
# This script generates a StructureDB using a list of nonredundant pdb
-# files. All pdb files get cleaned using some basic heuristics.
-# please note, that the values for the structure profile in the produced
+# files. All pdb files get cleaned using Molck from openstructure with
+# with settings specified below.
+# Please note, that the values for the structure profile in the produced
# db are only allocated and simply set to zero.
# You therefore need to create an initial db, from which you can create
# these structure profiles and set them in a second step.
@@ -125,7 +24,7 @@ def Clean(prot):
# file generated by get_data_from_smtl.py (or by yourself)
# every line requires to be in the format: pdb_id chain_name
# e.g. 5UZG A
-data = open("data_extracted_from_smtl.txt",'r').readlines()
+data = open("cullpdb_pc60_res2.5_R1.0_d180524_chains25634_data_extracted_from_smtl.txt", 'r').readlines()
# directory containing the structures. naming: pdb_id.pdb
# (pdb_id in upper case!) e.g. 5UZG.pdb
@@ -135,12 +34,22 @@ structure_dir = "structures"
# (pdb_id and chain_id in upper case!) e.g. 5UZGA.hhm
profile_dir = "hmms"
+# molck settings to process the input structures
+molck_settings = mol.alg.MolckSettings()
+molck_settings.rm_unk_atoms = True
+molck_settings.rm_non_std = True
+molck_settings.rm_hyd_atoms = True
+molck_settings.rm_oxt_atoms = True
+molck_settings.rm_zero_occ_atoms = True
+molck_settings.map_nonstd_res = True
+molck_settings.assign_elem = True
-path_to_msms_binary = "/scicore/soft/apps/msms/2.6.1-linux-x86_64/msms.x86_64Linux2.2.6.1"
-
+# Assumes that a proper compound lib has been specified when
+# compiling openstructure
+compound_lib = conop.GetDefaultLib()
# Do it!!
-structure_db = loop.StructureDB()
+structure_db = loop.StructureDB(loop.StructureDBDataType.All)
for i,line in enumerate(data):
@@ -149,6 +58,7 @@ for i,line in enumerate(data):
chain_id = split_line[1]
try:
+
print 'processing: ',prot_id,' on line: ',i
prot_path = os.path.join(structure_dir, prot_id+'.pdb')
@@ -161,25 +71,27 @@ for i,line in enumerate(data):
print "Could not find hhm file... skip..."
continue
- prot = io.LoadPDB(prot_path).Select('peptide=true')
+ # load and clean full structure
+ prot = io.LoadPDB(prot_path)
+ mol.alg.Molck(prot, compound_lib, molck_settings)
+
+ # we're only interested in the peptide chains...
+ prot = prot.Select("peptide=true")
+
+ # get profile and seqres
hmm = io.LoadSequenceProfile(hhm_path)
+ raw_seqres = hmm.sequence
+ seqres = seq.CreateSequence("seqres", raw_seqres)
- Clean(prot)
- AssignSecStruct(prot)
- Accessibility(prot, algorithm=mol.alg.AccessibilityAlgorithm.DSSP)
- surf = msms.CalculateSurface(prot, msms_exe=path_to_msms_binary)[0]
- prot_single_chain = prot.Select("cname="+chain_id)
- idx = structure_db.AddCoordinates(prot_id, chain_id,
- prot_single_chain.chains[0], surf, hmm,
- solvent_accessibility_string="asaAbs")
-
-
+ # add it
+ structure_db.AddCoordinates(prot_id, chain_id,
+ prot, seqres, hmm)
+
except:
traceback.print_exc()
structure_db.PrintStatistics()
-structure_db.Save('structure_db.dat')
-
+structure_db.SavePortable('portable_structure_db_60.dat')
diff --git a/extras/data_generation/structure_db/create_structure_profiles.py b/extras/data_generation/structure_db/create_structure_profiles.py
index ec227549785f97790208abaa3764af16eb06ea6c..a0e335925a4ed4fa5ced2e07a44bd0b379da4bb8 100644
--- a/extras/data_generation/structure_db/create_structure_profiles.py
+++ b/extras/data_generation/structure_db/create_structure_profiles.py
@@ -3,6 +3,7 @@ import sys
from promod3 import loop
from ost import seq
import time
+import traceback
if len(sys.argv) != 6:
@@ -47,14 +48,30 @@ profile_db = seq.ProfileDB()
for i in range(start,end):
print "processing chain with idx", i
- # generate fragment info object
- coord_info = structure_db.GetCoordInfo(i)
- fragment_info = loop.FragmentInfo(i,0,coord_info.size)
-
- # generate the structure profile given the source StructureDB
- profile = structure_db.GenerateStructureProfile(structure_db_source, fragment_info)
- profile_db.AddProfile(coord_info.pdb_id, profile)
+ try:
+ # generate fragment info object
+ coord_info = structure_db.GetCoordInfo(i)
+ fragment_info = loop.FragmentInfo(i,0,coord_info.size)
+ sequence = structure_db.GetSequence(fragment_info)
+ bb_list = structure_db.GetBackboneList(fragment_info, sequence)
+ residue_depths = structure_db.GetResidueDepths(fragment_info)
+ print "id: ", coord_info.id
+ print "chain_name: ", coord_info.chain_name
+ print "sequence length: ", len(sequence)
+
+ # generate the structure profile given the source StructureDB
+ start = time.time()
+ profile = structure_db_source.GenerateStructureProfile(bb_list, residue_depths)
+ end = time.time()
+
+ print "it took: ", end-start
+
+ profile_db.AddProfile('_'.join([coord_info.id, coord_info.chain_name]), profile)
+
+ except:
+ traceback.print_exc()
+ print "failed to create structure profile... skip..."
profile_db.Save(profile_db_out_path)
diff --git a/extras/data_generation/structure_db/get_data_from_smtl.py b/extras/data_generation/structure_db/get_data_from_smtl.py
index a881e5206502bd07fe11234d0162d7e4dc274fa7..7965046a728bd55260ab275073d7449ce7147db7 100644
--- a/extras/data_generation/structure_db/get_data_from_smtl.py
+++ b/extras/data_generation/structure_db/get_data_from_smtl.py
@@ -15,7 +15,7 @@ from sm import smtl
# 2. Fetch the data manually from the PDB and obtain the profiles with
# the hh-suite available at: https://github.com/soedinglab/hh-suite.
-pisces_path = "cullpdb_pc20_res1.8_R0.25_d170820_chains4892"
+pisces_path = "cullpdb_pc20_res2.0_R0.25_d180524_chains6670"
smtl_path = "/scicore/data/databases/SMTL/"
profile_out_dir = "hmms"
@@ -29,13 +29,11 @@ pisces_data = open(pisces_path).readlines()
# in here we store pdb id and chain name relative to the SMTL
fetched_structures = list()
-
if not os.path.exists(profile_out_dir):
os.makedirs(profile_out_dir)
if not os.path.exists(structure_out_dir):
os.makedirs(structure_out_dir)
-
for i,line in enumerate(pisces_data[1:]):
prot_id = line[:4]
@@ -76,8 +74,8 @@ for i,line in enumerate(pisces_data[1:]):
structure = ch.structure
profile_path = tpl_lib.ProfileForTemplate(unique_name)
- profile_out_path = os.path.join(profile_out_dir, prot_id+ch.name+".hhm")
- structure_out_path = os.path.join(structure_out_dir, prot_id+".pdb")
+ profile_out_path = os.path.join(profile_out_dir, prot_id + ch.name + ".hhm")
+ structure_out_path = os.path.join(structure_out_dir, prot_id + ".pdb")
# copy over the profile
os.system(' '.join(["cp", profile_path, profile_out_path]))
@@ -98,7 +96,7 @@ for i,line in enumerate(pisces_data[1:]):
-outfile = open("data_extracted_from_smtl.txt",'w')
+outfile = open(pisces_path + "_data_extracted_from_smtl.txt",'w')
outfile.write('\n'.join([(x[0] + ' ' + x[1]) for x in fetched_structures]))
outfile.close()
diff --git a/extras/data_generation/structure_db/prepare_slurm_submission_structure_profiles.py b/extras/data_generation/structure_db/prepare_slurm_submission_structure_profiles.py
new file mode 100644
index 0000000000000000000000000000000000000000..d982a468161a2ccfbcceb994961f4f7e706f543d
--- /dev/null
+++ b/extras/data_generation/structure_db/prepare_slurm_submission_structure_profiles.py
@@ -0,0 +1,57 @@
+from promod3 import loop
+import os
+
+profiles_per_job = 60
+structure_db_path = "/scicore/home/schwede/studga00/data/promod3_databases/final_shit/structure_db_60.dat"
+source_structure_db_path = "/scicore/home/schwede/studga00/data/promod3_databases/final_shit/structure_db_20.dat"
+profile_db_out_dir = "/scicore/home/schwede/studga00/data/promod3_databases/final_shit/structure_profile_dbs"
+awesome_script = "/scicore/home/schwede/studga00/data/promod3_databases/final_shit/create_structure_profiles.py"
+
+
+structure_db = loop.StructureDB.Load(structure_db_path)
+n_entries = structure_db.GetNumCoords()
+
+from_idx = 0
+to_idx = profiles_per_job
+
+n_jobs = int(n_entries / profiles_per_job) + 1
+
+commands = list()
+
+for job_idx in range(n_jobs):
+
+ current_cmd = list()
+ current_cmd.append("pm")
+ current_cmd.append(awesome_script)
+ current_cmd.append(structure_db_path)
+ current_cmd.append(source_structure_db_path)
+ current_cmd.append(str(from_idx))
+ current_cmd.append(str(to_idx))
+ current_cmd.append(os.path.join(profile_db_out_dir, str(job_idx)+".dat"))
+
+ commands.append(' '.join(current_cmd))
+
+ from_idx = min(n_entries - 1, from_idx + profiles_per_job)
+ to_idx = min(n_entries, to_idx + profiles_per_job)
+
+outfile = open("structure_profile_generation.cmd", 'w')
+outfile.write('\n'.join(commands))
+outfile.close()
+
+stuff_to_write = list()
+stuff_to_write.append("#!/bin/bash")
+stuff_to_write.append("#SBATCH --job-name=structure_scoring_array")
+stuff_to_write.append("#SBATCH --time=06:00:00")
+stuff_to_write.append("#SBATCH --output=%s"%(os.path.join("stdout", "%A_%a.out")))
+stuff_to_write.append("#SBATCH --mem=8G")
+stuff_to_write.append("#SBATCH --array=1-%i"%(len(commands)))
+stuff_to_write.append("source /scicore/home/schwede/studga00/data/promod3_databases/final_shit/setup_bc2_centos7")
+stuff_to_write.append("SEEDFILE=%s"%(os.path.join(os.getcwd(), "structure_profile_generation.cmd")))
+stuff_to_write.append("SEED=$(sed -n ${SLURM_ARRAY_TASK_ID}p $SEEDFILE)")
+stuff_to_write.append("eval $SEED")
+
+outfile = open("structure_profile_generation_array.sh", 'w')
+outfile.write('\n'.join(stuff_to_write))
+outfile.close()
+
+
diff --git a/extras/data_generation/structure_db/submit_structure_profile_calculations.py b/extras/data_generation/structure_db/submit_structure_profile_calculations.py
deleted file mode 100644
index 87f26a5f99cd2df34a38958f6a5f8acaf54a7fd2..0000000000000000000000000000000000000000
--- a/extras/data_generation/structure_db/submit_structure_profile_calculations.py
+++ /dev/null
@@ -1,115 +0,0 @@
-import os, math
-from promod3 import loop
-
-# path to StructureDB for which you want to calculate the profiles:
-# (relative to current working directory!)
-structure_db_path = "structure_db.dat"
-
-# path to StructureDB from which you extract the structural information
-# if the StructureDB above is very large, you might want to give it a smaller
-# database here to limit CPU time. A database with around 5000 chains should
-# be sufficient
-# (relative to current working directory!)
-structure_db_source_path = "structure_db.dat"
-
-# the profiles that get generated end up here:
-# (relative to current working directory!)
-out_dir = "profile_dbs"
-
-# number of jobs
-num_jobs = 100
-
-# all stdout, stderr and submission_script files will go here
-# (relative to current working directory!)
-submission_workspace = "submission_workspace"
-
-
-# path to the pm bash script
-# Once we have the latest and greatest ProMod3 module, this should not
-# be necessary anymore and we can simply call pm
-pm_path = "/scicore/home/schwede/studga00/prog/promod3_dev/build/stage/bin/pm"
-
-
-# This is stuff relevant for the submission script
-max_runtime = "13:00:00"
-membycore = "3G"
-my_email = "gabriel.studer@unibas.ch"
-
-# we only need ost and promod3 as soon as they're released...
-required_modules = ["Boost/1.53.0-goolf-1.4.10-Python-2.7.5",
- "Python/2.7.5-goolf-1.4.10",
- "OpenMM/7.1.1-goolf-1.4.10-Python-2.7.5"]
-
-# they won't be necessary anymore as soon as there are ost
-# and promod3 modules
-ost_python_path = "/scicore/home/schwede/studga00/prog/ost_dev/build/stage/lib64/python2.7/site-packages"
-promod_python_path = "/scicore/home/schwede/studga00/prog/promod3_dev/build/stage/lib64/python2.7/site-packages"
-
-
-#################################################################
-# NO EDITING BELOW THIS POINT (EXCEPT ON DIFFERENT SYSTEMS ;) ) #
-#################################################################
-
-if not os.path.exists(submission_workspace):
- os.makedirs(submission_workspace)
-
-if not os.path.exists(out_dir):
- os.makedirs(out_dir)
-
-structure_db = loop.StructureDB.Load(structure_db_path)
-num_coords = structure_db.GetNumCoords()
-chunk_size = math.ceil(float(num_coords ) / num_jobs)
-current_start = 0
-current_end = chunk_size
-
-for job_idx in range(num_jobs):
-
- start = current_start
- end = current_end
- if end > num_coords:
- end = num_coords
-
- # we estimate the chunk size with a ceil => we might get away with even
- # less jobs...
- if start >= end:
- break
-
- start = int(start)
- end = int(end)
-
- current_start += chunk_size
- current_end += chunk_size
-
- cmd = [pm_path, \
- os.path.join(os.getcwd(),"create_structure_profiles.py"), \
- os.path.join(os.getcwd(),structure_db_path), \
- os.path.join(os.getcwd(),structure_db_source_path), \
- str(start), str(end), \
- os.path.join(os.getcwd(), out_dir, str(job_idx)+".dat")]
-
- stdout_path = os.path.join(os.getcwd(), submission_workspace, str(job_idx) + ".stdout")
- stderr_path = os.path.join(os.getcwd(), submission_workspace, str(job_idx) + ".stderr")
-
- content = list()
- content.append("#!/bin/bash")
- content.append("#$ -o " + stdout_path)
- content.append("#$ -e " + stderr_path)
- content.append("#$ -l runtime=" + max_runtime)
- content.append("#$ -l membycore=" + membycore)
- content.append("#$ -m as -M " + my_email)
-
- for module in required_modules:
- content.append("ml " + module)
-
- content.append("export PYTHONPATH=" + ost_python_path + ":PYTHONPATH")
- content.append("export PYTHONPATH=" + promod_python_path + ":PYTHONPATH")
- content.append(' '.join(cmd))
-
- s_script_path = os.path.join(submission_workspace, "sub_"+str(job_idx)+".sh")
- outfile = open(s_script_path,'w')
- outfile.write('\n'.join(content))
- outfile.close()
-
- # FIRE!!!
- os.system("qsub "+ s_script_path)
-
diff --git a/extras/data_generation/torsion_sampler/train_torsion_sampler.py b/extras/data_generation/torsion_sampler/train_torsion_sampler.py
index 4bba5cc57f66b86ac3f04bfcca8021065e29600c..1c6eb9d809068664075f554c9aa8a1dde93db2f1 100644
--- a/extras/data_generation/torsion_sampler/train_torsion_sampler.py
+++ b/extras/data_generation/torsion_sampler/train_torsion_sampler.py
@@ -1,40 +1,40 @@
from promod3 import loop
+from ost import mol
import os
import pickle
import traceback
-from ost.bindings import dssp
-#Tested group definitions are:
-# 1. simple_group_definitions.txt
-# 2. solis_group_definitions.txt
+# Tested group definitions are:
+# 1. simple_group_definitions.txt
+# 2. solis_group_definitions.txt
#
-#The first group definition file is taken from:
+# The first group definition file is taken from:
#
-#R. J. Read, P. D. Adams, W. B. Arendall, A. T. Brunger, P. Em-
-#sley, R. P. Joosten, G. J. Kleywegt, E. B. Krissinel, T. Lutteke,
-#Z. Otwinowski, A. Perrakis, J. S. Richardson, W. H. Sheffler, J. L.
-#Smith, I. J. Tickle, G. Vriend, and P. H. Zwart. A new genera-
-#tion of crystallographic validation tools for the protein data bank.
-#Structure, Oct 2011.
+# R. J. Read, P. D. Adams, W. B. Arendall, A. T. Brunger, P. Em-
+# sley, R. P. Joosten, G. J. Kleywegt, E. B. Krissinel, T. Lutteke,
+# Z. Otwinowski, A. Perrakis, J. S. Richardson, W. H. Sheffler, J. L.
+# Smith, I. J. Tickle, G. Vriend, and P. H. Zwart. A new genera-
+# tion of crystallographic validation tools for the protein data bank.
+# Structure, Oct 2011.
#
-#The latter from:
+# The latter from:
#
-#A. D. Solis and S. Rackovsky. Improvement of statistical poten-
-#tials and threading score functions using information maximiza-
-#tion. Proteins, Mar 2006.
+# A. D. Solis and S. Rackovsky. Improvement of statistical poten-
+# tials and threading score functions using information maximiza-
+# tion. Proteins, Mar 2006.
#
#
-#The file containing the prot data has been pulled from:
-#http://dunbrack.fccc.edu/PISCES.php
+# The file containing the prot data has been pulled from:
+# http://dunbrack.fccc.edu/PISCES.php
#
-#To finally train the torsion samplers using this information
-#you have to get the pdb structure files from somewhere and dump
-#them into the structure_dir defined below.
-#Their name must be in the format pdb_id + chain_id
-#e.g. 1AKEA.pdb
+# To finally train the torsion samplers using this information
+# you have to get the pdb structure files from somewhere and dump
+# them into the structure_dir defined below.
+# Their name must be in the format pdb_id + chain_id
+# e.g. 1AKEA.pdb
group_definition_file = "solis_group_definitions.txt"
-structure_dir = "/home/schdaude/workspace/promod_tests/structures"
+structure_dir = "/home/schdaude/workspace/promod_test/structures"
prot_data = open('cullpdb_pc50_res2.5_R1.0_d140401_chains19001','r').readlines()
@@ -43,58 +43,51 @@ group_data = open(group_definition_file,'r')
for line in group_data:
group_definitions.append(line.strip())
-#initialize one sampler being trained with all data
-#and three secondary structure dependent samplers
+# initialize one sampler being trained with all data
+# and three secondary structure dependent samplers
sampler = loop.TorsionSampler(group_definitions, 72,0)
coil_sampler = loop.TorsionSampler(group_definitions, 72,0)
helix_sampler = loop.TorsionSampler(group_definitions,72,0)
sheet_sampler = loop.TorsionSampler(group_definitions,72,0)
-#Internally, the TorsionHandles get used to extract the
-#phi/psi dihedrals. We have to make sure, that they're really
-#assigned when loading a structure
+# Internally, the TorsionHandles get used to extract the
+# phi/psi dihedrals. We have to make sure, that they're really
+# assigned when loading a structure
proc = conop.HeuristicProcessor(assign_torsions=True)
prof = io.IOProfile(dialect='PDB', fault_tolerant=False,
quack_mode=False, processor=proc)
for i,line in enumerate(prot_data[1:]):
- prot_id = line[:4]
- chain_id = line[4]
- try:
- print 'processing: ',prot_id,' on line: ',i
-
- prot = io.LoadPDB(os.path.join(structure_dir,prot_id+chain_id+'.pdb'), profile=prof).Select('peptide=true and cname='+chain_id)
-
- dssp.AssignDSSP(prot)
-
- for r in prot.residues:
- if r.GetSecStructure().IsHelical():
- r.SetIntProp('ss',0)
- continue
- if r.GetSecStructure().IsExtended():
- r.SetIntProp('ss',1)
- continue
- r.SetIntProp('ss',2)
-
- helix_selection = prot.Select('grss=0')
- extended_selection = prot.Select('grss=1')
- coil_selection = prot.Select('grss=2')
-
-
+ prot_id = line[:4]
+ chain_id = line[4]
try:
- sampler.ExtractStatistics(prot)
- helix_sampler.ExtractStatistics(helix_selection)
- coil_sampler.ExtractStatistics(coil_selection)
- sheet_sampler.ExtractStatistics(extended_selection)
+ print 'processing: ',prot_id,' on line: ',i
+ prot = io.LoadPDB(os.path.join(structure_dir,prot_id+chain_id+'.pdb'),
+ profile=prof).Select('peptide=true and cname='+chain_id)
+ mol.alg.AssignSecStruct(prot)
+ for r in prot.residues:
+ if r.GetSecStructure().IsHelical():
+ r.SetIntProp('ss',0)
+ continue
+ if r.GetSecStructure().IsExtended():
+ r.SetIntProp('ss',1)
+ continue
+ r.SetIntProp('ss',2)
+ helix_selection = prot.Select('grss=0')
+ extended_selection = prot.Select('grss=1')
+ coil_selection = prot.Select('grss=2')
+ try:
+ sampler.ExtractStatistics(prot)
+ helix_sampler.ExtractStatistics(helix_selection)
+ coil_sampler.ExtractStatistics(coil_selection)
+ sheet_sampler.ExtractStatistics(extended_selection)
+ except:
+ traceback.print_exc()
except:
- traceback.print_exc()
- except:
- traceback.print_exc()
+ traceback.print_exc()
sampler.Save('torsion_sampler.dat')
helix_sampler.Save('torsion_sampler_helical.dat')
sheet_sampler.Save('torsion_sampler_extended.dat')
coil_sampler.Save('torsion_sampler_coil.dat')
-
-
diff --git a/extras/sanity_checks/Makefile b/extras/sanity_checks/Makefile
index c3bba635362ed6e67810b0a9368c371c2b38ebbf..454cab058d2dafb2d214cbdc1dc5f96382581e81 100644
--- a/extras/sanity_checks/Makefile
+++ b/extras/sanity_checks/Makefile
@@ -26,7 +26,7 @@ INCLUDES = -I$(OST_ROOT)/include -I$(PROMOD3_ROOT)/include
LIB_DIRS = -L$(OST_ROOT)/lib64 -L$(PROMOD3_ROOT)/lib64
LIBS = -lpromod3_core -lpromod3_loop -lpromod3_modelling -lpromod3_sidechain
LIBS += -lost_io -lost_mol -lost_seq -lost_seq_alg -lost_mol_alg -lost_conop
-LIBS += -lost_base -lost_geom -lost_mol_mm
+LIBS += -lost_base -lost_geom -lost_mol_mm -lboost_system
# add rpath to find shared objects (req. gcc)
LDFLAGS += "-Wl,-rpath,$(PROMOD3_ROOT)/lib64:$(OST_ROOT)/lib64"
diff --git a/extras/sanity_checks/run_pipeline.py b/extras/sanity_checks/run_pipeline.py
index a1ebbc51571006b94eed4f5e1be19b6883d1da78..4fd77a97db72a32b82ede9b5a164b121cf69f1a7 100644
--- a/extras/sanity_checks/run_pipeline.py
+++ b/extras/sanity_checks/run_pipeline.py
@@ -1,6 +1,5 @@
import ost
-from ost import io
-from ost.bindings import dssp
+from ost import io, mol
from promod3 import modelling
import time
@@ -11,7 +10,7 @@ ost.PushVerbosityLevel(3)
aln = io.LoadAlignment("aln.fasta")
template = io.LoadPDB("template.pdb")
# add sec. structure
-dssp.AssignDSSP(template)
+mol.alg.AssignSecStruct(template)
# get raw model
aln.AttachView(1,template.Select('peptide=true'))
mhandle = modelling.BuildRawModel(aln)
diff --git a/extras/scoring_weight_training/generate_bft_chunks.py b/extras/scoring_weight_training/generate_bft_chunks.py
index 835e0368e05dd637bb16720c8080c24b7c8ff102..c31ca52f887e7e6704e7a053a67d2ef4102cf17f 100644
--- a/extras/scoring_weight_training/generate_bft_chunks.py
+++ b/extras/scoring_weight_training/generate_bft_chunks.py
@@ -130,7 +130,7 @@ def GetLoopData(lc):
start_res_num = start_idx + 1
for key in bb_scorers:
score_container = modelling.ScoreContainer()
- lc.CalculateBackboneScores(score_container, bb_scorer, [key], start_res_num)
+ lc.CalculateBackboneScores(score_container, bb_scorer, bb_score_env, [key], start_res_num)
lc_data[key] = score_container.Get(key)
##########################################################
diff --git a/extras/scoring_weight_training/generate_bft_testset.py b/extras/scoring_weight_training/generate_bft_testset.py
index 5dfefe5f42561e7c64dbfd278045a84f7ae2004c..d7fc423f3eba8c0bb8b908ed2bd9268def37a135 100644
--- a/extras/scoring_weight_training/generate_bft_testset.py
+++ b/extras/scoring_weight_training/generate_bft_testset.py
@@ -16,7 +16,7 @@ min_coord_size = 50 # min. size for StructureDB entry to be considered
terminal_res_to_skip = 2 # first and last x residues are never chosen for loop
num_chains = 4000 # get x random chains from structure DB
num_loops_per_len = 5000 # number of loops to pick for each loop length
-loop_range = range(3,13) # range of loop lengths (uniformly distributed)
+loop_range = range(3,15) # range of loop lengths (uniformly distributed)
random.seed(42) # fixed seed for reproducibilty
out_fragments = "fragments.json" # full path!
diff --git a/loop/data/portable_frag_db.dat b/loop/data/portable_frag_db.dat
index 802c3651567e94c49ffa483cab3827049869c141..f612b3cd9f7ae1d878363545027ea4158565b71e 100644
Binary files a/loop/data/portable_frag_db.dat and b/loop/data/portable_frag_db.dat differ
diff --git a/loop/data/portable_structure_db.dat b/loop/data/portable_structure_db.dat
index 73ab352c929d9c0c693b57f4a8da568c833d8cb5..0498195c094fbc0dae623c42903b5c91c5990a2c 100644
Binary files a/loop/data/portable_structure_db.dat and b/loop/data/portable_structure_db.dat differ
diff --git a/loop/doc/structure_db.rst b/loop/doc/structure_db.rst
index 631811ed79575c01da39b5dba4b94ad6a54729b2..a967d08a3823e6ae0eba26410ba7bdfa313ba358 100644
--- a/loop/doc/structure_db.rst
+++ b/loop/doc/structure_db.rst
@@ -3,30 +3,37 @@ Structural Data
.. currentmodule:: promod3.loop
-The structural database serves as a container for structural backbone
-and profile data. It can be filled with chains of pdb structures with their
-corresponding profiles as they are produced by the HHSuite tools [soding2005]_.
-Structural and profile data get complemented by with additional information.
-Following features get stored on a per residue basis:
-
-* The amino acid one letter code
-* The coordinates of the backbone atoms (N,CA,C,O)
-* The phi/psi dihedral angles
-* The secondary structure state as defined by dssp
-* The solvent accessibility in square Angstrom
-* The residue depth defined as the average distance from all atoms of a
- residue to the closest surface vertex as calculated by msms [sanner1996]_.
- This is a simplified version of the residue depth as discussed in
- [chakravarty1999]_ and gets directly calculated when structural information
- gets added to the StructureDB.
-* The amino acid frequencies as given by an input sequence profile
-* The amino acid frequency derived from structural alignments as described
- in [zhou2005]_ - Since the calculation of such a profile already requires a
- StructureDB, we end up in a hen and egg problem here... When adding
- structural information to the StructureDB, the according memory gets
- just allocated and set to zero. The usage of this information
- is therefore only meaningful if you calculate these profiles
- and manually set them (or load the provided default database).
+The structural database serves as a container for structural backbone and
+sequence data. Custom accessor objects can be implemented that relate
+arbitrary features to structural data. Examples provided by ProMod3 include
+accession using matching stem geometry (see: :class:`FragDB`) or sequence
+features (see: :class:`Fragger`).
+Besides backbone and sequence data, derived features can
+optionally be stored. E.g. sequence profiles or secondary structure information.
+Optional data includes:
+
+ * The phi/psi dihedral angles
+ * The secondary structure state as defined by dssp
+ * The solvent accessibility in square Angstrom
+ * The amino acid frequencies as given by an input sequence profile
+ * The residue depth - The residue depth is defined as the minimum distance of
+ a residue towards any of the exposed residues.
+ Distances are calculated using CB positions (artificially constructed in case
+ of glycine) and exposed is defined as:
+ relative solvent accessibility > 25% and at least one atom being exposed
+ to the OUTER surface. To determine whether an atom is part of that outer
+ surface, the full structure is placed into a 3D grid and a flood fill
+ algorithm is used to determine the atoms of interest.
+ Internal cavities are excluded by using this approach. This is a simplified
+ version of the residue depth as discussed in [chakravarty1999]_ and gets
+ directly calculated when structural information is added to the StructureDB.
+ * The amino acid frequency derived from structural alignments as described
+ in [zhou2005]_ - Since the calculation of such a profile already requires a
+ StructureDB, we end up in a hen and egg problem here... When adding
+ structural information to the StructureDB, the according memory gets
+ just allocated and set to zero. The usage of this information
+ is therefore only meaningful if you calculate these profiles
+ and manually set them (or load the provided default database).
Defining Chains and Fragments
--------------------------------------------------------------------------------
@@ -34,27 +41,45 @@ Defining Chains and Fragments
.. class:: CoordInfo()
The CoordInfo gets automatically generated when new chains are added to
- the structural database. It contains internal information of how
- the according chain is stored in the database.
+ the structural database. It contains internal information of how a
+ connected stretch of residues is stored in the database.
- .. attribute:: pdb_id
+ .. attribute:: id
- A character residue string containing the 4 character pdb_id and the
- 1 character chain_id. (:class:`str`)
+ An id string specified when adding the corresponding stretch to the
+ structure db
+
+ .. attribute:: chain_name
+
+ A chain name string specified when adding the corresponding stretch to the
+ structure db
.. attribute:: offset
- All residues of the added structures are stored in a linear memory layout.
- The offset parameter tells us where it exactly starts. (:class:`int`)
+ All residues of the added stretch are stored in a linear memory layout.
+ The offset parameter tells us where it exactly starts in the global data
+ structure. (:class:`int`)
.. attribute:: size
- The length of the stretch of residues. (:class:`int`)
+ The number of residues in that stretch (:class:`int`)
+
+ .. attribute:: start_resnum
+
+ Residue number of first residue in the added stretch. The residue number
+ is relative to the SEQRES provided in the input profile when adding the
+ stuff to the structure db.
+
+ .. attribute:: shift
+
+ Translation from original coordinates that has been applied before storing
+ structural information in db.
.. class:: FragmentInfo(chain_index, offset, length)
- The FragmentInfo defines a fragment in the structural database.
+ The FragmentInfo defines any fragment in the structural database. If you
+ implement your own accessor object, thats the information you want to store.
:param chain_index: Fills :attr:`chain_index`
@@ -64,17 +89,19 @@ Defining Chains and Fragments
.. attribute:: chain_index
- The index of the chain (defined by :class:`CoordInfo`) in the structure db this particle belongs to. (:class:`int`)
+ The index of the chain (defined by :class:`CoordInfo`) in the structure db
+ this particle belongs to. (:class:`int`)
.. attribute:: offset
- Index of residue in **chain** the fragment starts. (:class:`int`)
+ Index of residue in **chain** the fragment starts. (0-based, :class:`int`)
.. attribute:: length
Length of the fragment (:class:`int`)
+
The Structure Database
--------------------------------------------------------------------------------
@@ -83,18 +110,46 @@ and fill it with content.
.. literalinclude:: ../../../tests/doc/scripts/loop_structure_db.py
-Calculating the structural profiles is highly expensive and heavily depends on
+Calculating the structural profiles is expensive and heavily depends on
the size of the database used as source. If you want to do this for a larger
database, you might want to consider two things:
-1. Use a database of limited size as structural source (something
+1. Use a database of limited size to generate the actual profiles (something
in between 5000 and 10000 nonredundant chains is enough)
2. Use the :class:`ost.seq.ProfileDB` to gather profiles produced from jobs
running in parallel
-.. class:: StructureDB()
- .. staticmethod:: Load(filename, load_frequencies=True)
+.. class:: StructureDBDataType
+
+ The StructureDBDataType enum has to be passed at initialization of a
+ StructureDB in order to define what data you want to store additionally
+ to backbone coordinates and sequence.
+ If you want to store all data possible, use All. If you only want a subset,
+ you can combine some of the datatypes with a bitwise or operation
+ (see example script for StructureDB). One important note:
+ If you enable AAFrequenciesStruct, the actual information is not automatically
+ assigned. Only the according memory is allocated and set to zero, the actual
+ information must be assigned manually (see example script again...).
+
+ All, Dihedrals, SolventAccessibilities, ResidueDepths, DSSP, AAFrequencies,
+ AAFrequenciesStruct
+
+
+.. class:: StructureDB(data_to_store)
+
+ Generates an empty StructureDB that can be filled with content through
+ :func:`AddCoordinates`. The information extracted there is defined by
+ *data_to_store*. Have a look at the :class:`StructureDBDataType`
+ documentation and at the example script...
+
+ :param data_to_store: Specifies what data to store in the database, several
+ flags can be combined with a bitwise or operator.
+ :type data_to_store: :class:`StructureDBDataType`
+
+
+
+ .. staticmethod:: Load(filename)
LoadPortable(filename)
Loads raw binary file generated with :meth:`Save` (optimized for fast
@@ -103,13 +158,6 @@ database, you might want to consider two things:
:param filename: Path to the file from which to load the database.
:type filename: :class:`str`
- :param load_frequencies: If True, the full database including profile
- information for every position gets loaded.
- A database without profiles loads faster and
- requires less memory. But it's not possible
- to add new coordinates or call one of the
- profile dependent functions.
- :type load_frequencies: :class:`bool`
:returns: The loaded data base
:rtype: :class:`StructureDB`
@@ -117,6 +165,7 @@ database, you might want to consider two things:
:raises: :exc:`~exceptions.RuntimeError` if file cannot be opened or if
file cannot be parsed (see :ref:`here <portableIO>` for details).
+
.. method:: Save(filename)
SavePortable(filename)
@@ -127,73 +176,127 @@ database, you might want to consider two things:
:param filename: Path to the file where the database will be saved
:type filename: :class:`str`
- :raises: :exc:`~exceptions.RuntimeError` if file cannot be opened or if
- db has been loaded with load_frequencies=False (enforces only
- complete databases to be saved down)
-
- .. method:: AddCoordinates(pdb_id, chain_name, chain, surf, prof, \
- solvent_accessibility_string="solvent_accessibility")
-
- This method takes a structural chain and searches the longest stretch of
- connected residues containing all necessary backbone atoms. This stretch
- gets then added to the database. Due to technical reasons, The maximal
- extent along one of the base axis cannot exceed 650 A.
- Following features are expected to be set on a per residue level in *chain*:
- The secondary structure (e.g. call :meth:`ost.mol.alg.AssignSecStruct` on the
- full :class:`ost.mol.EntityView` the *chain* belongs to) and
- the solvent accessibility assigned using a float property with name
- *solvent_accessibility_string* as name on a per residue level (e.g. call
- :meth:`ost.mol.alg.Accessibility` on the full :class:`ost.mol.EntityView`
- the chain belongs to and take care to pass the appropriate
- *solvent_accessibility_string*).
-
- :param pdb_id: 4-letter code of the structure the chain belongs to
- :param chain_name: Name of the chain consisting of one letter
- :param chain: The actual chain
- :param surf: A surface describing the solvent accessible surface
- (we advise you to provide a surface estimated with the
- full :class:`ost.mol.EntityView` the *chain* belongs to)
- :param prof: Profile information for this *chain*.
- :param solvent_accessibility_string: Name of float property where the
- solvent accessibilities are stored
- on a per residue basis in *chain*
-
- :type pdb_id: :class:`str`
+ :raises: :exc:`~exceptions.RuntimeError` if file cannot be opened
+
+
+ .. method:: HasData(data_type)
+
+ Checks, whether requested data type is available in the current database.
+
+ :param data_type: Data type to check
+ :type data_type: :class:`StructureDBDataType`
+
+ :returns: Whether the requested datatype is available
+ :rtype: :class:`bool`
+
+
+ .. method:: AddCoordinates(id, chain_name, ent, seqres, prof=None, \
+ only_longest_stretch=True)
+
+ This method takes an entity and adds coordinates and the sequence
+ of one of its chains to the structural database. Additionally, all
+ data as specified at the initialization of the database is extracted
+ fully automatically by considering the full *ent* (e.g. when
+ calculating solvent accessibilities etc.).
+ The only exception is AAFrequencies, where a valid sequence profile
+ is expected in *prof* that has matching sequence with *seqres*
+ All residues in chain with name *chain_name* must have residue numbers
+ that directly relate them to the *seqres* with an indexing scheme
+ starting from one.
+ If this is not the case, an error gets thrown. You might want to
+ consider to use :meth:`ost.seq.Renumber` for proper numbering.
+ Based on consecutive numbering and additionally checking for valid
+ peptide bonds, connected stretches are identified
+ and every added connected stretch gets its own entry with
+ :class:`CoordInfo` as a descriptor.
+ To avoid cluttering the database with many small fragments, the flag:
+ *only_longest_stretch* can be used. Set it to False if all
+ connected stretches of chain with name *chain_name* should be added.
+ There is one final catch you have to consider: Due to the internal
+ lossy data compression for the positions, the extent in x, y and
+ z - direction for every connected stretch is limited to 655A. This should
+ be sufficient for most structures, but stretches exceeding this maximum
+ are discarded. For storing the structural data given these restraints,
+ a translation is applied that gets stored as the *shift* attribute
+ in the according :class:`CoordInfo` object.
+
+ :param id: identifier of the added structure (e.g. pdb id)
+ :param chain_name: Name of the chain in *ent* you want to add
+ :param ent: The full entity that must contain a chain named
+ as specified by *chain_name*.
+ :param seqres: The reference sequence of chain with name *chain_name*
+ :param prof: Profile information for the chain with name
+ *chain_name*. The profile sequence must match *seqres*.
+ :param only_longest_stretch: Flag whether you want to add only the longest
+ connected stretch of residues are all connected
+ stretches of residues
+
+ :type id: :class:`str`
:type chain_name: :class:`str`
- :type chain: :class:`ost.mol.ChainView`
- :type surf: :class:`ost.mol.SurfaceHandle`
+ :type ent: :class:`ost.mol.EntityView`
+ :type seqres: :class:`ost.seq.SequenceHandle`
:type prof: :class:`ost.seq.ProfileHandle`
- :type solvent_accessibility_string: :class:`str`
+ :type only_longest_strech: :class:`bool`
- :returns: DB index of added chain.
- :rtype: :class:`int`
+ :returns: indices of added stretches in db
+ :rtype: :class:`list` of `int`
- :raises: :exc:`~exceptions.RuntimeError` if size of chain is too large,
- when db has been loaded with load_frequencies=False or when the
- ATOMSEQ form the *chain* can't be aligned with the SEQRES from
- the *prof*.
+ :raises: :exc:`~exceptions.RuntimeError` if the residues in chain with
+ name *chain_name* do not match *seqres* given the
+ residue numbers, when AAFrequencies have to to be extracted and
+ the sequence in *prof* does not match the *seqres* or *prof* is
+ invalid.
- .. method:: GetCoordIndex(pdb_id, chain_name)
- :returns: The StructureDB index (in [0, :meth:`GetNumCoords`-1]) of the
- chain of interest, -1 if it cannot be found.
- :rtype: :class:`int`
+ .. method:: RemoveCoordinates(coord_idx)
+
+ Removes coordinates at specified location and all its associated data. This
+ has an impact on the offset values of all :class:`CoordInfo` objects
+ that are internally stored afterwards and on the actual coord indices
+ (all shifted by one). So make sure that you adapt your data access
+ accordingly!
+
+ :param coord_idx: Specifies coordinates to be removed
+ :type coord_idx: :class:`int`
- :param pdb_id: 4-letter code of the structure the chain belongs to
- :param chain_name: Name of the chain consisting of one letter
+ :raises: :exc:`~exceptions.RuntimeError` if *coord_idx* is invalid
+
+ .. method:: GetCoordIdx(id, chain_name)
+
+ :returns: The StructureDB indices (in [0, :meth:`GetNumCoords`-1]) of
+ of all coords (connected stretches) with matching
+ *id* / *chain_name*.
+ :rtype: :class:`list` of :class:`int`
+
+ :param id: Identifier given when calling :meth:`AddCoordinates`
+ :param chain_name: Name of chain given when calling :meth:`AddCoordinates`
:type pdb_id: :class:`str`
:type chain_name: :class:`str`
+
.. method:: GetCoordInfo(idx)
- :returns: Object describing the chain with index *idx*.
+ :returns: Object describing the stretch of connected residues with
+ index *idx*.
:rtype: :class:`CoordInfo`
:param idx: The StructureDB index (in [0, :meth:`GetNumCoords`-1])
:type idx: :class:`int`
+ .. method:: GetNumCoords()
+
+ :returns: Number of connected stretches of residues that have been added to
+ the database.
+ :rtype: :class:`int`
+
+
+ .. method:: PrintStatistics()
+
+ Prints out some information about the db.
+
+
.. method:: GetBackboneList(fragment, sequence)
GetBackboneList(n_stem, c_stem, fragment, sequence)
@@ -212,20 +315,9 @@ database, you might want to consider two things:
:type c_stem: :class:`ost.mol.ResidueHandle`
:raises: :exc:`~exceptions.RuntimeError` if fragment is invalid (happens
- if the fragment does not fully fit into one of the chains in the
- database) or if *sequence* contains a one letter code which is not
- one of the 20 default amino acids.
-
-
- .. method:: GetNumCoords()
-
- :returns: Number of chains that have been added to the database.
- :rtype: :class:`int`
-
-
- .. method:: PrintStatistics()
-
- Prints out some information about the db.
+ if the fragment does not fully fit into one of the connected
+ stretches in the database) or if *sequence* contains a one letter
+ code which is not one of the 20 default amino acids.
.. method:: GetSequence(fragment)
@@ -238,7 +330,7 @@ database, you might want to consider two things:
:raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
+ connected stretches of residues in the database.
.. method:: GetDSSPStates(fragment)
@@ -249,9 +341,10 @@ database, you might want to consider two things:
:param fragment: Fragment definition from which to extract the states.
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain dssp
+ data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
+ connected stretches of residues in the database.
.. method:: GetDihedralAngles(fragment)
@@ -262,9 +355,11 @@ database, you might want to consider two things:
:param fragment: Fragment definition from which to extract the dihedrals.
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ dihedral angle data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
+ connected stretches of residues in the database.
+
.. method:: GetResidueDepths(fragment)
@@ -275,9 +370,11 @@ database, you might want to consider two things:
depths
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ residue depth data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
+ connected stretches of residues in the database.
+
.. method:: GetSolventAccessibilitites(fragment)
@@ -289,9 +386,11 @@ database, you might want to consider two things:
accessibilities
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ solvent accessibility data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
+ connected stretches of residues in the database.
+
.. method:: GetSequenceProfile(fragment)
@@ -304,10 +403,12 @@ database, you might want to consider two things:
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
+ :raises: :exc:`~exceptions.RuntimeError` if database does not cotain
+ aa frequency data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
-
+ connected stretches of residues in the database.
+
+
.. method:: GetStructureProfile(fragment)
:returns: The structure profile for the residues defined by *fragment* with
@@ -319,44 +420,50 @@ database, you might want to consider two things:
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ aa frequencies struct data or if fragment is invalid. This is
the case when the fragment does not fully fit into one of the
- chains in the database.
+ connected stretches of residues in the database.
- .. method:: GenerateStructureProfile(other_db, fragment)
- Takes the CA positions and residue depths for *fragment* defined from
- *other_db* to calculate a structure profile using the full internal
- structural data of this database with their corresponding residue depths.
+ .. method:: GenerateStructureProfile(bb_list, residue_depths)
- :param fragment: Fragment definition from *other_db*.
- :type fragment: :class:`FragmentInfo`
- :param other_db: Structural database from which we extract CA positions and
- residue depths for *fragment*.
- :type other_db: :class:`StructureDB`
+ Calculates a structure profile for *bb_list* with given *residue_depths*
+ using the full internal data of this StructureDB.
+
+ :param bb_list: Positions for which to calculate the structural profile
+ :type bb_list: :class:`BackboneList`
+ :param residue_depths: The residue depth for each residue in *bb_list*
+ as you would extract it from any StructureDB
+ containing that data.
+ :type residue_depths: :class:`list` of :class:`float`
:returns: The structure profile for the input with the BLOSUM62
probabilities as NULL model.
:rtype: :class:`ost.seq.ProfileHandle`
:raises: :exc:`~exceptions.RuntimeError` if *bb_list* and
- *residue_depths* differ in size or when their size is 0
+ *residue_depths* differ in size, when their size is 0
+ or when database does not contain aa frequencies struct data.
- .. method:: SetStructureProfile(chain_idx, prof)
+
+ .. method:: SetStructureProfile(coord_idx, prof)
Takes the *prof* and sets the corresponding StructureProfile
- frequencies in entry with *chain_idx*
+ frequencies in entry with *coord_idx*
:param prof: Source of profile frequencies
- :param chain_idx: StructureDB index of entry for which to set frequencies
+ :param coord_idx: StructureDB index of entry for which to set frequencies
(in [0, :meth:`GetNumCoords`-1])
:type prof: :class:`ost.seq.ProfileHandle`
- :type chain_idx: :class:`int`
+ :type coord_idx: :class:`int`
+
+ :raises: :exc:`~exceptions.RuntimeError` if *coord_idx* does not match
+ any entry in the db, when the size of the *prof* does not
+ exactly match the size of entry at *coord_idx* or when database
+ does not contain aa frequency struct data.
- :raises: :exc:`~exceptions.RuntimeError` if *chain_idx* does not match
- any entry in the db or when the size of the *prof* does not
- exactly match the size of entry at *chain_idx*
.. method:: GetSubDB(indices)
@@ -437,6 +544,7 @@ This example illustrates how to create a custom FragDB based on a StructureDB:
:return: The bin size
:rtype: :class:`float`
+
.. method:: AddFragments(fragment_length, rmsd_cutoff, structure_db)
Iterates over all fragments of length **fragment_length** in the given structural database and adds them to the fragment database. Fragments will be skipped if there is already a fragment in the database that has an RMSD to the one being added smaller than **rmsd_cutoff**.
@@ -870,7 +978,6 @@ The PsipredPrediction class
.. [soding2005] Söding J (2005). Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.
-.. [sanner1996] Sanner M, Olson AJ, Spehner JC (1996). Reduced Surface: an Efficient Way to Compute Molecular Surfaces. Biopolymers 38 (3): 305-320.
.. [chakravarty1999] Chakravarty S, Varadarajan R (1999). Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7 (7): 723–732.
.. [zhou2005] Zhou H, Zhou Y (2005). Fold Recognition by Combining Sequence Profiles Derived From Evolution and From Depth-Dependent Structural Alignment of Fragments. Proteins 58 (2): 321–328.
.. [Jones1999] Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292: 195-202.
diff --git a/loop/pymod/export_loop_object_loader.cc b/loop/pymod/export_loop_object_loader.cc
index 276690cf9fabed11f24cb20c8ff3c11f16fffeb4..fb6cb09087e4950cb473d4255fd2dc1ad5731ccb 100644
--- a/loop/pymod/export_loop_object_loader.cc
+++ b/loop/pymod/export_loop_object_loader.cc
@@ -12,5 +12,5 @@ void export_LoopObjectLoader() {
(arg("seed")=0));
def("LoadTorsionSamplerCoil", &LoadTorsionSamplerCoil, (arg("seed")=0));
def("LoadFragDB", &LoadFragDB);
- def("LoadStructureDB", &LoadStructureDB, (arg("load_frequencies")=true));
+ def("LoadStructureDB", &LoadStructureDB);
}
diff --git a/loop/pymod/export_structure_db.cc b/loop/pymod/export_structure_db.cc
index 072ae4dd308069e7b304f075fc9515ef05106ab2..954614498a7b99168f1c1598211a7be1e7a86889 100644
--- a/loop/pymod/export_structure_db.cc
+++ b/loop/pymod/export_structure_db.cc
@@ -29,6 +29,16 @@ namespace {
return bb_list;
}
+ boost::python::list WrapGetCoordIdx(StructureDBPtr db,
+ const String& id,
+ const String& chain_name) {
+
+ std::vector<int> indices = db->GetCoordIdx(id, chain_name);
+ boost::python::list return_list;
+ core::AppendVectorToList(indices, return_list);
+ return return_list;
+ }
+
boost::python::list WrapGetDihedralAngles(StructureDBPtr db, FragmentInfo& info){
std::vector<std::pair<Real,Real> > dihedrals = db->GetDihedralAngles(info);
@@ -58,19 +68,30 @@ namespace {
return db->GetSubDB(v_indices);
}
+ ost::seq::ProfileHandlePtr WrapGenerateStructureProfile(StructureDBPtr db,
+ const BackboneList& bb_list,
+ const list& residue_depths) {
+ std::vector<Real> v_residue_depths;
+ core::ConvertListToVector(residue_depths, v_residue_depths);
+ return db->GenerateStructureProfile(bb_list, v_residue_depths);
+ }
+
}
void export_StructureDB(){
- class_<CoordInfo>("CoordInfo", init<>())
- .def_readonly("pdb_id", &CoordInfo::GetFullID)
+ class_<CoordInfo>("CoordInfo", no_init)
+ .def_readonly("id", &CoordInfo::id)
+ .def_readonly("chain_name", &CoordInfo::chain_name)
.def_readonly("offset", &CoordInfo::offset)
.def_readonly("size", &CoordInfo::size)
+ .def_readonly("start_resnum", &CoordInfo::start_resnum)
+ .def_readonly("shift", &CoordInfo::shift)
;
class_<FragmentInfo>
- ("FragmentInfo", init<unsigned short, unsigned short, unsigned short>())
+ ("FragmentInfo", init<unsigned int, unsigned short, unsigned short>())
.def_readwrite("chain_index", &FragmentInfo::chain_index)
.def_readwrite("offset", &FragmentInfo::offset)
.def_readwrite("length", &FragmentInfo::length)
@@ -78,25 +99,40 @@ void export_StructureDB(){
.def(self != self)
;
- class_<StructureDB, boost::noncopyable> ("StructureDB", init<>())
+ enum_<StructureDB::DBDataType>("StructureDBDataType")
+ .value("All", StructureDB::All)
+ .value("Dihedrals", StructureDB::Dihedrals)
+ .value("SolventAccessibilities", StructureDB::SolventAccessibilities)
+ .value("ResidueDepths", StructureDB::ResidueDepths)
+ .value("DSSP", StructureDB::DSSP)
+ .value("AAFrequencies", StructureDB::AAFrequencies)
+ .value("AAFrequenciesStruct", StructureDB::AAFrequenciesStruct)
+ ;
+
+ class_<StructureDB, boost::noncopyable> ("StructureDB", init<int>())
.def("Load", &StructureDB::Load,
- (arg("filename"), arg("load_frequencies")=true))
+ (arg("filename")))
.staticmethod("Load")
.def("Save", &StructureDB::Save, (arg("filename")))
.def("LoadPortable", &StructureDB::LoadPortable, (arg("filename")))
.staticmethod("LoadPortable")
.def("SavePortable", &StructureDB::SavePortable, (arg("filename")))
+ .def("HasData", &StructureDB::HasData, (arg("structure_db_data_type")))
.def("AddCoordinates", &StructureDB::AddCoordinates,
- (arg("pdb_id"), arg("chain_name"),
- arg("chain"), arg("surf"), arg("prof"),
- arg("solvent_accessibility_string")="solvent_accessibility"))
- .def("GetCoordIndex", &StructureDB::GetCoordIndex,
+ (arg("id"), arg("chain_name"),
+ arg("ent"), arg("seqres"),
+ arg("prof")=ost::seq::ProfileHandlePtr(),
+ arg("only_longest_stretch")=true))
+ .def("RemoveCoordinates", &StructureDB::RemoveCoordinates,
+ (arg("coord_idx")))
+ .def("GetCoordIndex", &WrapGetCoordIdx,
(arg("pdb_id"), arg("chain_name")))
.def("GetBackboneList", &wrap_get_bb_list_one,
(arg("fragment"), arg("sequence")))
.def("GetBackboneList", &wrap_get_bb_list_two,
(arg("stem_one"), arg("stem_two"), arg("fragment"), arg("sequence")))
- .def("GetCoordInfo", &StructureDB::GetCoordInfo,(arg("index")))
+ .def("GetCoordInfo", &StructureDB::GetCoordInfo,(arg("index")),
+ return_value_policy<reference_existing_object>())
.def("GetNumCoords", &StructureDB::GetNumCoords)
.def("PrintStatistics", &StructureDB::PrintStatistics)
.def("GetSequence", &StructureDB::GetSequence, (arg("fragment")))
@@ -109,8 +145,9 @@ void export_StructureDB(){
(arg("fragment")))
.def("GetStructureProfile", &StructureDB::GetStructureProfile,
(arg("fragment")))
- .def("GenerateStructureProfile", &StructureDB::GenerateStructureProfile,
- (arg("other_db"), arg("fragment")))
+ .def("GetStartResnum", &StructureDB::GetStartResnum, (arg("fragment")))
+ .def("GenerateStructureProfile", &WrapGenerateStructureProfile,
+ (arg("bb_list"), arg("residue_depths")))
.def("SetStructureProfile", &StructureDB::SetStructureProfile,
(arg("chain_idx"), arg("prof")))
.def("GetSubDB", &WrapGetSubDB,(arg("indices")))
diff --git a/loop/src/CMakeLists.txt b/loop/src/CMakeLists.txt
index 93597f2d68460db36f8f43d3cd474eb02bcc10a6..6c874f584b1f8b29cba7803c056a816c5a0ce365 100644
--- a/loop/src/CMakeLists.txt
+++ b/loop/src/CMakeLists.txt
@@ -19,13 +19,13 @@ set(LOOP_HEADERS
mm_system_creator.hh
paged_array.hh
psipred_prediction.hh
- sec_struct.hh
stem_geom.hh
structure_db.hh
torsion_sampler.hh
ushort_vec.hh
sidechain_atom_rule_lookup.hh
sidechain_atom_constructor.hh
+ structure_db_custom_types.hh
)
set(LOOP_SOURCES
@@ -44,7 +44,6 @@ set(LOOP_SOURCES
loop_object_loader.cc
mm_system_creator.cc
psipred_prediction.cc
- sec_struct.cc
structure_db.cc
torsion_sampler.cc
sidechain_atom_rule_lookup.cc
diff --git a/loop/src/all_atom_env.cc b/loop/src/all_atom_env.cc
index cb12451b065d2c54e89be6532767c138e1daec49..cef7b4eca18ebfd5ada74f84012cfd95807185f2 100644
--- a/loop/src/all_atom_env.cc
+++ b/loop/src/all_atom_env.cc
@@ -76,7 +76,7 @@ void AllAtomEnv::SetInitialEnvironment(const ost::mol::EntityHandle& env) {
const ost::conop::AminoAcid myaa = all_pos_->GetAA(res_idx);
if (myaa != ost::conop::OneLetterCodeToAminoAcid(olc)) {
- String err = "Sequence mismatch when settings loop scorers env! ";
+ String err = "Sequence mismatch when setting loop scorers env! ";
err += j->GetQualifiedName() + " should be a ";
err += ost::conop::AminoAcidToResidueName(myaa);
throw promod3::Error(err);
diff --git a/loop/src/frag_db.cc b/loop/src/frag_db.cc
index e69cf20f6d8930accd32e9a86b7e0c4f6c5fb3a1..73f75b903efc17f72edbf402f63acd58e989ec9c 100644
--- a/loop/src/frag_db.cc
+++ b/loop/src/frag_db.cc
@@ -30,7 +30,7 @@ FragDBPtr FragDB::Load(const String& file_name) {
// header for consistency checks
core::CheckMagicNumber(in_stream);
uint32_t version = core::GetVersionNumber(in_stream);
- if (version > 1) {
+ if (version != 2) {
std::stringstream ss;
ss << "Unsupported file version '" << version << "' in '" << file_name;
throw promod3::Error(ss.str());
@@ -84,7 +84,7 @@ void FragDB::Save(const String& filename) {
// header for consistency checks
core::WriteMagicNumber(out_stream);
- core::WriteVersionNumber(out_stream, 1);
+ core::WriteVersionNumber(out_stream, 2);
// required base types: int, Real, uint, char, unsigned int, unsigned short
// required structs: std::pair<StemPairGeom, BagInfo>, FragmentInfo
typedef FragmentData::BagInfo BI;
@@ -134,7 +134,7 @@ FragDBPtr FragDB::LoadPortable(const String& file_name) {
// header for consistency checks
core::CheckMagicNumber(in_stream);
uint32_t version = core::GetVersionNumber(in_stream);
- if (version > 1) {
+ if (version != 2) {
std::stringstream ss;
ss << "Unsupported file version '" << version << "' in '" << file_name;
throw promod3::Error(ss.str());
@@ -178,7 +178,7 @@ void FragDB::SavePortable(const String& filename) {
// header for consistency checks
core::WriteMagicNumber(out_stream);
- core::WriteVersionNumber(out_stream, 1);
+ core::WriteVersionNumber(out_stream, 2);
// here: only base-type-checks needed (we store Real as float!)
core::WriteTypeSize<int16_t>(out_stream);
core::WriteTypeSize<int32_t>(out_stream);
@@ -242,10 +242,11 @@ void FragDB::AddFragments(uint fragment_length,
//extract all stem information of this chain to create the
//stem geoms later on
+ const PagedArray<PeptideCoords, 65536>& db_coords = structure_db->GetCoords();
stem_coords.clear();
for(uint j = 0; j < size; ++j){
- const Peptide& peptide = structure_db->GetPeptide(offset+j);
- stem_coords.push_back(StemCoordsFromPeptides(peptide,peptide));
+ const PeptideCoords& coords = db_coords[offset + j];
+ stem_coords.push_back(StemCoordPairFromPeptideCoords(coords, coords));
}
//create a sliding window and go over all possible fragments
@@ -280,7 +281,7 @@ void FragDB::SearchDB(const ost::mol::ResidueHandle& n_stem,
uint frag_size, std::vector<FragmentInfo>& fragments,
uint extra_bins) {
- StemCoordPair stems = StemCoordsFromResidues(n_stem, c_stem);
+ StemCoordPair stems = StemCoordPairFromResidues(n_stem, c_stem);
SearchDB(stems, frag_size, fragments, extra_bins);
}
@@ -349,7 +350,7 @@ int FragDB::GetNumFragments(int length) const{
return count;
}
-FragDB::StemCoordPair FragDB::StemCoordsFromResidues(
+FragDB::StemCoordPair FragDB::StemCoordPairFromResidues(
const ost::mol::ResidueHandle& n_res,
const ost::mol::ResidueHandle& c_res) {
@@ -358,19 +359,20 @@ FragDB::StemCoordPair FragDB::StemCoordsFromResidues(
return std::make_pair(n_stem, c_stem);
}
-FragDB::StemCoordPair FragDB::StemCoordsFromPeptides(const Peptide& n_pep,
- const Peptide& c_pep) {
+FragDB::StemCoordPair FragDB::StemCoordPairFromPeptideCoords(
+ const PeptideCoords& n_coords,
+ const PeptideCoords& c_coords) {
core::StemCoords n_stem;
core::StemCoords c_stem;
- n_stem.n_coord = n_pep.coords.n.ToVec3();
- n_stem.ca_coord = n_pep.coords.ca.ToVec3();
- n_stem.c_coord = n_pep.coords.c.ToVec3();
+ n_stem.n_coord = n_coords.n.ToVec3();
+ n_stem.ca_coord = n_coords.ca.ToVec3();
+ n_stem.c_coord = n_coords.c.ToVec3();
- c_stem.n_coord = c_pep.coords.n.ToVec3();
- c_stem.ca_coord = c_pep.coords.ca.ToVec3();
- c_stem.c_coord = c_pep.coords.c.ToVec3();
+ c_stem.n_coord = c_coords.n.ToVec3();
+ c_stem.ca_coord = c_coords.ca.ToVec3();
+ c_stem.c_coord = c_coords.c.ToVec3();
return std::make_pair(n_stem,c_stem);
}
diff --git a/loop/src/frag_db.hh b/loop/src/frag_db.hh
index 4a53521edfb8adfea616d8bdecc45d0a4a9f4627..6bb3134df3e2084734a02dd8b5b27573ffa5b120 100644
--- a/loop/src/frag_db.hh
+++ b/loop/src/frag_db.hh
@@ -106,13 +106,11 @@ private:
std::vector<FragmentInfo>& fragments,
uint extra_bins = 0);
- FragDB(const FragDB& other) { };
+ StemCoordPair StemCoordPairFromResidues(const ost::mol::ResidueHandle& n_res,
+ const ost::mol::ResidueHandle& c_res);
- StemCoordPair StemCoordsFromResidues(const ost::mol::ResidueHandle& n_res,
- const ost::mol::ResidueHandle& c_res);
-
- StemCoordPair StemCoordsFromPeptides(const Peptide& n_pep,
- const Peptide& c_pep);
+ StemCoordPair StemCoordPairFromPeptideCoords(const PeptideCoords& n_coords,
+ const PeptideCoords& c_coords);
std::vector<StemPairGeom> MakeStemPairGeom(const core::StemCoords& n_stem,
const core::StemCoords& c_stem,
diff --git a/loop/src/fragger.cc b/loop/src/fragger.cc
index cf9f39164709b0963955f28b4f3ed41da75573f5..aa6bc18dd72ad8699eddf2493eac9dfc2353ef48 100644
--- a/loop/src/fragger.cc
+++ b/loop/src/fragger.cc
@@ -162,20 +162,6 @@ void Fragger::Fill(StructureDBPtr db, Real max_rmsd, uint num_fragments){
"type to fill Fragger!");
}
- // if there is any profile feature, we have to make sure the
- // db contains frequencies...
- for(std::vector<FraggerScoreType>::iterator i = score_types_.begin();
- i != score_types_.end(); ++i){
- if(*i == SequenceProfile || *i == StructureProfile){
- if(!db->HasFrequencies()){
- std::stringstream ss;
- ss << "You must provide a StructureDB with loaded frequencies ";
- ss << "to apply any profile features in the Fragger!";
- throw promod3::Error(ss.str());
- }
- }
- }
-
this->LinearFill(db, max_rmsd, num_fragments);
}
@@ -498,14 +484,14 @@ void Fragger::FillProfiles(StructureDBPtr db,
break;
}
case SequenceProfile:{
- const PagedArray<AAFreq,4096>& frequencies =
+ const PagedArray<AAFreq, 65536>& frequencies =
db->GetAAFrequencies();
this->GenerateProfileProfile(db, profiles[i], chain_idx, frequencies,
profiles_[i]);
break;
}
case StructureProfile:{
- const PagedArray<AAFreq,4096>& frequencies =
+ const PagedArray<AAFreq, 65536>& frequencies =
db->GetAAStructFrequencies();
this->GenerateProfileProfile(db, profiles[i], chain_idx, frequencies,
profiles_[i]);
@@ -551,7 +537,7 @@ void Fragger::GenerateSeqSimProfile(StructureDBPtr db,
const ost::seq::alg::SubstWeightMatrix& subst) const{
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
- const PagedArray<Peptide,4096>& coords = db->GetCoords();
+ const PagedArray<char, 65536>& full_db_seq = db->GetSeq();
profile.clear();
@@ -562,7 +548,7 @@ void Fragger::GenerateSeqSimProfile(StructureDBPtr db,
String db_seq(chain_size,'X');
uint coord_index = coord_toc[index].offset;
for(uint i = 0; i < chain_size; ++i, ++coord_index){
- db_seq[i] = coords[coord_index].olc;
+ db_seq[i] = full_db_seq[coord_index];
}
Real score = 0.0;
@@ -589,7 +575,7 @@ void Fragger::GenerateSeqIDProfile(StructureDBPtr db,
uint index) const{
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
- const PagedArray<Peptide,4096>& coords = db->GetCoords();
+ const PagedArray<char, 65536>& full_db_seq = db->GetSeq();
profile.clear();
@@ -600,7 +586,7 @@ void Fragger::GenerateSeqIDProfile(StructureDBPtr db,
String db_seq(chain_size,'X');
uint coord_index = coord_toc[index].offset;
for(uint i = 0; i < chain_size; ++i, ++coord_index){
- db_seq[i] = coords[coord_index].olc;
+ db_seq[i] = full_db_seq[coord_index];
}
int matches = 0;
@@ -620,7 +606,7 @@ void Fragger::GenerateSSAgreementProfile(StructureDBPtr db,
const std::vector<int>& confidence) const {
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
- const PagedArray<Peptide,4096>& coords = db->GetCoords();
+ const PagedArray<char, 65536>& full_db_dssp = db->GetDSSP();
profile.clear();
@@ -633,7 +619,7 @@ void Fragger::GenerateSSAgreementProfile(StructureDBPtr db,
uint coord_index = coord_toc[index].offset;
for(uint i = 0; i < chain_size; ++i){
- chain_dssp_states[i] = GetDSSPIdx(coords[coord_index].dssp_state);
+ chain_dssp_states[i] = GetDSSPIdx(full_db_dssp[coord_index]);
++coord_index;
}
@@ -656,7 +642,7 @@ void Fragger::GenerateTorsionProbabilityProfile(StructureDBPtr db,
const std::vector<int>& t_sampler_indices) const {
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
- const PagedArray<Peptide,4096>& coords = db->GetCoords();
+ const PagedArray<DihedralInfo, 65536>& full_db_dihedrals = db->GetDihedrals();
profile.clear();
@@ -669,8 +655,9 @@ void Fragger::GenerateTorsionProbabilityProfile(StructureDBPtr db,
uint coord_idx = coord_toc[index].offset;
for(uint i = 0; i < chain_size; ++i){
- phi_bins[i] = t_sampler[0]->GetAngleBin(coords[coord_idx].dihedrals.GetPhi());
- psi_bins[i] = t_sampler[0]->GetAngleBin(coords[coord_idx].dihedrals.GetPsi());
+ const DihedralInfo& db_dihedrals = full_db_dihedrals[coord_idx];
+ phi_bins[i] = t_sampler[0]->GetAngleBin(db_dihedrals.GetPhi());
+ psi_bins[i] = t_sampler[0]->GetAngleBin(db_dihedrals.GetPsi());
++coord_idx;
}
@@ -690,7 +677,7 @@ void Fragger::GenerateTorsionProbabilityProfile(StructureDBPtr db,
void Fragger::GenerateProfileProfile(StructureDBPtr db,
std::vector<Real>& profile,
uint index,
- const PagedArray<AAFreq,4096>& frequencies,
+ const PagedArray<AAFreq,65536>& frequencies,
short** prof) const {
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
diff --git a/loop/src/fragger.hh b/loop/src/fragger.hh
index 88e2d5e9164f2b6c749239f577afa0e573dd8f04..b109770cc5d2ace6a75d4da6d08e24d8355a8c04 100644
--- a/loop/src/fragger.hh
+++ b/loop/src/fragger.hh
@@ -118,7 +118,7 @@ private:
void GenerateProfileProfile(StructureDBPtr db, std::vector<Real>& profile,
uint index,
- const PagedArray<AAFreq,4096>& frequencies,
+ const PagedArray<AAFreq, 65536>& frequencies,
short** prof) const;
diff --git a/loop/src/idx_handler.cc b/loop/src/idx_handler.cc
index 5cee45a4da30b96e3c0c6e5be5943074290e15db..dfc50c26c159112638e248fde20750fa17ba362c 100644
--- a/loop/src/idx_handler.cc
+++ b/loop/src/idx_handler.cc
@@ -28,12 +28,12 @@ uint IdxHandler::ToIdx(uint resnum, uint chain_idx) const {
if (resnum == 0 || resnum - 1 >= chain_sizes_[chain_idx]) {
throw promod3::Error("Invalid resnum!");
}
-
return chain_start_idx_[chain_idx] + (resnum - 1);
}
std::vector<uint> IdxHandler::ToIdxVector(uint start_resnum, uint num_residues,
uint chain_idx) const {
+
// check/get start index
uint start_idx = ToIdx(start_resnum, chain_idx);
// check size
@@ -84,6 +84,71 @@ void IdxHandler::SetupScoreCalculation(const loop::BackboneList& bb_list,
start_idx, end_idx);
}
+void IdxHandler::SetupScoreCalculation(uint start_resnum, uint num_residues,
+ uint chain_idx, std::vector<uint>& indices,
+ std::vector<bool>& occupied) const {
+
+ indices = this->ToIdxVector(start_resnum, num_residues, chain_idx);
+ occupied.assign(this->GetNumResidues(), false);
+ for(std::vector<uint>::const_iterator i = indices.begin();
+ i != indices.end(); ++i) {
+ occupied[*i] = true;
+ }
+}
+
+void IdxHandler::SetupScoreCalculation(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<uint> >& indices,
+ std::vector<bool>& occupied) const {
+
+ if(start_resnum.size() != num_residues.size()) {
+ throw promod3::Error("Inconsistent input data in Score Setup!");
+ }
+
+ if(start_resnum.size() != chain_idx.size()) {
+ throw promod3::Error("Inconsistent input data in Score Setup!");
+ }
+
+ indices.resize(start_resnum.size());
+ occupied.assign(this->GetNumResidues(), false);
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ indices[i] = this->ToIdxVector(start_resnum[i], num_residues[i],
+ chain_idx[i]);
+ const std::vector<uint>& vec = indices[i];
+ for(std::vector<uint>::const_iterator j = vec.begin();
+ j != vec.end(); ++j) {
+ occupied[*j] = true;
+ }
+ }
+}
+
+void IdxHandler::SetupScoreCalculation(uint start_resnum, uint num_residues,
+ uint chain_idx, std::vector<uint>& indices) const {
+
+ indices = this->ToIdxVector(start_resnum, num_residues, chain_idx);
+}
+
+void IdxHandler::SetupScoreCalculation(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<uint> >& indices) const {
+
+ if(start_resnum.size() != num_residues.size()) {
+ throw promod3::Error("Inconsistent input data in Score Setup!");
+ }
+
+ if(start_resnum.size() != chain_idx.size()) {
+ throw promod3::Error("Inconsistent input data in Score Setup!");
+ }
+
+ indices.resize(start_resnum.size());
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ indices[i] = this->ToIdxVector(start_resnum[i], num_residues[i],
+ chain_idx[i]);
+ }
+}
+
void IdxHandler::SetupScoreCalculation(uint start_resnum, uint num_residues,
uint chain_idx, uint& start_idx,
uint& end_idx) const {
diff --git a/loop/src/idx_handler.hh b/loop/src/idx_handler.hh
index c16463f2f100a626206acdf50b78b480599e1c7b..193520286029bdf138bbd6c738a37405ef905d27 100644
--- a/loop/src/idx_handler.hh
+++ b/loop/src/idx_handler.hh
@@ -57,6 +57,20 @@ public:
uint start_resnum, uint chain_idx,
uint& bb_list_size, uint& start_idx,
uint& end_idx) const;
+ void SetupScoreCalculation(uint start_resnum, uint num_residues,
+ uint chain_idx, std::vector<uint>& indices,
+ std::vector<bool>& occupied) const;
+ void SetupScoreCalculation(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<uint> >& indices,
+ std::vector<bool>& occupied) const;
+ void SetupScoreCalculation(uint start_resnum, uint num_residues,
+ uint chain_idx, std::vector<uint>& indices) const;
+ void SetupScoreCalculation(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<uint> >& indices) const;
void SetupScoreCalculation(uint start_resnum, uint num_residues,
uint chain_idx, uint& start_idx,
uint& end_idx) const;
diff --git a/loop/src/loop_object_loader.cc b/loop/src/loop_object_loader.cc
index 671a0679747c2051d4a328643c0bd655dd34622f..4eeff56860e15a6603312f8fa62104ad1e3f87af 100644
--- a/loop/src/loop_object_loader.cc
+++ b/loop/src/loop_object_loader.cc
@@ -45,11 +45,11 @@ FragDBPtr LoadFragDB() {
return p;
}
-StructureDBPtr LoadStructureDB(bool load_frequencies) {
+StructureDBPtr LoadStructureDB() {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"loop::LoadStructureDB", 2);
String path = GetProMod3BinaryPath("loop_data", "structure_db.dat");
- StructureDBPtr p = StructureDB::Load(path, load_frequencies);
+ StructureDBPtr p = StructureDB::Load(path);
return p;
}
diff --git a/loop/src/loop_object_loader.hh b/loop/src/loop_object_loader.hh
index 66e9d7cca3cce744ff40efa5100ca2e1acea8d64..0b89e68a50ba2f96e453d3a3d1aab52b2fbe6d21 100644
--- a/loop/src/loop_object_loader.hh
+++ b/loop/src/loop_object_loader.hh
@@ -17,7 +17,7 @@ TorsionSamplerPtr LoadTorsionSamplerCoil(uint seed = 0);
FragDBPtr LoadFragDB();
-StructureDBPtr LoadStructureDB(bool load_frequencies = true);
+StructureDBPtr LoadStructureDB();
}} //ns
diff --git a/loop/src/paged_array.hh b/loop/src/paged_array.hh
index fbe20b91d30e2aebcae93dbaad190b2b42f10f6c..3591e2915fb9b3acc07ce9ffd10720860ada420c 100644
--- a/loop/src/paged_array.hh
+++ b/loop/src/paged_array.hh
@@ -61,6 +61,31 @@ public:
{
pages_.clear();
}
+
+ // clears everything in [from, to[ and shifts every datapoint after the specified
+ // range at the location defined by from
+ void ClearRange(uint64_t from, uint64_t to)
+ {
+ if(to <= from) return; // invalid range
+ uint64_t current_size = this->size();
+ if(from >= current_size) return; // nothing to delete
+ if(to > current_size) to = current_size; // from is in the valid range, but
+ // to is too large. Let's just kill
+ // [from, this->size()[
+
+ uint64_t num_elements_to_shift = current_size - to;
+ for(uint64_t i = 0; i < num_elements_to_shift; ++i) {
+ (*this)[from + i] = (*this)[to + i];
+ }
+
+ uint64_t num_elements_deleted = to - from;
+ uint64_t new_size = current_size - num_elements_deleted;
+ uint64_t new_last_element_idx = new_size - 1;
+ uint64_t new_last_page_idx = this->GetPage(new_last_element_idx);
+ pages_.resize(new_last_page_idx + 1);
+ uint64_t offset = this->GetOffset(new_last_element_idx);
+ pages_.back().resize(offset + 1);
+ }
void Write(std::ofstream& out_stream, bool treat_as_pod=true)
{
diff --git a/loop/src/sec_struct.cc b/loop/src/sec_struct.cc
deleted file mode 100644
index 08628dc1a32123c52de047b3ccc32774958d7001..0000000000000000000000000000000000000000
--- a/loop/src/sec_struct.cc
+++ /dev/null
@@ -1,405 +0,0 @@
-#include <promod3/loop/sec_struct.hh>
-
-namespace promod3{ namespace loop{
-
-void RawEstimateSS(const std::vector<geom::Vec3>& ca_positions,
- int start_idx,
- const std::vector<int>& donor_for_one,
- const std::vector<int>& donor_for_two,
- const std::vector<int>& acceptor_for_one,
- const std::vector<int>& acceptor_for_two,
- String& ss_assignment){
-
- int size = ca_positions.size();
-
- if(size != static_cast<int>(donor_for_one.size())){
- throw promod3::Error("Position and donor data are inconsistent for dssp calculation!");
- }
-
- if(size != static_cast<int>(donor_for_two.size())){
- throw promod3::Error("Position and donor data are inconsistent for dssp calculation!");
- }
-
- if(size != static_cast<int>(acceptor_for_one.size())){
- throw promod3::Error("Position and acceptor data are inconsistent for dssp calculation!");
- }
-
- if(size != static_cast<int>(acceptor_for_two.size())){
- throw promod3::Error("Position and acceptor data are inconsistent for dssp calculation!");
- }
-
- if(size < 3){
- throw promod3::Error("Size of input positions are too small!");
- }
-
- ss_assignment.assign(size,'C');
-
- int bends[size];
- int turn_3[size];
- int turn_4[size];
- int turn_5[size];
- int para_bridge[size];
- int antipara_bridge[size];
-
- memset(bends,0,size*sizeof(int));
- memset(turn_3,0,size*sizeof(int));
- memset(turn_4,0,size*sizeof(int));
- memset(turn_5,0,size*sizeof(int));
- memset(para_bridge,0,size*sizeof(int));
- memset(antipara_bridge,0,size*sizeof(int));
-
- //let's first search for the bends, i.e. pieces with high curvature
- Real angle;
- for(int i = 2; i < size-2; ++i){
- angle = geom::Angle(ca_positions[i]-ca_positions[i-2],
- ca_positions[i+2]-ca_positions[i]);
- if(angle > 1.2217) bends[i] = 1;
- }
-
- //let's search for turns
- int three = start_idx + 3;
- int four = start_idx + 4;
- int five = start_idx + 5;
- for(int i = 0; i < size; ++i, ++three, ++four, ++five){
- if(acceptor_for_one[i] == four) turn_4[i] = 1;
- if(acceptor_for_one[i] == three) turn_3[i] = 1;
- if(acceptor_for_one[i] == five) turn_5[i] = 1;
- if(acceptor_for_two[i] == four) turn_4[i] = 1;
- if(acceptor_for_two[i] == three) turn_3[i] = 1;
- if(acceptor_for_two[i] == five) turn_5[i] = 1;
- }
-
- //let's search for antiparallel beta bridges
- for(int i = 0; i < size; ++i){
- if(acceptor_for_one[i] != -1){
- if(acceptor_for_one[i] == donor_for_one[i]) antipara_bridge[i] = 1;
- if(acceptor_for_one[i] == donor_for_two[i]) antipara_bridge[i] = 1;
- }
- if(acceptor_for_two[i] != -1){
- if(acceptor_for_two[i] == donor_for_one[i]) antipara_bridge[i] = 1;
- if(acceptor_for_two[i] == donor_for_two[i]) antipara_bridge[i] = 1;
- }
- }
-
- for(int i = 1; i < size-1; ++i){
- if(donor_for_one[i+1] != -1){
- if(donor_for_one[i+1] + 2 == acceptor_for_one[i-1]) antipara_bridge[i] = 1;
- if(donor_for_one[i+1] + 2 == acceptor_for_two[i-1]) antipara_bridge[i] = 1;
- }
-
- if(donor_for_two[i+1] != -1){
- if(donor_for_two[i+1] + 2 == acceptor_for_one[i-1]) antipara_bridge[i] = 1;
- if(donor_for_two[i+1] + 2 == acceptor_for_two[i-1]) antipara_bridge[i] = 1;
- }
- }
-
- //let's search for parallel beta bridges
- for(int i = 1; i < size-1; ++i){
- if(acceptor_for_one[i-1] != -1){
- if(acceptor_for_one[i-1] == donor_for_one[i+1]) para_bridge[i] = 1;
- if(acceptor_for_one[i-1] == donor_for_two[i+1]) para_bridge[i] = 1;
- }
- if(acceptor_for_two[i-1] != -1){
- if(acceptor_for_two[i-1] == donor_for_one[i+1]) para_bridge[i] = 1;
- if(acceptor_for_two[i-1] == donor_for_two[i+1]) para_bridge[i] = 1;
- }
- }
-
- for(int i = 0; i < size; ++i){
- if(donor_for_one[i] != -1){
- if(donor_for_one[i] + 2 == acceptor_for_one[i]) para_bridge[i] = 1;
- if(donor_for_one[i] + 2 == acceptor_for_two[i]) para_bridge[i] = 1;
- }
-
- if(donor_for_two[i] != -1){
- if(donor_for_two[i] + 2 == acceptor_for_one[i]) para_bridge[i] = 1;
- if(donor_for_two[i] + 2 == acceptor_for_two[i]) para_bridge[i] = 1;
- }
- }
-
- //priority according to the dssp paper is: H,B,E,G,I,T,S
- //we therefore start to assign from lowest to highest priority,
- //potentially overwriting low priority elements
-
- //do S
- for(int i = 0; i < size; ++i){
- if(bends[i]) ss_assignment[i] = 'S';
- }
-
- //do T
- for(int i = 0; i < size - 2; ++i){
- if(turn_3[i]){
- ss_assignment[i+1] = 'T';
- ss_assignment[i+2] = 'T';
- }
- }
-
- for(int i = 0; i < size - 3; ++i){
- if(turn_4[i]){
- ss_assignment[i+1] = 'T';
- ss_assignment[i+2] = 'T';
- ss_assignment[i+3] = 'T';
- }
- }
-
- for(int i = 0; i < size - 4; ++i){
- if(turn_5[i]){
- ss_assignment[i+1] = 'T';
- ss_assignment[i+2] = 'T';
- ss_assignment[i+3] = 'T';
- ss_assignment[i+4] = 'T';
- }
- }
-
- //let's do the helices... we use the bend arrays to fill helices
- //and start with H, we then fill in G if there is no space occupied by H
- //and finally I if there is nothing in that range occupied.
- memset(bends,0,size*sizeof(int));
- for(int i = 1; i < size-4; ++i){
- if(turn_4[i-1] && turn_4[i]){
- bends[i] = 1;
- bends[i+1] = 1;
- bends[i+2] = 1;
- bends[i+3] = 1;
- }
- }
-
- int start;
- int end;
- for(int i = 1; i < size-3; ++i){
- if(turn_3[i-1] && turn_3[i]){
- start = i;
- end = i+3;
- //let's search how long it continues...
- while(true && end < size){
- if(turn_3[end-3] && turn_3[end-2]){
- ++end;
- }
- else break;
- }
- //check, whether there already is something in this range
- bool empty = true;
- for(int j = start; j < end; ++j){
- if(bends[j]){
- empty = false;
- break;
- }
- }
- if(empty){
- //let's fill!
- for(int j = start; j < end; ++j){
- bends[j] = 2;
- }
- }
- }
- }
-
- for(int i = 1; i < size-5; ++i){
- if(turn_5[i-1] && turn_5[i]){
- start = i;
- end = i+5;
- //let's search how long it continues...
- while(true && end < size){
- if(turn_5[end-5] && turn_5[end-4]){
- ++end;
- }
- else break;
- }
- //check, whether there already is something in this range
- bool empty = true;
- for(int j = start; j < end; ++j){
- if(bends[j]){
- empty = false;
- break;
- }
- }
- if(empty){
- //let's fill!
- for(int j = start; j < end; ++j){
- bends[j] = 3;
- }
- }
- }
- }
-
- //do I
- for(int i = 0; i < size; ++i){
- if(bends[i] == 3) ss_assignment[i] = 'I';
- }
-
- //do G
- for(int i = 0; i < size; ++i){
- if(bends[i] == 2) ss_assignment[i] = 'G';
- }
-
- //do E
- if(para_bridge[0]){
- if(para_bridge[1]) ss_assignment[0] = 'E';
- }
- if(antipara_bridge[0]){
- if(antipara_bridge[1]) ss_assignment[0] = 'E';
- }
-
- for(int i = 1; i < size - 1; ++i){
- if(para_bridge[i]){
- if(para_bridge[i-1] || para_bridge[i+1]) ss_assignment[i] = 'E';
- }
- if(antipara_bridge[i]){
- if(antipara_bridge[i-1] || antipara_bridge[i+1]) ss_assignment[i] = 'E';
- }
- }
-
- if(para_bridge[size-1]){
- if(para_bridge[size-2]) ss_assignment[size-1] = 'E';
- }
- if(antipara_bridge[size-1]){
- if(antipara_bridge[size-2]) ss_assignment[size-1] = 'E';
- }
-
- //do B
- if(para_bridge[0]){
- if(!para_bridge[1]) ss_assignment[0] = 'B';
- }
- if(antipara_bridge[0]){
- if(!antipara_bridge[1]) ss_assignment[0] = 'B';
- }
-
- for(int i = 1; i < size-1; ++i){
- if(para_bridge[i]){
- if(!(para_bridge[i-1] || para_bridge[i+1])) ss_assignment[i] = 'B';
- }
- if(antipara_bridge[i]){
- if(!(antipara_bridge[i-1] ||antipara_bridge[i+1])) ss_assignment[i] = 'B';
- }
- }
-
- if(para_bridge[size-1]){
- if(!para_bridge[size-2]) ss_assignment[size-1] = 'B';
- }
- if(antipara_bridge[size-1]){
- if(!antipara_bridge[size-2]) ss_assignment[size-1] = 'B';
- }
-
- //do H
- for(int i = 0; i < size; ++i){
- if(bends[i] == 1) ss_assignment[i] = 'H';
- }
-}
-
-void EstimateSS(const BackboneList& bb_list, String& ss_assignment){
-
- int size = bb_list.size();
-
- if(size == 0){
- throw promod3::Error("Cannot estimate SS with empty BackboneList!");
- }
-
- std::vector<int> donor_for_one(size,-1);
- std::vector<int> donor_for_two(size,-1);
- std::vector<int> acceptor_for_one(size,-1);
- std::vector<int> acceptor_for_two(size,-1);
- std::vector<Real> donor_one_energies(size,std::numeric_limits<Real>::max());
- std::vector<Real> donor_two_energies(size,std::numeric_limits<Real>::max());
- std::vector<Real> acceptor_one_energies(size,std::numeric_limits<Real>::max());
- std::vector<Real> acceptor_two_energies(size,std::numeric_limits<Real>::max());
- std::vector<geom::Vec3> ca_positions(size,geom::Vec3(0,0,0));
- std::vector<geom::Vec3> h_positions(size,geom::Vec3(0,0,0));
-
- //first residue is expected not to be an hbond donor,
- //we don't do anything for the first h_position...
- ca_positions[0] = bb_list.GetCA(0);
-
- geom::Vec3 co_vec;
- for(int i = 1; i < size; ++i){
- ca_positions[i] = bb_list.GetCA(i);
- co_vec = geom::Normalize(bb_list.GetO(i-1) - bb_list.GetC(i-1));
- h_positions[i] = bb_list.GetN(i) - co_vec;
- }
-
- Real e;
- for(int i = 0; i < size-3; ++i){
- for(int j = i+3; j < size; ++j){
- if(geom::Length2(ca_positions[i]-ca_positions[j]) < 81.0){
- //i as acceptor ; j as donor
- if(bb_list.GetOLC(j) != 'P'){
- e = DSSPHBondEnergy(h_positions[j], bb_list.GetN(j),
- bb_list.GetC(i), bb_list.GetO(i));
-
- if(e < -0.5){
- //it is an hbond... let's see, whether it is the best for i as acceptor
- if(e < acceptor_two_energies[i]){
- if(e < acceptor_one_energies[i]){
- acceptor_two_energies[i] = acceptor_one_energies[i];
- acceptor_for_two[i] = acceptor_for_one[i];
- acceptor_one_energies[i] = e;
- acceptor_for_one[i] = j;
- }
- else{
- acceptor_two_energies[i] = e;
- acceptor_for_two[i] = j;
- }
- }
-
- //let's see, whether it is the best for j as donor
- if(e < donor_two_energies[j]){
- if(e < donor_one_energies[j]){
- donor_two_energies[j] = donor_one_energies[j];
- donor_for_two[j] = donor_for_one[j];
- donor_one_energies[j] = e;
- donor_for_one[j] = i;
- }
- else{
- donor_two_energies[j] = e;
- donor_for_two[j] = i;
- }
- }
- }
- }
-
- //i as donor, j as acceptor
- // note, that the first residue is not considered for donor
- // and last element not as acceptor
- if(bb_list.GetOLC(i) != 'P' && i > 0 && j < size-1){
-
- e = DSSPHBondEnergy(h_positions[i], bb_list.GetN(i),
- bb_list.GetC(j), bb_list.GetO(j));
-
- if(e < -0.5){
- //it is an hbond... let's see, whether it is the best for i as donor
- if(e < donor_two_energies[i]){
- if(e < donor_one_energies[i]){
- donor_two_energies[i] = donor_one_energies[i];
- donor_for_two[i] = donor_for_one[i];
- donor_one_energies[i] = e;
- donor_for_one[i] = j;
- }
- else{
- donor_two_energies[i] = e;
- donor_for_two[i] = j;
- }
- }
-
- //let's see, whether it is the best for j as acceptor
- if(e < acceptor_two_energies[j]){
- if(e < acceptor_one_energies[j]){
- acceptor_two_energies[j] = acceptor_one_energies[j];
- acceptor_for_two[j] = acceptor_for_one[j];
- acceptor_one_energies[j] = e;
- acceptor_for_one[j] = i;
- }
- else{
- acceptor_two_energies[j] = e;
- acceptor_for_two[j] = i;
- }
- }
- }
- }
- }
- }
- }
-
- RawEstimateSS(ca_positions, 0, donor_for_one, donor_for_two,
- acceptor_for_one, acceptor_for_two, ss_assignment);
-}
-
-}} //ns
diff --git a/loop/src/sec_struct.hh b/loop/src/sec_struct.hh
deleted file mode 100644
index b808265bfe6869c5c0dbaa8ec8d88499512f2448..0000000000000000000000000000000000000000
--- a/loop/src/sec_struct.hh
+++ /dev/null
@@ -1,63 +0,0 @@
-#ifndef PROMOD_LOOP_SEC_STRUCT_HH
-#define PROMOD_LOOP_SEC_STRUCT_HH
-
-#include <promod3/loop/backbone.hh>
-#include <algorithm>
-#include <limits>
-#include <math.h>
-
-namespace promod3 { namespace loop {
-
-inline Real DSSPHBondEnergy(const geom::Vec3& h_pos, const geom::Vec3& n_pos,
- const geom::Vec3& c_pos, const geom::Vec3& o_pos){
- Real on = 1.0/geom::Distance(o_pos,n_pos);
- Real ch = 1.0/geom::Distance(c_pos,h_pos);
- Real oh = 1.0/geom::Distance(o_pos,h_pos);
- Real cn = 1.0/geom::Distance(c_pos,n_pos);
- return 27.888 * (on+ch-oh-cn);
-}
-
-//Raw estimation of secondary structure
-//
-// This function is not intended for Python export, since the
-// input has to be prepared carefully. It basically estimates
-// the secondary structure based on the hydrogen pattern as
-// described for the dssp tool. Some simplifications lead to
-// same estimation for roughly 98-99 % of the residues.
-// Please note, that there is absolutely no handling of chain
-// breaks!
-//
-// The idea is, that secondary structure estimation can be performed
-// for a small stretch in the environment of a full structure.
-// ca_positions contains the CA-positions of this stretch.
-// Every residue is considered to serve as donor/acceptor
-// for two other residues (note, that Proline cannot be a donor,
-// you have to consider that in the input data!!).
-// This acceptor/donor information is
-// given in the other four vectors. donor_for_one[i] means,
-// that residue i of the stretch is donor for the corresponding
-// entry, where a value of -1 means that i is NOT a donor at all.
-// The entry indices are based on the residue index in
-// the full structure. For the proper positioning of the stretch
-// in the full structure, the parameter start_idx is used.
-//
-//
-// Some points to consider when preparing the input data:
-// Only check for hbonds of residue i beginning at i+3
-// => at least 3 residue apart... Only consider HBonds
-// with DSSPHBondEnergy < -0.5
-
-
-void RawEstimateSS(const std::vector<geom::Vec3>& ca_positions,
- int start_idx,
- const std::vector<int>& donor_for_one,
- const std::vector<int>& donor_for_two,
- const std::vector<int>& acceptor_for_one,
- const std::vector<int>& acceptor_for_two,
- String& ss_assignment);
-
-void EstimateSS(const BackboneList& bb_list, String& ss_assignment);
-
-}} //ns
-
-#endif
diff --git a/loop/src/sidechain_atom_constructor.cc b/loop/src/sidechain_atom_constructor.cc
index 5648ea0f0489f11b186c60caf9709f4f6001af67..0fb09cefbb5367fd9b24103448f62ee32a3db2dc 100644
--- a/loop/src/sidechain_atom_constructor.cc
+++ b/loop/src/sidechain_atom_constructor.cc
@@ -67,10 +67,26 @@ void ConstructSidechainAtoms(AllAtomPositions& all_pos, uint res_idx,
throw promod3::Error("Invalid res_idx in ConstructSidechainAtoms!");
}
+ ost::conop::AminoAcid aa = all_pos.GetAA(res_idx);
+
+ // We make sure that ALL backbone positions are present of ALL heavy atoms
+ // This way we can guarantee that all heavy atoms of the FULL residue are
+ // set when this function ran through.
if(!(all_pos.IsSet(res_idx, BB_N_INDEX) &&
all_pos.IsSet(res_idx, BB_CA_INDEX) &&
- all_pos.IsSet(res_idx, BB_CB_INDEX))){
- throw promod3::Error("N, CA and CB must be set in ConstructSidechainAtoms!");
+ all_pos.IsSet(res_idx, BB_C_INDEX) &&
+ all_pos.IsSet(res_idx, BB_O_INDEX)) ||
+ (aa != ost::conop::GLY && !all_pos.IsSet(res_idx, BB_CB_INDEX))) {
+ throw promod3::Error("All backbone heavy atoms must be set in "
+ "ConstructSidechainAtoms!");
+ }
+
+ const std::vector<SidechainAtomRule>& rules =
+ SidechainAtomRuleLookup::GetInstance().GetRules(aa);
+
+ if(rules.empty()) {
+ // no sidechain atoms to construct! (e.g. ALA or GLY)
+ return;
}
Real chi_angles[5];
@@ -80,9 +96,6 @@ void ConstructSidechainAtoms(AllAtomPositions& all_pos, uint res_idx,
chi_angles[3] = chi4;
chi_angles[4] = 0.0;
- const std::vector<SidechainAtomRule>& rules =
- SidechainAtomRuleLookup::GetInstance().GetRules(all_pos.GetAA(res_idx));
-
for(uint rule_idx = 0; rule_idx < rules.size(); ++rule_idx){
const SidechainAtomRule& rule = rules[rule_idx];
@@ -90,7 +103,7 @@ void ConstructSidechainAtoms(AllAtomPositions& all_pos, uint res_idx,
Real dihedral_angle = chi_angles[rule.dihedral_idx];
if(dihedral_angle != dihedral_angle){
- if(all_pos.GetAA(res_idx) == ost::conop::PRO && rule.dihedral_idx == 1){
+ if(aa == ost::conop::PRO && rule.dihedral_idx == 1){
dihedral_angle = ProlineChi2Fallback(all_pos, res_idx, rule);
}
else{
diff --git a/loop/src/structure_db.cc b/loop/src/structure_db.cc
index 20f37d00500c07318bf57717114b4908d41160ae..7eb3fe33e6c722c526f44403d9f1c727c1c30cd1 100644
--- a/loop/src/structure_db.cc
+++ b/loop/src/structure_db.cc
@@ -2,132 +2,349 @@
#include <promod3/core/portable_binary_serializer.hh>
#include <promod3/core/check_io.hh>
#include <promod3/core/runtime_profiling.hh>
+#include <ost/mol/alg/accessibility.hh>
+#include <ost/mol/alg/sec_struct.hh>
namespace {
-//returns the number of connnected residues ongoing from start with all backbone
-//atoms present
-uint cont_fragment_length(const ost::mol::ResidueViewList& rvl, uint start) {
- if(rvl.empty() || start >= rvl.size()) return 0;
- uint size=0;
- while (true) {
- ost::mol::AtomView n = rvl[start].FindAtom("N");
- ost::mol::AtomView ca = rvl[start].FindAtom("CA");
- ost::mol::AtomView c=rvl[start].FindAtom("C");
- ost::mol::AtomView o = rvl[start].FindAtom("O");
- if(!n.IsValid() || !ca.IsValid() || !c.IsValid() || !o.IsValid()) break;
- ++size;
- ++start;
- if(start>=rvl.size()) break;
- ost::mol::AtomView n_next=rvl[start].FindAtom("N");
- if (!BondExists(c.GetHandle(), n_next.GetHandle())) break;
- }
- return size;
-}
-std::pair<uint,uint> max_cont_fragment_length(const ost::mol::ResidueViewList& rvl){
+void FloodLevel(char* data, int x_start, int y_start,
+ int x_extent, int y_extent,
+ int orig_value, int dest_value) {
+
+ //http://lodev.org/cgtutor/floodfill.html
+ if(orig_value != data[x_start*y_extent + y_start]) {
+ return;
+ }
- uint actual_start = 0;
- uint actual_length = cont_fragment_length(rvl,actual_start);
- uint max_start = actual_start;
- uint max_length = actual_length;
+ std::vector<std::pair<int,int> > queue;
+ queue.push_back(std::make_pair(x_start, y_start));
+
+ int y1,y,x;
+ bool spanLeft, spanRight;
+ std::pair<int,int> actual_position;
+
+ while(!queue.empty()){
- while(actual_start + actual_length < rvl.size()){
- if(actual_length == 0) ++actual_start;
- else actual_start += actual_length;
- actual_length = cont_fragment_length(rvl,actual_start);
- if(actual_length > max_length){
- max_start = actual_start;
- max_length = actual_length;
+ actual_position = queue.back();
+ queue.pop_back();
+ x = actual_position.first;
+ y = actual_position.second;
+
+ y1 = y;
+
+ while(y1 >= 0 && data[x*y_extent + y1] == orig_value) {
+ --y1;
}
- }
- return std::make_pair(max_start,max_length);
-}
+ y1++;
+ spanLeft = spanRight = 0;
-Real FindClosestDist(const geom::Vec3& pos,
- const std::vector<geom::Vec3>& surrounding){
-
- Real dist = std::numeric_limits<Real>::max();
- for(std::vector<geom::Vec3>::const_iterator i = surrounding.begin(),
- e = surrounding.end(); i != e; ++i){
- Real actual_dist = geom::Length2(pos-(*i));
- if(actual_dist < dist) dist = actual_dist;
+ while(y1 < y_extent &&
+ data[x*y_extent + y1] == orig_value ) {
+
+ data[x*y_extent + y1] = dest_value;
+
+ if(!spanLeft && x > 0 &&
+ data[(x-1)*y_extent + y1] == orig_value) {
+ queue.push_back(std::make_pair(x-1,y1));
+ spanLeft = 1;
+ }
+ else if(spanLeft && x > 0 &&
+ data[(x-1)*y_extent + y1] != orig_value) {
+ spanLeft = 0;
+ }
+
+ if(!spanRight && x < x_extent - 1 &&
+ data[(x+1)*y_extent + y1] == orig_value) {
+ queue.push_back(std::make_pair(x+1,y1));
+ spanRight = 1;
+ }
+ else if(spanRight && x < x_extent - 1 &&
+ data[(x+1)*y_extent + y1] != orig_value) {
+ spanRight = 0;
+ }
+ ++y1;
+ }
}
- return std::sqrt(dist);
}
-void FillVertexPositions(const ost::mol::SurfaceHandle& surf,
- std::vector<geom::Vec3>& positions){
- ost::mol::SurfaceVertexIDList v_id_list = surf.GetVertexIDList();
- positions.clear();
- positions.reserve(v_id_list.size());
- for(ost::mol::SurfaceVertexIDList::iterator i = v_id_list.begin(),
- e = v_id_list.end(); i!=e; ++i){
- ost::mol::SurfaceVertex v = surf.GetVertex(*i);
- positions.push_back(v.position);
+
+void AssignResidueDepths(const ost::mol::EntityView& ent,
+ const ost::mol::ChainView& chain) {
+
+
+ // sum of approx. vdw radius of the present heavy atoms (1.8)
+ // plus 1.4 for water.
+ Real radius = 3.2;
+ Real one_over_radius = Real(1.0) / radius;
+
+ // lets setup a grid in which we place the atoms
+ Real min_x = std::numeric_limits<Real>::max();
+ Real max_x = -min_x;
+
+ Real min_y = std::numeric_limits<Real>::max();
+ Real max_y = -min_y;
+
+ Real min_z = std::numeric_limits<Real>::max();
+ Real max_z = -min_z;
+
+ std::vector<geom::Vec3> atom_positions;
+ ost::mol::AtomViewList atom_list = ent.GetAtomList();
+
+ for(ost::mol::AtomViewList::iterator it = atom_list.begin();
+ it != atom_list.end(); ++it) {
+ geom::Vec3 pos = it->GetPos();
+ min_x = std::min(min_x, pos[0]);
+ max_x = std::max(max_x, pos[0]);
+ min_y = std::min(min_y, pos[1]);
+ max_y = std::max(max_y, pos[1]);
+ min_z = std::min(min_z, pos[2]);
+ max_z = std::max(max_z, pos[2]);
+ atom_positions.push_back(pos);
}
-}
-Real SingleResidueDepth(const ost::mol::ResidueView& res,
- const std::vector<geom::Vec3>& surface_positions){
- ost::mol::AtomViewList atom_list = res.GetAtomList();
- Real depth = 0.0;
- for(ost::mol::AtomViewList::iterator i = atom_list.begin(),
- e = atom_list.end(); i!=e; ++i){
- depth += FindClosestDist(i->GetPos(),surface_positions);
+ // we guarantee that the thing is properly solvated in the x-y plane and add
+ // some space around this is also necessary to avoid overflow checks in
+ // different places
+ min_x -= Real(2.1) * radius;
+ min_y -= Real(2.1) * radius;
+ min_z -= Real(2.1) * radius;
+ max_x += Real(2.1) * radius;
+ max_y += Real(2.1) * radius;
+ max_z += Real(2.1) * radius;
+
+ int num_xbins = std::ceil((max_x - min_x) * one_over_radius);
+ int num_ybins = std::ceil((max_y - min_y) * one_over_radius);
+ int num_zbins = std::ceil((max_z - min_z) * one_over_radius);
+ int num_bins = num_xbins * num_ybins * num_zbins;
+ char* grid = new char[num_bins];
+ memset(grid, 0, num_bins);
+
+ for(uint i = 0; i < atom_positions.size(); ++i) {
+
+ const geom::Vec3& pos = atom_positions[i];
+ int x_bin = (pos[0] - min_x) * one_over_radius;
+ int y_bin = (pos[1] - min_y) * one_over_radius;
+ int z_bin = (pos[2] - min_z) * one_over_radius;
+
+ // we're really crude here and simply set all 27 cubes with central
+ // cube defined by x_bin, y_bin and z_bin to one
+ for(int z = z_bin - 1; z <= z_bin + 1; ++z) {
+ for(int x = x_bin - 1; x <= x_bin + 1; ++x) {
+ for(int y = y_bin - 1; y <= y_bin + 1; ++y) {
+ grid[z*num_xbins*num_ybins + x*num_ybins + y] = 1;
+ }
+ }
+ }
+ }
+
+ // lets call flood fill for every layer along the z-axis from every
+ // corner in the x-y plane.
+ for(int z = 0; z < num_zbins; ++z) {
+ char* level = &grid[z*num_xbins*num_ybins];
+ FloodLevel(level, 0, 0, num_xbins, num_ybins, 0, 2);
+ FloodLevel(level, 0, num_ybins - 1, num_xbins, num_ybins, 0, 2);
+ FloodLevel(level, num_xbins - 1, 0, num_xbins, num_ybins, 0, 2);
+ FloodLevel(level, num_xbins - 1, num_ybins - 1, num_xbins, num_ybins, 0, 2);
}
- return (depth/atom_list.size() + 1.4);
-}
-void ResidueDepth(const ost::mol::ChainView& chain, const ost::mol::SurfaceHandle& surf,
- std::vector<Real>& depth){
+ // we filled the xy-planes but we also need to consider stuff along the z-axis
+ bool something_happened = true;
+ while(something_happened) {
+
+ something_happened = false;
+
+ char* level;
+ char* upper_level;
+ char* lower_level;
+ int idx;
+
+ // do first layer
+ level = &grid[0];
+ upper_level = &grid[num_xbins*num_ybins];
+ idx = 0;
+ for(int x = 0; x < num_xbins; ++x) {
+ for(int y = 0; y < num_ybins; ++y, ++idx) {
+ if(level[idx] == 2 && upper_level[idx] == 0) {
+ FloodLevel(upper_level, x, y, num_xbins, num_ybins, 0, 2);
+ something_happened = true;
+ }
+ }
+ }
- ost::mol::ResidueViewList res_list = chain.GetResidueList();
- depth.clear();
- depth.reserve(res_list.size());
- std::vector<geom::Vec3> vertex_positions;
- FillVertexPositions(surf,vertex_positions);
- for(ost::mol::ResidueViewList::iterator i = res_list.begin(),
- e = res_list.end(); i != e; ++i){
- depth.push_back(SingleResidueDepth(*i,vertex_positions));
+ // do all layers in between
+ for(int z = 1; z < num_zbins - 1; ++z) {
+ level = &grid[z*num_xbins*num_ybins];
+ upper_level = &grid[(z+1)*num_xbins*num_ybins];
+ lower_level = &grid[(z-1)*num_xbins*num_ybins];
+ idx = 0;
+ for(int x = 0; x < num_xbins; ++x) {
+ for(int y = 0; y < num_ybins; ++y, ++idx) {
+ if(level[idx] == 2 && upper_level[idx] == 0) {
+ FloodLevel(upper_level, x, y, num_xbins, num_ybins, 0, 2);
+ something_happened = true;
+ }
+ if(level[idx] == 2 && lower_level[idx] == 0) {
+ FloodLevel(lower_level, x, y, num_xbins, num_ybins, 0, 2);
+ something_happened = true;
+ }
+ }
+ }
+ }
+
+ // do last layer
+ level = &grid[(num_zbins - 1) * num_xbins*num_ybins];
+ lower_level = &grid[(num_zbins - 2) * num_xbins*num_ybins];
+ idx = 0;
+ for(int x = 0; x < num_xbins; ++x) {
+ for(int y = 0; y < num_ybins; ++y, ++idx) {
+ if(level[idx] == 2 && lower_level[idx] == 0) {
+ FloodLevel(lower_level, x, y, num_xbins, num_ybins, 0, 2);
+ something_happened = true;
+ }
+ }
+ }
+ }
+
+ // every cube in every layer that has currently value 1 that has a city-block
+ // distance below 3 to any cube with value 2 is considered to be in contact
+ // with the outer surface... lets set them to a value of three
+ for(int z = 0; z < num_zbins; ++z) {
+ for(int x = 0; x < num_xbins; ++x) {
+ for(int y = 0; y < num_ybins; ++y) {
+ if(grid[z*num_xbins*num_ybins + x*num_ybins + y] == 1) {
+ int x_from = std::max(0, x - 3);
+ int x_to = std::min(num_xbins-1, x + 3);
+ int y_from = std::max(0, y - 3);
+ int y_to = std::min(num_ybins-1, y + 3);
+ int z_from = std::max(0, z - 3);
+ int z_to = std::min(num_zbins-1, z + 3);
+ bool exposed = false;
+ for(int i = x_from; i <= x_to && !exposed; ++i) {
+ for(int j = y_from; j <= y_to; ++j) {
+ for(int k = z_from; k < z_to; ++k) {
+ if(grid[k*num_xbins*num_ybins + i*num_ybins + j] == 2) {
+ grid[z*num_xbins*num_ybins + x*num_ybins + y] = 3;
+ exposed = true;
+ break;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
}
-}
+ // All residues that have at least one atom in a cube with value 3 AND have a
+ // relative solvent accessibility > 0.25 are considered to be exposed.
+ // To finally calculate a distance, we use the CB position.
+ ost::mol::ResidueViewList all_residues = ent.GetResidueList();
+ std::vector<geom::Vec3> exposed_positions;
+
+ for(ost::mol::ResidueViewList::iterator res_it = all_residues.begin();
+ res_it != all_residues.end(); ++res_it) {
+
+ if(res_it->HasProp("asaRel") && res_it->GetFloatProp("asaRel") > Real(25)) {
+
+ bool has_exposed_atom = false;
+ ost::mol::AtomViewList at_list = res_it->GetAtomList();
+ for(ost::mol::AtomViewList::iterator at_it = at_list.begin();
+ at_it != at_list.end(); ++at_it) {
+ const geom::Vec3& pos = at_it->GetPos();
+ int x_bin = (pos[0] - min_x) * one_over_radius;
+ int y_bin = (pos[1] - min_y) * one_over_radius;
+ int z_bin = (pos[2] - min_z) * one_over_radius;
+ if(grid[z_bin*num_xbins*num_ybins + x_bin*num_ybins + y_bin] == 3) {
+ has_exposed_atom = true;
+ break;
+ }
+ }
-}
+ if(has_exposed_atom) {
+ ost::mol::AtomView cb = res_it->FindAtom("CB");
+ if(cb.IsValid()) {
+ exposed_positions.push_back(cb.GetPos());
+ } else {
+ ost::mol::AtomView n = res_it->FindAtom("N");
+ ost::mol::AtomView ca = res_it->FindAtom("CA");
+ ost::mol::AtomView c = res_it->FindAtom("C");
+ if(n.IsValid() && ca.IsValid() && c.IsValid()) {
+ geom::Vec3 cb_pos;
+ promod3::core::ConstructCBetaPos(n.GetPos(), ca.GetPos(),
+ c.GetPos(), cb_pos);
+ exposed_positions.push_back(cb_pos);
+ }
+ }
+ }
+ }
+ }
-namespace promod3 { namespace loop {
+ ost::mol::ResidueViewList chain_residues = chain.GetResidueList();
+ for(ost::mol::ResidueViewList::iterator res_it = chain_residues.begin();
+ res_it != chain_residues.end(); ++res_it) {
+
+ Real min_dist_2 = std::numeric_limits<Real>::max();
+
+ bool valid_pos = false;
+ geom::Vec3 pos;
+
+ ost::mol::AtomView cb = res_it->FindAtom("CB");
+ if(cb.IsValid()) {
+ pos = cb.GetPos();
+ valid_pos = true;
+ } else {
+ ost::mol::AtomView n = res_it->FindAtom("N");
+ ost::mol::AtomView ca = res_it->FindAtom("CA");
+ ost::mol::AtomView c = res_it->FindAtom("C");
+ if(n.IsValid() && ca.IsValid() && c.IsValid()) {
+ promod3::core::ConstructCBetaPos(n.GetPos(), ca.GetPos(),
+ c.GetPos(), pos);
+ valid_pos = true;
+ }
+ }
+ if(valid_pos) {
+ for(uint i = 0; i < exposed_positions.size(); ++i) {
+ min_dist_2 = std::min(min_dist_2,
+ geom::Length2(pos - exposed_positions[i]));
+ }
+ } else {
+ // dont do anything, we just leave it at the max value...
+ }
-void AAFreq::AssignProfileColumn(const ost::seq::ProfileColumn& col) {
- const Real* col_freq_ptr = col.freqs_begin();
- short* freq_ptr = &freqs[0];
- for(uint i = 0; i < 20; ++i){
- *freq_ptr = (*col_freq_ptr)*10000;
- ++freq_ptr;
- ++col_freq_ptr;
+ res_it->SetFloatProp("residue_depth", std::sqrt(min_dist_2));
}
+
+ // cleanup
+ delete [] grid;
+}
+
}
-StructureDBPtr StructureDB::Load(const String& file_name,
- bool load_frequencies) {
+namespace promod3 { namespace loop {
+
+StructureDBPtr StructureDB::Load(const String& file_name) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"StructureDB::Load", 2);
- std::ifstream in_stream(file_name.c_str(), std::ios::binary);
- if (!in_stream) {
+ std::ifstream in_stream_(file_name.c_str(), std::ios::binary);
+ if (!in_stream_) {
std::stringstream ss;
ss << "The file '" << file_name << "' does not exist.";
throw promod3::Error(ss.str());
}
+ core::PortableBinaryDataSource in_stream(in_stream_);
+
// header for consistency checks
core::CheckMagicNumber(in_stream);
uint32_t version = core::GetVersionNumber(in_stream);
- if (version > 1) {
+ if (version != 2) {
std::stringstream ss;
ss << "Unsupported file version '" << version << "' in '" << file_name;
throw promod3::Error(ss.str());
}
+
// see Save for required types...
typedef ost::FixedString<5> MyString;
core::CheckTypeSize<uint>(in_stream);
@@ -137,7 +354,6 @@ StructureDBPtr StructureDB::Load(const String& file_name,
core::CheckTypeSize<short>(in_stream);
core::CheckTypeSize<MyString>(in_stream);
core::CheckTypeSize<CoordInfo>(in_stream);
- core::CheckTypeSize<Peptide>(in_stream);
core::CheckTypeSize<AAFreq>(in_stream);
core::CheckTypeSize<PeptideCoords>(in_stream);
core::CheckTypeSize<UShortVec>(in_stream);
@@ -151,40 +367,55 @@ StructureDBPtr StructureDB::Load(const String& file_name,
core::CheckBaseType<short>(in_stream);
// raw data
StructureDBPtr db_p(new StructureDB);
- uint toc_len;
- in_stream.read(reinterpret_cast<char*>(&toc_len), sizeof(uint));
- db_p->coord_toc_.resize(toc_len);
- in_stream.read(reinterpret_cast<char*>(&db_p->coord_toc_.front()),
- sizeof(CoordInfo)*toc_len);
- db_p->coords_.Read(in_stream);
- if(load_frequencies){
- db_p->aa_frequencies_.Read(in_stream);
- db_p->aa_frequencies_struct_.Read(in_stream);
- }
- db_p->frequencies_present_ = load_frequencies;
- in_stream.close();
+
+ in_stream & db_p->stored_data_;
+ in_stream & db_p->coord_toc_;
+ db_p->seq_.Read(in_stream.Stream());
+ db_p->coords_.Read(in_stream.Stream());
+
+ if(db_p->HasData(Dihedrals)) {
+ db_p->dihedrals_.Read(in_stream.Stream());
+ }
+
+ if(db_p->HasData(SolventAccessibilities)) {
+ db_p->solv_acc_.Read(in_stream.Stream());
+ }
+
+ if(db_p->HasData(ResidueDepths)) {
+ db_p->res_depths_.Read(in_stream.Stream());
+ }
+
+ if(db_p->HasData(DSSP)) {
+ db_p->dssp_.Read(in_stream.Stream());
+ }
+
+ if(db_p->HasData(AAFrequencies)) {
+ db_p->aa_frequencies_.Read(in_stream.Stream());
+ }
+
+ if(db_p->HasData(AAFrequenciesStruct)) {
+ db_p->aa_frequencies_struct_.Read(in_stream.Stream());
+ }
+
+ in_stream_.close();
return db_p;
}
void StructureDB::Save(const String& filename) {
- if (!frequencies_present_) {
- std::stringstream ss;
- ss << "Can only save a database that has newly been created ";
- ss << "or loaded with load_frequencies=true!";
- throw promod3::Error(ss.str());
- }
- std::ofstream out_stream(filename.c_str(), std::ios::binary);
- if (!out_stream) {
+ std::ofstream out_stream_(filename.c_str(), std::ios::binary);
+ if (!out_stream_) {
std::stringstream ss;
ss << "The file '" << filename << "' cannot be opened.";
throw promod3::Error(ss.str());
}
+ core::PortableBinaryDataSink out_stream(out_stream_);
+
// header for consistency checks
core::WriteMagicNumber(out_stream);
- core::WriteVersionNumber(out_stream, 1);
+ core::WriteVersionNumber(out_stream, 2);
// required base types: uint, char, unsigned short, uint64_t, short
- // required structs: ost::FixedString<5>, CoordInfo, Peptide, AAFreq
+ // required structs: ost::FixedString<5>, CoordInfo, AAFreq
// PeptideCoords, UShortVec, DihedralInfo
typedef ost::FixedString<5> MyString;
core::WriteTypeSize<uint>(out_stream);
@@ -194,7 +425,6 @@ void StructureDB::Save(const String& filename) {
core::WriteTypeSize<short>(out_stream);
core::WriteTypeSize<MyString>(out_stream);
core::WriteTypeSize<CoordInfo>(out_stream);
- core::WriteTypeSize<Peptide>(out_stream);
core::WriteTypeSize<AAFreq>(out_stream);
core::WriteTypeSize<PeptideCoords>(out_stream);
core::WriteTypeSize<UShortVec>(out_stream);
@@ -207,14 +437,37 @@ void StructureDB::Save(const String& filename) {
core::WriteBaseType<uint64_t>(out_stream);
core::WriteBaseType<short>(out_stream);
// raw data
- uint toc_len=coord_toc_.size();
- out_stream.write(reinterpret_cast<char*>(&toc_len), sizeof(uint));
- out_stream.write(reinterpret_cast<char*>(&coord_toc_.front()),
- sizeof(CoordInfo)*toc_len);
- coords_.Write(out_stream);
- aa_frequencies_.Write(out_stream);
- aa_frequencies_struct_.Write(out_stream);
- out_stream.close();
+
+ out_stream & stored_data_;
+ out_stream & coord_toc_;
+ seq_.Write(out_stream.Stream());
+ coords_.Write(out_stream.Stream());
+
+ if(this->HasData(Dihedrals)) {
+ dihedrals_.Write(out_stream.Stream());
+ }
+
+ if(this->HasData(SolventAccessibilities)) {
+ solv_acc_.Write(out_stream.Stream());
+ }
+
+ if(this->HasData(ResidueDepths)) {
+ res_depths_.Write(out_stream.Stream());
+ }
+
+ if(this->HasData(DSSP)) {
+ dssp_.Write(out_stream.Stream());
+ }
+
+ if(this->HasData(AAFrequencies)) {
+ aa_frequencies_.Write(out_stream.Stream());
+ }
+
+ if(this->HasData(AAFrequenciesStruct)) {
+ aa_frequencies_struct_.Write(out_stream.Stream());
+ }
+
+ out_stream_.close();
}
StructureDBPtr StructureDB::LoadPortable(const String& file_name) {
@@ -230,7 +483,7 @@ StructureDBPtr StructureDB::LoadPortable(const String& file_name) {
// header for consistency checks
core::CheckMagicNumber(in_stream);
uint32_t version = core::GetVersionNumber(in_stream);
- if (version > 1) {
+ if (version != 2) {
std::stringstream ss;
ss << "Unsupported file version '" << version << "' in '" << file_name;
throw promod3::Error(ss.str());
@@ -247,23 +500,44 @@ StructureDBPtr StructureDB::LoadPortable(const String& file_name) {
// data
StructureDBPtr db_p(new StructureDB);
+ in_stream & db_p->stored_data_;
in_stream & db_p->coord_toc_;
+ // seq_ has fundamental type
+ db_p->seq_.Read(in_stream.Stream());
in_stream & db_p->coords_;
- in_stream & db_p->aa_frequencies_;
- in_stream & db_p->aa_frequencies_struct_;
- db_p->frequencies_present_ = true;
+
+ if(db_p->HasData(Dihedrals)) {
+ in_stream & db_p->dihedrals_;
+ }
+
+ if(db_p->HasData(SolventAccessibilities)) {
+ // solv_acc_ has fundamental type
+ db_p->solv_acc_.Read(in_stream.Stream());
+ }
+
+ if(db_p->HasData(ResidueDepths)) {
+ // res_depths_ has fundamental type
+ db_p->res_depths_.Read(in_stream.Stream());
+ }
+
+ if(db_p->HasData(DSSP)) {
+ // dssp_ has fundamental type
+ db_p->dssp_.Read(in_stream.Stream());
+ }
+
+ if(db_p->HasData(AAFrequencies)) {
+ in_stream & db_p->aa_frequencies_;
+ }
+ if(db_p->HasData(AAFrequenciesStruct)) {
+ in_stream & db_p->aa_frequencies_struct_;
+ }
+
in_stream_.close();
return db_p;
}
void StructureDB::SavePortable(const String& filename) {
- if (!frequencies_present_) {
- std::stringstream ss;
- ss << "Can only save a database that has newly been created ";
- ss << "or loaded with load_frequencies=true!";
- throw promod3::Error(ss.str());
- }
// open file
std::ofstream out_stream_(filename.c_str(), std::ios::binary);
if (!out_stream_) {
@@ -275,7 +549,7 @@ void StructureDB::SavePortable(const String& filename) {
// header for consistency checks
core::WriteMagicNumber(out_stream);
- core::WriteVersionNumber(out_stream, 1);
+ core::WriteVersionNumber(out_stream, 2);
// here: only base-type-checks needed
core::WriteTypeSize<int16_t>(out_stream);
core::WriteTypeSize<int32_t>(out_stream);
@@ -287,10 +561,38 @@ void StructureDB::SavePortable(const String& filename) {
core::WriteBaseType<char>(out_stream);
// data
+ out_stream & stored_data_;
out_stream & coord_toc_;
- out_stream & coords_;
- out_stream & aa_frequencies_;
- out_stream & aa_frequencies_struct_;
+ // seq_ has fundamental type
+ seq_.Write(out_stream.Stream());
+ out_stream & coords_;
+
+ if(this->HasData(Dihedrals)) {
+ out_stream & dihedrals_;
+ }
+
+ if(this->HasData(SolventAccessibilities)) {
+ // solv_acc_ has fundamental type
+ solv_acc_.Write(out_stream.Stream());
+ }
+
+ if(this->HasData(ResidueDepths)) {
+ // res_depths_ has fundamental type
+ res_depths_.Write(out_stream.Stream());
+ }
+
+ if(this->HasData(DSSP)) {
+ // dssp_ has fundamental type
+ dssp_.Write(out_stream.Stream());
+ }
+
+ if(this->HasData(AAFrequencies)) {
+ out_stream & aa_frequencies_;
+ }
+
+ if(this->HasData(AAFrequenciesStruct)) {
+ out_stream & aa_frequencies_struct_;
+ }
out_stream_.close();
}
@@ -299,221 +601,343 @@ bool StructureDB::operator==(const StructureDB& rhs) const {
return coord_toc_ == rhs.coord_toc_
&& coords_ == rhs.coords_
&& aa_frequencies_ == rhs.aa_frequencies_
- && aa_frequencies_struct_ == rhs.aa_frequencies_struct_
- && frequencies_present_ == rhs.frequencies_present_;
+ && aa_frequencies_struct_ == rhs.aa_frequencies_struct_;
}
-int StructureDB::AddCoordinates(const String& pdb_id,
- const String& chain_name,
- const ost::mol::ChainView& chain,
- const ost::mol::SurfaceHandle& surf,
- ost::seq::ProfileHandlePtr prof,
- const String& solvent_accessibility_string) {
+std::vector<int> StructureDB::AddCoordinates(const String& id,
+ const String& chain_name,
+ ost::mol::EntityView& ent,
+ ost::seq::SequenceHandle& seqres,
+ ost::seq::ProfileHandlePtr prof,
+ bool only_longest_stretch) {
- if(!frequencies_present_){
- std::stringstream ss;
- ss << "Can only add coordinates if database has newly been created ";
- ss << "or loaded with load_frequencies=true!";
- throw promod3::Error(ss.str());
- }
+ ost::mol::ChainView chain = ent.FindChain(chain_name);
- uint chain_index = coord_toc_.size();
- if(chain_index > std::numeric_limits<unsigned int>::max()){
- std::stringstream ss;
- ss << "Due to technical reasons, the database can only contain ";
- ss << std::numeric_limits<unsigned int>::max();
- ss << " chains.";
- throw promod3::Error(ss.str());
+ if(!chain.IsValid()) {
+ throw promod3::Error("Could not find specified chain in input entity!");
}
- ost::mol::ResidueViewList res_list = chain.GetResidueList();
- uint offset=coords_.size();
+ // if we want the amino acid frequencies, we must ensure a valid profile
+ // that has matching sequence with seqres
+ if(this->HasData(AAFrequencies)) {
- //Let's find the longest connected stretch of residues in the provided chain
- std::pair<uint,uint> subfrag_info = max_cont_fragment_length(res_list);
- uint frag_start = subfrag_info.first;
- uint connected_size = subfrag_info.second;
+ if(!prof) {
+ throw promod3::Error("You must provide a valid sequence profile when you"
+ " add coordinates to this StructureDB!");
+ }
- if(connected_size > std::numeric_limits<unsigned short>::max()){
- std::stringstream ss;
- ss << "Due to technical reasons, the max number of residues per chain is: ";
- ss << std::numeric_limits<unsigned short>::max();
- throw promod3::Error(ss.str());
+ if(prof->GetSequence() != seqres.GetString()) {
+ std::stringstream ss;
+ ss << "Profile sequence does not match with seqres: ";
+ ss << prof->GetSequence() << " vs " << seqres.GetString();
+ throw promod3::Error(ss.str());
+ }
}
- if(connected_size == 0) return -1;
- geom::AlignedCuboid bounds=chain.GetBounds();
- geom::Vec3 cuboid_size = bounds.GetSize();
- Real max_extent = std::max(cuboid_size[0],std::max(cuboid_size[1],cuboid_size[2]));
- if(max_extent >= std::floor(std::numeric_limits<unsigned short>::max()*0.01)){
- std::stringstream ss;
- ss << "Max extent of structure to be added must not exceed ";
- ss << std::floor(std::numeric_limits<unsigned short>::max()*0.01);
- ss <<" Angstrom!";
- throw promod3::Error(ss.str());
+ std::vector<int> return_vec;
+ ost::mol::ResidueViewList residues = chain.GetResidueList();
+
+ if(residues.empty()) {
+ return return_vec;
}
- //extract according sequences
- String prof_seq = prof->GetSequence();
- String structure_seq(connected_size,'X');
- for(uint j = 0; j < connected_size; ++j){
- structure_seq[j] = res_list[j].GetOneLetterCode();
- }
-
- //generate sequence handles and generate the alignment
- ost::seq::SequenceHandle prof_seq_handle = ost::seq::CreateSequence("A",prof_seq);
- ost::seq::SequenceHandle structure_seq_handle = ost::seq::CreateSequence("B",structure_seq);
- ost::seq::alg::SubstWeightMatrixPtr subst(new ost::seq::alg::SubstWeightMatrix);
- subst->AssignPreset(ost::seq::alg::SubstWeightMatrix::BLOSUM100);
- ost::seq::AlignmentHandle aln = ost::seq::alg::SemiGlobalAlign(prof_seq_handle,structure_seq_handle,subst)[0];
-
- //get the profile column indices of the aligned structural residues
- std::vector<int> prof_indices;
- prof_indices.reserve(connected_size);
- bool invalid_sequence = false;
- char a,b;
- int aln_pos_idx = 0;
- for(ost::seq::AlignmentHandle::iterator col_it = aln.begin();
- col_it != aln.end(); ++col_it){
- a = (*col_it)[0];
- b = (*col_it)[1];
- if(a == '-' || a == '?'){
- invalid_sequence = true; // "SEQRES" olcs must be valid and not a gap!
+ // check for consistency of the residue numbers with seqres
+ int seqres_size = seqres.GetLength();
+ std::vector<int> resnums;
+ ost::mol::AtomView c_prev;
+ Real optimal_peptide_bond_length = 1.348435;
+ std::vector<bool> connected_to_prev;
+
+ for(ost::mol::ResidueViewList::iterator it = residues.begin();
+ it != residues.end(); ++it) {
+ int rnum = it->GetNumber().GetNum();
+ char olc = it->GetOneLetterCode();
+ if(rnum < 1 || rnum > seqres_size || olc != seqres[rnum-1]) {
+ std::stringstream ss;
+ ss << "Residue " << *it << " doesnt match with seqres: ";
+ ss << seqres;
+ throw promod3::Error(ss.str());
}
- if(a != b && b != '-'){
- if(!(b == 'X' || b == '?')){
- if(a != 'X'){
- invalid_sequence = true; //let's allow alignment mismatch if '?' or 'X' is allowed
- }
+ // only consider residue if all required backbone atoms are present
+ ost::mol::AtomView n = it->FindAtom("N");
+ ost::mol::AtomView ca = it->FindAtom("CA");
+ ost::mol::AtomView c = it->FindAtom("C");
+ ost::mol::AtomView o = it->FindAtom("O");
+
+ if(!(n.IsValid() && ca.IsValid() && c.IsValid() && o.IsValid())) {
+ continue;
+ }
+
+ resnums.push_back(rnum);
+
+ Real d = 0.0;
+ if(c_prev.IsValid()) {
+ d = geom::Distance(c_prev.GetPos(), n.GetPos());
+ }
+ if(std::abs(d - optimal_peptide_bond_length) > 0.5) {
+ connected_to_prev.push_back(false);
+ } else {
+ connected_to_prev.push_back(true);
+ }
+ c_prev = c;
+ }
+
+ // find connected stretches of residue numbers
+ std::vector<std::vector<int> > connected_stretches;
+ std::vector<int> current_resnums;
+ current_resnums.push_back(resnums[0]);
+ for(uint i = 1; i < resnums.size(); ++i) {
+ if(resnums[i] == current_resnums.back() + 1 && connected_to_prev[i]) {
+ current_resnums.push_back(resnums[i]);
+ } else {
+ connected_stretches.push_back(current_resnums);
+ current_resnums = std::vector<int>();
+ current_resnums.push_back(resnums[i]);
+ }
+ }
+ if(!current_resnums.empty()) {
+ connected_stretches.push_back(current_resnums);
+ }
+
+ // depending on the only_longest_stretch flag, we only add one stretch
+ // or all of them
+ std::vector<int> stretches_to_add;
+ if(only_longest_stretch) {
+ uint max_size = 0;
+ int max_idx = 0;
+ for(uint i = 0; i < connected_stretches.size(); ++i) {
+ if(connected_stretches[i].size() > max_size) {
+ max_size = connected_stretches[i].size();
+ max_idx = i;
}
- }
+ }
+ stretches_to_add.push_back(max_idx);
+ } else {
+ for(uint i = 0; i < connected_stretches.size(); ++i) {
+ stretches_to_add.push_back(i);
+ }
+ }
- if(b != '-') prof_indices.push_back(aln_pos_idx);
- ++aln_pos_idx;
- }
+ // If required, we assign secondary structures, solvent accessibilities and
+ // residue depths given the full complex. Since they relate
+ // to the same underlying data, the stuff will also be accessible from the
+ // residues in the ChainView.
+ if(this->HasData(DSSP)) {
+ ost::mol::alg::AssignSecStruct(ent);
+ }
- if(invalid_sequence){
- std::stringstream ss;
- ss << "Could not align the ATOMSEQ from the given chain to the ";
- ss << "SEQRES given by the profile!";
- throw promod3::Error(ss.str());
+ if(this->HasData(SolventAccessibilities) ||
+ this->HasData(ResidueDepths)) {
+ ost::mol::alg::Accessibility(ent);
}
- //extract dssp information, solvent accessibilities and residue depths
- std::vector<char> dssp_states;
- std::vector<unsigned short> solvent_accessibilities;
- std::vector<Real> residue_depths;
- ResidueDepth(chain,surf,residue_depths);
- String valid_dssp_states = "GHIBETSC";
- for(ost::mol::ResidueViewList::const_iterator i = res_list.begin(),
- e = res_list.end(); i != e; ++i){
- char dssp_state = char(i->GetSecStructure());
- if(valid_dssp_states.find(dssp_state) == String::npos){
+ if(this->HasData(ResidueDepths)) {
+ AssignResidueDepths(ent, chain);
+ }
+
+ /////////////////
+ // Lets do it! //
+ /////////////////
+
+ for(std::vector<int>::iterator stretch_idx_it = stretches_to_add.begin();
+ stretch_idx_it != stretches_to_add.end(); ++stretch_idx_it) {
+
+ const std::vector<int>& stretch = connected_stretches[*stretch_idx_it];
+
+ // chain must not exceed length...
+ if(stretch.size() >= std::numeric_limits<unsigned short>::max()) {
std::stringstream ss;
- ss << "Residue \"" << i->GetQualifiedName() <<"\" has invalid dssp state \'";
- ss << dssp_state << "\'. Adding \'C\' instead!";
- std::cerr<<ss.str()<<std::endl;
- dssp_state = 'C';
+ ss << "Due to technical reasons, the maximum length of added chains is ";
+ ss << std::numeric_limits<unsigned short>::max() << ". skip...";
+ LOG_ERROR(ss.str());
+ continue;
}
- dssp_states.push_back(dssp_state);
- if(i->HasProp(solvent_accessibility_string)){
- Real acc = i->GetFloatProp(solvent_accessibility_string);
- solvent_accessibilities.push_back(acc);
+
+ // lets build a BackboneList of the stretch to simplify feature extraction
+ ost::mol::ResidueHandleList stretch_residues;
+ String stretch_sequence(stretch.size(), 'X');
+
+ for(uint rnum_idx = 0; rnum_idx < stretch.size(); ++rnum_idx) {
+ ost::mol::ResNum rnum(stretch[rnum_idx]);
+ ost::mol::ResidueView res = chain.FindResidue(rnum);
+ stretch_residues.push_back(res.GetHandle());
+ stretch_sequence[rnum_idx] = res.GetOneLetterCode();
}
- else{
- String err = "Residue \"" + i->GetQualifiedName() + "\" has no ";
- err += ("property " + solvent_accessibility_string + " describing ");
- err += "its solvent accessibility. Adding 0.0 instead.";
- std::cerr<<err<<std::endl;
- solvent_accessibilities.push_back(0.0);
+
+ promod3::loop::BackboneList bb_list(stretch_sequence, stretch_residues);
+
+ // get the bounds and check whether they're small enough for our custom
+ // position data type
+ geom::AlignedCuboid bounds = bb_list.GetBounds();
+ geom::Vec3 cuboid_size = bounds.GetSize();
+ Real max_extent = std::max(cuboid_size[0],
+ std::max(cuboid_size[1],
+ cuboid_size[2]));
+ Real max_v = std::floor(std::numeric_limits<unsigned short>::max() * 0.01);
+ if(max_extent >= max_v) {
+ std::stringstream ss;
+ ss << "Max extent of stretch to be added must not exceed ";
+ ss << std::floor(std::numeric_limits<unsigned short>::max() * 0.01);
+ ss <<" Angstrom! skip...";
+ LOG_ERROR(ss.str());
+ continue;
}
- }
- coord_toc_.push_back(CoordInfo(pdb_id, chain_name, offset, connected_size));
-
- std::vector<Peptide> peptides;
- for(uint i = 0; i < connected_size; ++i){
- ost::mol::ResidueView r=res_list[frag_start+i];
- Peptide peptide;
- peptide.coords.n=UShortVec(r.FindAtom("N").GetPos()-bounds.GetMin());
- peptide.coords.ca=UShortVec(r.FindAtom("CA").GetPos()-bounds.GetMin());
- peptide.coords.c=UShortVec(r.FindAtom("C").GetPos()-bounds.GetMin());
- peptide.coords.o=UShortVec(r.FindAtom("O").GetPos()-bounds.GetMin());
- peptide.olc=r.GetOneLetterCode();
- peptide.dssp_state=dssp_states[frag_start+i];
- peptide.solv_acc=solvent_accessibilities[frag_start+i];
- Real transformed_residue_depth = residue_depths[frag_start+i]*10;
- if(transformed_residue_depth >= std::numeric_limits<unsigned short>::max()){
- peptide.res_depth = std::numeric_limits<unsigned short>::max();
+ // we're ready to go, from now on we should have no errors anymore
+ uint offset = coords_.size();
+ geom::Vec3 shift = -bounds.GetMin();
+ coord_toc_.push_back(CoordInfo(id, chain_name, offset,
+ bb_list.size(), stretch[0], shift));
+
+ for(uint rnum_idx = 0; rnum_idx < bb_list.size(); ++rnum_idx) {
+ PeptideCoords coords;
+ coords.n = UShortVec(bb_list.GetN(rnum_idx) + shift);
+ coords.ca = UShortVec(bb_list.GetCA(rnum_idx) + shift);
+ coords.c = UShortVec(bb_list.GetC(rnum_idx) + shift);
+ coords.o = UShortVec(bb_list.GetO(rnum_idx) + shift);
+ seq_.push_back(bb_list.GetOLC(rnum_idx));
+ coords_.push_back(coords);
+ }
+
+ if(this->HasData(Dihedrals)) {
+
+ dihedrals_.push_back(DihedralInfo(-1.0472,
+ bb_list.GetPsiTorsion(0)));
+ for(uint i = 1; i < bb_list.size() - 1; ++i) {
+ dihedrals_.push_back(DihedralInfo(bb_list.GetPhiTorsion(i),
+ bb_list.GetPsiTorsion(i)));
+ }
+ dihedrals_.push_back(DihedralInfo(bb_list.GetPhiTorsion(bb_list.size()-1),
+ -0.78540));
+ }
+
+ if(this->HasData(SolventAccessibilities)) {
+ for(ost::mol::ResidueHandleList::iterator it = stretch_residues.begin();
+ it != stretch_residues.end(); ++it) {
+ if(it->HasProp("asaAbs")) {
+ Real acc = static_cast<unsigned short>(it->GetFloatProp("asaAbs"));
+ solv_acc_.push_back(acc);
+ } else {
+ std::stringstream ss;
+ ss << "Residue " << *it << " has no valid solvent accessibility ";
+ ss << "assigned. Use 0.0..."<<std::endl;
+ LOG_ERROR(ss.str());
+
+ solv_acc_.push_back(0);
+ }
+ }
}
- else peptide.res_depth = static_cast<unsigned short>(transformed_residue_depth);
- peptides.push_back(peptide);
+
+ if(this->HasData(ResidueDepths)) {
+ for(ost::mol::ResidueHandleList::iterator it = stretch_residues.begin();
+ it != stretch_residues.end(); ++it) {
+ Real residue_depth = it->GetFloatProp("residue_depth");
+ Real transformed_r_depth = residue_depth * 10;
+ unsigned short final_depth;
+ if(transformed_r_depth >= std::numeric_limits<unsigned short>::max()) {
+ final_depth = std::numeric_limits<unsigned short>::max();
+ } else {
+ final_depth = static_cast<unsigned short>(transformed_r_depth);
+ }
+ res_depths_.push_back(final_depth);
+ }
+ }
+
+ if(this->HasData(DSSP)) {
+ for(ost::mol::ResidueHandleList::const_iterator it =
+ stretch_residues.begin(); it != stretch_residues.end(); ++it) {
+ char dssp_state = char(it->GetSecStructure());
+ dssp_.push_back(dssp_state);
+ }
+ }
+
+ if(this->HasData(AAFrequencies)) {
+ for(uint rnum_idx = 0; rnum_idx < bb_list.size(); ++rnum_idx) {
+ AAFreq aa_freq;
+ const ost::seq::ProfileColumn& col = (*prof)[stretch[rnum_idx] - 1];
+ aa_freq.AssignProfileColumn(col);
+ aa_frequencies_.push_back(aa_freq);
+ }
+ }
+
+ if(this->HasData(AAFrequenciesStruct)) {
+ for(uint rnum_idx = 0; rnum_idx < bb_list.size(); ++rnum_idx) {
+ AAFreq aa_freq_struct;
+ aa_frequencies_struct_.push_back(aa_freq_struct);
+ }
+ }
+
+ return_vec.push_back(coord_toc_.size() - 1);
}
- //calculate all dihedrals
- Real phi,psi;
+ return return_vec;
+}
- //first one
- phi = -1.0472;
- psi = geom::DihedralAngle(peptides[0].coords.n.ToVec3(),
- peptides[0].coords.ca.ToVec3(),
- peptides[0].coords.c.ToVec3(),
- peptides[1].coords.n.ToVec3());
- peptides[0].dihedrals = DihedralInfo(phi,psi);
+void StructureDB::RemoveCoordinates(uint coord_idx) {
- //the middle stuff
- for(uint i = 1; i < peptides.size()-1; ++i){
- phi = geom::DihedralAngle(peptides[i-1].coords.c.ToVec3(),
- peptides[i].coords.n.ToVec3(),
- peptides[i].coords.ca.ToVec3(),
- peptides[i].coords.c.ToVec3());
- psi = geom::DihedralAngle(peptides[i].coords.n.ToVec3(),
- peptides[i].coords.ca.ToVec3(),
- peptides[i].coords.c.ToVec3(),
- peptides[i+1].coords.n.ToVec3());
- peptides[i].dihedrals = DihedralInfo(phi,psi);
+ if(coord_idx >= coord_toc_.size()) {
+ throw promod3::Error("Invalid input idx!");
}
- //last one
- phi = geom::DihedralAngle(peptides[peptides.size()-1-1].coords.c.ToVec3(),
- peptides[peptides.size()-1].coords.n.ToVec3(),
- peptides[peptides.size()-1].coords.ca.ToVec3(),
- peptides[peptides.size()-1].coords.c.ToVec3());
- psi = -0.78540;
+ // lets first remove everything from the paged arrays
+ uint64_t from = coord_toc_[coord_idx].offset;
+ uint64_t to = from + coord_toc_[coord_idx].size;
- peptides[peptides.size()-1].dihedrals = DihedralInfo(phi,psi);
+ seq_.ClearRange(from, to);
+ coords_.ClearRange(from, to);
+ if(this->HasData(Dihedrals)) {
+ dihedrals_.ClearRange(from, to);
+ }
- //finally add all peptides to the coords_ and the frequencies to
- //aa_frequencies_
- for(std::vector<Peptide>::iterator i = peptides.begin();
- i != peptides.end(); ++i){
- coords_.push_back(*i);
+ if(this->HasData(SolventAccessibilities)) {
+ solv_acc_.ClearRange(from, to);
}
- for(uint i = 0; i < connected_size; ++i){
- AAFreq aa_freq;
- const ost::seq::ProfileColumn& col = (*prof)[prof_indices[i]];
- aa_freq.AssignProfileColumn(col);
- aa_frequencies_.push_back(aa_freq);
- AAFreq aa_freq_struct;
- aa_frequencies_struct_.push_back(aa_freq_struct);
+ if(this->HasData(ResidueDepths)) {
+ res_depths_.ClearRange(from, to);
}
- return chain_index;
+ if(this->HasData(DSSP)) {
+ dssp_.ClearRange(from, to);
+ }
+
+ if(this->HasData(AAFrequencies)) {
+ aa_frequencies_.ClearRange(from, to);
+ }
+
+ if(this->HasData(AAFrequenciesStruct)) {
+ aa_frequencies_struct_.ClearRange(from, to);
+ }
+
+ // correct all offset values of the coords that are stored afterwards
+ for(uint i = coord_idx + 1; i < coord_toc_.size(); ++i) {
+ coord_toc_[i].offset -= coord_toc_[coord_idx].size;
+ }
+
+ // and finally kill the CoordInfo itself
+ coord_toc_.erase(coord_toc_.begin() + coord_idx);
}
-int StructureDB::GetCoordIndex(const String& pdb_id, const String& chain_name) const{
- ost::FixedString<5> id(pdb_id+chain_name);
+
+std::vector<int> StructureDB::GetCoordIdx(const String& id,
+ const String& chain_name) const{
+
+ std::vector<int> return_vec;
+
for(uint i = 0; i < coord_toc_.size(); ++i){
- if(coord_toc_[i].pdb_id == id) return i;
+ if(coord_toc_[i].id == id) {
+ if(coord_toc_[i].chain_name == chain_name) {
+ return_vec.push_back(i);
+ }
+ }
}
- return -1;
+ return return_vec;
}
-CoordInfo StructureDB::GetCoordInfo(int index) const{
+const CoordInfo& StructureDB::GetCoordInfo(int index) const{
if(static_cast<uint>(index) >= coord_toc_.size()){
throw promod3::Error("pdb index exceeds number of coord tocs in database!");
}
@@ -544,61 +968,28 @@ Real StructureDB::CARMSD(const FragmentInfo& info_one,
core::EMatX3 pos_one = core::EMatX3::Zero(6,3);
core::EMatX3 pos_two = core::EMatX3::Zero(6,3);
- Peptide start_peptide = coords_[start_one];
- Peptide end_peptide = coords_[start_one + static_cast<uint>(info_one.length) - 1];
-
- pos_one(0,0) = start_peptide.coords.n.x * 0.01;
- pos_one(0,1) = start_peptide.coords.n.y * 0.01;
- pos_one(0,2) = start_peptide.coords.n.z * 0.01;
-
- pos_one(1,0) = start_peptide.coords.ca.x * 0.01;
- pos_one(1,1) = start_peptide.coords.ca.y * 0.01;
- pos_one(1,2) = start_peptide.coords.ca.z * 0.01;
-
- pos_one(2,0) = start_peptide.coords.c.x * 0.01;
- pos_one(2,1) = start_peptide.coords.c.y * 0.01;
- pos_one(2,2) = start_peptide.coords.c.z * 0.01;
+ PeptideCoords start_coords = coords_[start_one];
+ PeptideCoords end_coords = coords_[start_one +
+ static_cast<uint>(info_one.length) - 1];
- pos_one(3,0) = end_peptide.coords.n.x * 0.01;
- pos_one(3,1) = end_peptide.coords.n.y * 0.01;
- pos_one(3,2) = end_peptide.coords.n.z * 0.01;
+ core::EMatFillRow(pos_one, 0, start_coords.n.ToVec3());
+ core::EMatFillRow(pos_one, 1, start_coords.ca.ToVec3());
+ core::EMatFillRow(pos_one, 2, start_coords.c.ToVec3());
+ core::EMatFillRow(pos_one, 3, end_coords.n.ToVec3());
+ core::EMatFillRow(pos_one, 4, end_coords.ca.ToVec3());
+ core::EMatFillRow(pos_one, 5, end_coords.c.ToVec3());
- pos_one(4,0) = end_peptide.coords.ca.x * 0.01;
- pos_one(4,1) = end_peptide.coords.ca.y * 0.01;
- pos_one(4,2) = end_peptide.coords.ca.z * 0.01;
+ start_coords = coords_[start_two];
+ end_coords = coords_[start_two + static_cast<uint>(info_two.length) - 1];
- pos_one(5,0) = end_peptide.coords.c.x * 0.01;
- pos_one(5,1) = end_peptide.coords.c.y * 0.01;
- pos_one(5,2) = end_peptide.coords.c.z * 0.01;
+ core::EMatFillRow(pos_two, 0, start_coords.n.ToVec3());
+ core::EMatFillRow(pos_two, 1, start_coords.ca.ToVec3());
+ core::EMatFillRow(pos_two, 2, start_coords.c.ToVec3());
+ core::EMatFillRow(pos_two, 3, end_coords.n.ToVec3());
+ core::EMatFillRow(pos_two, 4, end_coords.ca.ToVec3());
+ core::EMatFillRow(pos_two, 5, end_coords.c.ToVec3());
- start_peptide = coords_[start_two];
- end_peptide = coords_[start_two + static_cast<uint>(info_two.length) - 1];
-
- pos_two(0,0) = start_peptide.coords.n.x * 0.01;
- pos_two(0,1) = start_peptide.coords.n.y * 0.01;
- pos_two(0,2) = start_peptide.coords.n.z * 0.01;
-
- pos_two(1,0) = start_peptide.coords.ca.x * 0.01;
- pos_two(1,1) = start_peptide.coords.ca.y * 0.01;
- pos_two(1,2) = start_peptide.coords.ca.z * 0.01;
-
- pos_two(2,0) = start_peptide.coords.c.x * 0.01;
- pos_two(2,1) = start_peptide.coords.c.y * 0.01;
- pos_two(2,2) = start_peptide.coords.c.z * 0.01;
-
- pos_two(3,0) = end_peptide.coords.n.x * 0.01;
- pos_two(3,1) = end_peptide.coords.n.y * 0.01;
- pos_two(3,2) = end_peptide.coords.n.z * 0.01;
-
- pos_two(4,0) = end_peptide.coords.ca.x * 0.01;
- pos_two(4,1) = end_peptide.coords.ca.y * 0.01;
- pos_two(4,2) = end_peptide.coords.ca.z * 0.01;
-
- pos_two(5,0) = end_peptide.coords.c.x * 0.01;
- pos_two(5,1) = end_peptide.coords.c.y * 0.01;
- pos_two(5,2) = end_peptide.coords.c.z * 0.01;
-
- geom::Mat4 t = core::MinRMSDSuperposition(pos_one,pos_two);
+ geom::Mat4 t = core::MinRMSDSuperposition(pos_one, pos_two);
Real msd = 0.0;
Real temp;
@@ -606,39 +997,42 @@ Real StructureDB::CARMSD(const FragmentInfo& info_one,
geom::Vec3 ca_pos_two;
for(int i = 0; i < info_one.length; ++i){
- ca_pos_one = coords_[start_one+i].coords.ca.ToVec3();
- ca_pos_two = coords_[start_two+i].coords.ca.ToVec3();
+ ca_pos_one = coords_[start_one+i].ca.ToVec3();
+ ca_pos_two = coords_[start_two+i].ca.ToVec3();
- temp = t(0,0)*ca_pos_one[0]+t(0,1)*ca_pos_one[1]+t(0,2)*ca_pos_one[2]+t(0,3);
+ temp = t(0,0) * ca_pos_one[0] +
+ t(0,1) * ca_pos_one[1] +
+ t(0,2) * ca_pos_one[2] +
+ t(0,3);
temp -= ca_pos_two[0];
msd += temp * temp;
- temp = t(1,0)*ca_pos_one[0]+t(1,1)*ca_pos_one[1]+t(1,2)*ca_pos_one[2]+t(1,3);
+ temp = t(1,0) * ca_pos_one[0] +
+ t(1,1) * ca_pos_one[1] +
+ t(1,2) * ca_pos_one[2] +
+ t(1,3);
temp -= ca_pos_two[1];
msd += temp * temp;
- temp = t(2,0)*ca_pos_one[0]+t(2,1)*ca_pos_one[1]+t(2,2)*ca_pos_one[2]+t(2,3);
+ temp = t(2,0) * ca_pos_one[0] +
+ t(2,1) * ca_pos_one[1] +
+ t(2,2) * ca_pos_one[2] +
+ t(2,3);
temp -= ca_pos_two[2];
msd += temp * temp;
}
- return std::sqrt(msd/info_one.length);
+ return std::sqrt(msd / info_one.length);
}
core::EMatX3 pos_one = core::EMatX3::Zero(info_one.length,3);
core::EMatX3 pos_two = core::EMatX3::Zero(info_one.length,3);
for(int i = 0; i < info_one.length; ++i){
- const Peptide& pep = coords_[start_one+i];
- pos_one(i,0) = pep.coords.ca.x * 0.01;
- pos_one(i,1) = pep.coords.ca.y * 0.01;
- pos_one(i,2) = pep.coords.ca.z * 0.01;
+ core::EMatFillRow(pos_one, i, coords_[start_one + i].ca.ToVec3());
}
for(int i = 0; i < info_two.length; ++i){
- const Peptide& pep = coords_[start_two+i];
- pos_two(i,0) = pep.coords.ca.x * 0.01;
- pos_two(i,1) = pep.coords.ca.y * 0.01;
- pos_two(i,2) = pep.coords.ca.z * 0.01;
+ core::EMatFillRow(pos_two, i, coords_[start_two + i].ca.ToVec3());
}
return core::SuperposedRMSD(pos_one,pos_two);
@@ -656,10 +1050,10 @@ void StructureDB::FillBackbone(BackboneList& bb_list, const FragmentInfo& info,
uint coord_start = GetStartIndex(info);
for (uint i = 0; i < info.length; ++i) {
// NOTE: CB pos. and AA (must be non-XXX) are set in push_back
- bb_list.push_back(coords_[coord_start+i].coords.n.ToVec3(),
- coords_[coord_start+i].coords.ca.ToVec3(),
- coords_[coord_start+i].coords.c.ToVec3(),
- coords_[coord_start+i].coords.o.ToVec3(),
+ bb_list.push_back(coords_[coord_start+i].n.ToVec3(),
+ coords_[coord_start+i].ca.ToVec3(),
+ coords_[coord_start+i].c.ToVec3(),
+ coords_[coord_start+i].o.ToVec3(),
sequence[i]);
}
}
@@ -692,10 +1086,9 @@ void StructureDB::FillBackbone(BackboneList& bb_list,
"backbone atoms!");
}
- // note, that GetPos() on an atomhandle gets a reference to the internal pos
- pos_one.row(0) = core::ERVec3(&(n.GetPos()[0]));
- pos_one.row(1) = core::ERVec3(&(ca.GetPos()[0]));
- pos_one.row(2) = core::ERVec3(&(c.GetPos()[0]));
+ core::EMatFillRow(pos_one, 0, n.GetPos());
+ core::EMatFillRow(pos_one, 1, ca.GetPos());
+ core::EMatFillRow(pos_one, 2, c.GetPos());
n = stem_two.FindAtom("N");
ca = stem_two.FindAtom("CA");
@@ -706,37 +1099,20 @@ void StructureDB::FillBackbone(BackboneList& bb_list,
"backbone atoms!");
}
- pos_one.row(3) = core::ERVec3(&(n.GetPos()[0]));
- pos_one.row(4) = core::ERVec3(&(ca.GetPos()[0]));
- pos_one.row(5) = core::ERVec3(&(c.GetPos()[0]));
+ core::EMatFillRow(pos_one, 3, n.GetPos());
+ core::EMatFillRow(pos_one, 4, ca.GetPos());
+ core::EMatFillRow(pos_one, 5, c.GetPos());
int start = GetStartIndex(info);
- const Peptide& start_peptide = coords_[start];
- const Peptide& end_peptide = coords_[start + info.length - 1];
-
- pos_two(0,0) = start_peptide.coords.n.x * 0.01;
- pos_two(0,1) = start_peptide.coords.n.y * 0.01;
- pos_two(0,2) = start_peptide.coords.n.z * 0.01;
+ const PeptideCoords& start_coords = coords_[start];
+ const PeptideCoords& end_coords = coords_[start + info.length - 1];
- pos_two(1,0) = start_peptide.coords.ca.x * 0.01;
- pos_two(1,1) = start_peptide.coords.ca.y * 0.01;
- pos_two(1,2) = start_peptide.coords.ca.z * 0.01;
-
- pos_two(2,0) = start_peptide.coords.c.x * 0.01;
- pos_two(2,1) = start_peptide.coords.c.y * 0.01;
- pos_two(2,2) = start_peptide.coords.c.z * 0.01;
-
- pos_two(3,0) = end_peptide.coords.n.x * 0.01;
- pos_two(3,1) = end_peptide.coords.n.y * 0.01;
- pos_two(3,2) = end_peptide.coords.n.z * 0.01;
-
- pos_two(4,0) = end_peptide.coords.ca.x * 0.01;
- pos_two(4,1) = end_peptide.coords.ca.y * 0.01;
- pos_two(4,2) = end_peptide.coords.ca.z * 0.01;
-
- pos_two(5,0) = end_peptide.coords.c.x * 0.01;
- pos_two(5,1) = end_peptide.coords.c.y * 0.01;
- pos_two(5,2) = end_peptide.coords.c.z * 0.01;
+ core::EMatFillRow(pos_two, 0, start_coords.n.ToVec3());
+ core::EMatFillRow(pos_two, 1, start_coords.ca.ToVec3());
+ core::EMatFillRow(pos_two, 2, start_coords.c.ToVec3());
+ core::EMatFillRow(pos_two, 3, end_coords.n.ToVec3());
+ core::EMatFillRow(pos_two, 4, end_coords.ca.ToVec3());
+ core::EMatFillRow(pos_two, 5, end_coords.c.ToVec3());
geom::Mat4 t = core::MinRMSDSuperposition(pos_two,pos_one);
@@ -752,13 +1128,17 @@ String StructureDB::GetSequence(const FragmentInfo& info) const{
int end = start+info.length;
int pos = 0;
for (; start < end; ++start, ++pos) {
- return_sequence[pos] = coords_[start].olc;
+ return_sequence[pos] = seq_[start];
}
return return_sequence;
}
String StructureDB::GetDSSPStates(const FragmentInfo& info) const{
+ if(!this->HasData(DSSP)) {
+ throw promod3::Error("StructureDB does not contain dssp assignments!");
+ }
+
this->CheckFragmentInfo(info);
String return_states(static_cast<uint>(info.length),'C');
@@ -766,12 +1146,17 @@ String StructureDB::GetDSSPStates(const FragmentInfo& info) const{
int end = start+info.length;
int pos = 0;
for (; start < end; ++start, ++pos) {
- return_states[pos] = coords_[start].dssp_state;
+ return_states[pos] = dssp_[start];
}
return return_states;
}
-std::vector<std::pair<Real,Real> > StructureDB::GetDihedralAngles(const FragmentInfo& info) const{
+std::vector<std::pair<Real,Real> >
+StructureDB::GetDihedralAngles(const FragmentInfo& info) const{
+
+ if(!this->HasData(Dihedrals)) {
+ throw promod3::Error("StructureDB does not contain dihedrals!");
+ }
this->CheckFragmentInfo(info);
@@ -780,14 +1165,19 @@ std::vector<std::pair<Real,Real> > StructureDB::GetDihedralAngles(const Fragment
int end = start+info.length;
int pos = 0;
for (; start < end; ++start, ++pos) {
- return_vec[pos] = std::make_pair(coords_[start].dihedrals.GetPhi(),
- coords_[start].dihedrals.GetPsi());
+ const DihedralInfo& dihedrals = dihedrals_[start];
+ return_vec[pos] = std::make_pair(dihedrals.GetPhi(),
+ dihedrals.GetPsi());
}
return return_vec;
}
std::vector<Real> StructureDB::GetResidueDepths(const FragmentInfo& info) const{
+ if(!this->HasData(ResidueDepths)) {
+ throw promod3::Error("StructureDB does not contain residue depths!");
+ }
+
this->CheckFragmentInfo(info);
std::vector<Real> return_depths;
@@ -795,13 +1185,18 @@ std::vector<Real> StructureDB::GetResidueDepths(const FragmentInfo& info) const{
int start = GetStartIndex(info);
int end = start+info.length;
for (; start < end; ++start) {
- return_depths.push_back(0.1 * coords_[start].res_depth);
+ return_depths.push_back(0.1 * res_depths_[start]);
}
return return_depths;
}
std::vector<int> StructureDB::GetSolventAccessibilities(const FragmentInfo& info) const{
+ if(!this->HasData(SolventAccessibilities)) {
+ throw promod3::Error("StructureDB does not contain "
+ "solvent accessibilities!");
+ }
+
this->CheckFragmentInfo(info);
std::vector<int> return_accessibilities;
@@ -809,7 +1204,7 @@ std::vector<int> StructureDB::GetSolventAccessibilities(const FragmentInfo& info
int start = GetStartIndex(info);
int end = start+info.length;
for (; start < end; ++start) {
- return_accessibilities.push_back(coords_[start].solv_acc);
+ return_accessibilities.push_back(solv_acc_[start]);
}
return return_accessibilities;
}
@@ -817,9 +1212,9 @@ std::vector<int> StructureDB::GetSolventAccessibilities(const FragmentInfo& info
ost::seq::ProfileHandlePtr
StructureDB::GetSequenceProfile(const FragmentInfo& info) const {
- if (!frequencies_present_) {
- throw promod3::Error("Cannot access profile information in database "
- "loaded with load_frequencies = false!");
+ if(!this->HasData(AAFrequencies)) {
+ throw promod3::Error("StructureDB does not contain amino acid "
+ "frequencies!");
}
this->CheckFragmentInfo(info);
@@ -835,7 +1230,7 @@ StructureDB::GetSequenceProfile(const FragmentInfo& info) const {
for (uint i = 0; i < 20; ++i) {
col_data[i] = static_cast<Real>(0.0001 * freqs[i]);
}
- prof->AddColumn(col, coords_[start].olc);
+ prof->AddColumn(col, seq_[start]);
}
return prof;
}
@@ -843,9 +1238,9 @@ StructureDB::GetSequenceProfile(const FragmentInfo& info) const {
ost::seq::ProfileHandlePtr
StructureDB::GetStructureProfile(const FragmentInfo& info) const {
- if (!frequencies_present_) {
- throw promod3::Error("Cannot access profile information in database "
- "loaded with load_frequencies = false!");
+ if(!this->HasData(AAFrequenciesStruct)) {
+ throw promod3::Error("StructureDB does not contain amino acid "
+ "frequencies derived from structural information!");
}
this->CheckFragmentInfo(info);
@@ -861,15 +1256,21 @@ StructureDB::GetStructureProfile(const FragmentInfo& info) const {
for (uint i = 0; i < 20; ++i) {
col_data[i] = static_cast<Real>(0.0001 * freqs[i]);
}
- prof->AddColumn(col, coords_[start].olc);
+ prof->AddColumn(col, seq_[start]);
}
return prof;
}
+int StructureDB::GetStartResnum(const FragmentInfo& info) const {
+
+ this->CheckFragmentInfo(info);
+
+ return coord_toc_[info.chain_index].start_resnum + info.offset;
+}
+
StructureDBPtr StructureDB::GetSubDB(const std::vector<uint>& indices) const{
- StructureDBPtr ret_db(new StructureDB);
- ret_db->frequencies_present_ = frequencies_present_;
+ StructureDBPtr sub_db(new StructureDB(stored_data_));
for(std::vector<uint>::const_iterator i = indices.begin();
i != indices.end(); ++i){
@@ -878,110 +1279,139 @@ StructureDBPtr StructureDB::GetSubDB(const std::vector<uint>& indices) const{
throw promod3::Error("Invalid idx observed when creating SubDB!");
}
- ret_db->coord_toc_.push_back(coord_toc_[*i]);
- ret_db->coord_toc_.back().offset = ret_db->coords_.size();
+ sub_db->coord_toc_.push_back(coord_toc_[*i]);
+ sub_db->coord_toc_.back().offset = sub_db->coords_.size();
uint start = coord_toc_[*i].offset;
uint end = start + coord_toc_[*i].size;
- for(uint j = start; j < end; ++j){
- ret_db->coords_.push_back(coords_[j]);
+ for(uint j = start; j < end; ++j) {
+ sub_db->seq_.push_back(seq_[j]);
+ sub_db->coords_.push_back(coords_[j]);
}
- if(frequencies_present_){
- for(uint j = start; j < end; ++j){
- ret_db->aa_frequencies_.push_back(aa_frequencies_[j]);
- ret_db->aa_frequencies_struct_.push_back(aa_frequencies_struct_[j]);
- }
+ if(this->HasData(Dihedrals)) {
+ for(uint j = start; j < end; ++j) {
+ sub_db->dihedrals_.push_back(dihedrals_[j]);
+ }
+ }
+
+ if(this->HasData(SolventAccessibilities)) {
+ for(uint j = start; j < end; ++j) {
+ sub_db->solv_acc_.push_back(solv_acc_[j]);
+ }
+ }
+
+ if(this->HasData(ResidueDepths)) {
+ for(uint j = start; j < end; ++j) {
+ sub_db->res_depths_.push_back(res_depths_[j]);
+ }
+ }
+
+ if(this->HasData(DSSP)) {
+ for(uint j = start; j < end; ++j) {
+ sub_db->dssp_.push_back(dssp_[j]);
+ }
+ }
+
+ if(this->HasData(AAFrequencies)) {
+ for(uint j = start; j < end; ++j) {
+ sub_db->aa_frequencies_.push_back(aa_frequencies_[j]);
+ }
+ }
+
+ if(this->HasData(AAFrequenciesStruct)) {
+ for(uint j = start; j < end; ++j) {
+ sub_db->aa_frequencies_struct_.push_back(aa_frequencies_struct_[j]);
+ }
}
}
- return ret_db;
+ return sub_db;
}
void StructureDB::PrintStatistics() const{
- std::cout << "number of pdb chains : " << coord_toc_.size() << std::endl;
+ std::cout << "number of chains : " << coord_toc_.size() << std::endl;
std::cout << "number of backbone coords :" << coords_.size() << std::endl;
}
ost::seq::ProfileHandlePtr StructureDB::GenerateStructureProfile(
- const StructureDB& other_db,
- const FragmentInfo& info) const {
+ const BackboneList& bb_list,
+ const std::vector<Real>& residue_depths) const {
- if (info.length == 0) {
- throw promod3::Error("Cannot generate structural profile from empty input!");
+ if(!this->HasData(ResidueDepths)) {
+ throw promod3::Error("StructureDB does not contain residue depths!");
}
- other_db.CheckFragmentInfo(info);
- // get data from other_db
- std::vector<Real> residue_depths = other_db.GetResidueDepths(info);
- assert(residue_depths.size() == info.length);
- std::vector<geom::Vec3> ca_pos;
- ca_pos.reserve(info.length);
- uint coord_start = other_db.GetStartIndex(info);
- for (uint i = 0; i < info.length; ++i) {
- ca_pos.push_back(other_db.GetPeptide(coord_start+i).coords.ca.ToVec3());
+ if(bb_list.size() != residue_depths.size()) {
+ throw promod3::Error("BackboneList and residue depths must be of same "
+ "size!");
}
- uint frag_length = std::min(9, static_cast<int>(info.length));
- FragmentInfo inf(0,0,frag_length);
+ uint bb_list_size = bb_list.size();
+ uint frag_length = std::min(9, static_cast<int>(bb_list.size()));
+ FragmentInfo inf(0, 0, frag_length);
std::vector<std::vector<char> > close_sequences;
- close_sequences.assign(info.length, std::vector<char>());
+ close_sequences.assign(bb_list_size, std::vector<char>());
std::list<std::pair<Real,FragmentInfo> > similar_frags;
// let's create a buffer for the exponential depth terms in the db
+ // as well as the extracted positions
uint longest_chain = 0;
for(uint i = 0; i < coord_toc_.size(); ++i){
longest_chain = std::max(longest_chain,static_cast<uint>(coord_toc_[i].size));
}
- std::vector<Real> db_depths(longest_chain);
+ std::vector<Real> db_depths_full_chain(longest_chain);
+ std::vector<geom::Vec3> ca_pos_full_chain(longest_chain);
// the exponential depth values can be precalculated
- std::vector<Real> depths(info.length);
- for(uint i = 0; i < info.length; ++i){
+ std::vector<Real> depths(bb_list_size);
+ for(uint i = 0; i < bb_list_size; ++i){
depths[i] = std::exp(-residue_depths[i] * 0.35714);
}
// positions for rmsd calculations will be stored in here
- core::EMatX3 pos = core::EMatX3::Zero(frag_length,3);
- core::EMatX3 db_pos = core::EMatX3::Zero(frag_length,3);
+ core::EMatX3 pos = core::EMatX3::Zero(frag_length, 3);
+ core::EMatX3 db_pos = core::EMatX3::Zero(frag_length, 3);
- for(uint i = 0; i <= info.length-frag_length; ++i){
+ for(uint i = 0; i <= bb_list_size - frag_length; ++i){
similar_frags.clear();
Real worst_score = std::numeric_limits<Real>::max();
// set the positions for query fragments
for (uint j = 0; j < frag_length; ++j) {
- core::EMatFillRow(pos, j, ca_pos[i+j]);
+ core::EMatFillRow(pos, j, bb_list.GetCA(i+j));
}
inf.chain_index = 0;
// let's search through all chains of the db
for(uint j = 0; j < coord_toc_.size(); ++j, ++inf.chain_index){
+
if(coord_toc_[j].size < frag_length) continue;
+
inf.offset = 0;
// the depth exp value of the full chain can be precalculated
+ // at the same time we're extracting the positions here
uint db_chain_offset = coord_toc_[j].offset;
for(uint k = 0; k < coord_toc_[j].size; ++k){
- db_depths[k] = std::exp(-coords_[db_chain_offset + k].res_depth * 0.035714);
+ db_depths_full_chain[k] = std::exp(-res_depths_[db_chain_offset + k] * 0.035714);
+ ca_pos_full_chain[k] = coords_[db_chain_offset + k].ca.ToVec3();
}
+
// let's finally iterate over all possible fragments in this chain
- for(uint k = 0; k <= coord_toc_[j].size-frag_length; ++k, ++inf.offset){
+ for(uint k = 0; k <= coord_toc_[j].size - frag_length; ++k, ++inf.offset){
for(uint l = 0; l < frag_length; ++l){
- const Peptide& pep = coords_[db_chain_offset + k + l];
- db_pos(l,0) = pep.coords.ca.x * 0.01;
- db_pos(l,1) = pep.coords.ca.y * 0.01;
- db_pos(l,2) = pep.coords.ca.z * 0.01;
+ core::EMatFillRow(db_pos, l, ca_pos_full_chain[k+l]);
}
- Real rmsd = core::SuperposedRMSD(pos,db_pos);
+ Real rmsd = core::SuperposedRMSD(pos, db_pos);
Real summed_squared_depth_diff = 0.0;
for(uint l = 0; l < frag_length; ++l){
- Real temp = depths[i+l]-db_depths[k+l];
+ Real temp = depths[i+l] - db_depths_full_chain[k+l];
summed_squared_depth_diff += temp*temp;
}
@@ -1017,30 +1447,36 @@ ost::seq::ProfileHandlePtr StructureDB::GenerateStructureProfile(
// set profile
ost::seq::ProfileHandlePtr return_prof(new ost::seq::ProfileHandle);
return_prof->SetNullModel(ost::seq::ProfileColumn::HHblitsNullModel());
- String other_sequence = other_db.GetSequence(info);
+ String reference_sequence = bb_list.GetSequence();
Real frequencies[20];
- for(uint i = 0; i < info.length; ++i){
+ for(uint i = 0; i < bb_list_size; ++i) {
// sum up a value of one for every position
memset(frequencies,0,sizeof(Real)*20);
- for(uint j = 0; j < close_sequences[i].size(); ++j){
+ for(uint j = 0; j < close_sequences[i].size(); ++j) {
int idx = ost::seq::ProfileColumn::GetIndex(close_sequences[i][j]);
- if(idx != -1) frequencies[idx] += 1.0;
+ if(idx != -1) {
+ frequencies[idx] += 1.0;
+ }
}
// normalize it
Real sum = 0.0;
- for(uint j = 0; j < 20; ++j) sum += frequencies[j];
-
- if(sum != 0){
+ for(uint j = 0; j < 20; ++j) {
+ sum += frequencies[j];
+ }
+
+ if(sum != 0) {
Real factor = 1.0/sum;
- for(uint j = 0; j < 20; ++j) frequencies[j] *= factor;
+ for(uint j = 0; j < 20; ++j) {
+ frequencies[j] *= factor;
+ }
}
// and add it to the profile
ost::seq::ProfileColumn actual_col;
Real* prof_col_data = actual_col.freqs_begin();
- for(uint j = 0; j < 20; ++j){
+ for(uint j = 0; j < 20; ++j) {
prof_col_data[j] = frequencies[j];
}
- return_prof->AddColumn(actual_col, other_sequence[i]);
+ return_prof->AddColumn(actual_col, reference_sequence[i]);
}
return return_prof;
@@ -1049,9 +1485,9 @@ ost::seq::ProfileHandlePtr StructureDB::GenerateStructureProfile(
void StructureDB::SetStructureProfile(uint chain_idx,
ost::seq::ProfileHandlePtr prof) {
- if(!frequencies_present_){
- throw promod3::Error("Cannot set profile information in database "
- "loaded with load_frequencies = false!");
+ if(!this->HasData(AAFrequenciesStruct)) {
+ throw promod3::Error("StructureDB does not contain amino acid "
+ "frequencies derived from structural information!");
}
if(chain_idx >= coord_toc_.size()){
diff --git a/loop/src/structure_db.hh b/loop/src/structure_db.hh
index 2068c60624444ac29bc42c1c36890f6006bcef54..a11db69ef12d31a3669ea5c986933ebadd94e640 100644
--- a/loop/src/structure_db.hh
+++ b/loop/src/structure_db.hh
@@ -19,10 +19,10 @@
#include <ost/mol/surface_handle.hh>
#include <promod3/loop/paged_array.hh>
-#include <promod3/loop/ushort_vec.hh>
#include <promod3/loop/backbone.hh>
#include <promod3/core/message.hh>
#include <promod3/core/superpose.hh>
+#include <promod3/loop/structure_db_custom_types.hh>
#include <promod3/core/portable_binary_serializer.hh>
@@ -31,60 +31,57 @@ namespace promod3 { namespace loop {
class StructureDB;
typedef boost::shared_ptr<StructureDB> StructureDBPtr;
+
struct CoordInfo {
- CoordInfo(): offset(0), size(0) {}
+ CoordInfo() { }
CoordInfo(const String& id, const String& chain_name,
- uint off=0, uint s=0):
- pdb_id(id+chain_name), offset(off), size(s)
- { }
+ uint off, uint s, uint sr, const geom::Vec3 sh):
+ id(id), chain_name(chain_name),
+ offset(off), size(s),
+ start_resnum(sr), shift(sh) { }
+
/// pdb id plus chain all lowercase letters
- String GetFullID() const{
- String id = "";
- for(uint i = 0; i < pdb_id.size(); ++i){
- id += pdb_id[i];
- }
- return id;
+ String GetFullID() const {
+ return id + "_" + chain_name;
}
// portable serialization
// (cleanly element by element with fixed-width base-types)
template <typename DS>
void Serialize(DS& ds) {
- if (ds.IsSource()) {
- // load ID
- String id;
- ds & id;
- // ensure appropriate length of pdb_id
- if (id.length() > pdb_id.capacity()) {
- throw promod3::Error(String("Serialize-load failed for ID ") + id);
- } else {
- pdb_id = id;
- }
- } else {
- String id(pdb_id.c_str());
- ds & id;
- }
+ core::ConvertBaseType<String> (ds, id);
+ core::ConvertBaseType<String> (ds, chain_name);
core::ConvertBaseType<uint32_t>(ds, offset);
core::ConvertBaseType<uint16_t>(ds, size);
+ core::ConvertBaseType<uint16_t>(ds, start_resnum);
+ core::ConvertBaseType<float>(ds, shift[0]);
+ core::ConvertBaseType<float>(ds, shift[1]);
+ core::ConvertBaseType<float>(ds, shift[2]);
}
bool operator==(const CoordInfo& rhs) const {
- return pdb_id == rhs.pdb_id
+ return id == rhs.id
+ && chain_name == rhs.chain_name
&& offset == rhs.offset
- && size == rhs.size;
+ && size == rhs.size
+ && start_resnum == rhs.start_resnum;
}
bool operator!=(const CoordInfo& rhs) const {
return !this->operator==(rhs);
}
- ost::FixedString<5> pdb_id;
+ String id;
+ String chain_name;
uint offset;
unsigned short size;
+ unsigned short start_resnum;
+ geom::Vec3 shift;
};
+
struct FragmentInfo {
FragmentInfo() { }
- FragmentInfo(unsigned short c_i,
+ FragmentInfo(unsigned int c_i,
unsigned short o,
unsigned short l): chain_index(c_i),
offset(o),
@@ -94,7 +91,7 @@ struct FragmentInfo {
// (cleanly element by element with fixed-width base-types)
template <typename DS>
void Serialize(DS& ds) {
- core::ConvertBaseType<uint16_t>(ds, chain_index);
+ core::ConvertBaseType<uint32_t>(ds, chain_index);
core::ConvertBaseType<uint16_t>(ds, offset);
core::ConvertBaseType<uint16_t>(ds, length);
}
@@ -108,172 +105,54 @@ struct FragmentInfo {
return !this->operator==(rhs);
}
- unsigned short chain_index;
+ unsigned int chain_index;
unsigned short offset;
unsigned short length;
};
-struct PeptideCoords {
- // portable serialization
- // (cleanly element by element with fixed-width base-types)
- template <typename DS>
- void Serialize(DS& ds) {
- ds & n;
- ds & ca;
- ds & c;
- ds & o;
- }
-
- bool operator==(const PeptideCoords& rhs) const {
- return n == rhs.n
- && ca == rhs.ca
- && c == rhs.c
- && o == rhs.o;
- }
- bool operator!=(const PeptideCoords& rhs) const {
- return !this->operator==(rhs);
- }
-
- UShortVec n;
- UShortVec ca;
- UShortVec c;
- UShortVec o;
-};
-
-struct DihedralInfo {
- DihedralInfo() { }
- DihedralInfo(Real a, Real b){
- phi = a * 1000;
- psi = b * 1000;
- }
-
- inline Real GetPhi() const { return static_cast<Real>(phi) * Real(0.001); }
-
- inline Real GetPsi() const { return static_cast<Real>(psi) * Real(0.001); }
-
- // portable serialization
- // (cleanly element by element with fixed-width base-types)
- template <typename DS>
- void Serialize(DS& ds) {
- core::ConvertBaseType<int16_t>(ds, phi);
- core::ConvertBaseType<int16_t>(ds, psi);
- }
-
- bool operator==(const DihedralInfo& rhs) const {
- return phi == rhs.phi
- && psi == rhs.psi;
- }
- bool operator!=(const DihedralInfo& rhs) const {
- return !this->operator==(rhs);
- }
-
- short phi;
- short psi;
-};
-
-struct AAFreq {
-
- AAFreq() {
- memset(freqs, 0, sizeof(short)*20);
- }
-
- void AssignProfileColumn(const ost::seq::ProfileColumn& col);
- const short* data() const { return freqs; }
- short* data() { return freqs; }
-
- // portable serialization
- // (cleanly element by element with fixed-width base-types)
- template <typename DS>
- void Serialize(DS& ds) {
- for (int i = 0; i < 20; ++i) {
- core::ConvertBaseType<int16_t>(ds, freqs[i]);
- }
- }
-
- bool operator==(const AAFreq& rhs) const {
- return !memcmp(freqs, rhs.freqs, sizeof(short)*20);
- }
- bool operator!=(const AAFreq& rhs) const {
- return !this->operator==(rhs);
- }
-
- short freqs[20];
-};
-
-struct Peptide {
- // portable serialization
- // (cleanly element by element with fixed-width base-types)
- template <typename DS>
- void Serialize(DS& ds) {
- ds & coords;
- ds & dihedrals;
- core::ConvertBaseType<uint16_t>(ds, solv_acc);
- core::ConvertBaseType<uint16_t>(ds, res_depth);
- ds & olc;
- ds & dssp_state;
- }
-
- bool operator==(const Peptide& rhs) const {
- return coords == rhs.coords
- && dihedrals == rhs.dihedrals
- && solv_acc == rhs.solv_acc
- && res_depth == rhs.res_depth
- && olc == rhs.olc
- && dssp_state == rhs.dssp_state;
- }
- bool operator!=(const Peptide& rhs) const {
- return !this->operator==(rhs);
- }
-
- PeptideCoords coords; //contains all backbone coordinates
- DihedralInfo dihedrals; //contains phi and psi dihedral angles
- unsigned short solv_acc; //solvent accessibility in A^2 as calculated by dssp
- unsigned short res_depth; //average distance of the atoms to closest surface in A
- //multiplied by a value of 10 to allow an accuracy of 0.1
- char olc; //the one letter code
- char dssp_state; //the dssp state, which should be a member of
- // {H,B,E,G,I,T,S}
-};
class StructureDB {
public:
- StructureDB(): frequencies_present_(true) { }
+ enum DBDataType {All = -1, Dihedrals = 1, SolventAccessibilities = 2,
+ ResidueDepths = 4, DSSP = 8, AAFrequencies = 16,
+ AAFrequenciesStruct = 32};
- static StructureDBPtr Load(const String& file_name,
- bool load_frequencies);
+ StructureDB(int32_t stored_data = -1): stored_data_(stored_data) { }
+
+ static StructureDBPtr Load(const String& file_name);
void Save(const String& filename);
- // only with frequencies (otherwise we cannot use Save)
static StructureDBPtr LoadPortable(const String& file_name);
void SavePortable(const String& filename);
+ bool HasData(DBDataType data_type) const {
+ return (data_type & stored_data_) == data_type;
+ }
+
bool operator==(const StructureDB& rhs) const;
bool operator!=(const StructureDB& rhs) const {
return !this->operator==(rhs);
}
- bool HasFrequencies() { return frequencies_present_; }
+ std::vector<int> AddCoordinates(const String& id, const String& chain_name,
+ ost::mol::EntityView& ent,
+ ost::seq::SequenceHandle& seqres,
+ ost::seq::ProfileHandlePtr prof =
+ ost::seq::ProfileHandlePtr(),
+ bool only_longest_stretch = true);
- int AddCoordinates(const String& pdb_id, const String& chain_name,
- const ost::mol::ChainView& chain,
- const ost::mol::SurfaceHandle& surf,
- ost::seq::ProfileHandlePtr prof,
- const String& solvent_accessibilty_string =
- "solvent_accessibility");
+ void RemoveCoordinates(uint coord_idx);
- int GetCoordIndex(const String& pdb_id, const String& chain_name) const;
+ std::vector<int> GetCoordIdx(const String& id,
+ const String& chain_name) const;
- CoordInfo GetCoordInfo(int index) const;
+ const CoordInfo& GetCoordInfo(int index) const;
size_t GetNumCoords() const { return coord_toc_.size(); }
- Peptide& GetPeptide(int index) { return coords_[index]; }
-
- const Peptide& GetPeptide(int index) const { return coords_[index]; }
-
Real CARMSD(const FragmentInfo& info_one,
const FragmentInfo& info_two,
bool superpose_stems = true) const;
@@ -303,36 +182,92 @@ public:
ost::seq::ProfileHandlePtr GetStructureProfile(const FragmentInfo& info) const;
+ int GetStartResnum(const FragmentInfo& info) const;
+
StructureDBPtr GetSubDB(const std::vector<uint>& indices) const;
void PrintStatistics() const;
ost::seq::ProfileHandlePtr GenerateStructureProfile(
- const StructureDB& other_db,
- const FragmentInfo& info) const;
+ const BackboneList& other_db,
+ const std::vector<Real>& residue_depths) const;
void SetStructureProfile(uint chain_idx, ost::seq::ProfileHandlePtr prof);
- //functions to gain direct access to db internals, not intended for python export
+
+ // functions to gain direct access to db internals, not intended for python
+ // export
+
const std::vector<CoordInfo>& GetCoordToc() const { return coord_toc_; }
- const PagedArray<Peptide,4096>& GetCoords() const { return coords_; }
- const PagedArray<AAFreq, 4096>& GetAAFrequencies() const {
- if(!frequencies_present_){
- throw promod3::Error("Cannot access profile information in database "
- "loaded with load_frequencies = false!");
- }
+
+ const PagedArray<char, 65536>& GetSeq() const {
+ return seq_;
+ }
+
+ const PagedArray<PeptideCoords, 65536>& GetCoords() const {
+ return coords_;
+ }
+
+ const PagedArray<DihedralInfo, 65536>& GetDihedrals() const {
+
+ if(!this->HasData(Dihedrals)) {
+ throw promod3::Error("StructureDB does not contain dihedrals!");
+ }
+
+ return dihedrals_;
+ }
+
+ const PagedArray<unsigned short, 65536>& GetSolvAcc() const {
+
+ if(!this->HasData(SolventAccessibilities)) {
+ throw promod3::Error("StructureDB does not contain "
+ "solvent accessibilities!");
+ }
+
+ return solv_acc_;
+ }
+
+ const PagedArray<unsigned short, 65536>& GetResDepth() const {
+
+ if(!this->HasData(ResidueDepths)) {
+ throw promod3::Error("StructureDB does not contain residue depths!");
+ }
+
+ return res_depths_;
+ }
+
+ const PagedArray<char, 65536>& GetDSSP() const {
+
+ if(!this->HasData(DSSP)) {
+ throw promod3::Error("StructureDB does not contain dssp assignments!");
+ }
+
+ return dssp_;
+ }
+
+ const PagedArray<AAFreq, 65536>& GetAAFrequencies() const {
+
+ if(!this->HasData(AAFrequencies)) {
+ throw promod3::Error("StructureDB does not contain amino acid "
+ "frequencies!");
+ }
+
return aa_frequencies_;
}
- const PagedArray<AAFreq, 4096>& GetAAStructFrequencies() const {
- if(!frequencies_present_){
- throw promod3::Error("Cannot access profile information in database "
- "loaded with load_frequencies = false!");
+
+ const PagedArray<AAFreq, 65536>& GetAAStructFrequencies() const {
+
+ if(!this->HasData(AAFrequenciesStruct)) {
+ throw promod3::Error("StructureDB does not contain amino acid "
+ "frequencies derived from structural information!");
}
+
return aa_frequencies_struct_;
}
private:
+ // just don't allow it...
StructureDB(const StructureDB& other) { };
// get start index into paged arrays
@@ -341,11 +276,41 @@ private:
}
void CheckFragmentInfo(const FragmentInfo& info) const;
- std::vector<CoordInfo> coord_toc_;
- PagedArray<Peptide, 4096> coords_;
- PagedArray<AAFreq, 4096> aa_frequencies_;
- PagedArray<AAFreq, 4096> aa_frequencies_struct_;
- bool frequencies_present_;
+ ///////////////////
+ // INTERNAL DATA //
+ ///////////////////
+
+ // bitfield that defines what kind of data is stored in the database
+ int32_t stored_data_;
+
+ // stores information about full stretches
+ std::vector<CoordInfo> coord_toc_;
+
+ // one letter codes
+ PagedArray<char, 65536> seq_;
+
+ // backbone coordinates
+ PagedArray<PeptideCoords, 65536> coords_;
+
+ // phi and psi dihedrals
+ PagedArray<DihedralInfo, 65536> dihedrals_;
+
+ // solvent accessibility in A^2 as calculated by Lee & Richards implementation
+ // in ost
+ PagedArray<uint16_t, 65536> solv_acc_;
+
+ // distance towards closest surface residue in A multiplied by 10 to allow
+ // accuracy of 0.1
+ PagedArray<uint16_t, 65536> res_depths_;
+
+ // dssp state, which is a member of {H,B,E,G,I,T,S}
+ PagedArray<char, 65536> dssp_;
+
+ // Amino acid frequencies as given as input profile
+ PagedArray<AAFreq, 65536> aa_frequencies_;
+
+ // Amino acid frequencies as derived from structural information
+ PagedArray<AAFreq, 65536> aa_frequencies_struct_;
};
}}
diff --git a/loop/src/structure_db_custom_types.hh b/loop/src/structure_db_custom_types.hh
new file mode 100644
index 0000000000000000000000000000000000000000..d636c7dbd21edb8a335fb91f51f4d2003a064548
--- /dev/null
+++ b/loop/src/structure_db_custom_types.hh
@@ -0,0 +1,110 @@
+#ifndef PROMOD_LOOP_STRUCTURE_DB_CUSTOM_TYPES
+#define PROMOD_LOOP_STRUCTURE_DB_CUSTOM_TYPES
+
+#include <promod3/loop/ushort_vec.hh>
+#include <promod3/core/portable_binary_serializer.hh>
+
+namespace promod3 { namespace loop {
+
+struct PeptideCoords {
+ // portable serialization
+ // (cleanly element by element with fixed-width base-types)
+ template <typename DS>
+ void Serialize(DS& ds) {
+ ds & n;
+ ds & ca;
+ ds & c;
+ ds & o;
+ }
+
+ bool operator==(const PeptideCoords& rhs) const {
+ return n == rhs.n
+ && ca == rhs.ca
+ && c == rhs.c
+ && o == rhs.o;
+ }
+ bool operator!=(const PeptideCoords& rhs) const {
+ return !this->operator==(rhs);
+ }
+
+ UShortVec n;
+ UShortVec ca;
+ UShortVec c;
+ UShortVec o;
+};
+
+
+struct DihedralInfo {
+ DihedralInfo() { }
+ DihedralInfo(Real a, Real b){
+ phi = a * 1000;
+ psi = b * 1000;
+ }
+
+ inline Real GetPhi() const { return static_cast<Real>(phi) * Real(0.001); }
+
+ inline Real GetPsi() const { return static_cast<Real>(psi) * Real(0.001); }
+
+ // portable serialization
+ // (cleanly element by element with fixed-width base-types)
+ template <typename DS>
+ void Serialize(DS& ds) {
+ core::ConvertBaseType<int16_t>(ds, phi);
+ core::ConvertBaseType<int16_t>(ds, psi);
+ }
+
+ bool operator==(const DihedralInfo& rhs) const {
+ return phi == rhs.phi
+ && psi == rhs.psi;
+ }
+ bool operator!=(const DihedralInfo& rhs) const {
+ return !this->operator==(rhs);
+ }
+
+ short phi;
+ short psi;
+};
+
+
+struct AAFreq {
+
+ AAFreq() {
+ memset(freqs, 0, sizeof(short)*20);
+ }
+
+ void AssignProfileColumn(const ost::seq::ProfileColumn& col) {
+ const Real* col_freq_ptr = col.freqs_begin();
+ short* freq_ptr = &freqs[0];
+ for(uint i = 0; i < 20; ++i){
+ *freq_ptr = (*col_freq_ptr)*10000;
+ ++freq_ptr;
+ ++col_freq_ptr;
+ }
+ }
+
+ const short* data() const { return freqs; }
+
+ short* data() { return freqs; }
+
+ // portable serialization
+ // (cleanly element by element with fixed-width base-types)
+ template <typename DS>
+ void Serialize(DS& ds) {
+ for (int i = 0; i < 20; ++i) {
+ core::ConvertBaseType<int16_t>(ds, freqs[i]);
+ }
+ }
+
+ bool operator==(const AAFreq& rhs) const {
+ return !memcmp(freqs, rhs.freqs, sizeof(short)*20);
+ }
+ bool operator!=(const AAFreq& rhs) const {
+ return !this->operator==(rhs);
+ }
+
+ short freqs[20];
+};
+
+}} // ns
+
+#endif
diff --git a/loop/tests/CMakeLists.txt b/loop/tests/CMakeLists.txt
index a1fc21f8cd2bc1724524f7a3b6eec43e6df825fb..04bfa9f35a4b9c0d3f5b37874d4af9ae11963c3d 100644
--- a/loop/tests/CMakeLists.txt
+++ b/loop/tests/CMakeLists.txt
@@ -9,13 +9,15 @@ set(LOOP_UNIT_TESTS
test_mm_system_creator.cc
test_psipred_prediction.cc
test_sidechain_construction.cc
- test_ss_assignment.cc
test_torsion_sampler.cc
+ test_structuredb.cc
tests.cc
)
set(LOOP_TEST_DATA
data/1A88A.hhm
+ data/1A88A.pdb
+ data/1A88A_with_gap.pdb
data/1akyA.horiz
data/1CRN.pdb
data/3DEFA.pdb
diff --git a/loop/tests/data/1A88A.pdb b/loop/tests/data/1A88A.pdb
new file mode 100755
index 0000000000000000000000000000000000000000..dd8be93e1726e36315e7300e13e6747c31eb2ef5
--- /dev/null
+++ b/loop/tests/data/1A88A.pdb
@@ -0,0 +1,2107 @@
+ATOM 1 N GLY A 1 31.764 53.257 -5.145 1.00 21.92 N
+ATOM 2 CA GLY A 1 31.661 51.955 -4.451 1.00 20.38 C
+ATOM 3 C GLY A 1 30.228 51.594 -4.213 1.00 22.43 C
+ATOM 4 O GLY A 1 29.301 52.280 -4.687 1.00 20.07 O
+ATOM 5 N THR A 2 29.953 50.447 -3.576 1.00 20.81 N
+ATOM 6 CA THR A 2 28.571 50.144 -3.254 1.00 24.30 C
+ATOM 7 C THR A 2 28.510 49.528 -1.854 1.00 24.57 C
+ATOM 8 O THR A 2 29.507 48.974 -1.349 1.00 24.04 O
+ATOM 9 CB THR A 2 27.886 49.192 -4.253 1.00 28.12 C
+ATOM 10 OG1 THR A 2 28.529 47.925 -4.086 1.00 31.49 O
+ATOM 11 CG2 THR A 2 27.965 49.541 -5.730 1.00 27.46 C
+ATOM 12 N VAL A 3 27.370 49.622 -1.203 1.00 22.42 N
+ATOM 13 CA VAL A 3 27.147 49.017 0.095 1.00 24.30 C
+ATOM 14 C VAL A 3 25.861 48.228 -0.035 1.00 23.74 C
+ATOM 15 O VAL A 3 24.906 48.622 -0.722 1.00 22.67 O
+ATOM 16 CB VAL A 3 27.028 49.956 1.302 1.00 25.50 C
+ATOM 17 CG1 VAL A 3 28.381 50.584 1.663 1.00 27.68 C
+ATOM 18 CG2 VAL A 3 26.103 51.113 1.034 1.00 27.65 C
+ATOM 19 N THR A 4 25.854 47.062 0.574 1.00 23.05 N
+ATOM 20 CA THR A 4 24.672 46.202 0.570 1.00 26.31 C
+ATOM 21 C THR A 4 23.829 46.421 1.812 1.00 26.75 C
+ATOM 22 O THR A 4 24.377 46.407 2.918 1.00 29.12 O
+ATOM 23 CB THR A 4 25.103 44.726 0.458 1.00 27.13 C
+ATOM 24 OG1 THR A 4 25.713 44.592 -0.829 1.00 27.43 O
+ATOM 25 CG2 THR A 4 23.903 43.814 0.614 1.00 28.43 C
+ATOM 26 N THR A 5 22.536 46.692 1.686 1.00 24.64 N
+ATOM 27 CA THR A 5 21.727 46.951 2.868 1.00 26.94 C
+ATOM 28 C THR A 5 21.173 45.630 3.423 1.00 28.87 C
+ATOM 29 O THR A 5 21.359 44.560 2.825 1.00 28.63 O
+ATOM 30 CB THR A 5 20.563 47.904 2.493 1.00 25.62 C
+ATOM 31 OG1 THR A 5 19.773 47.127 1.610 1.00 22.98 O
+ATOM 32 CG2 THR A 5 21.081 49.182 1.837 1.00 26.21 C
+ATOM 33 N SER A 6 20.416 45.706 4.512 1.00 32.07 N
+ATOM 34 CA SER A 6 19.914 44.475 5.151 1.00 34.50 C
+ATOM 35 C SER A 6 19.034 43.646 4.242 1.00 34.88 C
+ATOM 36 O SER A 6 19.264 42.413 4.164 1.00 35.66 O
+ATOM 37 CB SER A 6 19.260 44.760 6.491 1.00 36.17 C
+ATOM 38 OG SER A 6 18.258 45.742 6.449 1.00 38.37 O
+ATOM 39 N ASP A 7 18.170 44.274 3.432 1.00 32.57 N
+ATOM 40 CA ASP A 7 17.369 43.488 2.491 1.00 29.56 C
+ATOM 41 C ASP A 7 18.127 43.106 1.244 1.00 28.25 C
+ATOM 42 O ASP A 7 17.502 42.669 0.288 1.00 27.90 O
+ATOM 43 CB ASP A 7 16.076 44.231 2.182 1.00 30.52 C
+ATOM 44 CG ASP A 7 16.170 45.511 1.376 1.00 30.30 C
+ATOM 45 OD1 ASP A 7 17.263 45.876 0.931 1.00 29.25 O
+ATOM 46 OD2 ASP A 7 15.127 46.180 1.159 1.00 30.59 O
+ATOM 47 N GLY A 8 19.443 43.249 1.129 1.00 28.74 N
+ATOM 48 CA GLY A 8 20.172 42.928 -0.091 1.00 26.98 C
+ATOM 49 C GLY A 8 20.152 44.009 -1.155 1.00 26.24 C
+ATOM 50 O GLY A 8 20.644 43.753 -2.272 1.00 27.20 O
+ATOM 51 N THR A 9 19.679 45.229 -0.886 1.00 24.00 N
+ATOM 52 CA THR A 9 19.710 46.283 -1.920 1.00 21.61 C
+ATOM 53 C THR A 9 21.108 46.857 -2.041 1.00 21.67 C
+ATOM 54 O THR A 9 21.691 47.226 -0.998 1.00 23.64 O
+ATOM 55 CB THR A 9 18.718 47.393 -1.543 1.00 20.75 C
+ATOM 56 OG1 THR A 9 17.407 46.802 -1.546 1.00 19.41 O
+ATOM 57 CG2 THR A 9 18.638 48.560 -2.556 1.00 20.13 C
+ATOM 58 N ASN A 10 21.661 47.017 -3.238 1.00 20.77 N
+ATOM 59 CA ASN A 10 22.961 47.660 -3.391 1.00 19.56 C
+ATOM 60 C ASN A 10 22.762 49.172 -3.633 1.00 19.39 C
+ATOM 61 O ASN A 10 21.969 49.567 -4.476 1.00 17.13 O
+ATOM 62 CB ASN A 10 23.826 47.103 -4.513 1.00 21.53 C
+ATOM 63 CG ASN A 10 24.198 45.658 -4.181 1.00 25.77 C
+ATOM 64 OD1 ASN A 10 24.782 45.354 -3.145 1.00 26.65 O
+ATOM 65 ND2 ASN A 10 23.789 44.748 -5.050 1.00 27.54 N
+ATOM 66 N ILE A 11 23.488 49.953 -2.852 1.00 16.01 N
+ATOM 67 CA ILE A 11 23.473 51.404 -2.847 1.00 16.13 C
+ATOM 68 C ILE A 11 24.788 51.907 -3.415 1.00 16.10 C
+ATOM 69 O ILE A 11 25.885 51.559 -2.908 1.00 16.08 O
+ATOM 70 CB ILE A 11 23.303 51.881 -1.391 1.00 17.18 C
+ATOM 71 CG1 ILE A 11 21.912 51.467 -0.888 1.00 19.25 C
+ATOM 72 CG2 ILE A 11 23.543 53.372 -1.267 1.00 18.69 C
+ATOM 73 CD1 ILE A 11 20.760 52.090 -1.647 1.00 20.48 C
+ATOM 74 N PHE A 12 24.721 52.715 -4.453 1.00 13.95 N
+ATOM 75 CA PHE A 12 25.910 53.287 -5.056 1.00 14.01 C
+ATOM 76 C PHE A 12 26.339 54.517 -4.270 1.00 12.98 C
+ATOM 77 O PHE A 12 25.429 55.281 -3.898 1.00 13.88 O
+ATOM 78 CB PHE A 12 25.591 53.711 -6.492 1.00 15.02 C
+ATOM 79 CG PHE A 12 26.707 54.477 -7.135 1.00 14.64 C
+ATOM 80 CD1 PHE A 12 27.755 53.821 -7.735 1.00 17.30 C
+ATOM 81 CD2 PHE A 12 26.704 55.871 -7.114 1.00 16.10 C
+ATOM 82 CE1 PHE A 12 28.803 54.564 -8.314 1.00 19.46 C
+ATOM 83 CE2 PHE A 12 27.731 56.593 -7.686 1.00 16.45 C
+ATOM 84 CZ PHE A 12 28.800 55.939 -8.274 1.00 17.84 C
+ATOM 85 N TYR A 13 27.618 54.770 -4.068 1.00 12.68 N
+ATOM 86 CA TYR A 13 28.049 56.000 -3.392 1.00 13.94 C
+ATOM 87 C TYR A 13 29.396 56.458 -3.960 1.00 14.49 C
+ATOM 88 O TYR A 13 30.149 55.633 -4.485 1.00 17.10 O
+ATOM 89 CB TYR A 13 28.088 55.911 -1.875 1.00 14.70 C
+ATOM 90 CG TYR A 13 29.266 55.041 -1.436 1.00 15.23 C
+ATOM 91 CD1 TYR A 13 29.092 53.684 -1.286 1.00 18.01 C
+ATOM 92 CD2 TYR A 13 30.494 55.626 -1.162 1.00 15.71 C
+ATOM 93 CE1 TYR A 13 30.171 52.871 -0.884 1.00 19.66 C
+ATOM 94 CE2 TYR A 13 31.567 54.830 -0.767 1.00 18.64 C
+ATOM 95 CZ TYR A 13 31.375 53.471 -0.630 1.00 20.23 C
+ATOM 96 OH TYR A 13 32.456 52.691 -0.281 1.00 22.12 O
+ATOM 97 N LYS A 14 29.691 57.735 -3.805 1.00 12.68 N
+ATOM 98 CA LYS A 14 30.973 58.308 -4.186 1.00 13.28 C
+ATOM 99 C LYS A 14 31.725 58.680 -2.905 1.00 13.70 C
+ATOM 100 O LYS A 14 31.028 59.140 -1.993 1.00 11.22 O
+ATOM 101 CB LYS A 14 30.729 59.646 -4.936 1.00 13.56 C
+ATOM 102 CG LYS A 14 30.055 59.407 -6.293 1.00 17.04 C
+ATOM 103 CD LYS A 14 29.598 60.791 -6.803 1.00 16.95 C
+ATOM 104 CE LYS A 14 28.859 60.613 -8.109 1.00 16.88 C
+ATOM 105 NZ LYS A 14 29.275 61.643 -9.079 1.00 11.46 N
+ATOM 106 N ASP A 15 33.039 58.630 -2.881 1.00 13.17 N
+ATOM 107 CA ASP A 15 33.772 58.981 -1.642 1.00 13.31 C
+ATOM 108 C ASP A 15 35.071 59.625 -2.089 1.00 11.64 C
+ATOM 109 O ASP A 15 35.924 58.884 -2.645 1.00 14.33 O
+ATOM 110 CB ASP A 15 33.950 57.676 -0.842 1.00 12.42 C
+ATOM 111 CG ASP A 15 34.829 57.878 0.408 1.00 15.23 C
+ATOM 112 OD1 ASP A 15 35.255 58.979 0.772 1.00 13.01 O
+ATOM 113 OD2 ASP A 15 35.082 56.850 1.085 1.00 16.31 O
+ATOM 114 N TRP A 16 35.150 60.930 -2.143 1.00 10.20 N
+ATOM 115 CA TRP A 16 36.325 61.577 -2.730 1.00 12.29 C
+ATOM 116 C TRP A 16 37.051 62.386 -1.642 1.00 14.41 C
+ATOM 117 O TRP A 16 36.387 62.801 -0.682 1.00 13.69 O
+ATOM 118 CB TRP A 16 35.855 62.542 -3.828 1.00 10.66 C
+ATOM 119 CG TRP A 16 35.204 61.854 -5.012 1.00 12.83 C
+ATOM 120 CD1 TRP A 16 35.261 60.566 -5.385 1.00 12.58 C
+ATOM 121 CD2 TRP A 16 34.300 62.500 -5.933 1.00 11.99 C
+ATOM 122 NE1 TRP A 16 34.476 60.347 -6.517 1.00 12.31 N
+ATOM 123 CE2 TRP A 16 33.894 61.529 -6.854 1.00 12.96 C
+ATOM 124 CE3 TRP A 16 33.863 63.805 -6.096 1.00 12.84 C
+ATOM 125 CZ2 TRP A 16 33.033 61.840 -7.937 1.00 12.24 C
+ATOM 126 CZ3 TRP A 16 32.989 64.124 -7.129 1.00 12.81 C
+ATOM 127 CH2 TRP A 16 32.614 63.126 -8.056 1.00 11.63 C
+ATOM 128 N GLY A 17 38.327 62.678 -1.836 1.00 17.50 N
+ATOM 129 CA GLY A 17 39.037 63.578 -0.895 1.00 18.73 C
+ATOM 130 C GLY A 17 39.896 62.740 0.057 1.00 19.98 C
+ATOM 131 O GLY A 17 39.945 61.518 0.012 1.00 19.39 O
+ATOM 132 N PRO A 18 40.568 63.427 0.981 1.00 21.84 N
+ATOM 133 CA PRO A 18 41.467 62.747 1.912 1.00 24.40 C
+ATOM 134 C PRO A 18 40.740 61.715 2.730 1.00 25.93 C
+ATOM 135 O PRO A 18 39.695 61.992 3.327 1.00 26.51 O
+ATOM 136 CB PRO A 18 41.998 63.853 2.817 1.00 23.82 C
+ATOM 137 CG PRO A 18 41.579 65.134 2.222 1.00 24.48 C
+ATOM 138 CD PRO A 18 40.595 64.888 1.118 1.00 22.83 C
+ATOM 139 N ARG A 19 41.340 60.569 2.940 1.00 29.28 N
+ATOM 140 CA ARG A 19 40.778 59.511 3.765 1.00 33.09 C
+ATOM 141 C ARG A 19 40.643 59.898 5.228 1.00 34.57 C
+ATOM 142 O ARG A 19 39.830 59.339 5.967 1.00 35.74 O
+ATOM 143 CB ARG A 19 41.688 58.277 3.594 1.00 34.45 C
+ATOM 144 CG ARG A 19 42.010 58.013 2.119 1.00 34.65 C
+ATOM 145 CD ARG A 19 40.747 57.360 1.506 1.00 34.26 C
+ATOM 146 NE ARG A 19 39.918 58.420 0.927 1.00 33.29 N
+ATOM 147 CZ ARG A 19 38.596 58.415 0.770 1.00 31.02 C
+ATOM 148 NH1 ARG A 19 37.937 57.349 1.196 1.00 29.19 N
+ATOM 149 NH2 ARG A 19 38.013 59.470 0.217 1.00 26.29 N
+ATOM 150 N ASP A 20 41.426 60.851 5.702 1.00 35.79 N
+ATOM 151 CA ASP A 20 41.387 61.357 7.068 1.00 37.11 C
+ATOM 152 C ASP A 20 40.755 62.737 7.157 1.00 34.73 C
+ATOM 153 O ASP A 20 40.793 63.389 8.201 1.00 36.97 O
+ATOM 154 CB ASP A 20 42.832 61.443 7.612 1.00 40.20 C
+ATOM 155 CG ASP A 20 43.625 62.280 6.614 1.00 44.16 C
+ATOM 156 OD1 ASP A 20 43.852 61.807 5.473 1.00 46.24 O
+ATOM 157 OD2 ASP A 20 43.975 63.426 6.958 1.00 46.14 O
+ATOM 158 N GLY A 21 40.147 63.261 6.100 1.00 30.99 N
+ATOM 159 CA GLY A 21 39.492 64.571 6.194 1.00 26.89 C
+ATOM 160 C GLY A 21 38.152 64.415 6.929 1.00 22.01 C
+ATOM 161 O GLY A 21 37.607 63.326 7.088 1.00 22.45 O
+ATOM 162 N LEU A 22 37.637 65.525 7.423 1.00 20.89 N
+ATOM 163 CA LEU A 22 36.318 65.546 8.044 1.00 20.96 C
+ATOM 164 C LEU A 22 35.310 65.216 6.920 1.00 18.65 C
+ATOM 165 O LEU A 22 35.317 65.884 5.892 1.00 16.52 O
+ATOM 166 CB LEU A 22 36.062 66.963 8.579 1.00 23.41 C
+ATOM 167 CG LEU A 22 34.860 67.108 9.534 1.00 26.98 C
+ATOM 168 CD1 LEU A 22 35.133 68.301 10.477 1.00 29.41 C
+ATOM 169 CD2 LEU A 22 33.525 67.302 8.834 1.00 24.72 C
+ATOM 170 N PRO A 23 34.436 64.282 7.178 1.00 19.30 N
+ATOM 171 CA PRO A 23 33.458 63.817 6.200 1.00 18.80 C
+ATOM 172 C PRO A 23 32.221 64.691 6.196 1.00 18.74 C
+ATOM 173 O PRO A 23 31.644 65.078 7.210 1.00 17.64 O
+ATOM 174 CB PRO A 23 33.177 62.378 6.574 1.00 18.76 C
+ATOM 175 CG PRO A 23 33.526 62.281 8.023 1.00 19.59 C
+ATOM 176 CD PRO A 23 34.437 63.395 8.370 1.00 19.10 C
+ATOM 177 N VAL A 24 31.857 65.067 4.984 1.00 15.22 N
+ATOM 178 CA VAL A 24 30.666 65.851 4.685 1.00 14.77 C
+ATOM 179 C VAL A 24 29.880 64.955 3.716 1.00 15.60 C
+ATOM 180 O VAL A 24 30.435 64.510 2.703 1.00 12.24 O
+ATOM 181 CB VAL A 24 30.995 67.164 3.996 1.00 15.38 C
+ATOM 182 CG1 VAL A 24 29.745 67.975 3.657 1.00 16.66 C
+ATOM 183 CG2 VAL A 24 32.014 67.988 4.776 1.00 16.14 C
+ATOM 184 N VAL A 25 28.661 64.613 4.100 1.00 11.81 N
+ATOM 185 CA VAL A 25 27.855 63.658 3.382 1.00 13.59 C
+ATOM 186 C VAL A 25 26.637 64.372 2.797 1.00 15.07 C
+ATOM 187 O VAL A 25 25.956 65.085 3.546 1.00 13.74 O
+ATOM 188 CB VAL A 25 27.373 62.567 4.382 1.00 14.11 C
+ATOM 189 CG1 VAL A 25 26.587 61.507 3.632 1.00 14.74 C
+ATOM 190 CG2 VAL A 25 28.546 61.944 5.155 1.00 15.09 C
+ATOM 191 N PHE A 26 26.376 64.183 1.506 1.00 13.58 N
+ATOM 192 CA PHE A 26 25.329 64.934 0.801 1.00 11.26 C
+ATOM 193 C PHE A 26 24.176 64.016 0.412 1.00 12.76 C
+ATOM 194 O PHE A 26 24.410 62.857 -0.004 1.00 11.00 O
+ATOM 195 CB PHE A 26 25.949 65.535 -0.478 1.00 14.11 C
+ATOM 196 CG PHE A 26 26.984 66.586 -0.199 1.00 15.39 C
+ATOM 197 CD1 PHE A 26 26.593 67.910 -0.023 1.00 15.42 C
+ATOM 198 CD2 PHE A 26 28.326 66.268 -0.162 1.00 16.48 C
+ATOM 199 CE1 PHE A 26 27.545 68.903 0.193 1.00 16.22 C
+ATOM 200 CE2 PHE A 26 29.256 67.257 0.076 1.00 17.18 C
+ATOM 201 CZ PHE A 26 28.879 68.565 0.233 1.00 15.49 C
+ATOM 202 N HIS A 27 22.953 64.479 0.700 1.00 10.40 N
+ATOM 203 CA HIS A 27 21.741 63.695 0.513 1.00 10.97 C
+ATOM 204 C HIS A 27 20.861 64.399 -0.532 1.00 10.19 C
+ATOM 205 O HIS A 27 20.268 65.444 -0.288 1.00 10.60 O
+ATOM 206 CB HIS A 27 20.928 63.555 1.820 1.00 12.16 C
+ATOM 207 CG HIS A 27 21.690 62.862 2.925 1.00 13.43 C
+ATOM 208 ND1 HIS A 27 21.303 61.629 3.408 1.00 11.63 N
+ATOM 209 CD2 HIS A 27 22.799 63.260 3.606 1.00 13.24 C
+ATOM 210 CE1 HIS A 27 22.178 61.292 4.370 1.00 13.22 C
+ATOM 211 NE2 HIS A 27 23.080 62.246 4.517 1.00 14.11 N
+ATOM 212 N HIS A 28 20.768 63.845 -1.739 1.00 11.74 N
+ATOM 213 CA HIS A 28 20.054 64.500 -2.869 1.00 8.78 C
+ATOM 214 C HIS A 28 18.543 64.493 -2.752 1.00 8.92 C
+ATOM 215 O HIS A 28 17.962 63.740 -1.978 1.00 9.63 O
+ATOM 216 CB HIS A 28 20.461 63.767 -4.174 1.00 8.31 C
+ATOM 217 CG HIS A 28 19.935 62.361 -4.287 1.00 8.02 C
+ATOM 218 ND1 HIS A 28 18.647 62.097 -4.703 1.00 9.36 N
+ATOM 219 CD2 HIS A 28 20.522 61.136 -4.096 1.00 8.03 C
+ATOM 220 CE1 HIS A 28 18.444 60.776 -4.717 1.00 8.99 C
+ATOM 221 NE2 HIS A 28 19.585 60.178 -4.340 1.00 8.20 N
+ATOM 222 N GLY A 29 17.882 65.397 -3.499 1.00 8.82 N
+ATOM 223 CA GLY A 29 16.399 65.383 -3.410 1.00 11.02 C
+ATOM 224 C GLY A 29 15.779 64.461 -4.433 1.00 13.10 C
+ATOM 225 O GLY A 29 16.456 63.745 -5.198 1.00 12.97 O
+ATOM 226 N TRP A 30 14.453 64.507 -4.480 1.00 11.76 N
+ATOM 227 CA TRP A 30 13.667 63.723 -5.426 1.00 11.49 C
+ATOM 228 C TRP A 30 13.596 64.520 -6.749 1.00 12.32 C
+ATOM 229 O TRP A 30 13.446 65.735 -6.728 1.00 10.33 O
+ATOM 230 CB TRP A 30 12.257 63.685 -4.834 1.00 12.65 C
+ATOM 231 CG TRP A 30 11.208 63.037 -5.713 1.00 13.04 C
+ATOM 232 CD1 TRP A 30 10.897 61.720 -5.802 1.00 11.74 C
+ATOM 233 CD2 TRP A 30 10.368 63.738 -6.638 1.00 13.91 C
+ATOM 234 NE1 TRP A 30 9.873 61.558 -6.709 1.00 14.39 N
+ATOM 235 CE2 TRP A 30 9.548 62.789 -7.242 1.00 14.52 C
+ATOM 236 CE3 TRP A 30 10.229 65.091 -6.973 1.00 16.58 C
+ATOM 237 CZ2 TRP A 30 8.570 63.121 -8.189 1.00 15.85 C
+ATOM 238 CZ3 TRP A 30 9.282 65.445 -7.944 1.00 18.55 C
+ATOM 239 CH2 TRP A 30 8.470 64.454 -8.512 1.00 17.00 C
+ATOM 240 N PRO A 31 13.619 63.836 -7.877 1.00 11.13 N
+ATOM 241 CA PRO A 31 13.850 62.395 -8.042 1.00 10.21 C
+ATOM 242 C PRO A 31 15.280 62.256 -8.606 1.00 12.56 C
+ATOM 243 O PRO A 31 15.545 61.719 -9.664 1.00 10.78 O
+ATOM 244 CB PRO A 31 12.805 62.060 -9.113 1.00 9.67 C
+ATOM 245 CG PRO A 31 12.619 63.311 -9.931 1.00 12.03 C
+ATOM 246 CD PRO A 31 13.339 64.463 -9.208 1.00 10.61 C
+ATOM 247 N LEU A 32 16.312 62.805 -7.940 1.00 11.12 N
+ATOM 248 CA LEU A 32 17.635 62.897 -8.514 1.00 12.32 C
+ATOM 249 C LEU A 32 18.632 61.817 -8.119 1.00 11.18 C
+ATOM 250 O LEU A 32 18.288 60.643 -8.044 1.00 10.82 O
+ATOM 251 CB LEU A 32 18.163 64.345 -8.223 1.00 9.98 C
+ATOM 252 CG LEU A 32 17.094 65.384 -8.657 1.00 11.19 C
+ATOM 253 CD1 LEU A 32 17.453 66.788 -8.236 1.00 13.84 C
+ATOM 254 CD2 LEU A 32 16.988 65.391 -10.195 1.00 14.00 C
+ATOM 255 N SER A 33 19.906 62.179 -7.957 1.00 11.30 N
+ATOM 256 CA SER A 33 20.965 61.240 -7.666 1.00 9.67 C
+ATOM 257 C SER A 33 22.110 61.972 -6.953 1.00 8.43 C
+ATOM 258 O SER A 33 22.070 63.215 -6.846 1.00 7.20 O
+ATOM 259 CB SER A 33 21.403 60.628 -9.007 1.00 10.41 C
+ATOM 260 OG SER A 33 22.293 61.521 -9.675 1.00 10.51 O
+ATOM 261 N ALA A 34 23.177 61.302 -6.599 1.00 9.22 N
+ATOM 262 CA ALA A 34 24.351 61.885 -6.019 1.00 9.62 C
+ATOM 263 C ALA A 34 25.020 62.837 -7.012 1.00 10.11 C
+ATOM 264 O ALA A 34 25.658 63.792 -6.552 1.00 8.62 O
+ATOM 265 CB ALA A 34 25.363 60.804 -5.587 1.00 10.36 C
+ATOM 266 N ASP A 35 24.741 62.725 -8.306 1.00 10.17 N
+ATOM 267 CA ASP A 35 25.338 63.652 -9.285 1.00 10.79 C
+ATOM 268 C ASP A 35 24.786 65.055 -9.195 1.00 10.13 C
+ATOM 269 O ASP A 35 25.395 65.975 -9.752 1.00 10.35 O
+ATOM 270 CB ASP A 35 25.128 63.125 -10.716 1.00 10.95 C
+ATOM 271 CG ASP A 35 26.036 61.950 -10.989 1.00 13.32 C
+ATOM 272 OD1 ASP A 35 26.762 61.509 -10.074 1.00 13.54 O
+ATOM 273 OD2 ASP A 35 25.999 61.432 -12.143 1.00 15.25 O
+ATOM 274 N ASP A 36 23.653 65.296 -8.506 1.00 8.36 N
+ATOM 275 CA ASP A 36 23.147 66.659 -8.307 1.00 8.03 C
+ATOM 276 C ASP A 36 24.109 67.504 -7.475 1.00 9.21 C
+ATOM 277 O ASP A 36 23.956 68.727 -7.446 1.00 11.05 O
+ATOM 278 CB ASP A 36 21.751 66.553 -7.614 1.00 10.47 C
+ATOM 279 CG ASP A 36 20.924 67.813 -7.861 1.00 16.13 C
+ATOM 280 OD1 ASP A 36 20.773 68.227 -9.024 1.00 17.12 O
+ATOM 281 OD2 ASP A 36 20.439 68.471 -6.912 1.00 15.32 O
+ATOM 282 N TRP A 37 25.079 66.931 -6.753 1.00 10.46 N
+ATOM 283 CA TRP A 37 25.984 67.664 -5.858 1.00 7.76 C
+ATOM 284 C TRP A 37 27.297 68.042 -6.484 1.00 9.56 C
+ATOM 285 O TRP A 37 28.193 68.574 -5.791 1.00 11.85 O
+ATOM 286 CB TRP A 37 26.253 66.742 -4.622 1.00 7.60 C
+ATOM 287 CG TRP A 37 25.001 66.543 -3.784 1.00 9.11 C
+ATOM 288 CD1 TRP A 37 24.267 65.410 -3.597 1.00 8.67 C
+ATOM 289 CD2 TRP A 37 24.403 67.551 -2.961 1.00 8.08 C
+ATOM 290 NE1 TRP A 37 23.223 65.663 -2.717 1.00 10.07 N
+ATOM 291 CE2 TRP A 37 23.291 66.972 -2.332 1.00 10.35 C
+ATOM 292 CE3 TRP A 37 24.710 68.902 -2.760 1.00 7.63 C
+ATOM 293 CZ2 TRP A 37 22.447 67.674 -1.470 1.00 8.35 C
+ATOM 294 CZ3 TRP A 37 23.891 69.609 -1.890 1.00 11.31 C
+ATOM 295 CH2 TRP A 37 22.793 68.985 -1.258 1.00 10.30 C
+ATOM 296 N ASP A 38 27.525 67.787 -7.774 1.00 9.33 N
+ATOM 297 CA ASP A 38 28.799 68.073 -8.410 1.00 11.16 C
+ATOM 298 C ASP A 38 29.467 69.360 -7.886 1.00 12.35 C
+ATOM 299 O ASP A 38 30.620 69.352 -7.489 1.00 12.36 O
+ATOM 300 CB ASP A 38 28.729 68.134 -9.915 1.00 11.22 C
+ATOM 301 CG ASP A 38 28.618 66.748 -10.584 1.00 14.58 C
+ATOM 302 OD1 ASP A 38 28.801 65.679 -9.939 1.00 11.78 O
+ATOM 303 OD2 ASP A 38 28.316 66.810 -11.796 1.00 14.06 O
+ATOM 304 N ASN A 39 28.773 70.486 -7.986 1.00 11.87 N
+ATOM 305 CA ASN A 39 29.347 71.774 -7.620 1.00 13.12 C
+ATOM 306 C ASN A 39 29.858 71.808 -6.175 1.00 12.64 C
+ATOM 307 O ASN A 39 30.969 72.304 -5.934 1.00 12.56 O
+ATOM 308 CB ASN A 39 28.246 72.828 -7.881 1.00 12.86 C
+ATOM 309 CG ASN A 39 28.735 74.207 -7.488 1.00 16.95 C
+ATOM 310 OD1 ASN A 39 28.991 74.427 -6.302 1.00 17.51 O
+ATOM 311 ND2 ASN A 39 28.936 75.144 -8.422 1.00 13.94 N
+ATOM 312 N GLN A 40 29.005 71.401 -5.228 1.00 10.79 N
+ATOM 313 CA GLN A 40 29.310 71.388 -3.802 1.00 12.37 C
+ATOM 314 C GLN A 40 30.359 70.336 -3.532 1.00 13.56 C
+ATOM 315 O GLN A 40 31.222 70.596 -2.672 1.00 14.85 O
+ATOM 316 CB GLN A 40 28.073 71.098 -2.903 1.00 10.94 C
+ATOM 317 CG GLN A 40 27.177 72.304 -2.752 1.00 12.64 C
+ATOM 318 CD GLN A 40 26.363 72.654 -3.968 1.00 13.95 C
+ATOM 319 OE1 GLN A 40 25.892 71.692 -4.634 1.00 12.38 O
+ATOM 320 NE2 GLN A 40 26.198 73.969 -4.228 1.00 11.57 N
+ATOM 321 N MET A 41 30.361 69.216 -4.265 1.00 9.82 N
+ATOM 322 CA MET A 41 31.420 68.252 -3.999 1.00 12.73 C
+ATOM 323 C MET A 41 32.790 68.783 -4.357 1.00 14.38 C
+ATOM 324 O MET A 41 33.713 68.665 -3.538 1.00 15.37 O
+ATOM 325 CB MET A 41 31.096 66.887 -4.643 1.00 15.27 C
+ATOM 326 CG MET A 41 30.171 66.198 -3.570 1.00 19.95 C
+ATOM 327 SD MET A 41 29.527 64.729 -4.235 1.00 30.23 S
+ATOM 328 CE MET A 41 30.795 63.508 -3.872 1.00 20.16 C
+ATOM 329 N LEU A 42 32.919 69.481 -5.499 1.00 13.84 N
+ATOM 330 CA LEU A 42 34.198 70.049 -5.851 1.00 13.52 C
+ATOM 331 C LEU A 42 34.587 71.209 -4.916 1.00 14.94 C
+ATOM 332 O LEU A 42 35.767 71.348 -4.584 1.00 14.55 O
+ATOM 333 CB LEU A 42 34.098 70.552 -7.285 1.00 13.38 C
+ATOM 334 CG LEU A 42 33.957 69.466 -8.388 1.00 15.26 C
+ATOM 335 CD1 LEU A 42 34.392 70.007 -9.736 1.00 15.85 C
+ATOM 336 CD2 LEU A 42 34.821 68.241 -8.130 1.00 15.96 C
+ATOM 337 N PHE A 43 33.602 71.998 -4.533 1.00 13.32 N
+ATOM 338 CA PHE A 43 33.891 73.166 -3.644 1.00 15.81 C
+ATOM 339 C PHE A 43 34.440 72.729 -2.294 1.00 16.66 C
+ATOM 340 O PHE A 43 35.503 73.159 -1.864 1.00 17.10 O
+ATOM 341 CB PHE A 43 32.595 73.964 -3.487 1.00 15.51 C
+ATOM 342 CG PHE A 43 32.710 75.058 -2.429 1.00 17.53 C
+ATOM 343 CD1 PHE A 43 33.261 76.274 -2.776 1.00 19.11 C
+ATOM 344 CD2 PHE A 43 32.234 74.829 -1.149 1.00 19.38 C
+ATOM 345 CE1 PHE A 43 33.370 77.294 -1.822 1.00 20.88 C
+ATOM 346 CE2 PHE A 43 32.326 75.840 -0.194 1.00 18.55 C
+ATOM 347 CZ PHE A 43 32.873 77.056 -0.549 1.00 17.92 C
+ATOM 348 N PHE A 44 33.809 71.736 -1.660 1.00 15.71 N
+ATOM 349 CA PHE A 44 34.273 71.205 -0.385 1.00 15.06 C
+ATOM 350 C PHE A 44 35.601 70.485 -0.464 1.00 17.32 C
+ATOM 351 O PHE A 44 36.489 70.536 0.432 1.00 18.03 O
+ATOM 352 CB PHE A 44 33.145 70.346 0.225 1.00 14.43 C
+ATOM 353 CG PHE A 44 32.209 71.241 1.023 1.00 15.08 C
+ATOM 354 CD1 PHE A 44 32.585 71.597 2.326 1.00 16.70 C
+ATOM 355 CD2 PHE A 44 31.065 71.730 0.481 1.00 14.94 C
+ATOM 356 CE1 PHE A 44 31.741 72.407 3.075 1.00 17.78 C
+ATOM 357 CE2 PHE A 44 30.214 72.551 1.232 1.00 17.65 C
+ATOM 358 CZ PHE A 44 30.566 72.898 2.530 1.00 18.75 C
+ATOM 359 N LEU A 45 35.814 69.714 -1.516 1.00 14.91 N
+ATOM 360 CA LEU A 45 37.072 69.069 -1.820 1.00 18.79 C
+ATOM 361 C LEU A 45 38.202 70.104 -1.871 1.00 18.00 C
+ATOM 362 O LEU A 45 39.295 69.831 -1.389 1.00 19.90 O
+ATOM 363 CB LEU A 45 37.067 68.428 -3.221 1.00 17.38 C
+ATOM 364 CG LEU A 45 36.611 66.991 -3.302 1.00 19.50 C
+ATOM 365 CD1 LEU A 45 36.562 66.566 -4.776 1.00 17.84 C
+ATOM 366 CD2 LEU A 45 37.585 66.165 -2.472 1.00 21.51 C
+ATOM 367 N SER A 46 37.947 71.227 -2.524 1.00 19.84 N
+ATOM 368 CA SER A 46 38.955 72.267 -2.609 1.00 22.20 C
+ATOM 369 C SER A 46 39.293 72.862 -1.231 1.00 24.61 C
+ATOM 370 O SER A 46 40.319 73.529 -1.110 1.00 23.74 O
+ATOM 371 CB SER A 46 38.529 73.380 -3.552 1.00 22.83 C
+ATOM 372 OG SER A 46 37.650 74.268 -2.896 1.00 29.36 O
+ATOM 373 N HIS A 47 38.435 72.677 -0.217 1.00 22.29 N
+ATOM 374 CA HIS A 47 38.714 73.191 1.106 1.00 22.20 C
+ATOM 375 C HIS A 47 39.197 72.068 2.028 1.00 22.23 C
+ATOM 376 O HIS A 47 39.283 72.314 3.240 1.00 22.21 O
+ATOM 377 CB HIS A 47 37.510 73.910 1.714 1.00 19.45 C
+ATOM 378 CG HIS A 47 37.353 75.211 1.008 1.00 21.06 C
+ATOM 379 ND1 HIS A 47 38.075 76.309 1.399 1.00 21.99 N
+ATOM 380 CD2 HIS A 47 36.571 75.599 -0.040 1.00 21.66 C
+ATOM 381 CE1 HIS A 47 37.783 77.329 0.616 1.00 22.57 C
+ATOM 382 NE2 HIS A 47 36.881 76.923 -0.265 1.00 22.90 N
+ATOM 383 N GLY A 48 39.580 70.947 1.422 1.00 21.01 N
+ATOM 384 CA GLY A 48 40.180 69.832 2.096 1.00 20.70 C
+ATOM 385 C GLY A 48 39.247 68.872 2.804 1.00 21.71 C
+ATOM 386 O GLY A 48 39.735 68.092 3.647 1.00 22.39 O
+ATOM 387 N TYR A 49 37.965 68.836 2.460 1.00 19.45 N
+ATOM 388 CA TYR A 49 37.060 67.879 3.116 1.00 18.69 C
+ATOM 389 C TYR A 49 36.949 66.587 2.335 1.00 18.08 C
+ATOM 390 O TYR A 49 37.309 66.479 1.169 1.00 19.13 O
+ATOM 391 CB TYR A 49 35.657 68.503 3.299 1.00 18.85 C
+ATOM 392 CG TYR A 49 35.695 69.660 4.286 1.00 20.92 C
+ATOM 393 CD1 TYR A 49 35.571 69.406 5.649 1.00 22.05 C
+ATOM 394 CD2 TYR A 49 35.870 70.964 3.868 1.00 21.65 C
+ATOM 395 CE1 TYR A 49 35.623 70.443 6.578 1.00 23.11 C
+ATOM 396 CE2 TYR A 49 35.939 72.011 4.774 1.00 22.46 C
+ATOM 397 CZ TYR A 49 35.802 71.725 6.127 1.00 23.54 C
+ATOM 398 OH TYR A 49 35.844 72.792 7.013 1.00 24.88 O
+ATOM 399 N ARG A 50 36.557 65.521 3.016 1.00 16.04 N
+ATOM 400 CA ARG A 50 36.229 64.239 2.430 1.00 16.01 C
+ATOM 401 C ARG A 50 34.742 64.366 2.059 1.00 15.33 C
+ATOM 402 O ARG A 50 33.974 64.921 2.866 1.00 14.61 O
+ATOM 403 CB ARG A 50 36.459 63.081 3.351 1.00 14.64 C
+ATOM 404 CG ARG A 50 36.198 61.698 2.748 1.00 14.58 C
+ATOM 405 CD ARG A 50 36.284 60.686 3.911 1.00 14.44 C
+ATOM 406 NE ARG A 50 35.910 59.347 3.508 1.00 13.80 N
+ATOM 407 CZ ARG A 50 35.864 58.283 4.280 1.00 16.31 C
+ATOM 408 NH1 ARG A 50 36.284 58.411 5.553 1.00 18.83 N
+ATOM 409 NH2 ARG A 50 35.431 57.118 3.862 1.00 15.18 N
+ATOM 410 N VAL A 51 34.388 64.016 0.811 1.00 14.78 N
+ATOM 411 CA VAL A 51 33.006 64.310 0.374 1.00 13.11 C
+ATOM 412 C VAL A 51 32.385 63.009 -0.096 1.00 14.09 C
+ATOM 413 O VAL A 51 33.049 62.179 -0.759 1.00 12.81 O
+ATOM 414 CB VAL A 51 32.915 65.397 -0.724 1.00 14.40 C
+ATOM 415 CG1 VAL A 51 33.250 66.769 -0.120 1.00 12.81 C
+ATOM 416 CG2 VAL A 51 33.876 65.101 -1.892 1.00 12.06 C
+ATOM 417 N ILE A 52 31.222 62.741 0.547 1.00 13.24 N
+ATOM 418 CA ILE A 52 30.505 61.490 0.279 1.00 12.71 C
+ATOM 419 C ILE A 52 29.086 61.792 -0.194 1.00 12.59 C
+ATOM 420 O ILE A 52 28.398 62.678 0.330 1.00 12.28 O
+ATOM 421 CB ILE A 52 30.463 60.671 1.600 1.00 13.98 C
+ATOM 422 CG1 ILE A 52 31.922 60.262 1.942 1.00 16.07 C
+ATOM 423 CG2 ILE A 52 29.585 59.445 1.464 1.00 13.36 C
+ATOM 424 CD1 ILE A 52 32.153 60.127 3.447 1.00 17.69 C
+ATOM 425 N ALA A 53 28.601 60.985 -1.147 1.00 10.28 N
+ATOM 426 CA ALA A 53 27.216 61.184 -1.632 1.00 8.98 C
+ATOM 427 C ALA A 53 26.727 59.861 -2.201 1.00 10.37 C
+ATOM 428 O ALA A 53 27.502 59.254 -2.974 1.00 10.18 O
+ATOM 429 CB ALA A 53 27.159 62.271 -2.691 1.00 9.23 C
+ATOM 430 N HIS A 54 25.538 59.424 -1.835 1.00 9.75 N
+ATOM 431 CA HIS A 54 25.032 58.180 -2.300 1.00 10.49 C
+ATOM 432 C HIS A 54 23.820 58.433 -3.213 1.00 10.00 C
+ATOM 433 O HIS A 54 23.120 59.451 -3.072 1.00 12.24 O
+ATOM 434 CB HIS A 54 24.611 57.227 -1.152 1.00 10.17 C
+ATOM 435 CG HIS A 54 23.445 57.748 -0.360 1.00 15.03 C
+ATOM 436 ND1 HIS A 54 23.518 58.948 0.309 1.00 16.75 N
+ATOM 437 CD2 HIS A 54 22.190 57.271 -0.134 1.00 17.52 C
+ATOM 438 CE1 HIS A 54 22.394 59.226 0.914 1.00 17.95 C
+ATOM 439 NE2 HIS A 54 21.572 58.229 0.645 1.00 18.90 N
+ATOM 440 N ASP A 55 23.496 57.437 -4.036 1.00 9.81 N
+ATOM 441 CA ASP A 55 22.204 57.427 -4.751 1.00 8.89 C
+ATOM 442 C ASP A 55 21.190 56.723 -3.863 1.00 10.25 C
+ATOM 443 O ASP A 55 21.345 55.518 -3.493 1.00 9.90 O
+ATOM 444 CB ASP A 55 22.333 56.595 -6.057 1.00 9.35 C
+ATOM 445 CG ASP A 55 23.176 57.300 -7.110 1.00 10.41 C
+ATOM 446 OD1 ASP A 55 23.432 58.516 -7.031 1.00 11.07 O
+ATOM 447 OD2 ASP A 55 23.583 56.640 -8.101 1.00 13.40 O
+ATOM 448 N ARG A 56 20.081 57.388 -3.549 1.00 9.91 N
+ATOM 449 CA ARG A 56 18.999 56.735 -2.828 1.00 11.19 C
+ATOM 450 C ARG A 56 18.509 55.507 -3.574 1.00 12.76 C
+ATOM 451 O ARG A 56 18.561 55.394 -4.806 1.00 11.30 O
+ATOM 452 CB ARG A 56 17.870 57.727 -2.625 1.00 11.77 C
+ATOM 453 CG ARG A 56 16.705 57.275 -1.749 1.00 14.73 C
+ATOM 454 CD ARG A 56 15.812 58.475 -1.410 1.00 11.41 C
+ATOM 455 NE ARG A 56 16.636 59.407 -0.677 1.00 11.61 N
+ATOM 456 CZ ARG A 56 16.963 60.632 -1.020 1.00 12.74 C
+ATOM 457 NH1 ARG A 56 16.422 61.207 -2.128 1.00 11.30 N
+ATOM 458 NH2 ARG A 56 17.817 61.305 -0.288 1.00 9.77 N
+ATOM 459 N ARG A 57 18.034 54.489 -2.841 1.00 11.59 N
+ATOM 460 CA ARG A 57 17.554 53.270 -3.462 1.00 11.95 C
+ATOM 461 C ARG A 57 16.476 53.640 -4.511 1.00 11.10 C
+ATOM 462 O ARG A 57 15.688 54.546 -4.275 1.00 11.20 O
+ATOM 463 CB ARG A 57 16.901 52.256 -2.513 1.00 13.57 C
+ATOM 464 CG ARG A 57 15.752 52.707 -1.643 1.00 16.84 C
+ATOM 465 CD ARG A 57 15.027 51.450 -1.048 1.00 15.52 C
+ATOM 466 NE ARG A 57 15.916 50.739 -0.135 1.00 16.36 N
+ATOM 467 CZ ARG A 57 15.871 49.511 0.349 1.00 18.20 C
+ATOM 468 NH1 ARG A 57 14.931 48.652 -0.033 1.00 16.83 N
+ATOM 469 NH2 ARG A 57 16.809 49.053 1.218 1.00 14.46 N
+ATOM 470 N GLY A 58 16.570 52.946 -5.635 1.00 10.12 N
+ATOM 471 CA GLY A 58 15.677 53.236 -6.739 1.00 10.60 C
+ATOM 472 C GLY A 58 16.030 54.514 -7.501 1.00 12.64 C
+ATOM 473 O GLY A 58 15.229 55.037 -8.289 1.00 10.99 O
+ATOM 474 N HIS A 59 17.210 55.088 -7.279 1.00 10.50 N
+ATOM 475 CA HIS A 59 17.596 56.321 -7.908 1.00 12.35 C
+ATOM 476 C HIS A 59 19.013 56.112 -8.483 1.00 11.51 C
+ATOM 477 O HIS A 59 19.823 55.335 -7.953 1.00 12.39 O
+ATOM 478 CB HIS A 59 17.703 57.517 -6.933 1.00 10.93 C
+ATOM 479 CG HIS A 59 16.404 57.959 -6.334 1.00 11.57 C
+ATOM 480 ND1 HIS A 59 15.663 57.055 -5.561 1.00 11.08 N
+ATOM 481 CD2 HIS A 59 15.722 59.144 -6.363 1.00 10.20 C
+ATOM 482 CE1 HIS A 59 14.557 57.704 -5.174 1.00 10.17 C
+ATOM 483 NE2 HIS A 59 14.592 58.946 -5.616 1.00 9.32 N
+ATOM 484 N GLY A 60 19.320 56.942 -9.479 1.00 10.42 N
+ATOM 485 CA GLY A 60 20.652 56.902 -10.083 1.00 10.86 C
+ATOM 486 C GLY A 60 21.107 55.513 -10.457 1.00 12.19 C
+ATOM 487 O GLY A 60 20.488 54.778 -11.237 1.00 12.14 O
+ATOM 488 N ARG A 61 22.260 55.118 -9.880 1.00 11.29 N
+ATOM 489 CA ARG A 61 22.891 53.831 -10.138 1.00 11.62 C
+ATOM 490 C ARG A 61 22.610 52.796 -9.048 1.00 13.15 C
+ATOM 491 O ARG A 61 23.199 51.709 -9.085 1.00 13.99 O
+ATOM 492 CB ARG A 61 24.424 54.022 -10.215 1.00 13.31 C
+ATOM 493 CG ARG A 61 24.869 54.879 -11.400 1.00 14.55 C
+ATOM 494 CD ARG A 61 26.024 55.827 -11.120 1.00 17.01 C
+ATOM 495 NE ARG A 61 25.549 56.911 -10.209 1.00 17.03 N
+ATOM 496 CZ ARG A 61 25.917 58.162 -10.189 1.00 16.70 C
+ATOM 497 NH1 ARG A 61 26.861 58.590 -11.048 1.00 15.95 N
+ATOM 498 NH2 ARG A 61 25.412 59.028 -9.296 1.00 14.51 N
+ATOM 499 N SER A 62 21.828 53.136 -8.030 1.00 12.83 N
+ATOM 500 CA SER A 62 21.476 52.138 -7.014 1.00 11.39 C
+ATOM 501 C SER A 62 20.502 51.121 -7.582 1.00 14.15 C
+ATOM 502 O SER A 62 19.868 51.367 -8.630 1.00 15.29 O
+ATOM 503 CB SER A 62 20.891 52.847 -5.765 1.00 7.46 C
+ATOM 504 OG SER A 62 21.998 53.564 -5.200 1.00 10.03 O
+ATOM 505 N ASP A 63 20.282 50.006 -6.905 1.00 13.37 N
+ATOM 506 CA ASP A 63 19.352 48.989 -7.346 1.00 13.66 C
+ATOM 507 C ASP A 63 17.945 49.568 -7.386 1.00 13.82 C
+ATOM 508 O ASP A 63 17.725 50.578 -6.697 1.00 14.80 O
+ATOM 509 CB ASP A 63 19.307 47.844 -6.333 1.00 14.50 C
+ATOM 510 CG ASP A 63 20.470 46.874 -6.460 1.00 20.41 C
+ATOM 511 OD1 ASP A 63 21.342 47.019 -7.311 1.00 19.01 O
+ATOM 512 OD2 ASP A 63 20.551 45.974 -5.600 1.00 21.85 O
+ATOM 513 N GLN A 64 17.002 48.902 -8.037 1.00 10.61 N
+ATOM 514 CA GLN A 64 15.623 49.389 -8.075 1.00 14.00 C
+ATOM 515 C GLN A 64 14.743 48.255 -7.487 1.00 15.71 C
+ATOM 516 O GLN A 64 14.178 47.458 -8.232 1.00 14.95 O
+ATOM 517 CB GLN A 64 15.189 49.636 -9.520 1.00 15.19 C
+ATOM 518 CG GLN A 64 16.210 50.338 -10.413 1.00 16.24 C
+ATOM 519 CD GLN A 64 15.614 50.878 -11.703 1.00 16.57 C
+ATOM 520 OE1 GLN A 64 14.652 50.305 -12.262 1.00 14.89 O
+ATOM 521 NE2 GLN A 64 16.176 52.005 -12.176 1.00 13.26 N
+ATOM 522 N PRO A 65 14.705 48.137 -6.173 1.00 15.24 N
+ATOM 523 CA PRO A 65 13.975 47.093 -5.494 1.00 15.11 C
+ATOM 524 C PRO A 65 12.494 47.338 -5.537 1.00 14.85 C
+ATOM 525 O PRO A 65 12.042 48.417 -5.865 1.00 15.52 O
+ATOM 526 CB PRO A 65 14.471 47.185 -4.047 1.00 14.78 C
+ATOM 527 CG PRO A 65 14.822 48.628 -3.868 1.00 16.59 C
+ATOM 528 CD PRO A 65 15.331 49.113 -5.221 1.00 15.09 C
+ATOM 529 N SER A 66 11.713 46.308 -5.209 1.00 15.98 N
+ATOM 530 CA SER A 66 10.274 46.407 -5.248 1.00 18.01 C
+ATOM 531 C SER A 66 9.716 47.229 -4.103 1.00 17.99 C
+ATOM 532 O SER A 66 8.650 47.851 -4.183 1.00 18.04 O
+ATOM 533 CB SER A 66 9.746 44.948 -4.997 1.00 19.08 C
+ATOM 534 OG SER A 66 8.331 45.114 -5.016 1.00 24.82 O
+ATOM 535 N THR A 67 10.422 47.149 -2.963 1.00 17.08 N
+ATOM 536 CA THR A 67 9.934 47.775 -1.740 1.00 19.31 C
+ATOM 537 C THR A 67 10.996 48.608 -1.030 1.00 18.68 C
+ATOM 538 O THR A 67 12.126 48.750 -1.492 1.00 18.47 O
+ATOM 539 CB THR A 67 9.470 46.694 -0.712 1.00 22.72 C
+ATOM 540 OG1 THR A 67 10.568 45.822 -0.383 1.00 25.78 O
+ATOM 541 CG2 THR A 67 8.418 45.758 -1.272 1.00 24.64 C
+ATOM 542 N GLY A 68 10.544 49.264 0.050 1.00 18.44 N
+ATOM 543 CA GLY A 68 11.410 50.070 0.881 1.00 18.48 C
+ATOM 544 C GLY A 68 11.430 51.513 0.425 1.00 18.03 C
+ATOM 545 O GLY A 68 12.341 52.225 0.869 1.00 17.43 O
+ATOM 546 N HIS A 69 10.386 51.958 -0.298 1.00 15.63 N
+ATOM 547 CA HIS A 69 10.355 53.371 -0.688 1.00 14.93 C
+ATOM 548 C HIS A 69 9.757 54.226 0.416 1.00 17.11 C
+ATOM 549 O HIS A 69 8.638 54.710 0.233 1.00 17.45 O
+ATOM 550 CB HIS A 69 9.572 53.474 -2.035 1.00 15.52 C
+ATOM 551 CG HIS A 69 10.239 52.528 -2.995 1.00 17.07 C
+ATOM 552 ND1 HIS A 69 11.567 52.724 -3.352 1.00 16.36 N
+ATOM 553 CD2 HIS A 69 9.833 51.360 -3.537 1.00 17.57 C
+ATOM 554 CE1 HIS A 69 11.915 51.713 -4.163 1.00 17.29 C
+ATOM 555 NE2 HIS A 69 10.894 50.860 -4.272 1.00 15.49 N
+ATOM 556 N ASP A 70 10.401 54.382 1.579 1.00 17.34 N
+ATOM 557 CA ASP A 70 9.849 55.101 2.717 1.00 18.16 C
+ATOM 558 C ASP A 70 11.016 55.692 3.544 1.00 16.30 C
+ATOM 559 O ASP A 70 12.116 55.163 3.410 1.00 13.01 O
+ATOM 560 CB ASP A 70 8.928 54.178 3.541 1.00 20.28 C
+ATOM 561 CG ASP A 70 9.746 53.058 4.173 1.00 23.91 C
+ATOM 562 OD1 ASP A 70 10.450 53.230 5.194 1.00 24.82 O
+ATOM 563 OD2 ASP A 70 9.798 51.942 3.629 1.00 27.21 O
+ATOM 564 N MET A 71 10.727 56.674 4.374 1.00 16.04 N
+ATOM 565 CA MET A 71 11.751 57.382 5.138 1.00 17.42 C
+ATOM 566 C MET A 71 12.489 56.507 6.126 1.00 18.97 C
+ATOM 567 O MET A 71 13.668 56.733 6.391 1.00 19.57 O
+ATOM 568 CB MET A 71 11.113 58.595 5.817 1.00 17.57 C
+ATOM 569 CG MET A 71 10.799 59.737 4.828 1.00 19.70 C
+ATOM 570 SD MET A 71 12.346 60.497 4.262 1.00 23.19 S
+ATOM 571 CE MET A 71 11.642 61.291 2.798 1.00 21.28 C
+ATOM 572 N ASP A 72 11.775 55.560 6.792 1.00 18.86 N
+ATOM 573 CA ASP A 72 12.473 54.698 7.726 1.00 20.01 C
+ATOM 574 C ASP A 72 13.515 53.867 6.990 1.00 17.50 C
+ATOM 575 O ASP A 72 14.636 53.699 7.436 1.00 17.67 O
+ATOM 576 CB ASP A 72 11.540 53.702 8.440 1.00 21.15 C
+ATOM 577 CG ASP A 72 10.651 54.414 9.426 1.00 23.56 C
+ATOM 578 OD1 ASP A 72 11.007 55.456 9.999 1.00 25.29 O
+ATOM 579 OD2 ASP A 72 9.544 53.929 9.677 1.00 26.30 O
+ATOM 580 N THR A 73 13.175 53.274 5.861 1.00 17.67 N
+ATOM 581 CA THR A 73 14.185 52.520 5.103 1.00 16.73 C
+ATOM 582 C THR A 73 15.262 53.441 4.560 1.00 16.33 C
+ATOM 583 O THR A 73 16.445 53.092 4.560 1.00 15.98 O
+ATOM 584 CB THR A 73 13.467 51.793 3.952 1.00 19.40 C
+ATOM 585 OG1 THR A 73 12.385 51.035 4.527 1.00 19.44 O
+ATOM 586 CG2 THR A 73 14.438 50.906 3.183 1.00 20.03 C
+ATOM 587 N TYR A 74 14.901 54.643 4.086 1.00 14.43 N
+ATOM 588 CA TYR A 74 15.942 55.537 3.560 1.00 14.73 C
+ATOM 589 C TYR A 74 16.957 55.842 4.662 1.00 15.63 C
+ATOM 590 O TYR A 74 18.142 55.858 4.393 1.00 13.39 O
+ATOM 591 CB TYR A 74 15.344 56.863 3.076 1.00 12.85 C
+ATOM 592 CG TYR A 74 14.417 56.781 1.865 1.00 13.05 C
+ATOM 593 CD1 TYR A 74 14.461 55.725 0.994 1.00 13.06 C
+ATOM 594 CD2 TYR A 74 13.504 57.830 1.665 1.00 11.61 C
+ATOM 595 CE1 TYR A 74 13.591 55.676 -0.092 1.00 13.74 C
+ATOM 596 CE2 TYR A 74 12.613 57.756 0.570 1.00 13.06 C
+ATOM 597 CZ TYR A 74 12.688 56.699 -0.283 1.00 12.46 C
+ATOM 598 OH TYR A 74 11.843 56.599 -1.381 1.00 15.66 O
+ATOM 599 N ALA A 75 16.454 56.130 5.890 1.00 14.81 N
+ATOM 600 CA ALA A 75 17.414 56.440 6.971 1.00 15.93 C
+ATOM 601 C ALA A 75 18.205 55.188 7.368 1.00 17.41 C
+ATOM 602 O ALA A 75 19.366 55.333 7.761 1.00 19.66 O
+ATOM 603 CB ALA A 75 16.636 56.997 8.152 1.00 17.42 C
+ATOM 604 N ALA A 76 17.653 53.997 7.255 1.00 16.77 N
+ATOM 605 CA ALA A 76 18.407 52.784 7.602 1.00 18.34 C
+ATOM 606 C ALA A 76 19.466 52.475 6.548 1.00 17.45 C
+ATOM 607 O ALA A 76 20.572 51.981 6.804 1.00 15.95 O
+ATOM 608 CB ALA A 76 17.468 51.599 7.773 1.00 18.78 C
+ATOM 609 N ASP A 77 19.139 52.844 5.291 1.00 15.37 N
+ATOM 610 CA ASP A 77 20.136 52.652 4.211 1.00 13.81 C
+ATOM 611 C ASP A 77 21.277 53.630 4.498 1.00 13.34 C
+ATOM 612 O ASP A 77 22.424 53.249 4.306 1.00 16.53 O
+ATOM 613 CB ASP A 77 19.494 52.994 2.858 1.00 13.74 C
+ATOM 614 CG ASP A 77 18.513 51.988 2.327 1.00 17.10 C
+ATOM 615 OD1 ASP A 77 18.425 50.849 2.881 1.00 16.29 O
+ATOM 616 OD2 ASP A 77 17.788 52.307 1.343 1.00 15.78 O
+ATOM 617 N VAL A 78 21.051 54.844 4.975 1.00 13.30 N
+ATOM 618 CA VAL A 78 22.112 55.774 5.317 1.00 13.87 C
+ATOM 619 C VAL A 78 22.995 55.177 6.445 1.00 15.32 C
+ATOM 620 O VAL A 78 24.221 55.230 6.400 1.00 14.19 O
+ATOM 621 CB VAL A 78 21.571 57.143 5.763 1.00 14.43 C
+ATOM 622 CG1 VAL A 78 22.714 57.985 6.298 1.00 15.65 C
+ATOM 623 CG2 VAL A 78 20.904 57.852 4.554 1.00 14.95 C
+ATOM 624 N ALA A 79 22.342 54.591 7.449 1.00 14.95 N
+ATOM 625 CA ALA A 79 23.102 53.964 8.557 1.00 15.95 C
+ATOM 626 C ALA A 79 23.934 52.847 8.022 1.00 15.19 C
+ATOM 627 O ALA A 79 25.079 52.715 8.472 1.00 17.54 O
+ATOM 628 CB ALA A 79 22.124 53.500 9.656 1.00 16.85 C
+ATOM 629 N ALA A 80 23.456 52.027 7.093 1.00 14.80 N
+ATOM 630 CA ALA A 80 24.236 50.967 6.501 1.00 17.47 C
+ATOM 631 C ALA A 80 25.499 51.562 5.868 1.00 17.32 C
+ATOM 632 O ALA A 80 26.583 50.993 6.093 1.00 19.66 O
+ATOM 633 CB ALA A 80 23.454 50.067 5.575 1.00 17.72 C
+ATOM 634 N LEU A 81 25.450 52.649 5.130 1.00 15.51 N
+ATOM 635 CA LEU A 81 26.623 53.274 4.528 1.00 15.62 C
+ATOM 636 C LEU A 81 27.582 53.880 5.552 1.00 16.94 C
+ATOM 637 O LEU A 81 28.808 53.700 5.418 1.00 18.22 O
+ATOM 638 CB LEU A 81 26.102 54.456 3.671 1.00 16.49 C
+ATOM 639 CG LEU A 81 27.157 55.396 3.066 1.00 19.29 C
+ATOM 640 CD1 LEU A 81 27.932 54.622 2.007 1.00 21.95 C
+ATOM 641 CD2 LEU A 81 26.473 56.621 2.490 1.00 22.69 C
+ATOM 642 N THR A 82 27.065 54.575 6.550 1.00 14.71 N
+ATOM 643 CA THR A 82 27.980 55.227 7.505 1.00 18.33 C
+ATOM 644 C THR A 82 28.678 54.214 8.422 1.00 19.91 C
+ATOM 645 O THR A 82 29.841 54.412 8.805 1.00 19.40 O
+ATOM 646 CB THR A 82 27.335 56.325 8.359 1.00 16.68 C
+ATOM 647 OG1 THR A 82 26.292 55.847 9.185 1.00 18.54 O
+ATOM 648 CG2 THR A 82 26.849 57.480 7.498 1.00 16.27 C
+ATOM 649 N GLU A 83 28.048 53.063 8.588 1.00 21.58 N
+ATOM 650 CA GLU A 83 28.658 51.958 9.340 1.00 25.23 C
+ATOM 651 C GLU A 83 29.713 51.272 8.482 1.00 24.69 C
+ATOM 652 O GLU A 83 30.819 51.012 8.961 1.00 23.50 O
+ATOM 653 CB GLU A 83 27.568 50.963 9.751 1.00 27.95 C
+ATOM 654 CG GLU A 83 28.084 49.713 10.444 1.00 33.90 C
+ATOM 655 CD GLU A 83 26.905 48.776 10.709 1.00 38.78 C
+ATOM 656 OE1 GLU A 83 26.519 48.018 9.785 1.00 40.54 O
+ATOM 657 OE2 GLU A 83 26.371 48.884 11.836 1.00 41.13 O
+ATOM 658 N ALA A 84 29.419 50.976 7.208 1.00 20.78 N
+ATOM 659 CA ALA A 84 30.450 50.419 6.330 1.00 19.99 C
+ATOM 660 C ALA A 84 31.664 51.318 6.205 1.00 20.70 C
+ATOM 661 O ALA A 84 32.793 50.773 6.143 1.00 22.41 O
+ATOM 662 CB ALA A 84 29.839 50.024 4.963 1.00 18.65 C
+ATOM 663 N LEU A 85 31.571 52.650 6.272 1.00 18.54 N
+ATOM 664 CA LEU A 85 32.699 53.528 6.145 1.00 19.39 C
+ATOM 665 C LEU A 85 33.261 53.914 7.518 1.00 19.27 C
+ATOM 666 O LEU A 85 34.291 54.579 7.531 1.00 21.45 O
+ATOM 667 CB LEU A 85 32.306 54.856 5.426 1.00 20.66 C
+ATOM 668 CG LEU A 85 31.663 54.697 4.046 1.00 23.58 C
+ATOM 669 CD1 LEU A 85 31.411 56.053 3.395 1.00 24.14 C
+ATOM 670 CD2 LEU A 85 32.588 53.894 3.145 1.00 23.29 C
+ATOM 671 N ASP A 86 32.514 53.615 8.539 1.00 20.86 N
+ATOM 672 CA ASP A 86 32.806 53.988 9.929 1.00 23.39 C
+ATOM 673 C ASP A 86 33.019 55.472 10.098 1.00 22.50 C
+ATOM 674 O ASP A 86 34.055 55.964 10.581 1.00 20.76 O
+ATOM 675 CB ASP A 86 34.038 53.213 10.432 1.00 26.61 C
+ATOM 676 CG ASP A 86 34.220 53.280 11.931 1.00 31.20 C
+ATOM 677 OD1 ASP A 86 33.267 53.429 12.719 1.00 29.69 O
+ATOM 678 OD2 ASP A 86 35.409 53.170 12.353 1.00 33.56 O
+ATOM 679 N LEU A 87 32.008 56.260 9.689 1.00 19.97 N
+ATOM 680 CA LEU A 87 32.208 57.705 9.781 1.00 19.09 C
+ATOM 681 C LEU A 87 31.999 58.169 11.221 1.00 19.84 C
+ATOM 682 O LEU A 87 31.084 57.671 11.897 1.00 19.74 O
+ATOM 683 CB LEU A 87 31.177 58.411 8.887 1.00 18.71 C
+ATOM 684 CG LEU A 87 31.249 58.071 7.387 1.00 19.32 C
+ATOM 685 CD1 LEU A 87 30.308 59.050 6.653 1.00 19.65 C
+ATOM 686 CD2 LEU A 87 32.639 58.230 6.800 1.00 19.00 C
+ATOM 687 N ARG A 88 32.733 59.164 11.620 1.00 19.63 N
+ATOM 688 CA ARG A 88 32.583 59.767 12.939 1.00 23.48 C
+ATOM 689 C ARG A 88 32.615 61.266 12.788 1.00 20.52 C
+ATOM 690 O ARG A 88 33.367 61.762 11.941 1.00 21.55 O
+ATOM 691 CB ARG A 88 33.748 59.318 13.859 1.00 25.09 C
+ATOM 692 CG ARG A 88 33.681 57.870 14.334 1.00 30.33 C
+ATOM 693 CD ARG A 88 32.394 57.510 15.074 1.00 34.04 C
+ATOM 694 NE ARG A 88 32.267 56.084 15.232 1.00 38.78 N
+ATOM 695 CZ ARG A 88 31.458 55.214 15.805 1.00 40.77 C
+ATOM 696 NH1 ARG A 88 30.364 55.549 16.484 1.00 40.44 N
+ATOM 697 NH2 ARG A 88 31.729 53.897 15.680 1.00 42.08 N
+ATOM 698 N GLY A 89 31.834 62.045 13.514 1.00 20.15 N
+ATOM 699 CA GLY A 89 31.858 63.465 13.455 1.00 17.54 C
+ATOM 700 C GLY A 89 31.500 64.049 12.081 1.00 18.79 C
+ATOM 701 O GLY A 89 32.003 65.107 11.684 1.00 16.87 O
+ATOM 702 N ALA A 90 30.643 63.348 11.355 1.00 17.83 N
+ATOM 703 CA ALA A 90 30.297 63.763 10.001 1.00 15.52 C
+ATOM 704 C ALA A 90 29.336 64.899 9.940 1.00 16.33 C
+ATOM 705 O ALA A 90 28.558 65.115 10.883 1.00 16.82 O
+ATOM 706 CB ALA A 90 29.561 62.547 9.393 1.00 17.00 C
+ATOM 707 N VAL A 91 29.393 65.720 8.871 1.00 13.67 N
+ATOM 708 CA VAL A 91 28.366 66.742 8.683 1.00 13.22 C
+ATOM 709 C VAL A 91 27.402 66.248 7.590 1.00 15.06 C
+ATOM 710 O VAL A 91 27.920 65.809 6.536 1.00 16.66 O
+ATOM 711 CB VAL A 91 28.974 68.075 8.297 1.00 16.04 C
+ATOM 712 CG1 VAL A 91 27.865 69.095 8.026 1.00 17.56 C
+ATOM 713 CG2 VAL A 91 29.861 68.570 9.447 1.00 16.48 C
+ATOM 714 N HIS A 92 26.113 66.229 7.807 1.00 11.63 N
+ATOM 715 CA HIS A 92 25.144 65.719 6.845 1.00 12.18 C
+ATOM 716 C HIS A 92 24.390 66.886 6.224 1.00 14.67 C
+ATOM 717 O HIS A 92 23.679 67.641 6.923 1.00 16.35 O
+ATOM 718 CB HIS A 92 24.212 64.719 7.527 1.00 12.33 C
+ATOM 719 CG HIS A 92 24.897 63.407 7.758 1.00 12.93 C
+ATOM 720 ND1 HIS A 92 24.708 62.309 6.964 1.00 12.24 N
+ATOM 721 CD2 HIS A 92 25.856 63.057 8.714 1.00 12.63 C
+ATOM 722 CE1 HIS A 92 25.485 61.284 7.376 1.00 13.63 C
+ATOM 723 NE2 HIS A 92 26.187 61.759 8.423 1.00 13.06 N
+ATOM 724 N ILE A 93 24.414 66.994 4.881 1.00 11.18 N
+ATOM 725 CA ILE A 93 23.709 68.114 4.203 1.00 9.98 C
+ATOM 726 C ILE A 93 22.616 67.515 3.326 1.00 11.23 C
+ATOM 727 O ILE A 93 22.892 66.634 2.469 1.00 10.49 O
+ATOM 728 CB ILE A 93 24.745 68.932 3.406 1.00 13.14 C
+ATOM 729 CG1 ILE A 93 25.852 69.482 4.320 1.00 14.06 C
+ATOM 730 CG2 ILE A 93 24.042 70.097 2.677 1.00 14.50 C
+ATOM 731 CD1 ILE A 93 26.903 70.365 3.678 1.00 15.40 C
+ATOM 732 N GLY A 94 21.366 67.912 3.536 1.00 10.62 N
+ATOM 733 CA GLY A 94 20.292 67.240 2.765 1.00 12.88 C
+ATOM 734 C GLY A 94 19.501 68.350 2.052 1.00 16.16 C
+ATOM 735 O GLY A 94 19.190 69.361 2.686 1.00 15.14 O
+ATOM 736 N HIS A 95 19.136 68.044 0.795 1.00 13.09 N
+ATOM 737 CA HIS A 95 18.354 69.000 0.020 1.00 13.32 C
+ATOM 738 C HIS A 95 17.014 68.337 -0.282 1.00 12.35 C
+ATOM 739 O HIS A 95 16.868 67.134 -0.584 1.00 11.34 O
+ATOM 740 CB HIS A 95 19.055 69.391 -1.297 1.00 15.02 C
+ATOM 741 CG HIS A 95 18.167 70.144 -2.238 1.00 16.82 C
+ATOM 742 ND1 HIS A 95 17.703 69.564 -3.414 1.00 17.88 N
+ATOM 743 CD2 HIS A 95 17.651 71.394 -2.174 1.00 14.59 C
+ATOM 744 CE1 HIS A 95 16.917 70.432 -4.040 1.00 18.81 C
+ATOM 745 NE2 HIS A 95 16.871 71.550 -3.318 1.00 17.88 N
+ATOM 746 N SER A 96 15.998 69.172 -0.067 1.00 14.04 N
+ATOM 747 CA SER A 96 14.618 68.802 -0.390 1.00 15.68 C
+ATOM 748 C SER A 96 14.201 67.538 0.301 1.00 14.88 C
+ATOM 749 O SER A 96 14.305 67.430 1.548 1.00 15.16 O
+ATOM 750 CB SER A 96 14.612 68.763 -1.957 1.00 15.50 C
+ATOM 751 OG SER A 96 13.280 68.544 -2.353 1.00 18.71 O
+ATOM 752 N THR A 97 13.778 66.487 -0.386 1.00 15.07 N
+ATOM 753 CA THR A 97 13.509 65.168 0.216 1.00 14.67 C
+ATOM 754 C THR A 97 14.711 64.635 0.982 1.00 15.48 C
+ATOM 755 O THR A 97 14.515 63.911 1.974 1.00 13.67 O
+ATOM 756 CB THR A 97 13.245 64.127 -0.904 1.00 15.45 C
+ATOM 757 OG1 THR A 97 11.997 64.541 -1.527 1.00 18.38 O
+ATOM 758 CG2 THR A 97 13.111 62.695 -0.449 1.00 15.51 C
+ATOM 759 N GLY A 98 15.948 64.972 0.540 1.00 12.55 N
+ATOM 760 CA GLY A 98 17.127 64.504 1.268 1.00 13.01 C
+ATOM 761 C GLY A 98 17.175 65.171 2.668 1.00 13.48 C
+ATOM 762 O GLY A 98 17.769 64.575 3.564 1.00 13.47 O
+ATOM 763 N GLY A 99 16.551 66.331 2.823 1.00 11.31 N
+ATOM 764 CA GLY A 99 16.509 66.993 4.126 1.00 12.15 C
+ATOM 765 C GLY A 99 15.628 66.175 5.084 1.00 14.00 C
+ATOM 766 O GLY A 99 16.046 66.003 6.243 1.00 17.52 O
+ATOM 767 N GLY A 100 14.603 65.494 4.591 1.00 12.96 N
+ATOM 768 CA GLY A 100 13.783 64.630 5.428 1.00 13.74 C
+ATOM 769 C GLY A 100 14.562 63.397 5.850 1.00 16.67 C
+ATOM 770 O GLY A 100 14.514 62.950 7.015 1.00 12.89 O
+ATOM 771 N GLU A 101 15.294 62.790 4.888 1.00 11.79 N
+ATOM 772 CA GLU A 101 16.136 61.641 5.177 1.00 12.41 C
+ATOM 773 C GLU A 101 17.190 62.010 6.223 1.00 11.59 C
+ATOM 774 O GLU A 101 17.465 61.163 7.080 1.00 13.66 O
+ATOM 775 CB GLU A 101 16.845 61.224 3.872 1.00 11.32 C
+ATOM 776 CG GLU A 101 17.903 60.135 3.989 1.00 12.29 C
+ATOM 777 CD GLU A 101 18.353 59.709 2.596 1.00 11.09 C
+ATOM 778 OE1 GLU A 101 17.684 58.906 1.932 1.00 12.25 O
+ATOM 779 OE2 GLU A 101 19.368 60.280 2.164 1.00 11.73 O
+ATOM 780 N VAL A 102 17.798 63.183 6.104 1.00 12.63 N
+ATOM 781 CA VAL A 102 18.799 63.629 7.065 1.00 14.35 C
+ATOM 782 C VAL A 102 18.122 63.741 8.461 1.00 16.40 C
+ATOM 783 O VAL A 102 18.707 63.289 9.448 1.00 17.06 O
+ATOM 784 CB VAL A 102 19.464 64.953 6.700 1.00 13.42 C
+ATOM 785 CG1 VAL A 102 20.226 65.622 7.859 1.00 14.21 C
+ATOM 786 CG2 VAL A 102 20.515 64.672 5.568 1.00 13.88 C
+ATOM 787 N ALA A 103 16.983 64.407 8.540 1.00 14.66 N
+ATOM 788 CA ALA A 103 16.350 64.567 9.878 1.00 16.92 C
+ATOM 789 C ALA A 103 16.100 63.217 10.552 1.00 18.96 C
+ATOM 790 O ALA A 103 16.526 63.086 11.728 1.00 19.92 O
+ATOM 791 CB ALA A 103 15.035 65.312 9.745 1.00 13.74 C
+ATOM 792 N ARG A 104 15.546 62.223 9.872 1.00 16.46 N
+ATOM 793 CA ARG A 104 15.300 60.914 10.427 1.00 18.30 C
+ATOM 794 C ARG A 104 16.570 60.126 10.722 1.00 20.67 C
+ATOM 795 O ARG A 104 16.637 59.523 11.812 1.00 21.85 O
+ATOM 796 CB ARG A 104 14.374 60.048 9.567 1.00 18.66 C
+ATOM 797 CG ARG A 104 14.049 58.698 10.193 1.00 20.98 C
+ATOM 798 CD ARG A 104 12.603 58.316 10.017 1.00 21.99 C
+ATOM 799 NE ARG A 104 11.671 59.387 10.338 1.00 22.40 N
+ATOM 800 CZ ARG A 104 10.379 59.279 10.084 1.00 22.61 C
+ATOM 801 NH1 ARG A 104 9.932 58.170 9.524 1.00 24.41 N
+ATOM 802 NH2 ARG A 104 9.556 60.253 10.423 1.00 21.87 N
+ATOM 803 N TYR A 105 17.603 60.158 9.873 1.00 16.74 N
+ATOM 804 CA TYR A 105 18.826 59.467 10.174 1.00 17.07 C
+ATOM 805 C TYR A 105 19.526 60.064 11.388 1.00 17.78 C
+ATOM 806 O TYR A 105 20.034 59.322 12.264 1.00 19.08 O
+ATOM 807 CB TYR A 105 19.799 59.508 8.959 1.00 15.36 C
+ATOM 808 CG TYR A 105 21.215 59.137 9.390 1.00 15.12 C
+ATOM 809 CD1 TYR A 105 21.508 57.825 9.719 1.00 16.22 C
+ATOM 810 CD2 TYR A 105 22.214 60.067 9.473 1.00 15.78 C
+ATOM 811 CE1 TYR A 105 22.791 57.475 10.150 1.00 16.69 C
+ATOM 812 CE2 TYR A 105 23.511 59.756 9.850 1.00 13.42 C
+ATOM 813 CZ TYR A 105 23.779 58.438 10.170 1.00 16.63 C
+ATOM 814 OH TYR A 105 25.049 58.067 10.566 1.00 17.46 O
+ATOM 815 N VAL A 106 19.649 61.371 11.449 1.00 18.18 N
+ATOM 816 CA VAL A 106 20.361 62.081 12.506 1.00 20.66 C
+ATOM 817 C VAL A 106 19.665 61.827 13.838 1.00 22.94 C
+ATOM 818 O VAL A 106 20.336 61.536 14.817 1.00 23.69 O
+ATOM 819 CB VAL A 106 20.542 63.579 12.280 1.00 20.43 C
+ATOM 820 CG1 VAL A 106 21.154 64.247 13.510 1.00 21.56 C
+ATOM 821 CG2 VAL A 106 21.526 63.775 11.094 1.00 19.15 C
+ATOM 822 N ALA A 107 18.351 61.806 13.873 1.00 22.13 N
+ATOM 823 CA ALA A 107 17.619 61.540 15.127 1.00 24.16 C
+ATOM 824 C ALA A 107 17.904 60.150 15.661 1.00 24.09 C
+ATOM 825 O ALA A 107 17.879 59.949 16.878 1.00 26.11 O
+ATOM 826 CB ALA A 107 16.135 61.723 14.786 1.00 21.13 C
+ATOM 827 N ARG A 108 18.181 59.164 14.827 1.00 24.23 N
+ATOM 828 CA ARG A 108 18.403 57.793 15.229 1.00 27.39 C
+ATOM 829 C ARG A 108 19.857 57.319 15.183 1.00 24.90 C
+ATOM 830 O ARG A 108 20.095 56.113 15.363 1.00 23.81 O
+ATOM 831 CB ARG A 108 17.652 56.917 14.189 1.00 30.03 C
+ATOM 832 CG ARG A 108 16.143 56.892 14.376 1.00 35.83 C
+ATOM 833 CD ARG A 108 15.500 56.000 13.299 1.00 38.87 C
+ATOM 834 NE ARG A 108 14.064 56.229 13.238 1.00 41.87 N
+ATOM 835 CZ ARG A 108 13.112 55.774 12.436 1.00 43.22 C
+ATOM 836 NH1 ARG A 108 13.256 54.906 11.437 1.00 42.75 N
+ATOM 837 NH2 ARG A 108 11.866 56.217 12.661 1.00 44.61 N
+ATOM 838 N ALA A 109 20.781 58.196 14.821 1.00 21.52 N
+ATOM 839 CA ALA A 109 22.128 57.736 14.551 1.00 24.73 C
+ATOM 840 C ALA A 109 22.839 57.349 15.856 1.00 25.69 C
+ATOM 841 O ALA A 109 22.528 57.924 16.900 1.00 23.47 O
+ATOM 842 CB ALA A 109 22.905 58.824 13.831 1.00 23.45 C
+ATOM 843 N GLU A 110 23.769 56.423 15.755 1.00 28.23 N
+ATOM 844 CA GLU A 110 24.601 56.048 16.899 1.00 31.70 C
+ATOM 845 C GLU A 110 25.324 57.316 17.323 1.00 32.18 C
+ATOM 846 O GLU A 110 25.861 58.036 16.463 1.00 33.02 O
+ATOM 847 CB GLU A 110 25.691 55.061 16.459 1.00 35.35 C
+ATOM 848 CG GLU A 110 25.247 53.732 15.905 1.00 40.99 C
+ATOM 849 CD GLU A 110 26.474 52.906 15.518 1.00 45.41 C
+ATOM 850 OE1 GLU A 110 27.453 52.903 16.311 1.00 46.51 O
+ATOM 851 OE2 GLU A 110 26.437 52.312 14.415 1.00 47.09 O
+ATOM 852 N PRO A 111 25.385 57.628 18.593 1.00 32.76 N
+ATOM 853 CA PRO A 111 26.064 58.859 19.029 1.00 32.92 C
+ATOM 854 C PRO A 111 27.525 58.863 18.572 1.00 30.57 C
+ATOM 855 O PRO A 111 28.177 57.817 18.417 1.00 28.47 O
+ATOM 856 CB PRO A 111 25.832 58.843 20.542 1.00 35.07 C
+ATOM 857 CG PRO A 111 24.629 57.971 20.767 1.00 34.07 C
+ATOM 858 CD PRO A 111 24.754 56.872 19.718 1.00 33.77 C
+ATOM 859 N GLY A 112 28.067 60.009 18.191 1.00 30.19 N
+ATOM 860 CA GLY A 112 29.431 60.163 17.673 1.00 29.60 C
+ATOM 861 C GLY A 112 29.555 60.103 16.144 1.00 29.16 C
+ATOM 862 O GLY A 112 30.480 60.685 15.553 1.00 27.81 O
+ATOM 863 N ARG A 113 28.565 59.512 15.468 1.00 26.41 N
+ATOM 864 CA ARG A 113 28.576 59.431 14.025 1.00 26.06 C
+ATOM 865 C ARG A 113 28.300 60.801 13.383 1.00 23.47 C
+ATOM 866 O ARG A 113 28.790 61.008 12.289 1.00 21.34 O
+ATOM 867 CB ARG A 113 27.486 58.469 13.573 1.00 28.07 C
+ATOM 868 CG ARG A 113 27.700 57.000 13.894 1.00 28.06 C
+ATOM 869 CD ARG A 113 28.098 56.271 12.609 1.00 29.02 C
+ATOM 870 NE ARG A 113 28.332 54.847 12.862 1.00 30.94 N
+ATOM 871 CZ ARG A 113 29.542 54.292 12.942 1.00 31.35 C
+ATOM 872 NH1 ARG A 113 30.693 54.940 12.771 1.00 29.03 N
+ATOM 873 NH2 ARG A 113 29.575 52.980 13.180 1.00 31.95 N
+ATOM 874 N VAL A 114 27.489 61.652 14.010 1.00 19.46 N
+ATOM 875 CA VAL A 114 27.141 62.931 13.415 1.00 17.53 C
+ATOM 876 C VAL A 114 27.562 64.113 14.273 1.00 19.91 C
+ATOM 877 O VAL A 114 27.231 64.194 15.452 1.00 19.40 O
+ATOM 878 CB VAL A 114 25.604 63.059 13.247 1.00 15.39 C
+ATOM 879 CG1 VAL A 114 25.198 64.377 12.593 1.00 13.59 C
+ATOM 880 CG2 VAL A 114 25.068 61.889 12.413 1.00 14.34 C
+ATOM 881 N ALA A 115 28.163 65.123 13.644 1.00 16.23 N
+ATOM 882 CA ALA A 115 28.538 66.316 14.352 1.00 19.35 C
+ATOM 883 C ALA A 115 27.535 67.438 14.137 1.00 19.13 C
+ATOM 884 O ALA A 115 27.319 68.240 15.040 1.00 18.48 O
+ATOM 885 CB ALA A 115 29.903 66.879 13.936 1.00 19.47 C
+ATOM 886 N LYS A 116 27.083 67.657 12.889 1.00 19.00 N
+ATOM 887 CA LYS A 116 26.223 68.787 12.568 1.00 16.04 C
+ATOM 888 C LYS A 116 25.330 68.354 11.382 1.00 16.14 C
+ATOM 889 O LYS A 116 25.719 67.411 10.678 1.00 16.69 O
+ATOM 890 CB LYS A 116 27.043 69.958 12.040 1.00 20.65 C
+ATOM 891 CG LYS A 116 28.035 70.656 12.936 1.00 22.85 C
+ATOM 892 CD LYS A 116 28.758 71.804 12.264 1.00 25.09 C
+ATOM 893 CE LYS A 116 29.914 72.284 13.163 1.00 28.02 C
+ATOM 894 NZ LYS A 116 29.929 73.775 13.090 1.00 31.95 N
+ATOM 895 N ALA A 117 24.262 69.074 11.152 1.00 16.05 N
+ATOM 896 CA ALA A 117 23.399 68.717 10.002 1.00 15.76 C
+ATOM 897 C ALA A 117 22.900 69.977 9.336 1.00 16.26 C
+ATOM 898 O ALA A 117 22.890 71.045 9.959 1.00 15.86 O
+ATOM 899 CB ALA A 117 22.293 67.767 10.424 1.00 16.07 C
+ATOM 900 N VAL A 118 22.578 69.919 8.026 1.00 15.13 N
+ATOM 901 CA VAL A 118 22.140 71.108 7.298 1.00 13.37 C
+ATOM 902 C VAL A 118 20.890 70.657 6.530 1.00 15.18 C
+ATOM 903 O VAL A 118 20.919 69.584 5.885 1.00 15.17 O
+ATOM 904 CB VAL A 118 23.178 71.662 6.304 1.00 15.05 C
+ATOM 905 CG1 VAL A 118 22.614 72.842 5.495 1.00 14.19 C
+ATOM 906 CG2 VAL A 118 24.502 72.078 6.932 1.00 13.64 C
+ATOM 907 N LEU A 119 19.783 71.328 6.638 1.00 14.09 N
+ATOM 908 CA LEU A 119 18.560 71.101 5.910 1.00 15.14 C
+ATOM 909 C LEU A 119 18.329 72.253 4.919 1.00 15.74 C
+ATOM 910 O LEU A 119 18.074 73.387 5.312 1.00 19.06 O
+ATOM 911 CB LEU A 119 17.300 71.025 6.790 1.00 17.15 C
+ATOM 912 CG LEU A 119 17.423 70.088 8.009 1.00 21.07 C
+ATOM 913 CD1 LEU A 119 16.113 70.093 8.796 1.00 23.48 C
+ATOM 914 CD2 LEU A 119 17.921 68.706 7.682 1.00 19.76 C
+ATOM 915 N VAL A 120 18.545 71.997 3.640 1.00 16.09 N
+ATOM 916 CA VAL A 120 18.399 73.007 2.601 1.00 13.95 C
+ATOM 917 C VAL A 120 17.109 72.766 1.821 1.00 14.28 C
+ATOM 918 O VAL A 120 16.913 71.663 1.282 1.00 12.45 O
+ATOM 919 CB VAL A 120 19.578 72.966 1.595 1.00 16.45 C
+ATOM 920 CG1 VAL A 120 19.431 74.146 0.623 1.00 14.13 C
+ATOM 921 CG2 VAL A 120 20.958 72.961 2.231 1.00 14.24 C
+ATOM 922 N SER A 121 16.233 73.785 1.746 1.00 13.51 N
+ATOM 923 CA SER A 121 14.986 73.663 1.007 1.00 16.25 C
+ATOM 924 C SER A 121 14.283 72.381 1.389 1.00 15.98 C
+ATOM 925 O SER A 121 13.751 71.670 0.532 1.00 16.42 O
+ATOM 926 CB SER A 121 15.274 73.688 -0.529 1.00 15.59 C
+ATOM 927 OG SER A 121 16.228 74.729 -0.787 1.00 17.82 O
+ATOM 928 N ALA A 122 14.306 71.993 2.677 1.00 15.58 N
+ATOM 929 CA ALA A 122 13.901 70.673 3.083 1.00 13.61 C
+ATOM 930 C ALA A 122 12.438 70.544 3.422 1.00 15.75 C
+ATOM 931 O ALA A 122 11.781 71.492 3.836 1.00 15.81 O
+ATOM 932 CB ALA A 122 14.791 70.273 4.278 1.00 14.14 C
+ATOM 933 N VAL A 123 11.924 69.312 3.284 1.00 15.36 N
+ATOM 934 CA VAL A 123 10.527 69.027 3.512 1.00 18.14 C
+ATOM 935 C VAL A 123 9.974 69.164 4.923 1.00 19.99 C
+ATOM 936 O VAL A 123 8.776 69.479 5.035 1.00 21.14 O
+ATOM 937 CB VAL A 123 10.062 67.644 2.940 1.00 18.42 C
+ATOM 938 CG1 VAL A 123 10.238 67.646 1.421 1.00 19.16 C
+ATOM 939 CG2 VAL A 123 10.861 66.474 3.520 1.00 18.69 C
+ATOM 940 N PRO A 124 10.721 68.892 5.987 1.00 19.16 N
+ATOM 941 CA PRO A 124 10.182 69.032 7.342 1.00 20.59 C
+ATOM 942 C PRO A 124 9.628 70.397 7.654 1.00 20.01 C
+ATOM 943 O PRO A 124 10.109 71.434 7.171 1.00 22.48 O
+ATOM 944 CB PRO A 124 11.392 68.800 8.286 1.00 19.48 C
+ATOM 945 CG PRO A 124 12.323 67.936 7.435 1.00 19.07 C
+ATOM 946 CD PRO A 124 12.128 68.471 6.025 1.00 18.32 C
+ATOM 947 N PRO A 125 8.721 70.443 8.644 1.00 21.76 N
+ATOM 948 CA PRO A 125 8.219 69.310 9.380 1.00 20.46 C
+ATOM 949 C PRO A 125 7.308 68.302 8.697 1.00 20.38 C
+ATOM 950 O PRO A 125 7.375 67.082 8.880 1.00 18.46 O
+ATOM 951 CB PRO A 125 7.324 69.985 10.466 1.00 20.66 C
+ATOM 952 CG PRO A 125 7.877 71.352 10.605 1.00 22.04 C
+ATOM 953 CD PRO A 125 8.255 71.757 9.197 1.00 20.22 C
+ATOM 954 N VAL A 126 6.316 68.801 7.967 1.00 19.98 N
+ATOM 955 CA VAL A 126 5.353 68.009 7.227 1.00 21.55 C
+ATOM 956 C VAL A 126 4.727 68.878 6.123 1.00 22.41 C
+ATOM 957 O VAL A 126 4.335 70.045 6.330 1.00 22.55 O
+ATOM 958 CB VAL A 126 4.230 67.380 8.073 1.00 24.15 C
+ATOM 959 CG1 VAL A 126 3.540 68.441 8.942 1.00 24.05 C
+ATOM 960 CG2 VAL A 126 3.210 66.654 7.208 1.00 24.22 C
+ATOM 961 N MET A 127 4.625 68.324 4.915 1.00 20.38 N
+ATOM 962 CA MET A 127 4.112 69.139 3.815 1.00 21.43 C
+ATOM 963 C MET A 127 2.597 69.118 3.663 1.00 23.72 C
+ATOM 964 O MET A 127 2.009 70.163 3.364 1.00 25.21 O
+ATOM 965 CB MET A 127 4.718 68.684 2.467 1.00 22.06 C
+ATOM 966 CG MET A 127 6.210 69.033 2.339 1.00 23.44 C
+ATOM 967 SD MET A 127 6.785 68.631 0.633 1.00 23.31 S
+ATOM 968 CE MET A 127 6.062 69.979 -0.273 1.00 22.99 C
+ATOM 969 N VAL A 128 2.000 67.948 3.707 1.00 24.76 N
+ATOM 970 CA VAL A 128 0.589 67.847 3.367 1.00 26.65 C
+ATOM 971 C VAL A 128 -0.316 68.452 4.443 1.00 30.56 C
+ATOM 972 O VAL A 128 -0.016 68.420 5.630 1.00 28.24 O
+ATOM 973 CB VAL A 128 0.229 66.380 3.125 1.00 26.19 C
+ATOM 974 CG1 VAL A 128 0.157 65.553 4.402 1.00 25.58 C
+ATOM 975 CG2 VAL A 128 -1.079 66.284 2.332 1.00 26.20 C
+ATOM 976 N LYS A 129 -1.455 68.930 3.955 1.00 33.75 N
+ATOM 977 CA LYS A 129 -2.528 69.410 4.811 1.00 37.76 C
+ATOM 978 C LYS A 129 -3.114 68.230 5.578 1.00 38.61 C
+ATOM 979 O LYS A 129 -3.401 67.151 5.056 1.00 39.57 O
+ATOM 980 CB LYS A 129 -3.606 70.087 3.961 1.00 39.66 C
+ATOM 981 CG LYS A 129 -4.822 70.488 4.789 1.00 42.50 C
+ATOM 982 CD LYS A 129 -5.900 71.086 3.899 1.00 43.45 C
+ATOM 983 CE LYS A 129 -5.819 72.598 3.876 1.00 44.88 C
+ATOM 984 NZ LYS A 129 -5.178 73.126 2.641 1.00 45.64 N
+ATOM 985 N SER A 130 -3.283 68.410 6.883 1.00 38.84 N
+ATOM 986 CA SER A 130 -3.854 67.425 7.778 1.00 38.69 C
+ATOM 987 C SER A 130 -4.493 68.142 8.982 1.00 39.55 C
+ATOM 988 O SER A 130 -4.423 69.362 9.058 1.00 38.38 O
+ATOM 989 CB SER A 130 -2.760 66.504 8.347 1.00 37.38 C
+ATOM 990 OG SER A 130 -1.819 67.347 9.027 1.00 37.20 O
+ATOM 991 N ASP A 131 -4.953 67.365 9.948 1.00 43.09 N
+ATOM 992 CA ASP A 131 -5.550 67.875 11.165 1.00 47.90 C
+ATOM 993 C ASP A 131 -4.518 68.671 11.989 1.00 48.15 C
+ATOM 994 O ASP A 131 -4.889 69.577 12.705 1.00 47.07 O
+ATOM 995 CB ASP A 131 -6.077 66.856 12.146 1.00 49.76 C
+ATOM 996 CG ASP A 131 -6.898 65.680 11.761 1.00 53.37 C
+ATOM 997 OD1 ASP A 131 -8.018 65.812 11.202 1.00 54.42 O
+ATOM 998 OD2 ASP A 131 -6.379 64.566 12.083 1.00 55.34 O
+ATOM 999 N THR A 132 -3.268 68.235 11.891 1.00 50.01 N
+ATOM 1000 CA THR A 132 -2.186 68.888 12.615 1.00 50.68 C
+ATOM 1001 C THR A 132 -1.449 69.908 11.776 1.00 50.61 C
+ATOM 1002 O THR A 132 -0.586 70.594 12.349 1.00 52.20 O
+ATOM 1003 CB THR A 132 -1.238 67.812 13.162 1.00 52.11 C
+ATOM 1004 OG1 THR A 132 -0.694 67.033 12.076 1.00 54.39 O
+ATOM 1005 CG2 THR A 132 -1.995 66.843 14.062 1.00 52.04 C
+ATOM 1006 N ASN A 133 -1.786 70.083 10.503 1.00 48.26 N
+ATOM 1007 CA ASN A 133 -1.122 71.040 9.629 1.00 47.55 C
+ATOM 1008 C ASN A 133 -2.042 71.671 8.597 1.00 49.07 C
+ATOM 1009 O ASN A 133 -2.045 71.329 7.408 1.00 48.16 O
+ATOM 1010 CB ASN A 133 0.037 70.296 8.925 1.00 45.68 C
+ATOM 1011 CG ASN A 133 0.818 71.178 7.974 1.00 44.93 C
+ATOM 1012 OD1 ASN A 133 1.060 72.351 8.252 1.00 44.22 O
+ATOM 1013 ND2 ASN A 133 1.215 70.634 6.821 1.00 43.36 N
+ATOM 1014 N PRO A 134 -2.842 72.662 8.992 1.00 50.69 N
+ATOM 1015 CA PRO A 134 -3.792 73.363 8.147 1.00 50.45 C
+ATOM 1016 C PRO A 134 -3.214 74.285 7.093 1.00 50.20 C
+ATOM 1017 O PRO A 134 -3.880 74.595 6.098 1.00 50.56 O
+ATOM 1018 CB PRO A 134 -4.600 74.225 9.144 1.00 51.82 C
+ATOM 1019 CG PRO A 134 -3.567 74.517 10.205 1.00 52.01 C
+ATOM 1020 CD PRO A 134 -2.897 73.167 10.405 1.00 51.50 C
+ATOM 1021 N ASP A 135 -1.986 74.767 7.250 1.00 49.38 N
+ATOM 1022 CA ASP A 135 -1.376 75.621 6.231 1.00 49.28 C
+ATOM 1023 C ASP A 135 -0.669 74.792 5.163 1.00 46.05 C
+ATOM 1024 O ASP A 135 -0.143 75.332 4.189 1.00 46.07 O
+ATOM 1025 CB ASP A 135 -0.421 76.614 6.892 1.00 52.19 C
+ATOM 1026 CG ASP A 135 -1.096 77.685 7.735 1.00 55.03 C
+ATOM 1027 OD1 ASP A 135 -2.344 77.641 7.906 1.00 56.45 O
+ATOM 1028 OD2 ASP A 135 -0.377 78.592 8.231 1.00 55.00 O
+ATOM 1029 N GLY A 136 -0.638 73.472 5.304 1.00 43.89 N
+ATOM 1030 CA GLY A 136 0.011 72.587 4.340 1.00 40.79 C
+ATOM 1031 C GLY A 136 -0.607 72.638 2.949 1.00 39.43 C
+ATOM 1032 O GLY A 136 -1.544 73.385 2.650 1.00 39.15 O
+ATOM 1033 N LEU A 137 -0.041 71.877 2.008 1.00 35.97 N
+ATOM 1034 CA LEU A 137 -0.546 71.797 0.644 1.00 32.66 C
+ATOM 1035 C LEU A 137 -1.582 70.678 0.590 1.00 29.24 C
+ATOM 1036 O LEU A 137 -1.435 69.663 1.243 1.00 26.74 O
+ATOM 1037 CB LEU A 137 0.577 71.474 -0.348 1.00 32.81 C
+ATOM 1038 CG LEU A 137 1.599 72.592 -0.555 1.00 35.09 C
+ATOM 1039 CD1 LEU A 137 2.843 72.066 -1.253 1.00 34.97 C
+ATOM 1040 CD2 LEU A 137 0.972 73.766 -1.309 1.00 35.67 C
+ATOM 1041 N PRO A 138 -2.652 70.861 -0.170 1.00 29.45 N
+ATOM 1042 CA PRO A 138 -3.675 69.844 -0.304 1.00 30.23 C
+ATOM 1043 C PRO A 138 -3.107 68.606 -0.990 1.00 31.36 C
+ATOM 1044 O PRO A 138 -2.182 68.693 -1.822 1.00 32.13 O
+ATOM 1045 CB PRO A 138 -4.783 70.503 -1.102 1.00 29.06 C
+ATOM 1046 CG PRO A 138 -4.217 71.741 -1.663 1.00 30.42 C
+ATOM 1047 CD PRO A 138 -2.923 72.077 -0.982 1.00 29.28 C
+ATOM 1048 N LEU A 139 -3.672 67.458 -0.684 1.00 31.51 N
+ATOM 1049 CA LEU A 139 -3.265 66.176 -1.216 1.00 32.88 C
+ATOM 1050 C LEU A 139 -3.340 66.131 -2.741 1.00 31.99 C
+ATOM 1051 O LEU A 139 -2.504 65.504 -3.406 1.00 28.55 O
+ATOM 1052 CB LEU A 139 -4.092 65.037 -0.623 1.00 33.94 C
+ATOM 1053 CG LEU A 139 -3.372 63.699 -0.466 1.00 37.35 C
+ATOM 1054 CD1 LEU A 139 -3.117 63.063 -1.822 1.00 39.86 C
+ATOM 1055 CD2 LEU A 139 -2.017 63.789 0.231 1.00 37.96 C
+ATOM 1056 N GLU A 140 -4.318 66.831 -3.302 1.00 31.28 N
+ATOM 1057 CA GLU A 140 -4.527 66.920 -4.732 1.00 34.12 C
+ATOM 1058 C GLU A 140 -3.313 67.462 -5.475 1.00 31.45 C
+ATOM 1059 O GLU A 140 -3.031 67.028 -6.610 1.00 30.08 O
+ATOM 1060 CB GLU A 140 -5.794 67.732 -5.049 1.00 37.68 C
+ATOM 1061 CG GLU A 140 -6.040 68.878 -4.111 1.00 43.67 C
+ATOM 1062 CD GLU A 140 -7.019 68.713 -2.958 1.00 45.80 C
+ATOM 1063 OE1 GLU A 140 -7.115 67.641 -2.311 1.00 45.98 O
+ATOM 1064 OE2 GLU A 140 -7.718 69.740 -2.683 1.00 47.17 O
+ATOM 1065 N VAL A 141 -2.523 68.339 -4.866 1.00 28.37 N
+ATOM 1066 CA VAL A 141 -1.286 68.790 -5.493 1.00 27.33 C
+ATOM 1067 C VAL A 141 -0.410 67.546 -5.757 1.00 25.57 C
+ATOM 1068 O VAL A 141 0.194 67.413 -6.827 1.00 25.43 O
+ATOM 1069 CB VAL A 141 -0.540 69.789 -4.610 1.00 29.32 C
+ATOM 1070 CG1 VAL A 141 0.888 70.082 -5.057 1.00 29.44 C
+ATOM 1071 CG2 VAL A 141 -1.302 71.127 -4.543 1.00 31.16 C
+ATOM 1072 N PHE A 142 -0.337 66.631 -4.805 1.00 21.76 N
+ATOM 1073 CA PHE A 142 0.516 65.463 -4.882 1.00 21.71 C
+ATOM 1074 C PHE A 142 -0.097 64.394 -5.767 1.00 20.83 C
+ATOM 1075 O PHE A 142 0.623 63.660 -6.423 1.00 19.11 O
+ATOM 1076 CB PHE A 142 0.877 64.900 -3.471 1.00 20.89 C
+ATOM 1077 CG PHE A 142 1.543 66.015 -2.693 1.00 20.73 C
+ATOM 1078 CD1 PHE A 142 2.757 66.537 -3.093 1.00 20.49 C
+ATOM 1079 CD2 PHE A 142 0.877 66.575 -1.607 1.00 20.60 C
+ATOM 1080 CE1 PHE A 142 3.325 67.590 -2.410 1.00 22.14 C
+ATOM 1081 CE2 PHE A 142 1.453 67.642 -0.942 1.00 22.34 C
+ATOM 1082 CZ PHE A 142 2.686 68.155 -1.324 1.00 20.93 C
+ATOM 1083 N ASP A 143 -1.417 64.311 -5.833 1.00 22.05 N
+ATOM 1084 CA ASP A 143 -2.112 63.389 -6.697 1.00 22.94 C
+ATOM 1085 C ASP A 143 -1.835 63.782 -8.163 1.00 22.41 C
+ATOM 1086 O ASP A 143 -1.703 62.840 -8.927 1.00 23.26 O
+ATOM 1087 CB ASP A 143 -3.619 63.441 -6.447 1.00 27.10 C
+ATOM 1088 CG ASP A 143 -4.051 62.727 -5.176 1.00 29.44 C
+ATOM 1089 OD1 ASP A 143 -3.371 61.870 -4.594 1.00 29.15 O
+ATOM 1090 OD2 ASP A 143 -5.176 63.078 -4.763 1.00 31.30 O
+ATOM 1091 N GLU A 144 -1.766 65.045 -8.493 1.00 21.73 N
+ATOM 1092 CA GLU A 144 -1.374 65.485 -9.837 1.00 25.52 C
+ATOM 1093 C GLU A 144 0.040 65.073 -10.232 1.00 24.13 C
+ATOM 1094 O GLU A 144 0.208 64.690 -11.388 1.00 22.40 O
+ATOM 1095 CB GLU A 144 -1.421 67.006 -10.030 1.00 28.14 C
+ATOM 1096 CG GLU A 144 -2.869 67.480 -10.020 1.00 36.33 C
+ATOM 1097 CD GLU A 144 -3.033 68.985 -10.091 1.00 40.88 C
+ATOM 1098 OE1 GLU A 144 -2.047 69.768 -9.974 1.00 42.24 O
+ATOM 1099 OE2 GLU A 144 -4.217 69.376 -10.273 1.00 44.88 O
+ATOM 1100 N PHE A 145 1.036 65.242 -9.360 1.00 22.28 N
+ATOM 1101 CA PHE A 145 2.390 64.743 -9.629 1.00 20.58 C
+ATOM 1102 C PHE A 145 2.385 63.240 -9.889 1.00 18.51 C
+ATOM 1103 O PHE A 145 2.992 62.744 -10.867 1.00 19.78 O
+ATOM 1104 CB PHE A 145 3.316 64.959 -8.436 1.00 22.71 C
+ATOM 1105 CG PHE A 145 3.666 66.343 -8.007 1.00 26.44 C
+ATOM 1106 CD1 PHE A 145 3.575 67.430 -8.857 1.00 27.94 C
+ATOM 1107 CD2 PHE A 145 4.064 66.546 -6.686 1.00 28.67 C
+ATOM 1108 CE1 PHE A 145 3.895 68.699 -8.438 1.00 30.51 C
+ATOM 1109 CE2 PHE A 145 4.391 67.832 -6.253 1.00 31.78 C
+ATOM 1110 CZ PHE A 145 4.318 68.909 -7.123 1.00 31.64 C
+ATOM 1111 N ARG A 146 1.749 62.471 -8.993 1.00 14.95 N
+ATOM 1112 CA ARG A 146 1.594 61.053 -9.210 1.00 16.50 C
+ATOM 1113 C ARG A 146 1.000 60.747 -10.594 1.00 16.19 C
+ATOM 1114 O ARG A 146 1.537 59.853 -11.263 1.00 16.94 O
+ATOM 1115 CB ARG A 146 0.712 60.363 -8.159 1.00 15.44 C
+ATOM 1116 CG ARG A 146 1.448 59.903 -6.913 1.00 18.49 C
+ATOM 1117 CD ARG A 146 0.522 59.214 -5.904 1.00 19.25 C
+ATOM 1118 NE ARG A 146 -0.263 60.147 -5.116 1.00 18.99 N
+ATOM 1119 CZ ARG A 146 0.162 60.845 -4.055 1.00 22.00 C
+ATOM 1120 NH1 ARG A 146 1.417 60.708 -3.589 1.00 20.74 N
+ATOM 1121 NH2 ARG A 146 -0.666 61.682 -3.424 1.00 19.74 N
+ATOM 1122 N ALA A 147 -0.108 61.405 -10.930 1.00 15.41 N
+ATOM 1123 CA ALA A 147 -0.742 61.068 -12.224 1.00 16.02 C
+ATOM 1124 C ALA A 147 0.098 61.494 -13.424 1.00 15.60 C
+ATOM 1125 O ALA A 147 0.205 60.731 -14.389 1.00 15.55 O
+ATOM 1126 CB ALA A 147 -2.112 61.756 -12.317 1.00 17.78 C
+ATOM 1127 N ALA A 148 0.745 62.663 -13.374 1.00 13.66 N
+ATOM 1128 CA ALA A 148 1.608 63.038 -14.492 1.00 13.34 C
+ATOM 1129 C ALA A 148 2.797 62.104 -14.625 1.00 15.15 C
+ATOM 1130 O ALA A 148 3.231 61.756 -15.756 1.00 14.91 O
+ATOM 1131 CB ALA A 148 2.058 64.486 -14.318 1.00 14.20 C
+ATOM 1132 N LEU A 149 3.391 61.691 -13.481 1.00 14.37 N
+ATOM 1133 CA LEU A 149 4.554 60.815 -13.474 1.00 15.07 C
+ATOM 1134 C LEU A 149 4.182 59.482 -14.107 1.00 16.23 C
+ATOM 1135 O LEU A 149 4.885 58.970 -14.955 1.00 15.81 O
+ATOM 1136 CB LEU A 149 5.075 60.558 -12.059 1.00 16.20 C
+ATOM 1137 CG LEU A 149 6.412 59.846 -11.889 1.00 18.76 C
+ATOM 1138 CD1 LEU A 149 7.086 60.354 -10.615 1.00 17.72 C
+ATOM 1139 CD2 LEU A 149 6.246 58.348 -11.940 1.00 17.67 C
+ATOM 1140 N ALA A 150 3.075 58.893 -13.651 1.00 15.42 N
+ATOM 1141 CA ALA A 150 2.615 57.620 -14.189 1.00 15.16 C
+ATOM 1142 C ALA A 150 2.230 57.738 -15.673 1.00 13.78 C
+ATOM 1143 O ALA A 150 2.514 56.789 -16.397 1.00 19.26 O
+ATOM 1144 CB ALA A 150 1.364 57.251 -13.386 1.00 16.42 C
+ATOM 1145 N ALA A 151 1.636 58.823 -16.125 1.00 13.40 N
+ATOM 1146 CA ALA A 151 1.186 58.908 -17.525 1.00 15.13 C
+ATOM 1147 C ALA A 151 2.360 59.061 -18.521 1.00 15.01 C
+ATOM 1148 O ALA A 151 2.327 58.380 -19.543 1.00 17.01 O
+ATOM 1149 CB ALA A 151 0.202 60.066 -17.659 1.00 16.40 C
+ATOM 1150 N ASN A 152 3.331 59.915 -18.248 1.00 12.29 N
+ATOM 1151 CA ASN A 152 4.439 60.148 -19.182 1.00 13.18 C
+ATOM 1152 C ASN A 152 5.573 60.722 -18.357 1.00 10.57 C
+ATOM 1153 O ASN A 152 5.726 61.921 -18.232 1.00 11.29 O
+ATOM 1154 CB ASN A 152 3.982 61.130 -20.277 1.00 14.78 C
+ATOM 1155 CG ASN A 152 5.036 61.288 -21.358 1.00 16.16 C
+ATOM 1156 OD1 ASN A 152 6.178 60.853 -21.145 1.00 12.66 O
+ATOM 1157 ND2 ASN A 152 4.588 61.815 -22.497 1.00 15.63 N
+ATOM 1158 N ARG A 153 6.332 59.814 -17.706 1.00 9.65 N
+ATOM 1159 CA ARG A 153 7.398 60.294 -16.812 1.00 9.45 C
+ATOM 1160 C ARG A 153 8.406 61.123 -17.576 1.00 10.07 C
+ATOM 1161 O ARG A 153 8.902 62.130 -17.059 1.00 9.84 O
+ATOM 1162 CB ARG A 153 8.047 59.062 -16.122 1.00 9.95 C
+ATOM 1163 CG ARG A 153 9.129 59.432 -15.113 1.00 11.95 C
+ATOM 1164 CD ARG A 153 9.551 58.224 -14.256 1.00 13.02 C
+ATOM 1165 NE ARG A 153 10.347 57.245 -14.983 1.00 10.42 N
+ATOM 1166 CZ ARG A 153 11.605 56.976 -14.698 1.00 12.00 C
+ATOM 1167 NH1 ARG A 153 12.210 57.583 -13.658 1.00 11.11 N
+ATOM 1168 NH2 ARG A 153 12.259 56.076 -15.418 1.00 11.45 N
+ATOM 1169 N ALA A 154 8.807 60.640 -18.788 1.00 9.44 N
+ATOM 1170 CA ALA A 154 9.789 61.415 -19.576 1.00 9.28 C
+ATOM 1171 C ALA A 154 9.390 62.843 -19.851 1.00 8.79 C
+ATOM 1172 O ALA A 154 10.271 63.686 -19.920 1.00 9.13 O
+ATOM 1173 CB ALA A 154 10.040 60.700 -20.903 1.00 9.50 C
+ATOM 1174 N GLN A 155 8.137 63.191 -20.063 1.00 9.37 N
+ATOM 1175 CA GLN A 155 7.712 64.565 -20.311 1.00 10.37 C
+ATOM 1176 C GLN A 155 7.519 65.339 -19.000 1.00 9.78 C
+ATOM 1177 O GLN A 155 7.921 66.483 -18.873 1.00 11.62 O
+ATOM 1178 CB GLN A 155 6.341 64.590 -21.027 1.00 10.74 C
+ATOM 1179 CG GLN A 155 5.909 66.003 -21.439 1.00 9.94 C
+ATOM 1180 CD GLN A 155 6.902 66.609 -22.400 1.00 11.90 C
+ATOM 1181 OE1 GLN A 155 7.337 65.974 -23.381 1.00 14.39 O
+ATOM 1182 NE2 GLN A 155 7.351 67.806 -22.090 1.00 12.98 N
+ATOM 1183 N PHE A 156 7.013 64.634 -17.972 1.00 10.53 N
+ATOM 1184 CA PHE A 156 6.839 65.277 -16.659 1.00 11.74 C
+ATOM 1185 C PHE A 156 8.203 65.727 -16.154 1.00 9.48 C
+ATOM 1186 O PHE A 156 8.397 66.768 -15.554 1.00 10.94 O
+ATOM 1187 CB PHE A 156 6.256 64.245 -15.646 1.00 12.12 C
+ATOM 1188 CG PHE A 156 6.000 64.794 -14.241 1.00 13.48 C
+ATOM 1189 CD1 PHE A 156 5.211 65.908 -14.082 1.00 13.11 C
+ATOM 1190 CD2 PHE A 156 6.477 64.155 -13.111 1.00 15.50 C
+ATOM 1191 CE1 PHE A 156 4.970 66.445 -12.813 1.00 15.16 C
+ATOM 1192 CE2 PHE A 156 6.204 64.647 -11.834 1.00 13.39 C
+ATOM 1193 CZ PHE A 156 5.465 65.796 -11.690 1.00 13.21 C
+ATOM 1194 N TYR A 157 9.294 64.964 -16.487 1.00 9.39 N
+ATOM 1195 CA TYR A 157 10.626 65.323 -15.969 1.00 8.62 C
+ATOM 1196 C TYR A 157 11.296 66.373 -16.831 1.00 10.81 C
+ATOM 1197 O TYR A 157 12.368 66.844 -16.467 1.00 9.98 O
+ATOM 1198 CB TYR A 157 11.523 64.093 -15.831 1.00 8.88 C
+ATOM 1199 CG TYR A 157 11.170 63.193 -14.660 1.00 10.44 C
+ATOM 1200 CD1 TYR A 157 10.110 63.418 -13.807 1.00 11.47 C
+ATOM 1201 CD2 TYR A 157 12.026 62.108 -14.415 1.00 11.17 C
+ATOM 1202 CE1 TYR A 157 9.883 62.572 -12.727 1.00 12.14 C
+ATOM 1203 CE2 TYR A 157 11.781 61.252 -13.378 1.00 12.49 C
+ATOM 1204 CZ TYR A 157 10.724 61.517 -12.513 1.00 13.38 C
+ATOM 1205 OH TYR A 157 10.501 60.602 -11.501 1.00 13.61 O
+ATOM 1206 N ILE A 158 10.671 66.837 -17.923 1.00 11.10 N
+ATOM 1207 CA ILE A 158 11.089 68.071 -18.598 1.00 12.31 C
+ATOM 1208 C ILE A 158 10.292 69.254 -17.938 1.00 11.59 C
+ATOM 1209 O ILE A 158 10.835 70.306 -17.575 1.00 11.49 O
+ATOM 1210 CB ILE A 158 10.750 68.081 -20.098 1.00 14.66 C
+ATOM 1211 CG1 ILE A 158 11.572 66.972 -20.802 1.00 15.74 C
+ATOM 1212 CG2 ILE A 158 10.961 69.479 -20.712 1.00 14.05 C
+ATOM 1213 CD1 ILE A 158 11.294 66.947 -22.300 1.00 13.62 C
+ATOM 1214 N ASP A 159 9.015 69.001 -17.726 1.00 11.12 N
+ATOM 1215 CA ASP A 159 8.133 70.029 -17.174 1.00 14.77 C
+ATOM 1216 C ASP A 159 8.546 70.562 -15.812 1.00 14.63 C
+ATOM 1217 O ASP A 159 8.522 71.789 -15.625 1.00 14.25 O
+ATOM 1218 CB ASP A 159 6.680 69.568 -17.124 1.00 16.02 C
+ATOM 1219 CG ASP A 159 6.089 69.272 -18.514 1.00 18.51 C
+ATOM 1220 OD1 ASP A 159 6.635 69.648 -19.554 1.00 16.93 O
+ATOM 1221 OD2 ASP A 159 5.053 68.602 -18.482 1.00 21.22 O
+ATOM 1222 N VAL A 160 8.925 69.692 -14.850 1.00 12.85 N
+ATOM 1223 CA VAL A 160 9.310 70.214 -13.540 1.00 11.22 C
+ATOM 1224 C VAL A 160 10.503 71.122 -13.472 1.00 12.66 C
+ATOM 1225 O VAL A 160 10.469 72.246 -12.937 1.00 13.19 O
+ATOM 1226 CB VAL A 160 9.428 68.997 -12.593 1.00 11.11 C
+ATOM 1227 CG1 VAL A 160 9.929 69.425 -11.226 1.00 11.13 C
+ATOM 1228 CG2 VAL A 160 8.091 68.302 -12.477 1.00 11.30 C
+ATOM 1229 N PRO A 161 11.685 70.742 -14.006 1.00 12.43 N
+ATOM 1230 CA PRO A 161 12.865 71.568 -14.015 1.00 9.91 C
+ATOM 1231 C PRO A 161 12.738 72.752 -14.967 1.00 11.78 C
+ATOM 1232 O PRO A 161 13.416 73.744 -14.772 1.00 12.50 O
+ATOM 1233 CB PRO A 161 13.986 70.622 -14.404 1.00 11.67 C
+ATOM 1234 CG PRO A 161 13.286 69.625 -15.276 1.00 11.08 C
+ATOM 1235 CD PRO A 161 11.920 69.391 -14.600 1.00 11.57 C
+ATOM 1236 N SER A 162 11.928 72.722 -16.013 1.00 14.47 N
+ATOM 1237 CA SER A 162 11.728 73.853 -16.910 1.00 15.87 C
+ATOM 1238 C SER A 162 10.859 74.906 -16.214 1.00 16.10 C
+ATOM 1239 O SER A 162 10.962 76.062 -16.524 1.00 17.75 O
+ATOM 1240 CB SER A 162 10.907 73.440 -18.163 1.00 15.71 C
+ATOM 1241 OG SER A 162 11.778 72.620 -18.953 1.00 17.94 O
+ATOM 1242 N GLY A 163 10.051 74.517 -15.251 1.00 16.08 N
+ATOM 1243 CA GLY A 163 9.114 75.422 -14.610 1.00 15.70 C
+ATOM 1244 C GLY A 163 9.439 75.796 -13.184 1.00 13.60 C
+ATOM 1245 O GLY A 163 10.290 76.646 -12.907 1.00 17.17 O
+ATOM 1246 N PRO A 164 8.868 75.092 -12.239 1.00 13.87 N
+ATOM 1247 CA PRO A 164 9.008 75.470 -10.837 1.00 16.88 C
+ATOM 1248 C PRO A 164 10.303 75.134 -10.124 1.00 15.68 C
+ATOM 1249 O PRO A 164 10.732 75.912 -9.280 1.00 18.25 O
+ATOM 1250 CB PRO A 164 7.861 74.726 -10.159 1.00 15.51 C
+ATOM 1251 CG PRO A 164 7.482 73.607 -11.078 1.00 16.56 C
+ATOM 1252 CD PRO A 164 7.838 74.033 -12.470 1.00 13.98 C
+ATOM 1253 N PHE A 165 10.976 74.030 -10.462 1.00 12.34 N
+ATOM 1254 CA PHE A 165 12.148 73.659 -9.622 1.00 10.59 C
+ATOM 1255 C PHE A 165 13.198 74.691 -9.452 1.00 12.15 C
+ATOM 1256 O PHE A 165 13.771 74.818 -8.345 1.00 11.34 O
+ATOM 1257 CB PHE A 165 12.687 72.322 -10.141 1.00 10.42 C
+ATOM 1258 CG PHE A 165 13.442 71.439 -9.175 1.00 11.90 C
+ATOM 1259 CD1 PHE A 165 14.778 71.695 -8.921 1.00 10.94 C
+ATOM 1260 CD2 PHE A 165 12.765 70.417 -8.530 1.00 10.90 C
+ATOM 1261 CE1 PHE A 165 15.483 70.894 -8.028 1.00 10.77 C
+ATOM 1262 CE2 PHE A 165 13.485 69.589 -7.619 1.00 11.84 C
+ATOM 1263 CZ PHE A 165 14.809 69.854 -7.408 1.00 10.14 C
+ATOM 1264 N TYR A 166 13.663 75.363 -10.531 1.00 10.46 N
+ATOM 1265 CA TYR A 166 14.773 76.252 -10.531 1.00 10.78 C
+ATOM 1266 C TYR A 166 14.304 77.687 -10.721 1.00 12.77 C
+ATOM 1267 O TYR A 166 15.122 78.569 -10.885 1.00 12.36 O
+ATOM 1268 CB TYR A 166 15.787 75.939 -11.692 1.00 11.17 C
+ATOM 1269 CG TYR A 166 16.528 74.625 -11.458 1.00 11.96 C
+ATOM 1270 CD1 TYR A 166 17.380 74.452 -10.368 1.00 9.60 C
+ATOM 1271 CD2 TYR A 166 16.345 73.558 -12.345 1.00 11.53 C
+ATOM 1272 CE1 TYR A 166 18.063 73.266 -10.197 1.00 11.76 C
+ATOM 1273 CE2 TYR A 166 17.009 72.369 -12.141 1.00 10.68 C
+ATOM 1274 CZ TYR A 166 17.843 72.214 -11.080 1.00 12.29 C
+ATOM 1275 OH TYR A 166 18.480 71.014 -10.899 1.00 12.68 O
+ATOM 1276 N GLY A 167 12.999 77.909 -10.657 1.00 15.04 N
+ATOM 1277 CA GLY A 167 12.464 79.276 -10.833 1.00 15.35 C
+ATOM 1278 C GLY A 167 12.686 79.797 -12.233 1.00 18.42 C
+ATOM 1279 O GLY A 167 12.609 81.029 -12.452 1.00 18.56 O
+ATOM 1280 N PHE A 168 12.913 78.946 -13.257 1.00 16.77 N
+ATOM 1281 CA PHE A 168 13.139 79.499 -14.597 1.00 17.30 C
+ATOM 1282 C PHE A 168 11.827 80.019 -15.198 1.00 18.88 C
+ATOM 1283 O PHE A 168 11.829 80.544 -16.321 1.00 20.43 O
+ATOM 1284 CB PHE A 168 13.741 78.420 -15.516 1.00 13.57 C
+ATOM 1285 CG PHE A 168 15.090 77.911 -15.125 1.00 12.80 C
+ATOM 1286 CD1 PHE A 168 15.968 78.689 -14.402 1.00 12.39 C
+ATOM 1287 CD2 PHE A 168 15.496 76.641 -15.519 1.00 13.54 C
+ATOM 1288 CE1 PHE A 168 17.235 78.262 -14.064 1.00 13.46 C
+ATOM 1289 CE2 PHE A 168 16.756 76.190 -15.161 1.00 13.74 C
+ATOM 1290 CZ PHE A 168 17.634 77.005 -14.447 1.00 15.04 C
+ATOM 1291 N ASN A 169 10.683 79.833 -14.579 1.00 19.48 N
+ATOM 1292 CA ASN A 169 9.430 80.400 -15.026 1.00 19.75 C
+ATOM 1293 C ASN A 169 9.268 81.820 -14.475 1.00 22.95 C
+ATOM 1294 O ASN A 169 8.198 82.390 -14.727 1.00 25.06 O
+ATOM 1295 CB ASN A 169 8.225 79.540 -14.653 1.00 18.97 C
+ATOM 1296 CG ASN A 169 8.138 79.306 -13.144 1.00 19.69 C
+ATOM 1297 OD1 ASN A 169 8.983 79.792 -12.369 1.00 19.38 O
+ATOM 1298 ND2 ASN A 169 7.139 78.551 -12.712 1.00 20.25 N
+ATOM 1299 N ARG A 170 10.204 82.385 -13.737 1.00 23.31 N
+ATOM 1300 CA ARG A 170 10.128 83.741 -13.239 1.00 26.22 C
+ATOM 1301 C ARG A 170 10.757 84.695 -14.256 1.00 29.13 C
+ATOM 1302 O ARG A 170 11.840 84.460 -14.818 1.00 28.21 O
+ATOM 1303 CB ARG A 170 10.945 83.901 -11.942 1.00 26.41 C
+ATOM 1304 CG ARG A 170 10.421 83.225 -10.688 1.00 26.12 C
+ATOM 1305 CD ARG A 170 8.948 83.458 -10.439 1.00 27.65 C
+ATOM 1306 NE ARG A 170 8.461 82.948 -9.166 1.00 28.05 N
+ATOM 1307 CZ ARG A 170 7.304 82.334 -8.992 1.00 26.76 C
+ATOM 1308 NH1 ARG A 170 6.476 82.167 -10.018 1.00 28.15 N
+ATOM 1309 NH2 ARG A 170 6.945 81.890 -7.789 1.00 28.29 N
+ATOM 1310 N GLU A 171 10.145 85.866 -14.406 1.00 31.67 N
+ATOM 1311 CA GLU A 171 10.681 86.880 -15.319 1.00 34.31 C
+ATOM 1312 C GLU A 171 12.058 87.315 -14.869 1.00 32.61 C
+ATOM 1313 O GLU A 171 12.327 87.492 -13.675 1.00 32.62 O
+ATOM 1314 CB GLU A 171 9.723 88.065 -15.395 1.00 38.74 C
+ATOM 1315 CG GLU A 171 9.948 88.980 -16.605 1.00 44.51 C
+ATOM 1316 CD GLU A 171 9.069 90.213 -16.402 1.00 48.11 C
+ATOM 1317 OE1 GLU A 171 7.851 90.025 -16.152 1.00 49.29 O
+ATOM 1318 OE2 GLU A 171 9.609 91.345 -16.463 1.00 50.71 O
+ATOM 1319 N GLY A 172 12.982 87.400 -15.819 1.00 32.49 N
+ATOM 1320 CA GLY A 172 14.336 87.855 -15.516 1.00 32.07 C
+ATOM 1321 C GLY A 172 15.282 86.815 -14.974 1.00 31.91 C
+ATOM 1322 O GLY A 172 16.459 87.097 -14.734 1.00 33.27 O
+ATOM 1323 N ALA A 173 14.828 85.556 -14.816 1.00 30.17 N
+ATOM 1324 CA ALA A 173 15.752 84.549 -14.292 1.00 27.07 C
+ATOM 1325 C ALA A 173 16.775 84.203 -15.361 1.00 24.53 C
+ATOM 1326 O ALA A 173 16.487 84.219 -16.546 1.00 25.51 O
+ATOM 1327 CB ALA A 173 15.000 83.283 -13.904 1.00 25.63 C
+ATOM 1328 N THR A 174 17.932 83.752 -14.951 1.00 22.90 N
+ATOM 1329 CA THR A 174 18.928 83.202 -15.841 1.00 22.99 C
+ATOM 1330 C THR A 174 18.583 81.726 -16.073 1.00 23.99 C
+ATOM 1331 O THR A 174 18.592 80.919 -15.125 1.00 24.96 O
+ATOM 1332 CB THR A 174 20.312 83.282 -15.204 1.00 25.97 C
+ATOM 1333 OG1 THR A 174 20.521 84.676 -14.873 1.00 30.01 O
+ATOM 1334 CG2 THR A 174 21.319 82.728 -16.197 1.00 25.88 C
+ATOM 1335 N VAL A 175 18.273 81.328 -17.286 1.00 21.03 N
+ATOM 1336 CA VAL A 175 17.909 79.949 -17.552 1.00 20.73 C
+ATOM 1337 C VAL A 175 19.121 79.152 -18.014 1.00 22.27 C
+ATOM 1338 O VAL A 175 19.899 79.639 -18.845 1.00 24.88 O
+ATOM 1339 CB VAL A 175 16.759 79.908 -18.532 1.00 21.57 C
+ATOM 1340 CG1 VAL A 175 16.286 78.467 -18.747 1.00 22.84 C
+ATOM 1341 CG2 VAL A 175 15.576 80.732 -17.996 1.00 21.51 C
+ATOM 1342 N SER A 176 19.350 77.969 -17.430 1.00 18.64 N
+ATOM 1343 CA SER A 176 20.483 77.183 -17.964 1.00 16.78 C
+ATOM 1344 C SER A 176 19.890 75.925 -18.536 1.00 16.00 C
+ATOM 1345 O SER A 176 19.319 75.128 -17.780 1.00 14.12 O
+ATOM 1346 CB SER A 176 21.452 76.900 -16.810 1.00 19.20 C
+ATOM 1347 OG SER A 176 22.314 75.823 -17.131 1.00 21.14 O
+ATOM 1348 N GLN A 177 19.977 75.667 -19.843 1.00 14.92 N
+ATOM 1349 CA GLN A 177 19.442 74.434 -20.420 1.00 14.44 C
+ATOM 1350 C GLN A 177 20.191 73.241 -19.783 1.00 13.19 C
+ATOM 1351 O GLN A 177 19.582 72.186 -19.653 1.00 13.85 O
+ATOM 1352 CB GLN A 177 19.757 74.419 -21.930 1.00 16.12 C
+ATOM 1353 CG GLN A 177 19.085 73.308 -22.712 1.00 20.11 C
+ATOM 1354 CD GLN A 177 17.574 73.256 -22.528 1.00 22.45 C
+ATOM 1355 OE1 GLN A 177 16.935 74.312 -22.627 1.00 22.84 O
+ATOM 1356 NE2 GLN A 177 16.981 72.095 -22.254 1.00 20.44 N
+ATOM 1357 N GLY A 178 21.459 73.432 -19.453 1.00 10.51 N
+ATOM 1358 CA GLY A 178 22.223 72.341 -18.829 1.00 11.89 C
+ATOM 1359 C GLY A 178 21.577 71.808 -17.560 1.00 12.67 C
+ATOM 1360 O GLY A 178 21.528 70.599 -17.310 1.00 11.81 O
+ATOM 1361 N LEU A 179 21.088 72.738 -16.710 1.00 10.92 N
+ATOM 1362 CA LEU A 179 20.479 72.322 -15.433 1.00 13.02 C
+ATOM 1363 C LEU A 179 19.204 71.553 -15.733 1.00 11.34 C
+ATOM 1364 O LEU A 179 18.899 70.575 -15.080 1.00 11.30 O
+ATOM 1365 CB LEU A 179 20.235 73.531 -14.526 1.00 12.08 C
+ATOM 1366 CG LEU A 179 21.538 74.187 -13.986 1.00 12.17 C
+ATOM 1367 CD1 LEU A 179 21.116 75.288 -12.986 1.00 13.45 C
+ATOM 1368 CD2 LEU A 179 22.423 73.181 -13.302 1.00 12.26 C
+ATOM 1369 N ILE A 180 18.407 72.020 -16.673 1.00 9.92 N
+ATOM 1370 CA ILE A 180 17.211 71.274 -17.084 1.00 10.91 C
+ATOM 1371 C ILE A 180 17.512 69.852 -17.555 1.00 9.25 C
+ATOM 1372 O ILE A 180 16.937 68.845 -17.076 1.00 11.55 O
+ATOM 1373 CB ILE A 180 16.452 72.015 -18.204 1.00 12.44 C
+ATOM 1374 CG1 ILE A 180 16.020 73.421 -17.682 1.00 12.77 C
+ATOM 1375 CG2 ILE A 180 15.240 71.187 -18.595 1.00 12.48 C
+ATOM 1376 CD1 ILE A 180 15.408 74.297 -18.803 1.00 13.61 C
+ATOM 1377 N ASP A 181 18.442 69.744 -18.506 1.00 7.41 N
+ATOM 1378 CA ASP A 181 18.764 68.454 -19.090 1.00 8.73 C
+ATOM 1379 C ASP A 181 19.405 67.513 -18.048 1.00 8.90 C
+ATOM 1380 O ASP A 181 19.099 66.331 -18.061 1.00 9.63 O
+ATOM 1381 CB ASP A 181 19.726 68.557 -20.286 1.00 9.91 C
+ATOM 1382 CG ASP A 181 19.132 69.371 -21.466 1.00 14.59 C
+ATOM 1383 OD1 ASP A 181 17.919 69.647 -21.490 1.00 12.65 O
+ATOM 1384 OD2 ASP A 181 20.013 69.724 -22.304 1.00 15.86 O
+ATOM 1385 N HIS A 182 20.242 68.041 -17.182 1.00 9.27 N
+ATOM 1386 CA HIS A 182 20.826 67.163 -16.146 1.00 7.11 C
+ATOM 1387 C HIS A 182 19.775 66.675 -15.167 1.00 8.04 C
+ATOM 1388 O HIS A 182 19.841 65.538 -14.689 1.00 11.75 O
+ATOM 1389 CB HIS A 182 21.940 67.904 -15.391 1.00 6.65 C
+ATOM 1390 CG HIS A 182 22.826 66.915 -14.649 1.00 10.34 C
+ATOM 1391 ND1 HIS A 182 23.573 67.304 -13.582 1.00 10.88 N
+ATOM 1392 CD2 HIS A 182 23.079 65.590 -14.829 1.00 10.02 C
+ATOM 1393 CE1 HIS A 182 24.287 66.280 -13.134 1.00 10.72 C
+ATOM 1394 NE2 HIS A 182 23.991 65.223 -13.875 1.00 10.31 N
+ATOM 1395 N TRP A 183 18.799 67.492 -14.818 1.00 8.64 N
+ATOM 1396 CA TRP A 183 17.742 67.036 -13.890 1.00 9.94 C
+ATOM 1397 C TRP A 183 17.008 65.867 -14.517 1.00 9.97 C
+ATOM 1398 O TRP A 183 16.703 64.790 -13.960 1.00 8.51 O
+ATOM 1399 CB TRP A 183 16.859 68.266 -13.597 1.00 7.17 C
+ATOM 1400 CG TRP A 183 15.831 68.172 -12.524 1.00 8.96 C
+ATOM 1401 CD1 TRP A 183 15.894 68.916 -11.364 1.00 9.78 C
+ATOM 1402 CD2 TRP A 183 14.606 67.449 -12.427 1.00 9.64 C
+ATOM 1403 NE1 TRP A 183 14.791 68.653 -10.573 1.00 10.40 N
+ATOM 1404 CE2 TRP A 183 13.982 67.779 -11.201 1.00 9.11 C
+ATOM 1405 CE3 TRP A 183 13.925 66.582 -13.292 1.00 8.09 C
+ATOM 1406 CZ2 TRP A 183 12.738 67.272 -10.808 1.00 11.24 C
+ATOM 1407 CZ3 TRP A 183 12.737 66.018 -12.906 1.00 9.24 C
+ATOM 1408 CH2 TRP A 183 12.120 66.372 -11.665 1.00 12.29 C
+ATOM 1409 N TRP A 184 16.643 66.082 -15.783 1.00 8.52 N
+ATOM 1410 CA TRP A 184 15.920 65.065 -16.562 1.00 9.38 C
+ATOM 1411 C TRP A 184 16.713 63.754 -16.614 1.00 7.61 C
+ATOM 1412 O TRP A 184 16.143 62.696 -16.479 1.00 8.91 O
+ATOM 1413 CB TRP A 184 15.701 65.630 -18.008 1.00 9.25 C
+ATOM 1414 CG TRP A 184 14.886 64.663 -18.857 1.00 11.21 C
+ATOM 1415 CD1 TRP A 184 13.529 64.560 -18.972 1.00 11.89 C
+ATOM 1416 CD2 TRP A 184 15.424 63.658 -19.739 1.00 10.38 C
+ATOM 1417 NE1 TRP A 184 13.195 63.524 -19.839 1.00 9.26 N
+ATOM 1418 CE2 TRP A 184 14.352 62.989 -20.326 1.00 9.95 C
+ATOM 1419 CE3 TRP A 184 16.757 63.294 -20.054 1.00 12.74 C
+ATOM 1420 CZ2 TRP A 184 14.525 61.932 -21.241 1.00 11.15 C
+ATOM 1421 CZ3 TRP A 184 16.946 62.252 -20.973 1.00 11.45 C
+ATOM 1422 CH2 TRP A 184 15.819 61.608 -21.567 1.00 12.34 C
+ATOM 1423 N LEU A 185 17.999 63.833 -16.876 1.00 6.27 N
+ATOM 1424 CA LEU A 185 18.793 62.596 -17.049 1.00 10.24 C
+ATOM 1425 C LEU A 185 18.837 61.838 -15.719 1.00 10.43 C
+ATOM 1426 O LEU A 185 18.628 60.635 -15.698 1.00 10.91 O
+ATOM 1427 CB LEU A 185 20.218 62.983 -17.434 1.00 10.32 C
+ATOM 1428 CG LEU A 185 21.262 61.854 -17.427 1.00 11.18 C
+ATOM 1429 CD1 LEU A 185 20.894 60.860 -18.551 1.00 12.36 C
+ATOM 1430 CD2 LEU A 185 22.685 62.375 -17.666 1.00 10.10 C
+ATOM 1431 N GLN A 186 19.103 62.572 -14.626 1.00 8.89 N
+ATOM 1432 CA GLN A 186 19.199 61.907 -13.327 1.00 9.70 C
+ATOM 1433 C GLN A 186 17.846 61.266 -12.990 1.00 8.06 C
+ATOM 1434 O GLN A 186 17.798 60.153 -12.448 1.00 9.13 O
+ATOM 1435 CB GLN A 186 19.560 62.896 -12.199 1.00 9.42 C
+ATOM 1436 CG GLN A 186 20.957 63.535 -12.355 1.00 9.12 C
+ATOM 1437 CD GLN A 186 21.146 64.513 -11.195 1.00 11.83 C
+ATOM 1438 OE1 GLN A 186 21.292 64.093 -10.032 1.00 11.79 O
+ATOM 1439 NE2 GLN A 186 21.012 65.788 -11.535 1.00 10.13 N
+ATOM 1440 N GLY A 187 16.772 61.955 -13.267 1.00 8.35 N
+ATOM 1441 CA GLY A 187 15.461 61.414 -13.026 1.00 8.49 C
+ATOM 1442 C GLY A 187 15.194 60.162 -13.852 1.00 8.16 C
+ATOM 1443 O GLY A 187 14.716 59.112 -13.356 1.00 8.16 O
+ATOM 1444 N MET A 188 15.512 60.205 -15.135 1.00 9.94 N
+ATOM 1445 CA MET A 188 15.162 59.076 -16.026 1.00 12.01 C
+ATOM 1446 C MET A 188 16.050 57.871 -15.686 1.00 10.90 C
+ATOM 1447 O MET A 188 15.635 56.733 -15.965 1.00 13.40 O
+ATOM 1448 CB MET A 188 15.294 59.472 -17.494 1.00 12.71 C
+ATOM 1449 CG MET A 188 14.215 60.423 -18.048 1.00 13.39 C
+ATOM 1450 SD MET A 188 12.566 60.130 -17.425 1.00 15.53 S
+ATOM 1451 CE MET A 188 12.044 58.633 -18.268 1.00 14.29 C
+ATOM 1452 N MET A 189 17.237 58.080 -15.096 1.00 11.10 N
+ATOM 1453 CA MET A 189 18.030 56.919 -14.654 1.00 14.24 C
+ATOM 1454 C MET A 189 17.366 56.122 -13.534 1.00 12.37 C
+ATOM 1455 O MET A 189 17.601 54.901 -13.419 1.00 11.72 O
+ATOM 1456 CB MET A 189 19.440 57.310 -14.176 1.00 16.66 C
+ATOM 1457 CG MET A 189 20.245 58.044 -15.255 1.00 28.15 C
+ATOM 1458 SD MET A 189 21.010 56.974 -16.498 1.00 40.58 S
+ATOM 1459 CE MET A 189 19.638 56.414 -17.489 1.00 38.46 C
+ATOM 1460 N GLY A 190 16.678 56.814 -12.625 1.00 10.17 N
+ATOM 1461 CA GLY A 190 16.046 56.099 -11.531 1.00 9.20 C
+ATOM 1462 C GLY A 190 14.771 55.361 -11.921 1.00 11.93 C
+ATOM 1463 O GLY A 190 14.229 55.469 -13.014 1.00 10.60 O
+ATOM 1464 N ALA A 191 14.226 54.617 -10.962 1.00 11.31 N
+ATOM 1465 CA ALA A 191 13.091 53.725 -11.178 1.00 10.61 C
+ATOM 1466 C ALA A 191 11.760 54.417 -11.063 1.00 11.13 C
+ATOM 1467 O ALA A 191 11.487 55.155 -10.092 1.00 11.13 O
+ATOM 1468 CB ALA A 191 13.107 52.641 -10.089 1.00 11.42 C
+ATOM 1469 N ALA A 192 10.862 54.066 -11.979 1.00 9.45 N
+ATOM 1470 CA ALA A 192 9.531 54.735 -11.912 1.00 11.53 C
+ATOM 1471 C ALA A 192 8.732 54.395 -10.649 1.00 10.83 C
+ATOM 1472 O ALA A 192 8.132 55.314 -10.072 1.00 11.89 O
+ATOM 1473 CB ALA A 192 8.751 54.335 -13.177 1.00 9.77 C
+ATOM 1474 N ASN A 193 8.846 53.171 -10.144 1.00 10.66 N
+ATOM 1475 CA ASN A 193 8.076 52.841 -8.909 1.00 12.75 C
+ATOM 1476 C ASN A 193 8.661 53.572 -7.696 1.00 12.52 C
+ATOM 1477 O ASN A 193 7.890 54.174 -6.932 1.00 13.42 O
+ATOM 1478 CB ASN A 193 7.997 51.329 -8.712 1.00 11.36 C
+ATOM 1479 CG ASN A 193 9.355 50.722 -8.356 1.00 13.45 C
+ATOM 1480 OD1 ASN A 193 10.445 51.187 -8.706 1.00 11.68 O
+ATOM 1481 ND2 ASN A 193 9.298 49.706 -7.493 1.00 13.73 N
+ATOM 1482 N ALA A 194 9.985 53.589 -7.572 1.00 11.34 N
+ATOM 1483 CA ALA A 194 10.570 54.387 -6.453 1.00 13.24 C
+ATOM 1484 C ALA A 194 10.158 55.839 -6.484 1.00 13.82 C
+ATOM 1485 O ALA A 194 9.705 56.487 -5.504 1.00 13.38 O
+ATOM 1486 CB ALA A 194 12.096 54.295 -6.576 1.00 12.18 C
+ATOM 1487 N HIS A 195 10.275 56.465 -7.701 1.00 12.12 N
+ATOM 1488 CA HIS A 195 9.908 57.885 -7.768 1.00 10.89 C
+ATOM 1489 C HIS A 195 8.427 58.074 -7.444 1.00 12.44 C
+ATOM 1490 O HIS A 195 8.081 59.125 -6.923 1.00 12.87 O
+ATOM 1491 CB HIS A 195 10.263 58.461 -9.162 1.00 12.63 C
+ATOM 1492 CG HIS A 195 11.732 58.465 -9.437 1.00 11.63 C
+ATOM 1493 ND1 HIS A 195 12.300 58.796 -10.665 1.00 13.18 N
+ATOM 1494 CD2 HIS A 195 12.763 58.213 -8.578 1.00 12.01 C
+ATOM 1495 CE1 HIS A 195 13.608 58.700 -10.553 1.00 12.63 C
+ATOM 1496 NE2 HIS A 195 13.938 58.358 -9.290 1.00 11.68 N
+ATOM 1497 N TYR A 196 7.570 57.204 -7.923 1.00 11.14 N
+ATOM 1498 CA TYR A 196 6.138 57.326 -7.676 1.00 14.97 C
+ATOM 1499 C TYR A 196 5.817 57.247 -6.167 1.00 15.63 C
+ATOM 1500 O TYR A 196 5.234 58.169 -5.604 1.00 14.86 O
+ATOM 1501 CB TYR A 196 5.430 56.248 -8.482 1.00 15.46 C
+ATOM 1502 CG TYR A 196 3.910 56.330 -8.437 1.00 19.96 C
+ATOM 1503 CD1 TYR A 196 3.199 55.719 -7.404 1.00 21.21 C
+ATOM 1504 CD2 TYR A 196 3.208 57.050 -9.393 1.00 20.06 C
+ATOM 1505 CE1 TYR A 196 1.809 55.792 -7.362 1.00 21.13 C
+ATOM 1506 CE2 TYR A 196 1.824 57.104 -9.380 1.00 22.27 C
+ATOM 1507 CZ TYR A 196 1.145 56.479 -8.349 1.00 21.98 C
+ATOM 1508 OH TYR A 196 -0.227 56.565 -8.320 1.00 23.99 O
+ATOM 1509 N GLU A 197 6.325 56.205 -5.494 1.00 17.04 N
+ATOM 1510 CA GLU A 197 6.104 55.965 -4.078 1.00 19.99 C
+ATOM 1511 C GLU A 197 6.719 57.005 -3.172 1.00 19.94 C
+ATOM 1512 O GLU A 197 6.137 57.375 -2.153 1.00 19.19 O
+ATOM 1513 CB GLU A 197 6.646 54.576 -3.734 1.00 23.97 C
+ATOM 1514 CG GLU A 197 5.943 53.559 -4.658 1.00 31.50 C
+ATOM 1515 CD GLU A 197 5.869 52.224 -3.953 1.00 38.58 C
+ATOM 1516 OE1 GLU A 197 5.731 52.243 -2.689 1.00 41.22 O
+ATOM 1517 OE2 GLU A 197 5.981 51.193 -4.678 1.00 42.93 O
+ATOM 1518 N CYS A 198 7.855 57.575 -3.585 1.00 15.64 N
+ATOM 1519 CA CYS A 198 8.530 58.598 -2.852 1.00 14.07 C
+ATOM 1520 C CYS A 198 7.701 59.847 -2.670 1.00 15.20 C
+ATOM 1521 O CYS A 198 7.983 60.665 -1.779 1.00 15.38 O
+ATOM 1522 CB CYS A 198 9.915 58.926 -3.486 1.00 14.77 C
+ATOM 1523 SG CYS A 198 10.965 59.847 -2.309 1.00 17.95 S
+ATOM 1524 N ILE A 199 6.788 60.118 -3.601 1.00 14.16 N
+ATOM 1525 CA ILE A 199 6.000 61.354 -3.458 1.00 15.06 C
+ATOM 1526 C ILE A 199 5.212 61.263 -2.133 1.00 15.89 C
+ATOM 1527 O ILE A 199 5.246 62.248 -1.393 1.00 17.25 O
+ATOM 1528 CB ILE A 199 5.058 61.589 -4.646 1.00 14.31 C
+ATOM 1529 CG1 ILE A 199 5.919 61.773 -5.926 1.00 13.62 C
+ATOM 1530 CG2 ILE A 199 4.225 62.869 -4.453 1.00 16.62 C
+ATOM 1531 CD1 ILE A 199 5.116 61.665 -7.217 1.00 15.90 C
+ATOM 1532 N ALA A 200 4.605 60.103 -1.867 1.00 16.81 N
+ATOM 1533 CA ALA A 200 3.911 60.065 -0.551 1.00 18.97 C
+ATOM 1534 C ALA A 200 4.919 60.148 0.604 1.00 20.23 C
+ATOM 1535 O ALA A 200 4.620 60.781 1.655 1.00 19.90 O
+ATOM 1536 CB ALA A 200 2.986 58.884 -0.446 1.00 15.52 C
+ATOM 1537 N ALA A 201 6.089 59.528 0.449 1.00 18.68 N
+ATOM 1538 CA ALA A 201 7.069 59.520 1.538 1.00 18.65 C
+ATOM 1539 C ALA A 201 7.542 60.914 1.842 1.00 17.85 C
+ATOM 1540 O ALA A 201 7.725 61.253 2.998 1.00 19.21 O
+ATOM 1541 CB ALA A 201 8.328 58.714 1.156 1.00 17.95 C
+ATOM 1542 N PHE A 202 7.837 61.775 0.840 1.00 16.49 N
+ATOM 1543 CA PHE A 202 8.342 63.085 1.191 1.00 16.50 C
+ATOM 1544 C PHE A 202 7.212 64.031 1.627 1.00 18.56 C
+ATOM 1545 O PHE A 202 7.519 65.003 2.339 1.00 17.49 O
+ATOM 1546 CB PHE A 202 9.217 63.700 0.113 1.00 16.52 C
+ATOM 1547 CG PHE A 202 8.613 64.267 -1.135 1.00 18.72 C
+ATOM 1548 CD1 PHE A 202 7.809 65.387 -1.130 1.00 19.52 C
+ATOM 1549 CD2 PHE A 202 8.916 63.675 -2.378 1.00 18.96 C
+ATOM 1550 CE1 PHE A 202 7.287 65.924 -2.309 1.00 20.55 C
+ATOM 1551 CE2 PHE A 202 8.361 64.171 -3.545 1.00 19.53 C
+ATOM 1552 CZ PHE A 202 7.551 65.294 -3.514 1.00 20.22 C
+ATOM 1553 N SER A 203 5.995 63.867 1.125 1.00 16.75 N
+ATOM 1554 CA SER A 203 4.977 64.881 1.393 1.00 17.39 C
+ATOM 1555 C SER A 203 4.041 64.542 2.557 1.00 19.14 C
+ATOM 1556 O SER A 203 3.414 65.490 3.079 1.00 21.16 O
+ATOM 1557 CB SER A 203 4.115 65.074 0.111 1.00 16.63 C
+ATOM 1558 OG SER A 203 3.448 63.857 -0.213 1.00 15.32 O
+ATOM 1559 N GLU A 204 3.866 63.303 2.951 1.00 17.78 N
+ATOM 1560 CA GLU A 204 3.010 62.913 4.038 1.00 20.17 C
+ATOM 1561 C GLU A 204 3.746 62.459 5.301 1.00 22.47 C
+ATOM 1562 O GLU A 204 3.081 62.265 6.313 1.00 24.51 O
+ATOM 1563 CB GLU A 204 2.106 61.750 3.610 1.00 21.28 C
+ATOM 1564 CG GLU A 204 1.217 62.227 2.443 1.00 23.76 C
+ATOM 1565 CD GLU A 204 0.472 61.046 1.858 1.00 28.74 C
+ATOM 1566 OE1 GLU A 204 0.197 60.125 2.643 1.00 32.02 O
+ATOM 1567 OE2 GLU A 204 0.188 60.952 0.650 1.00 29.09 O
+ATOM 1568 N THR A 205 5.045 62.199 5.255 1.00 20.01 N
+ATOM 1569 CA THR A 205 5.714 61.810 6.487 1.00 20.70 C
+ATOM 1570 C THR A 205 5.803 63.033 7.398 1.00 19.77 C
+ATOM 1571 O THR A 205 6.177 64.112 6.971 1.00 18.85 O
+ATOM 1572 CB THR A 205 7.119 61.252 6.191 1.00 20.73 C
+ATOM 1573 OG1 THR A 205 6.899 60.206 5.265 1.00 19.14 O
+ATOM 1574 CG2 THR A 205 7.746 60.699 7.483 1.00 20.93 C
+ATOM 1575 N ASP A 206 5.485 62.849 8.673 1.00 20.72 N
+ATOM 1576 CA ASP A 206 5.619 63.949 9.636 1.00 22.29 C
+ATOM 1577 C ASP A 206 6.961 63.824 10.331 1.00 19.79 C
+ATOM 1578 O ASP A 206 7.212 62.782 10.929 1.00 21.12 O
+ATOM 1579 CB ASP A 206 4.480 63.899 10.659 1.00 23.33 C
+ATOM 1580 CG ASP A 206 4.416 65.167 11.478 1.00 24.70 C
+ATOM 1581 OD1 ASP A 206 5.392 65.891 11.719 1.00 24.33 O
+ATOM 1582 OD2 ASP A 206 3.282 65.485 11.893 1.00 26.52 O
+ATOM 1583 N PHE A 207 7.851 64.807 10.225 1.00 19.16 N
+ATOM 1584 CA PHE A 207 9.167 64.664 10.842 1.00 17.15 C
+ATOM 1585 C PHE A 207 9.212 65.387 12.191 1.00 20.05 C
+ATOM 1586 O PHE A 207 10.278 65.633 12.760 1.00 18.32 O
+ATOM 1587 CB PHE A 207 10.223 65.340 9.892 1.00 18.67 C
+ATOM 1588 CG PHE A 207 10.313 64.565 8.587 1.00 18.91 C
+ATOM 1589 CD1 PHE A 207 11.097 63.443 8.484 1.00 17.68 C
+ATOM 1590 CD2 PHE A 207 9.585 65.002 7.473 1.00 18.47 C
+ATOM 1591 CE1 PHE A 207 11.199 62.735 7.297 1.00 18.48 C
+ATOM 1592 CE2 PHE A 207 9.685 64.289 6.277 1.00 16.55 C
+ATOM 1593 CZ PHE A 207 10.461 63.151 6.192 1.00 16.53 C
+ATOM 1594 N THR A 208 8.087 65.900 12.677 1.00 19.62 N
+ATOM 1595 CA THR A 208 8.056 66.672 13.920 1.00 22.75 C
+ATOM 1596 C THR A 208 8.816 66.008 15.047 1.00 22.23 C
+ATOM 1597 O THR A 208 9.692 66.602 15.680 1.00 20.08 O
+ATOM 1598 CB THR A 208 6.586 66.962 14.258 1.00 23.60 C
+ATOM 1599 OG1 THR A 208 6.151 67.888 13.207 1.00 23.98 O
+ATOM 1600 CG2 THR A 208 6.477 67.664 15.627 1.00 23.88 C
+ATOM 1601 N ASP A 209 8.565 64.731 15.297 1.00 24.26 N
+ATOM 1602 CA ASP A 209 9.232 63.981 16.348 1.00 25.53 C
+ATOM 1603 C ASP A 209 10.725 63.806 16.139 1.00 26.38 C
+ATOM 1604 O ASP A 209 11.527 63.827 17.113 1.00 26.69 O
+ATOM 1605 CB ASP A 209 8.544 62.629 16.529 1.00 27.20 C
+ATOM 1606 CG ASP A 209 7.183 62.737 17.206 1.00 30.81 C
+ATOM 1607 OD1 ASP A 209 6.811 63.836 17.684 1.00 32.11 O
+ATOM 1608 OD2 ASP A 209 6.451 61.720 17.257 1.00 31.40 O
+ATOM 1609 N ASP A 210 11.146 63.603 14.882 1.00 23.96 N
+ATOM 1610 CA ASP A 210 12.577 63.470 14.618 1.00 23.14 C
+ATOM 1611 C ASP A 210 13.291 64.772 15.006 1.00 22.91 C
+ATOM 1612 O ASP A 210 14.370 64.794 15.623 1.00 21.36 O
+ATOM 1613 CB ASP A 210 12.858 63.222 13.139 1.00 22.22 C
+ATOM 1614 CG ASP A 210 12.268 61.954 12.618 1.00 25.56 C
+ATOM 1615 OD1 ASP A 210 12.476 60.862 13.164 1.00 26.63 O
+ATOM 1616 OD2 ASP A 210 11.498 61.961 11.641 1.00 28.94 O
+ATOM 1617 N LEU A 211 12.707 65.883 14.528 1.00 19.62 N
+ATOM 1618 CA LEU A 211 13.282 67.186 14.785 1.00 20.91 C
+ATOM 1619 C LEU A 211 13.461 67.510 16.262 1.00 23.01 C
+ATOM 1620 O LEU A 211 14.404 68.220 16.657 1.00 23.21 O
+ATOM 1621 CB LEU A 211 12.413 68.269 14.135 1.00 21.39 C
+ATOM 1622 CG LEU A 211 12.443 68.358 12.605 1.00 22.37 C
+ATOM 1623 CD1 LEU A 211 11.574 69.523 12.148 1.00 22.52 C
+ATOM 1624 CD2 LEU A 211 13.851 68.493 12.035 1.00 20.52 C
+ATOM 1625 N LYS A 212 12.524 67.051 17.099 1.00 23.93 N
+ATOM 1626 CA LYS A 212 12.613 67.267 18.539 1.00 27.10 C
+ATOM 1627 C LYS A 212 13.701 66.420 19.158 1.00 26.94 C
+ATOM 1628 O LYS A 212 14.160 66.700 20.264 1.00 28.31 O
+ATOM 1629 CB LYS A 212 11.233 66.948 19.160 1.00 28.04 C
+ATOM 1630 CG LYS A 212 10.321 68.136 18.854 1.00 31.50 C
+ATOM 1631 CD LYS A 212 8.855 67.798 18.978 1.00 35.44 C
+ATOM 1632 CE LYS A 212 8.312 68.047 20.379 1.00 37.51 C
+ATOM 1633 NZ LYS A 212 6.847 67.714 20.444 1.00 39.24 N
+ATOM 1634 N ARG A 213 14.109 65.349 18.509 1.00 26.06 N
+ATOM 1635 CA ARG A 213 15.149 64.474 18.985 1.00 28.52 C
+ATOM 1636 C ARG A 213 16.556 64.907 18.603 1.00 27.90 C
+ATOM 1637 O ARG A 213 17.500 64.329 19.120 1.00 27.40 O
+ATOM 1638 CB ARG A 213 14.945 63.046 18.442 1.00 31.62 C
+ATOM 1639 CG ARG A 213 13.654 62.428 18.982 1.00 36.82 C
+ATOM 1640 CD ARG A 213 13.496 61.001 18.446 1.00 38.77 C
+ATOM 1641 NE ARG A 213 14.651 60.228 18.815 1.00 42.52 N
+ATOM 1642 CZ ARG A 213 15.115 59.056 18.444 1.00 45.13 C
+ATOM 1643 NH1 ARG A 213 14.517 58.275 17.549 1.00 46.98 N
+ATOM 1644 NH2 ARG A 213 16.243 58.629 19.024 1.00 46.27 N
+ATOM 1645 N ILE A 214 16.726 65.834 17.666 1.00 26.80 N
+ATOM 1646 CA ILE A 214 18.081 66.162 17.254 1.00 26.11 C
+ATOM 1647 C ILE A 214 18.776 67.087 18.237 1.00 26.77 C
+ATOM 1648 O ILE A 214 18.273 68.191 18.442 1.00 28.67 O
+ATOM 1649 CB ILE A 214 18.013 66.777 15.827 1.00 23.81 C
+ATOM 1650 CG1 ILE A 214 17.546 65.680 14.869 1.00 23.81 C
+ATOM 1651 CG2 ILE A 214 19.367 67.329 15.454 1.00 23.71 C
+ATOM 1652 CD1 ILE A 214 17.282 66.138 13.453 1.00 22.80 C
+ATOM 1653 N ASP A 215 19.967 66.753 18.704 1.00 28.08 N
+ATOM 1654 CA ASP A 215 20.649 67.692 19.592 1.00 34.14 C
+ATOM 1655 C ASP A 215 21.857 68.372 18.962 1.00 32.68 C
+ATOM 1656 O ASP A 215 22.214 69.432 19.497 1.00 34.56 O
+ATOM 1657 CB ASP A 215 21.048 67.039 20.910 1.00 39.14 C
+ATOM 1658 CG ASP A 215 21.559 65.631 20.746 1.00 43.79 C
+ATOM 1659 OD1 ASP A 215 22.287 65.301 19.779 1.00 47.08 O
+ATOM 1660 OD2 ASP A 215 21.221 64.817 21.638 1.00 47.43 O
+ATOM 1661 N VAL A 216 22.436 67.867 17.873 1.00 27.40 N
+ATOM 1662 CA VAL A 216 23.567 68.627 17.293 1.00 23.33 C
+ATOM 1663 C VAL A 216 23.080 69.924 16.670 1.00 21.01 C
+ATOM 1664 O VAL A 216 21.882 70.069 16.381 1.00 21.10 O
+ATOM 1665 CB VAL A 216 24.142 67.722 16.184 1.00 25.27 C
+ATOM 1666 CG1 VAL A 216 24.665 66.398 16.740 1.00 24.58 C
+ATOM 1667 CG2 VAL A 216 23.061 67.457 15.116 1.00 22.61 C
+ATOM 1668 N PRO A 217 23.973 70.851 16.354 1.00 20.43 N
+ATOM 1669 CA PRO A 217 23.672 72.070 15.656 1.00 20.74 C
+ATOM 1670 C PRO A 217 23.181 71.759 14.217 1.00 20.77 C
+ATOM 1671 O PRO A 217 23.725 70.875 13.568 1.00 19.36 O
+ATOM 1672 CB PRO A 217 24.924 72.901 15.625 1.00 19.85 C
+ATOM 1673 CG PRO A 217 25.907 72.179 16.491 1.00 22.91 C
+ATOM 1674 CD PRO A 217 25.431 70.750 16.658 1.00 20.14 C
+ATOM 1675 N VAL A 218 22.165 72.504 13.838 1.00 20.18 N
+ATOM 1676 CA VAL A 218 21.468 72.332 12.571 1.00 20.06 C
+ATOM 1677 C VAL A 218 21.296 73.694 11.916 1.00 20.90 C
+ATOM 1678 O VAL A 218 20.879 74.704 12.497 1.00 21.77 O
+ATOM 1679 CB VAL A 218 20.110 71.636 12.636 1.00 18.64 C
+ATOM 1680 CG1 VAL A 218 19.455 71.501 11.244 1.00 19.81 C
+ATOM 1681 CG2 VAL A 218 20.143 70.267 13.292 1.00 16.52 C
+ATOM 1682 N LEU A 219 21.783 73.761 10.678 1.00 17.40 N
+ATOM 1683 CA LEU A 219 21.580 74.953 9.843 1.00 16.12 C
+ATOM 1684 C LEU A 219 20.366 74.734 8.974 1.00 14.45 C
+ATOM 1685 O LEU A 219 20.321 73.694 8.302 1.00 16.29 O
+ATOM 1686 CB LEU A 219 22.806 75.277 8.987 1.00 16.77 C
+ATOM 1687 CG LEU A 219 22.575 76.259 7.809 1.00 18.95 C
+ATOM 1688 CD1 LEU A 219 22.229 77.646 8.285 1.00 18.80 C
+ATOM 1689 CD2 LEU A 219 23.814 76.317 6.895 1.00 19.30 C
+ATOM 1690 N VAL A 220 19.356 75.585 8.970 1.00 14.90 N
+ATOM 1691 CA VAL A 220 18.137 75.427 8.176 1.00 16.15 C
+ATOM 1692 C VAL A 220 18.140 76.521 7.115 1.00 17.44 C
+ATOM 1693 O VAL A 220 18.195 77.698 7.480 1.00 19.42 O
+ATOM 1694 CB VAL A 220 16.835 75.526 8.989 1.00 15.89 C
+ATOM 1695 CG1 VAL A 220 15.593 75.365 8.113 1.00 17.38 C
+ATOM 1696 CG2 VAL A 220 16.838 74.463 10.070 1.00 16.33 C
+ATOM 1697 N ALA A 221 18.324 76.183 5.845 1.00 16.87 N
+ATOM 1698 CA ALA A 221 18.462 77.213 4.779 1.00 15.60 C
+ATOM 1699 C ALA A 221 17.278 77.086 3.838 1.00 16.91 C
+ATOM 1700 O ALA A 221 16.898 75.929 3.533 1.00 17.96 O
+ATOM 1701 CB ALA A 221 19.803 76.978 4.073 1.00 15.92 C
+ATOM 1702 N HIS A 222 16.754 78.167 3.270 1.00 17.41 N
+ATOM 1703 CA HIS A 222 15.587 78.015 2.391 1.00 17.26 C
+ATOM 1704 C HIS A 222 15.350 79.268 1.565 1.00 17.59 C
+ATOM 1705 O HIS A 222 15.612 80.387 2.021 1.00 19.47 O
+ATOM 1706 CB HIS A 222 14.387 77.681 3.244 1.00 15.92 C
+ATOM 1707 CG HIS A 222 13.331 76.813 2.640 1.00 15.70 C
+ATOM 1708 ND1 HIS A 222 13.013 75.584 3.175 1.00 13.82 N
+ATOM 1709 CD2 HIS A 222 12.483 77.019 1.588 1.00 13.84 C
+ATOM 1710 CE1 HIS A 222 12.021 75.044 2.500 1.00 13.64 C
+ATOM 1711 NE2 HIS A 222 11.686 75.892 1.528 1.00 14.68 N
+ATOM 1712 N GLY A 223 14.955 79.085 0.312 1.00 17.02 N
+ATOM 1713 CA GLY A 223 14.750 80.290 -0.538 1.00 17.05 C
+ATOM 1714 C GLY A 223 13.318 80.748 -0.316 1.00 18.82 C
+ATOM 1715 O GLY A 223 12.430 79.913 -0.190 1.00 18.60 O
+ATOM 1716 N THR A 224 13.092 82.064 -0.281 1.00 22.61 N
+ATOM 1717 CA THR A 224 11.712 82.541 -0.038 1.00 22.98 C
+ATOM 1718 C THR A 224 10.868 82.456 -1.297 1.00 24.29 C
+ATOM 1719 O THR A 224 9.629 82.546 -1.130 1.00 26.26 O
+ATOM 1720 CB THR A 224 11.687 83.980 0.522 1.00 22.43 C
+ATOM 1721 OG1 THR A 224 12.117 84.891 -0.469 1.00 21.09 O
+ATOM 1722 CG2 THR A 224 12.670 84.100 1.695 1.00 21.74 C
+ATOM 1723 N ASP A 225 11.419 82.183 -2.496 1.00 20.64 N
+ATOM 1724 CA ASP A 225 10.481 82.007 -3.621 1.00 22.70 C
+ATOM 1725 C ASP A 225 10.459 80.542 -4.053 1.00 22.61 C
+ATOM 1726 O ASP A 225 10.432 80.190 -5.232 1.00 22.64 O
+ATOM 1727 CB ASP A 225 10.839 82.992 -4.744 1.00 23.76 C
+ATOM 1728 CG ASP A 225 9.896 82.985 -5.926 1.00 26.05 C
+ATOM 1729 OD1 ASP A 225 8.713 82.638 -5.765 1.00 26.68 O
+ATOM 1730 OD2 ASP A 225 10.289 83.242 -7.083 1.00 27.90 O
+ATOM 1731 N ASP A 226 10.516 79.616 -3.099 1.00 21.34 N
+ATOM 1732 CA ASP A 226 10.518 78.186 -3.310 1.00 20.81 C
+ATOM 1733 C ASP A 226 9.157 77.729 -3.782 1.00 20.97 C
+ATOM 1734 O ASP A 226 8.183 77.809 -3.007 1.00 19.82 O
+ATOM 1735 CB ASP A 226 10.911 77.417 -2.032 1.00 17.80 C
+ATOM 1736 CG ASP A 226 11.235 75.974 -2.382 1.00 16.53 C
+ATOM 1737 OD1 ASP A 226 10.518 75.353 -3.189 1.00 16.31 O
+ATOM 1738 OD2 ASP A 226 12.232 75.442 -1.848 1.00 17.08 O
+ATOM 1739 N GLN A 227 9.075 77.263 -5.030 1.00 19.72 N
+ATOM 1740 CA GLN A 227 7.785 76.850 -5.564 1.00 17.43 C
+ATOM 1741 C GLN A 227 7.505 75.380 -5.385 1.00 19.38 C
+ATOM 1742 O GLN A 227 6.431 74.932 -5.805 1.00 21.65 O
+ATOM 1743 CB GLN A 227 7.668 77.195 -7.047 1.00 18.59 C
+ATOM 1744 CG GLN A 227 7.836 78.671 -7.388 1.00 20.16 C
+ATOM 1745 CD GLN A 227 7.893 78.869 -8.911 1.00 20.26 C
+ATOM 1746 OE1 GLN A 227 6.994 78.356 -9.582 1.00 23.64 O
+ATOM 1747 NE2 GLN A 227 8.911 79.538 -9.409 1.00 18.19 N
+ATOM 1748 N VAL A 228 8.395 74.601 -4.748 1.00 17.76 N
+ATOM 1749 CA VAL A 228 8.167 73.180 -4.567 1.00 17.48 C
+ATOM 1750 C VAL A 228 7.865 72.850 -3.117 1.00 19.55 C
+ATOM 1751 O VAL A 228 6.905 72.159 -2.817 1.00 21.20 O
+ATOM 1752 CB VAL A 228 9.446 72.393 -5.009 1.00 18.09 C
+ATOM 1753 CG1 VAL A 228 9.275 70.900 -4.720 1.00 17.92 C
+ATOM 1754 CG2 VAL A 228 9.678 72.682 -6.492 1.00 19.09 C
+ATOM 1755 N VAL A 229 8.722 73.353 -2.202 1.00 20.35 N
+ATOM 1756 CA VAL A 229 8.526 73.211 -0.766 1.00 19.77 C
+ATOM 1757 C VAL A 229 8.364 74.614 -0.207 1.00 19.13 C
+ATOM 1758 O VAL A 229 9.286 75.422 -0.083 1.00 16.92 O
+ATOM 1759 CB VAL A 229 9.679 72.480 -0.061 1.00 22.29 C
+ATOM 1760 CG1 VAL A 229 9.441 72.421 1.457 1.00 22.21 C
+ATOM 1761 CG2 VAL A 229 9.800 71.058 -0.573 1.00 21.99 C
+ATOM 1762 N PRO A 230 7.100 74.997 0.009 1.00 21.14 N
+ATOM 1763 CA PRO A 230 6.756 76.361 0.405 1.00 20.29 C
+ATOM 1764 C PRO A 230 7.479 76.816 1.653 1.00 22.08 C
+ATOM 1765 O PRO A 230 7.510 76.087 2.666 1.00 22.87 O
+ATOM 1766 CB PRO A 230 5.237 76.341 0.552 1.00 21.98 C
+ATOM 1767 CG PRO A 230 4.818 75.235 -0.360 1.00 21.77 C
+ATOM 1768 CD PRO A 230 5.889 74.148 -0.143 1.00 20.68 C
+ATOM 1769 N TYR A 231 8.106 77.969 1.560 1.00 21.53 N
+ATOM 1770 CA TYR A 231 8.970 78.480 2.591 1.00 23.86 C
+ATOM 1771 C TYR A 231 8.346 78.584 3.990 1.00 25.63 C
+ATOM 1772 O TYR A 231 8.976 78.174 4.966 1.00 23.52 O
+ATOM 1773 CB TYR A 231 9.527 79.834 2.156 1.00 25.37 C
+ATOM 1774 CG TYR A 231 10.300 80.493 3.290 1.00 27.01 C
+ATOM 1775 CD1 TYR A 231 11.633 80.262 3.478 1.00 26.19 C
+ATOM 1776 CD2 TYR A 231 9.634 81.343 4.191 1.00 28.75 C
+ATOM 1777 CE1 TYR A 231 12.331 80.823 4.524 1.00 27.73 C
+ATOM 1778 CE2 TYR A 231 10.312 81.938 5.239 1.00 28.59 C
+ATOM 1779 CZ TYR A 231 11.656 81.663 5.404 1.00 29.48 C
+ATOM 1780 OH TYR A 231 12.368 82.236 6.428 1.00 27.33 O
+ATOM 1781 N ALA A 232 7.177 79.208 4.086 1.00 26.31 N
+ATOM 1782 CA ALA A 232 6.561 79.498 5.381 1.00 27.61 C
+ATOM 1783 C ALA A 232 6.117 78.272 6.150 1.00 28.15 C
+ATOM 1784 O ALA A 232 6.191 78.309 7.380 1.00 29.95 O
+ATOM 1785 CB ALA A 232 5.453 80.529 5.171 1.00 25.94 C
+ATOM 1786 N ASP A 233 5.737 77.169 5.571 1.00 27.74 N
+ATOM 1787 CA ASP A 233 5.364 75.918 6.194 1.00 27.18 C
+ATOM 1788 C ASP A 233 6.568 75.006 6.432 1.00 23.34 C
+ATOM 1789 O ASP A 233 6.367 73.902 6.944 1.00 23.91 O
+ATOM 1790 CB ASP A 233 4.375 75.149 5.313 1.00 32.20 C
+ATOM 1791 CG ASP A 233 3.469 74.115 5.938 1.00 36.48 C
+ATOM 1792 OD1 ASP A 233 2.840 74.379 7.012 1.00 39.35 O
+ATOM 1793 OD2 ASP A 233 3.271 72.985 5.390 1.00 35.48 O
+ATOM 1794 N ALA A 234 7.783 75.418 6.056 1.00 20.43 N
+ATOM 1795 CA ALA A 234 8.892 74.518 6.269 1.00 20.37 C
+ATOM 1796 C ALA A 234 9.945 75.097 7.206 1.00 20.01 C
+ATOM 1797 O ALA A 234 9.884 74.815 8.408 1.00 22.38 O
+ATOM 1798 CB ALA A 234 9.489 74.028 4.954 1.00 18.32 C
+ATOM 1799 N ALA A 235 10.784 75.971 6.739 1.00 19.94 N
+ATOM 1800 CA ALA A 235 11.981 76.454 7.358 1.00 20.45 C
+ATOM 1801 C ALA A 235 11.815 77.097 8.726 1.00 22.59 C
+ATOM 1802 O ALA A 235 12.446 76.666 9.671 1.00 21.74 O
+ATOM 1803 CB ALA A 235 12.772 77.317 6.381 1.00 18.56 C
+ATOM 1804 N PRO A 236 10.991 78.124 8.872 1.00 25.79 N
+ATOM 1805 CA PRO A 236 10.774 78.725 10.197 1.00 26.29 C
+ATOM 1806 C PRO A 236 10.154 77.698 11.127 1.00 25.86 C
+ATOM 1807 O PRO A 236 10.560 77.668 12.294 1.00 27.68 O
+ATOM 1808 CB PRO A 236 9.968 79.968 9.867 1.00 26.42 C
+ATOM 1809 CG PRO A 236 9.187 79.572 8.664 1.00 27.90 C
+ATOM 1810 CD PRO A 236 10.167 78.759 7.825 1.00 25.69 C
+ATOM 1811 N LYS A 237 9.305 76.781 10.710 1.00 25.66 N
+ATOM 1812 CA LYS A 237 8.752 75.776 11.616 1.00 28.08 C
+ATOM 1813 C LYS A 237 9.768 74.746 12.073 1.00 28.23 C
+ATOM 1814 O LYS A 237 9.786 74.279 13.216 1.00 28.93 O
+ATOM 1815 CB LYS A 237 7.560 75.056 10.981 1.00 29.41 C
+ATOM 1816 CG LYS A 237 6.466 76.080 10.627 1.00 32.45 C
+ATOM 1817 CD LYS A 237 5.347 75.394 9.862 1.00 35.79 C
+ATOM 1818 CE LYS A 237 3.979 75.773 10.406 1.00 39.66 C
+ATOM 1819 NZ LYS A 237 3.130 76.428 9.378 1.00 42.19 N
+ATOM 1820 N SER A 238 10.634 74.344 11.128 1.00 26.02 N
+ATOM 1821 CA SER A 238 11.696 73.423 11.495 1.00 25.28 C
+ATOM 1822 C SER A 238 12.590 74.049 12.553 1.00 24.86 C
+ATOM 1823 O SER A 238 12.950 73.380 13.527 1.00 26.05 O
+ATOM 1824 CB SER A 238 12.539 73.182 10.214 1.00 23.43 C
+ATOM 1825 OG SER A 238 11.722 72.238 9.514 1.00 25.88 O
+ATOM 1826 N ALA A 239 13.000 75.289 12.296 1.00 24.46 N
+ATOM 1827 CA ALA A 239 13.920 75.973 13.201 1.00 26.21 C
+ATOM 1828 C ALA A 239 13.348 76.141 14.620 1.00 28.34 C
+ATOM 1829 O ALA A 239 14.106 76.104 15.585 1.00 29.57 O
+ATOM 1830 CB ALA A 239 14.251 77.333 12.615 1.00 24.77 C
+ATOM 1831 N GLU A 240 12.040 76.346 14.744 1.00 29.85 N
+ATOM 1832 CA GLU A 240 11.423 76.478 16.055 1.00 33.55 C
+ATOM 1833 C GLU A 240 11.382 75.163 16.800 1.00 31.62 C
+ATOM 1834 O GLU A 240 11.478 75.200 18.033 1.00 32.58 O
+ATOM 1835 CB GLU A 240 9.994 77.027 15.941 1.00 37.55 C
+ATOM 1836 CG GLU A 240 10.071 78.411 15.290 1.00 44.40 C
+ATOM 1837 CD GLU A 240 8.681 78.951 14.996 1.00 48.88 C
+ATOM 1838 OE1 GLU A 240 7.726 78.534 15.707 1.00 51.76 O
+ATOM 1839 OE2 GLU A 240 8.590 79.779 14.061 1.00 51.05 O
+ATOM 1840 N LEU A 241 11.307 74.030 16.123 1.00 29.85 N
+ATOM 1841 CA LEU A 241 11.293 72.736 16.794 1.00 27.12 C
+ATOM 1842 C LEU A 241 12.664 72.197 17.170 1.00 26.32 C
+ATOM 1843 O LEU A 241 12.793 71.336 18.043 1.00 26.70 O
+ATOM 1844 CB LEU A 241 10.623 71.704 15.872 1.00 27.11 C
+ATOM 1845 CG LEU A 241 9.154 71.997 15.538 1.00 28.57 C
+ATOM 1846 CD1 LEU A 241 8.699 71.181 14.356 1.00 27.01 C
+ATOM 1847 CD2 LEU A 241 8.301 71.633 16.763 1.00 29.28 C
+ATOM 1848 N LEU A 242 13.728 72.610 16.505 1.00 25.02 N
+ATOM 1849 CA LEU A 242 15.072 72.115 16.741 1.00 25.16 C
+ATOM 1850 C LEU A 242 15.682 72.868 17.923 1.00 25.16 C
+ATOM 1851 O LEU A 242 15.564 74.081 18.002 1.00 25.47 O
+ATOM 1852 CB LEU A 242 15.975 72.336 15.503 1.00 23.76 C
+ATOM 1853 CG LEU A 242 15.680 71.383 14.324 1.00 22.60 C
+ATOM 1854 CD1 LEU A 242 16.075 72.060 13.028 1.00 22.79 C
+ATOM 1855 CD2 LEU A 242 16.458 70.080 14.491 1.00 23.27 C
+ATOM 1856 N ALA A 243 16.354 72.138 18.778 1.00 26.16 N
+ATOM 1857 CA ALA A 243 17.012 72.689 19.958 1.00 27.21 C
+ATOM 1858 C ALA A 243 18.095 73.671 19.605 1.00 28.66 C
+ATOM 1859 O ALA A 243 18.093 74.829 20.062 1.00 29.92 O
+ATOM 1860 CB ALA A 243 17.585 71.499 20.730 1.00 28.40 C
+ATOM 1861 N ASN A 244 19.031 73.308 18.738 1.00 27.94 N
+ATOM 1862 CA ASN A 244 20.100 74.236 18.336 1.00 28.85 C
+ATOM 1863 C ASN A 244 20.052 74.542 16.846 1.00 28.46 C
+ATOM 1864 O ASN A 244 20.878 73.998 16.089 1.00 29.05 O
+ATOM 1865 CB ASN A 244 21.424 73.581 18.753 1.00 31.44 C
+ATOM 1866 CG ASN A 244 22.640 74.463 18.612 1.00 35.35 C
+ATOM 1867 OD1 ASN A 244 22.605 75.645 18.228 1.00 36.23 O
+ATOM 1868 ND2 ASN A 244 23.809 73.896 18.949 1.00 37.56 N
+ATOM 1869 N ALA A 245 19.116 75.361 16.359 1.00 27.26 N
+ATOM 1870 CA ALA A 245 19.108 75.601 14.914 1.00 26.46 C
+ATOM 1871 C ALA A 245 19.525 77.010 14.554 1.00 26.33 C
+ATOM 1872 O ALA A 245 19.373 77.925 15.365 1.00 27.04 O
+ATOM 1873 CB ALA A 245 17.716 75.331 14.367 1.00 28.39 C
+ATOM 1874 N THR A 246 20.056 77.231 13.378 1.00 23.76 N
+ATOM 1875 CA THR A 246 20.350 78.548 12.815 1.00 24.23 C
+ATOM 1876 C THR A 246 19.524 78.650 11.517 1.00 25.52 C
+ATOM 1877 O THR A 246 19.521 77.708 10.675 1.00 24.33 O
+ATOM 1878 CB THR A 246 21.835 78.733 12.507 1.00 24.82 C
+ATOM 1879 OG1 THR A 246 22.629 78.586 13.716 1.00 26.36 O
+ATOM 1880 CG2 THR A 246 22.118 80.075 11.868 1.00 22.82 C
+ATOM 1881 N LEU A 247 18.752 79.692 11.359 1.00 25.04 N
+ATOM 1882 CA LEU A 247 17.856 79.853 10.218 1.00 26.55 C
+ATOM 1883 C LEU A 247 18.430 80.853 9.231 1.00 28.97 C
+ATOM 1884 O LEU A 247 18.684 82.007 9.614 1.00 27.62 O
+ATOM 1885 CB LEU A 247 16.472 80.337 10.659 1.00 27.65 C
+ATOM 1886 CG LEU A 247 15.395 80.538 9.618 1.00 30.51 C
+ATOM 1887 CD1 LEU A 247 15.056 79.219 8.944 1.00 29.55 C
+ATOM 1888 CD2 LEU A 247 14.078 81.117 10.172 1.00 30.17 C
+ATOM 1889 N LYS A 248 18.620 80.426 7.981 1.00 25.07 N
+ATOM 1890 CA LYS A 248 19.107 81.324 6.944 1.00 26.55 C
+ATOM 1891 C LYS A 248 18.056 81.357 5.835 1.00 26.74 C
+ATOM 1892 O LYS A 248 17.672 80.324 5.277 1.00 22.68 O
+ATOM 1893 CB LYS A 248 20.474 80.925 6.404 1.00 28.26 C
+ATOM 1894 CG LYS A 248 21.616 81.357 7.307 1.00 33.64 C
+ATOM 1895 CD LYS A 248 22.960 81.381 6.603 1.00 36.94 C
+ATOM 1896 CE LYS A 248 23.573 82.783 6.755 1.00 39.86 C
+ATOM 1897 NZ LYS A 248 23.723 83.031 8.233 1.00 42.16 N
+ATOM 1898 N SER A 249 17.600 82.556 5.535 1.00 24.84 N
+ATOM 1899 CA SER A 249 16.586 82.837 4.546 1.00 24.86 C
+ATOM 1900 C SER A 249 17.204 83.500 3.310 1.00 23.82 C
+ATOM 1901 O SER A 249 18.019 84.403 3.566 1.00 21.16 O
+ATOM 1902 CB SER A 249 15.691 83.977 5.146 1.00 26.60 C
+ATOM 1903 OG SER A 249 14.521 83.315 5.573 1.00 31.36 O
+ATOM 1904 N TYR A 250 16.859 83.057 2.099 1.00 19.26 N
+ATOM 1905 CA TYR A 250 17.531 83.687 0.935 1.00 21.04 C
+ATOM 1906 C TYR A 250 16.448 84.307 0.075 1.00 21.32 C
+ATOM 1907 O TYR A 250 15.632 83.593 -0.538 1.00 19.98 O
+ATOM 1908 CB TYR A 250 18.336 82.649 0.129 1.00 19.11 C
+ATOM 1909 CG TYR A 250 19.527 82.131 0.907 1.00 19.35 C
+ATOM 1910 CD1 TYR A 250 19.341 81.030 1.729 1.00 19.89 C
+ATOM 1911 CD2 TYR A 250 20.775 82.733 0.882 1.00 20.02 C
+ATOM 1912 CE1 TYR A 250 20.384 80.505 2.480 1.00 19.18 C
+ATOM 1913 CE2 TYR A 250 21.816 82.237 1.641 1.00 20.59 C
+ATOM 1914 CZ TYR A 250 21.603 81.116 2.425 1.00 20.45 C
+ATOM 1915 OH TYR A 250 22.620 80.577 3.198 1.00 21.79 O
+ATOM 1916 N GLU A 251 16.357 85.626 0.123 1.00 23.34 N
+ATOM 1917 CA GLU A 251 15.334 86.351 -0.583 1.00 25.33 C
+ATOM 1918 C GLU A 251 15.278 86.023 -2.080 1.00 24.07 C
+ATOM 1919 O GLU A 251 16.288 86.165 -2.754 1.00 23.97 O
+ATOM 1920 CB GLU A 251 15.540 87.890 -0.477 1.00 29.45 C
+ATOM 1921 CG GLU A 251 14.167 88.574 -0.563 1.00 36.84 C
+ATOM 1922 CD GLU A 251 13.311 88.131 0.630 1.00 41.39 C
+ATOM 1923 OE1 GLU A 251 13.936 88.024 1.723 1.00 43.88 O
+ATOM 1924 OE2 GLU A 251 12.092 87.869 0.480 1.00 43.37 O
+ATOM 1925 N GLY A 252 14.103 85.637 -2.533 1.00 23.71 N
+ATOM 1926 CA GLY A 252 13.797 85.384 -3.929 1.00 22.29 C
+ATOM 1927 C GLY A 252 14.442 84.138 -4.539 1.00 22.08 C
+ATOM 1928 O GLY A 252 14.311 84.005 -5.774 1.00 17.92 O
+ATOM 1929 N LEU A 253 15.113 83.276 -3.746 1.00 18.87 N
+ATOM 1930 CA LEU A 253 15.782 82.129 -4.429 1.00 16.86 C
+ATOM 1931 C LEU A 253 14.840 80.969 -4.577 1.00 15.26 C
+ATOM 1932 O LEU A 253 13.916 80.801 -3.793 1.00 13.98 O
+ATOM 1933 CB LEU A 253 17.073 81.807 -3.678 1.00 17.62 C
+ATOM 1934 CG LEU A 253 18.170 82.874 -3.713 1.00 18.37 C
+ATOM 1935 CD1 LEU A 253 19.495 82.262 -3.294 1.00 17.40 C
+ATOM 1936 CD2 LEU A 253 18.181 83.594 -5.069 1.00 18.65 C
+ATOM 1937 N PRO A 254 15.091 80.055 -5.527 1.00 14.37 N
+ATOM 1938 CA PRO A 254 14.214 78.972 -5.827 1.00 13.57 C
+ATOM 1939 C PRO A 254 14.480 77.679 -5.056 1.00 13.95 C
+ATOM 1940 O PRO A 254 15.412 77.616 -4.256 1.00 13.92 O
+ATOM 1941 CB PRO A 254 14.532 78.682 -7.310 1.00 12.53 C
+ATOM 1942 CG PRO A 254 15.982 78.940 -7.381 1.00 13.12 C
+ATOM 1943 CD PRO A 254 16.215 80.175 -6.505 1.00 13.32 C
+ATOM 1944 N HIS A 255 13.705 76.654 -5.425 1.00 11.11 N
+ATOM 1945 CA HIS A 255 13.911 75.361 -4.770 1.00 14.52 C
+ATOM 1946 C HIS A 255 15.279 74.772 -5.064 1.00 13.83 C
+ATOM 1947 O HIS A 255 15.953 74.248 -4.166 1.00 13.63 O
+ATOM 1948 CB HIS A 255 12.793 74.411 -5.215 1.00 14.63 C
+ATOM 1949 CG HIS A 255 12.841 73.123 -4.440 1.00 15.65 C
+ATOM 1950 ND1 HIS A 255 12.661 73.118 -3.063 1.00 14.47 N
+ATOM 1951 CD2 HIS A 255 12.982 71.841 -4.821 1.00 14.90 C
+ATOM 1952 CE1 HIS A 255 12.728 71.871 -2.635 1.00 16.38 C
+ATOM 1953 NE2 HIS A 255 12.914 71.059 -3.672 1.00 16.38 N
+ATOM 1954 N GLY A 256 15.738 74.913 -6.317 1.00 12.47 N
+ATOM 1955 CA GLY A 256 17.052 74.301 -6.642 1.00 12.60 C
+ATOM 1956 C GLY A 256 18.140 75.335 -6.530 1.00 13.71 C
+ATOM 1957 O GLY A 256 19.067 75.356 -7.331 1.00 12.53 O
+ATOM 1958 N MET A 257 18.102 76.205 -5.467 1.00 11.47 N
+ATOM 1959 CA MET A 257 19.094 77.264 -5.378 1.00 11.88 C
+ATOM 1960 C MET A 257 20.504 76.798 -5.196 1.00 10.29 C
+ATOM 1961 O MET A 257 21.404 77.594 -5.462 1.00 11.06 O
+ATOM 1962 CB MET A 257 18.801 78.260 -4.206 1.00 14.18 C
+ATOM 1963 CG MET A 257 18.670 77.500 -2.869 1.00 15.11 C
+ATOM 1964 SD MET A 257 18.139 78.639 -1.535 1.00 15.54 S
+ATOM 1965 CE MET A 257 18.290 77.519 -0.105 1.00 15.63 C
+ATOM 1966 N LEU A 258 20.784 75.563 -4.755 1.00 11.32 N
+ATOM 1967 CA LEU A 258 22.186 75.150 -4.629 1.00 13.70 C
+ATOM 1968 C LEU A 258 22.841 75.027 -6.032 1.00 14.34 C
+ATOM 1969 O LEU A 258 24.087 74.955 -6.072 1.00 12.79 O
+ATOM 1970 CB LEU A 258 22.253 73.770 -3.966 1.00 14.69 C
+ATOM 1971 CG LEU A 258 21.924 73.823 -2.455 1.00 15.37 C
+ATOM 1972 CD1 LEU A 258 21.534 72.409 -2.065 1.00 16.20 C
+ATOM 1973 CD2 LEU A 258 23.103 74.332 -1.659 1.00 13.34 C
+ATOM 1974 N SER A 259 22.008 74.873 -7.055 1.00 12.71 N
+ATOM 1975 CA SER A 259 22.566 74.797 -8.418 1.00 14.13 C
+ATOM 1976 C SER A 259 22.454 76.123 -9.176 1.00 13.04 C
+ATOM 1977 O SER A 259 23.329 76.391 -10.009 1.00 13.89 O
+ATOM 1978 CB SER A 259 21.768 73.704 -9.173 1.00 14.12 C
+ATOM 1979 OG SER A 259 22.209 72.459 -8.637 1.00 15.46 O
+ATOM 1980 N THR A 260 21.486 76.988 -8.825 1.00 12.37 N
+ATOM 1981 CA THR A 260 21.375 78.240 -9.592 1.00 14.17 C
+ATOM 1982 C THR A 260 22.195 79.340 -8.927 1.00 16.88 C
+ATOM 1983 O THR A 260 22.782 80.222 -9.554 1.00 14.34 O
+ATOM 1984 CB THR A 260 19.914 78.694 -9.696 1.00 15.13 C
+ATOM 1985 OG1 THR A 260 19.341 78.786 -8.389 1.00 12.51 O
+ATOM 1986 CG2 THR A 260 19.047 77.700 -10.495 1.00 15.43 C
+ATOM 1987 N HIS A 261 22.357 79.243 -7.588 1.00 14.37 N
+ATOM 1988 CA HIS A 261 23.126 80.290 -6.900 1.00 14.38 C
+ATOM 1989 C HIS A 261 24.158 79.717 -5.953 1.00 14.70 C
+ATOM 1990 O HIS A 261 24.202 80.098 -4.757 1.00 14.22 O
+ATOM 1991 CB HIS A 261 22.090 81.091 -6.044 1.00 12.97 C
+ATOM 1992 CG HIS A 261 21.129 81.840 -6.895 1.00 14.62 C
+ATOM 1993 ND1 HIS A 261 19.997 81.283 -7.428 1.00 13.83 N
+ATOM 1994 CD2 HIS A 261 21.196 83.114 -7.399 1.00 16.52 C
+ATOM 1995 CE1 HIS A 261 19.356 82.163 -8.187 1.00 16.22 C
+ATOM 1996 NE2 HIS A 261 20.075 83.273 -8.173 1.00 16.57 N
+ATOM 1997 N PRO A 262 25.021 78.803 -6.384 1.00 12.56 N
+ATOM 1998 CA PRO A 262 26.010 78.176 -5.529 1.00 12.94 C
+ATOM 1999 C PRO A 262 26.982 79.194 -4.950 1.00 14.51 C
+ATOM 2000 O PRO A 262 27.566 79.026 -3.890 1.00 14.12 O
+ATOM 2001 CB PRO A 262 26.774 77.198 -6.471 1.00 11.50 C
+ATOM 2002 CG PRO A 262 26.644 77.927 -7.814 1.00 13.49 C
+ATOM 2003 CD PRO A 262 25.174 78.297 -7.767 1.00 13.60 C
+ATOM 2004 N GLU A 263 27.333 80.261 -5.684 1.00 14.87 N
+ATOM 2005 CA GLU A 263 28.260 81.269 -5.183 1.00 17.68 C
+ATOM 2006 C GLU A 263 27.686 81.975 -3.936 1.00 18.93 C
+ATOM 2007 O GLU A 263 28.471 82.408 -3.044 1.00 19.21 O
+ATOM 2008 CB GLU A 263 28.615 82.273 -6.296 1.00 17.10 C
+ATOM 2009 CG GLU A 263 27.452 83.187 -6.605 1.00 22.08 C
+ATOM 2010 CD GLU A 263 26.362 82.535 -7.472 1.00 26.54 C
+ATOM 2011 OE1 GLU A 263 26.613 81.423 -8.032 1.00 27.63 O
+ATOM 2012 OE2 GLU A 263 25.257 83.132 -7.613 1.00 27.42 O
+ATOM 2013 N VAL A 264 26.380 82.049 -3.779 1.00 17.24 N
+ATOM 2014 CA VAL A 264 25.798 82.618 -2.556 1.00 18.73 C
+ATOM 2015 C VAL A 264 25.769 81.586 -1.433 1.00 20.06 C
+ATOM 2016 O VAL A 264 26.226 81.820 -0.309 1.00 17.96 O
+ATOM 2017 CB VAL A 264 24.345 83.086 -2.827 1.00 19.60 C
+ATOM 2018 CG1 VAL A 264 23.656 83.555 -1.540 1.00 20.68 C
+ATOM 2019 CG2 VAL A 264 24.328 84.231 -3.829 1.00 20.42 C
+ATOM 2020 N LEU A 265 25.302 80.367 -1.716 1.00 17.50 N
+ATOM 2021 CA LEU A 265 25.102 79.334 -0.718 1.00 17.19 C
+ATOM 2022 C LEU A 265 26.328 78.624 -0.173 1.00 16.22 C
+ATOM 2023 O LEU A 265 26.385 78.374 1.046 1.00 16.14 O
+ATOM 2024 CB LEU A 265 24.179 78.257 -1.345 1.00 17.49 C
+ATOM 2025 CG LEU A 265 22.683 78.258 -1.058 1.00 21.30 C
+ATOM 2026 CD1 LEU A 265 22.400 78.031 0.427 1.00 23.41 C
+ATOM 2027 CD2 LEU A 265 22.010 79.539 -1.517 1.00 21.84 C
+ATOM 2028 N ASN A 266 27.319 78.338 -1.027 1.00 14.29 N
+ATOM 2029 CA ASN A 266 28.483 77.567 -0.680 1.00 14.50 C
+ATOM 2030 C ASN A 266 29.285 78.175 0.477 1.00 15.93 C
+ATOM 2031 O ASN A 266 29.642 77.462 1.405 1.00 13.70 O
+ATOM 2032 CB ASN A 266 29.387 77.283 -1.882 1.00 15.15 C
+ATOM 2033 CG ASN A 266 28.839 76.233 -2.856 1.00 16.40 C
+ATOM 2034 OD1 ASN A 266 27.768 75.674 -2.595 1.00 16.53 O
+ATOM 2035 ND2 ASN A 266 29.496 76.035 -3.987 1.00 17.41 N
+ATOM 2036 N PRO A 267 29.535 79.477 0.435 1.00 16.09 N
+ATOM 2037 CA PRO A 267 30.301 80.112 1.521 1.00 17.58 C
+ATOM 2038 C PRO A 267 29.577 79.998 2.862 1.00 16.92 C
+ATOM 2039 O PRO A 267 30.183 79.818 3.928 1.00 18.06 O
+ATOM 2040 CB PRO A 267 30.362 81.581 1.073 1.00 18.07 C
+ATOM 2041 CG PRO A 267 30.253 81.514 -0.437 1.00 17.37 C
+ATOM 2042 CD PRO A 267 29.220 80.411 -0.664 1.00 16.05 C
+ATOM 2043 N ASP A 268 28.261 80.080 2.895 1.00 16.99 N
+ATOM 2044 CA ASP A 268 27.429 79.945 4.080 1.00 17.51 C
+ATOM 2045 C ASP A 268 27.431 78.498 4.566 1.00 19.19 C
+ATOM 2046 O ASP A 268 27.490 78.286 5.791 1.00 18.17 O
+ATOM 2047 CB ASP A 268 25.958 80.324 3.878 1.00 18.39 C
+ATOM 2048 CG ASP A 268 25.819 81.826 3.658 1.00 21.89 C
+ATOM 2049 OD1 ASP A 268 26.795 82.562 3.864 1.00 23.14 O
+ATOM 2050 OD2 ASP A 268 24.732 82.256 3.232 1.00 22.88 O
+ATOM 2051 N LEU A 269 27.413 77.519 3.602 1.00 15.58 N
+ATOM 2052 CA LEU A 269 27.545 76.143 4.099 1.00 16.81 C
+ATOM 2053 C LEU A 269 28.913 75.931 4.741 1.00 16.08 C
+ATOM 2054 O LEU A 269 29.055 75.220 5.747 1.00 15.61 O
+ATOM 2055 CB LEU A 269 27.332 75.119 2.960 1.00 15.57 C
+ATOM 2056 CG LEU A 269 26.015 75.252 2.182 1.00 17.03 C
+ATOM 2057 CD1 LEU A 269 25.956 74.223 1.028 1.00 16.82 C
+ATOM 2058 CD2 LEU A 269 24.860 74.857 3.129 1.00 19.95 C
+ATOM 2059 N LEU A 270 29.963 76.462 4.113 1.00 13.05 N
+ATOM 2060 CA LEU A 270 31.321 76.362 4.554 1.00 15.60 C
+ATOM 2061 C LEU A 270 31.523 76.975 5.951 1.00 16.88 C
+ATOM 2062 O LEU A 270 32.149 76.339 6.808 1.00 18.26 O
+ATOM 2063 CB LEU A 270 32.313 77.096 3.612 1.00 17.08 C
+ATOM 2064 CG LEU A 270 33.794 76.980 3.956 1.00 17.88 C
+ATOM 2065 CD1 LEU A 270 34.284 75.540 4.059 1.00 17.42 C
+ATOM 2066 CD2 LEU A 270 34.647 77.758 2.938 1.00 18.93 C
+ATOM 2067 N ALA A 271 30.972 78.148 6.154 1.00 16.94 N
+ATOM 2068 CA ALA A 271 31.078 78.853 7.444 1.00 18.93 C
+ATOM 2069 C ALA A 271 30.507 78.005 8.584 1.00 21.00 C
+ATOM 2070 O ALA A 271 31.103 77.781 9.646 1.00 18.11 O
+ATOM 2071 CB ALA A 271 30.241 80.146 7.263 1.00 18.68 C
+ATOM 2072 N PHE A 272 29.367 77.364 8.278 1.00 20.97 N
+ATOM 2073 CA PHE A 272 28.690 76.486 9.230 1.00 21.95 C
+ATOM 2074 C PHE A 272 29.514 75.254 9.516 1.00 24.01 C
+ATOM 2075 O PHE A 272 29.686 74.851 10.663 1.00 25.21 O
+ATOM 2076 CB PHE A 272 27.276 76.155 8.733 1.00 21.93 C
+ATOM 2077 CG PHE A 272 26.507 75.280 9.698 1.00 22.54 C
+ATOM 2078 CD1 PHE A 272 25.909 75.842 10.827 1.00 23.69 C
+ATOM 2079 CD2 PHE A 272 26.407 73.925 9.494 1.00 21.33 C
+ATOM 2080 CE1 PHE A 272 25.211 75.033 11.713 1.00 22.50 C
+ATOM 2081 CE2 PHE A 272 25.695 73.113 10.359 1.00 22.51 C
+ATOM 2082 CZ PHE A 272 25.113 73.681 11.487 1.00 22.56 C
+ATOM 2083 N VAL A 273 30.092 74.614 8.488 1.00 22.45 N
+ATOM 2084 CA VAL A 273 30.925 73.452 8.729 1.00 23.66 C
+ATOM 2085 C VAL A 273 32.178 73.821 9.517 1.00 26.23 C
+ATOM 2086 O VAL A 273 32.595 72.962 10.320 1.00 25.36 O
+ATOM 2087 CB VAL A 273 31.223 72.725 7.427 1.00 21.42 C
+ATOM 2088 CG1 VAL A 273 32.125 71.532 7.647 1.00 22.68 C
+ATOM 2089 CG2 VAL A 273 29.877 72.277 6.838 1.00 19.99 C
+ATOM 2090 N LYS A 274 32.729 75.022 9.328 1.00 27.59 N
+ATOM 2091 CA LYS A 274 33.900 75.418 10.106 1.00 32.61 C
+ATOM 2092 C LYS A 274 33.630 75.908 11.526 1.00 35.38 C
+ATOM 2093 O LYS A 274 34.520 75.919 12.383 1.00 37.25 O
+ATOM 2094 CB LYS A 274 34.529 76.619 9.393 1.00 31.85 C
+ATOM 2095 CG LYS A 274 35.297 76.340 8.119 1.00 32.44 C
+ATOM 2096 CD LYS A 274 36.012 77.641 7.763 1.00 33.40 C
+ATOM 2097 CE LYS A 274 37.391 77.436 7.167 1.00 35.22 C
+ATOM 2098 NZ LYS A 274 37.759 78.681 6.408 1.00 36.95 N
+ATOM 2099 N SER A 275 32.469 76.450 11.830 1.00 37.38 N
+ATOM 2100 CA SER A 275 32.096 76.962 13.128 1.00 39.67 C
+ATOM 2101 C SER A 275 32.157 75.977 14.288 1.00 40.91 C
+ATOM 2102 O SER A 275 31.980 76.499 15.432 1.00 43.49 O
+ATOM 2103 CB SER A 275 30.648 77.488 13.091 1.00 39.47 C
+ATOM 2104 OG SER A 275 29.849 76.295 12.959 1.00 41.94 O
+ATOM 2105 OXT SER A 275 32.192 74.734 14.203 1.00 41.57 O
+TER 2106 SER A 275
+END
diff --git a/loop/tests/data/1A88A_with_gap.pdb b/loop/tests/data/1A88A_with_gap.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..bb1cca6d8cddfc94ef7c43c6fd3b6cb0ffea6480
--- /dev/null
+++ b/loop/tests/data/1A88A_with_gap.pdb
@@ -0,0 +1,2081 @@
+ATOM 1 N GLY A 1 31.764 53.257 -5.145 1.00 21.92 N
+ATOM 2 CA GLY A 1 31.661 51.955 -4.451 1.00 20.38 C
+ATOM 3 C GLY A 1 30.228 51.594 -4.213 1.00 22.43 C
+ATOM 4 O GLY A 1 29.301 52.280 -4.687 1.00 20.07 O
+ATOM 5 N THR A 2 29.953 50.447 -3.576 1.00 20.81 N
+ATOM 6 CA THR A 2 28.571 50.144 -3.254 1.00 24.30 C
+ATOM 7 C THR A 2 28.510 49.528 -1.854 1.00 24.57 C
+ATOM 8 O THR A 2 29.507 48.974 -1.349 1.00 24.04 O
+ATOM 9 CB THR A 2 27.886 49.192 -4.253 1.00 28.12 C
+ATOM 10 OG1 THR A 2 28.529 47.925 -4.086 1.00 31.49 O
+ATOM 11 CG2 THR A 2 27.965 49.541 -5.730 1.00 27.46 C
+ATOM 12 N VAL A 3 27.370 49.622 -1.203 1.00 22.42 N
+ATOM 13 CA VAL A 3 27.147 49.017 0.095 1.00 24.30 C
+ATOM 14 C VAL A 3 25.861 48.228 -0.035 1.00 23.74 C
+ATOM 15 O VAL A 3 24.906 48.622 -0.722 1.00 22.67 O
+ATOM 16 CB VAL A 3 27.028 49.956 1.302 1.00 25.50 C
+ATOM 17 CG1 VAL A 3 28.381 50.584 1.663 1.00 27.68 C
+ATOM 18 CG2 VAL A 3 26.103 51.113 1.034 1.00 27.65 C
+ATOM 19 N THR A 4 25.854 47.062 0.574 1.00 23.05 N
+ATOM 20 CA THR A 4 24.672 46.202 0.570 1.00 26.31 C
+ATOM 21 C THR A 4 23.829 46.421 1.812 1.00 26.75 C
+ATOM 22 O THR A 4 24.377 46.407 2.918 1.00 29.12 O
+ATOM 23 CB THR A 4 25.103 44.726 0.458 1.00 27.13 C
+ATOM 24 OG1 THR A 4 25.713 44.592 -0.829 1.00 27.43 O
+ATOM 25 CG2 THR A 4 23.903 43.814 0.614 1.00 28.43 C
+ATOM 26 N THR A 5 22.536 46.692 1.686 1.00 24.64 N
+ATOM 27 CA THR A 5 21.727 46.951 2.868 1.00 26.94 C
+ATOM 28 C THR A 5 21.173 45.630 3.423 1.00 28.87 C
+ATOM 29 O THR A 5 21.359 44.560 2.825 1.00 28.63 O
+ATOM 30 CB THR A 5 20.563 47.904 2.493 1.00 25.62 C
+ATOM 31 OG1 THR A 5 19.773 47.127 1.610 1.00 22.98 O
+ATOM 32 CG2 THR A 5 21.081 49.182 1.837 1.00 26.21 C
+ATOM 33 N SER A 6 20.416 45.706 4.512 1.00 32.07 N
+ATOM 34 CA SER A 6 19.914 44.475 5.151 1.00 34.50 C
+ATOM 35 C SER A 6 19.034 43.646 4.242 1.00 34.88 C
+ATOM 36 O SER A 6 19.264 42.413 4.164 1.00 35.66 O
+ATOM 37 CB SER A 6 19.260 44.760 6.491 1.00 36.17 C
+ATOM 38 OG SER A 6 18.258 45.742 6.449 1.00 38.37 O
+ATOM 39 N ASP A 7 18.170 44.274 3.432 1.00 32.57 N
+ATOM 40 CA ASP A 7 17.369 43.488 2.491 1.00 29.56 C
+ATOM 41 C ASP A 7 18.127 43.106 1.244 1.00 28.25 C
+ATOM 42 O ASP A 7 17.502 42.669 0.288 1.00 27.90 O
+ATOM 43 CB ASP A 7 16.076 44.231 2.182 1.00 30.52 C
+ATOM 44 CG ASP A 7 16.170 45.511 1.376 1.00 30.30 C
+ATOM 45 OD1 ASP A 7 17.263 45.876 0.931 1.00 29.25 O
+ATOM 46 OD2 ASP A 7 15.127 46.180 1.159 1.00 30.59 O
+ATOM 47 N GLY A 8 19.443 43.249 1.129 1.00 28.74 N
+ATOM 48 CA GLY A 8 20.172 42.928 -0.091 1.00 26.98 C
+ATOM 49 C GLY A 8 20.152 44.009 -1.155 1.00 26.24 C
+ATOM 50 O GLY A 8 20.644 43.753 -2.272 1.00 27.20 O
+ATOM 51 N THR A 9 19.679 45.229 -0.886 1.00 24.00 N
+ATOM 52 CA THR A 9 19.710 46.283 -1.920 1.00 21.61 C
+ATOM 53 C THR A 9 21.108 46.857 -2.041 1.00 21.67 C
+ATOM 54 O THR A 9 21.691 47.226 -0.998 1.00 23.64 O
+ATOM 55 CB THR A 9 18.718 47.393 -1.543 1.00 20.75 C
+ATOM 56 OG1 THR A 9 17.407 46.802 -1.546 1.00 19.41 O
+ATOM 57 CG2 THR A 9 18.638 48.560 -2.556 1.00 20.13 C
+ATOM 58 N ASN A 10 21.661 47.017 -3.238 1.00 20.77 N
+ATOM 59 CA ASN A 10 22.961 47.660 -3.391 1.00 19.56 C
+ATOM 60 C ASN A 10 22.762 49.172 -3.633 1.00 19.39 C
+ATOM 61 O ASN A 10 21.969 49.567 -4.476 1.00 17.13 O
+ATOM 62 CB ASN A 10 23.826 47.103 -4.513 1.00 21.53 C
+ATOM 63 CG ASN A 10 24.198 45.658 -4.181 1.00 25.77 C
+ATOM 64 OD1 ASN A 10 24.782 45.354 -3.145 1.00 26.65 O
+ATOM 65 ND2 ASN A 10 23.789 44.748 -5.050 1.00 27.54 N
+ATOM 66 N ILE A 11 23.488 49.953 -2.852 1.00 16.01 N
+ATOM 67 CA ILE A 11 23.473 51.404 -2.847 1.00 16.13 C
+ATOM 68 C ILE A 11 24.788 51.907 -3.415 1.00 16.10 C
+ATOM 69 O ILE A 11 25.885 51.559 -2.908 1.00 16.08 O
+ATOM 70 CB ILE A 11 23.303 51.881 -1.391 1.00 17.18 C
+ATOM 71 CG1 ILE A 11 21.912 51.467 -0.888 1.00 19.25 C
+ATOM 72 CG2 ILE A 11 23.543 53.372 -1.267 1.00 18.69 C
+ATOM 73 CD1 ILE A 11 20.760 52.090 -1.647 1.00 20.48 C
+ATOM 74 N PHE A 12 24.721 52.715 -4.453 1.00 13.95 N
+ATOM 75 CA PHE A 12 25.910 53.287 -5.056 1.00 14.01 C
+ATOM 76 C PHE A 12 26.339 54.517 -4.270 1.00 12.98 C
+ATOM 77 O PHE A 12 25.429 55.281 -3.898 1.00 13.88 O
+ATOM 78 CB PHE A 12 25.591 53.711 -6.492 1.00 15.02 C
+ATOM 79 CG PHE A 12 26.707 54.477 -7.135 1.00 14.64 C
+ATOM 80 CD1 PHE A 12 27.755 53.821 -7.735 1.00 17.30 C
+ATOM 81 CD2 PHE A 12 26.704 55.871 -7.114 1.00 16.10 C
+ATOM 82 CE1 PHE A 12 28.803 54.564 -8.314 1.00 19.46 C
+ATOM 83 CE2 PHE A 12 27.731 56.593 -7.686 1.00 16.45 C
+ATOM 84 CZ PHE A 12 28.800 55.939 -8.274 1.00 17.84 C
+ATOM 85 N TYR A 13 27.618 54.770 -4.068 1.00 12.68 N
+ATOM 86 CA TYR A 13 28.049 56.000 -3.392 1.00 13.94 C
+ATOM 87 C TYR A 13 29.396 56.458 -3.960 1.00 14.49 C
+ATOM 88 O TYR A 13 30.149 55.633 -4.485 1.00 17.10 O
+ATOM 89 CB TYR A 13 28.088 55.911 -1.875 1.00 14.70 C
+ATOM 90 CG TYR A 13 29.266 55.041 -1.436 1.00 15.23 C
+ATOM 91 CD1 TYR A 13 29.092 53.684 -1.286 1.00 18.01 C
+ATOM 92 CD2 TYR A 13 30.494 55.626 -1.162 1.00 15.71 C
+ATOM 93 CE1 TYR A 13 30.171 52.871 -0.884 1.00 19.66 C
+ATOM 94 CE2 TYR A 13 31.567 54.830 -0.767 1.00 18.64 C
+ATOM 95 CZ TYR A 13 31.375 53.471 -0.630 1.00 20.23 C
+ATOM 96 OH TYR A 13 32.456 52.691 -0.281 1.00 22.12 O
+ATOM 97 N LYS A 14 29.691 57.735 -3.805 1.00 12.68 N
+ATOM 98 CA LYS A 14 30.973 58.308 -4.186 1.00 13.28 C
+ATOM 99 C LYS A 14 31.725 58.680 -2.905 1.00 13.70 C
+ATOM 100 O LYS A 14 31.028 59.140 -1.993 1.00 11.22 O
+ATOM 101 CB LYS A 14 30.729 59.646 -4.936 1.00 13.56 C
+ATOM 102 CG LYS A 14 30.055 59.407 -6.293 1.00 17.04 C
+ATOM 103 CD LYS A 14 29.598 60.791 -6.803 1.00 16.95 C
+ATOM 104 CE LYS A 14 28.859 60.613 -8.109 1.00 16.88 C
+ATOM 105 NZ LYS A 14 29.275 61.643 -9.079 1.00 11.46 N
+ATOM 106 N ASP A 15 33.039 58.630 -2.881 1.00 13.17 N
+ATOM 107 CA ASP A 15 33.772 58.981 -1.642 1.00 13.31 C
+ATOM 108 C ASP A 15 35.071 59.625 -2.089 1.00 11.64 C
+ATOM 109 O ASP A 15 35.924 58.884 -2.645 1.00 14.33 O
+ATOM 110 CB ASP A 15 33.950 57.676 -0.842 1.00 12.42 C
+ATOM 111 CG ASP A 15 34.829 57.878 0.408 1.00 15.23 C
+ATOM 112 OD1 ASP A 15 35.255 58.979 0.772 1.00 13.01 O
+ATOM 113 OD2 ASP A 15 35.082 56.850 1.085 1.00 16.31 O
+ATOM 114 N TRP A 16 35.150 60.930 -2.143 1.00 10.20 N
+ATOM 115 CA TRP A 16 36.325 61.577 -2.730 1.00 12.29 C
+ATOM 116 C TRP A 16 37.051 62.386 -1.642 1.00 14.41 C
+ATOM 117 O TRP A 16 36.387 62.801 -0.682 1.00 13.69 O
+ATOM 118 CB TRP A 16 35.855 62.542 -3.828 1.00 10.66 C
+ATOM 119 CG TRP A 16 35.204 61.854 -5.012 1.00 12.83 C
+ATOM 120 CD1 TRP A 16 35.261 60.566 -5.385 1.00 12.58 C
+ATOM 121 CD2 TRP A 16 34.300 62.500 -5.933 1.00 11.99 C
+ATOM 122 NE1 TRP A 16 34.476 60.347 -6.517 1.00 12.31 N
+ATOM 123 CE2 TRP A 16 33.894 61.529 -6.854 1.00 12.96 C
+ATOM 124 CE3 TRP A 16 33.863 63.805 -6.096 1.00 12.84 C
+ATOM 125 CZ2 TRP A 16 33.033 61.840 -7.937 1.00 12.24 C
+ATOM 126 CZ3 TRP A 16 32.989 64.124 -7.129 1.00 12.81 C
+ATOM 127 CH2 TRP A 16 32.614 63.126 -8.056 1.00 11.63 C
+ATOM 128 N GLY A 17 38.327 62.678 -1.836 1.00 17.50 N
+ATOM 129 CA GLY A 17 39.037 63.578 -0.895 1.00 18.73 C
+ATOM 130 C GLY A 17 39.896 62.740 0.057 1.00 19.98 C
+ATOM 131 O GLY A 17 39.945 61.518 0.012 1.00 19.39 O
+ATOM 158 N GLY A 21 40.147 63.261 6.100 1.00 30.99 N
+ATOM 159 CA GLY A 21 39.492 64.571 6.194 1.00 26.89 C
+ATOM 160 C GLY A 21 38.152 64.415 6.929 1.00 22.01 C
+ATOM 161 O GLY A 21 37.607 63.326 7.088 1.00 22.45 O
+ATOM 162 N LEU A 22 37.637 65.525 7.423 1.00 20.89 N
+ATOM 163 CA LEU A 22 36.318 65.546 8.044 1.00 20.96 C
+ATOM 164 C LEU A 22 35.310 65.216 6.920 1.00 18.65 C
+ATOM 165 O LEU A 22 35.317 65.884 5.892 1.00 16.52 O
+ATOM 166 CB LEU A 22 36.062 66.963 8.579 1.00 23.41 C
+ATOM 167 CG LEU A 22 34.860 67.108 9.534 1.00 26.98 C
+ATOM 168 CD1 LEU A 22 35.133 68.301 10.477 1.00 29.41 C
+ATOM 169 CD2 LEU A 22 33.525 67.302 8.834 1.00 24.72 C
+ATOM 170 N PRO A 23 34.436 64.282 7.178 1.00 19.30 N
+ATOM 171 CA PRO A 23 33.458 63.817 6.200 1.00 18.80 C
+ATOM 172 C PRO A 23 32.221 64.691 6.196 1.00 18.74 C
+ATOM 173 O PRO A 23 31.644 65.078 7.210 1.00 17.64 O
+ATOM 174 CB PRO A 23 33.177 62.378 6.574 1.00 18.76 C
+ATOM 175 CG PRO A 23 33.526 62.281 8.023 1.00 19.59 C
+ATOM 176 CD PRO A 23 34.437 63.395 8.370 1.00 19.10 C
+ATOM 177 N VAL A 24 31.857 65.067 4.984 1.00 15.22 N
+ATOM 178 CA VAL A 24 30.666 65.851 4.685 1.00 14.77 C
+ATOM 179 C VAL A 24 29.880 64.955 3.716 1.00 15.60 C
+ATOM 180 O VAL A 24 30.435 64.510 2.703 1.00 12.24 O
+ATOM 181 CB VAL A 24 30.995 67.164 3.996 1.00 15.38 C
+ATOM 182 CG1 VAL A 24 29.745 67.975 3.657 1.00 16.66 C
+ATOM 183 CG2 VAL A 24 32.014 67.988 4.776 1.00 16.14 C
+ATOM 184 N VAL A 25 28.661 64.613 4.100 1.00 11.81 N
+ATOM 185 CA VAL A 25 27.855 63.658 3.382 1.00 13.59 C
+ATOM 186 C VAL A 25 26.637 64.372 2.797 1.00 15.07 C
+ATOM 187 O VAL A 25 25.956 65.085 3.546 1.00 13.74 O
+ATOM 188 CB VAL A 25 27.373 62.567 4.382 1.00 14.11 C
+ATOM 189 CG1 VAL A 25 26.587 61.507 3.632 1.00 14.74 C
+ATOM 190 CG2 VAL A 25 28.546 61.944 5.155 1.00 15.09 C
+ATOM 191 N PHE A 26 26.376 64.183 1.506 1.00 13.58 N
+ATOM 192 CA PHE A 26 25.329 64.934 0.801 1.00 11.26 C
+ATOM 193 C PHE A 26 24.176 64.016 0.412 1.00 12.76 C
+ATOM 194 O PHE A 26 24.410 62.857 -0.004 1.00 11.00 O
+ATOM 195 CB PHE A 26 25.949 65.535 -0.478 1.00 14.11 C
+ATOM 196 CG PHE A 26 26.984 66.586 -0.199 1.00 15.39 C
+ATOM 197 CD1 PHE A 26 26.593 67.910 -0.023 1.00 15.42 C
+ATOM 198 CD2 PHE A 26 28.326 66.268 -0.162 1.00 16.48 C
+ATOM 199 CE1 PHE A 26 27.545 68.903 0.193 1.00 16.22 C
+ATOM 200 CE2 PHE A 26 29.256 67.257 0.076 1.00 17.18 C
+ATOM 201 CZ PHE A 26 28.879 68.565 0.233 1.00 15.49 C
+ATOM 202 N HIS A 27 22.953 64.479 0.700 1.00 10.40 N
+ATOM 203 CA HIS A 27 21.741 63.695 0.513 1.00 10.97 C
+ATOM 204 C HIS A 27 20.861 64.399 -0.532 1.00 10.19 C
+ATOM 205 O HIS A 27 20.268 65.444 -0.288 1.00 10.60 O
+ATOM 206 CB HIS A 27 20.928 63.555 1.820 1.00 12.16 C
+ATOM 207 CG HIS A 27 21.690 62.862 2.925 1.00 13.43 C
+ATOM 208 ND1 HIS A 27 21.303 61.629 3.408 1.00 11.63 N
+ATOM 209 CD2 HIS A 27 22.799 63.260 3.606 1.00 13.24 C
+ATOM 210 CE1 HIS A 27 22.178 61.292 4.370 1.00 13.22 C
+ATOM 211 NE2 HIS A 27 23.080 62.246 4.517 1.00 14.11 N
+ATOM 212 N HIS A 28 20.768 63.845 -1.739 1.00 11.74 N
+ATOM 213 CA HIS A 28 20.054 64.500 -2.869 1.00 8.78 C
+ATOM 214 C HIS A 28 18.543 64.493 -2.752 1.00 8.92 C
+ATOM 215 O HIS A 28 17.962 63.740 -1.978 1.00 9.63 O
+ATOM 216 CB HIS A 28 20.461 63.767 -4.174 1.00 8.31 C
+ATOM 217 CG HIS A 28 19.935 62.361 -4.287 1.00 8.02 C
+ATOM 218 ND1 HIS A 28 18.647 62.097 -4.703 1.00 9.36 N
+ATOM 219 CD2 HIS A 28 20.522 61.136 -4.096 1.00 8.03 C
+ATOM 220 CE1 HIS A 28 18.444 60.776 -4.717 1.00 8.99 C
+ATOM 221 NE2 HIS A 28 19.585 60.178 -4.340 1.00 8.20 N
+ATOM 222 N GLY A 29 17.882 65.397 -3.499 1.00 8.82 N
+ATOM 223 CA GLY A 29 16.399 65.383 -3.410 1.00 11.02 C
+ATOM 224 C GLY A 29 15.779 64.461 -4.433 1.00 13.10 C
+ATOM 225 O GLY A 29 16.456 63.745 -5.198 1.00 12.97 O
+ATOM 226 N TRP A 30 14.453 64.507 -4.480 1.00 11.76 N
+ATOM 227 CA TRP A 30 13.667 63.723 -5.426 1.00 11.49 C
+ATOM 228 C TRP A 30 13.596 64.520 -6.749 1.00 12.32 C
+ATOM 229 O TRP A 30 13.446 65.735 -6.728 1.00 10.33 O
+ATOM 230 CB TRP A 30 12.257 63.685 -4.834 1.00 12.65 C
+ATOM 231 CG TRP A 30 11.208 63.037 -5.713 1.00 13.04 C
+ATOM 232 CD1 TRP A 30 10.897 61.720 -5.802 1.00 11.74 C
+ATOM 233 CD2 TRP A 30 10.368 63.738 -6.638 1.00 13.91 C
+ATOM 234 NE1 TRP A 30 9.873 61.558 -6.709 1.00 14.39 N
+ATOM 235 CE2 TRP A 30 9.548 62.789 -7.242 1.00 14.52 C
+ATOM 236 CE3 TRP A 30 10.229 65.091 -6.973 1.00 16.58 C
+ATOM 237 CZ2 TRP A 30 8.570 63.121 -8.189 1.00 15.85 C
+ATOM 238 CZ3 TRP A 30 9.282 65.445 -7.944 1.00 18.55 C
+ATOM 239 CH2 TRP A 30 8.470 64.454 -8.512 1.00 17.00 C
+ATOM 240 N PRO A 31 13.619 63.836 -7.877 1.00 11.13 N
+ATOM 241 CA PRO A 31 13.850 62.395 -8.042 1.00 10.21 C
+ATOM 242 C PRO A 31 15.280 62.256 -8.606 1.00 12.56 C
+ATOM 243 O PRO A 31 15.545 61.719 -9.664 1.00 10.78 O
+ATOM 244 CB PRO A 31 12.805 62.060 -9.113 1.00 9.67 C
+ATOM 245 CG PRO A 31 12.619 63.311 -9.931 1.00 12.03 C
+ATOM 246 CD PRO A 31 13.339 64.463 -9.208 1.00 10.61 C
+ATOM 247 N LEU A 32 16.312 62.805 -7.940 1.00 11.12 N
+ATOM 248 CA LEU A 32 17.635 62.897 -8.514 1.00 12.32 C
+ATOM 249 C LEU A 32 18.632 61.817 -8.119 1.00 11.18 C
+ATOM 250 O LEU A 32 18.288 60.643 -8.044 1.00 10.82 O
+ATOM 251 CB LEU A 32 18.163 64.345 -8.223 1.00 9.98 C
+ATOM 252 CG LEU A 32 17.094 65.384 -8.657 1.00 11.19 C
+ATOM 253 CD1 LEU A 32 17.453 66.788 -8.236 1.00 13.84 C
+ATOM 254 CD2 LEU A 32 16.988 65.391 -10.195 1.00 14.00 C
+ATOM 255 N SER A 33 19.906 62.179 -7.957 1.00 11.30 N
+ATOM 256 CA SER A 33 20.965 61.240 -7.666 1.00 9.67 C
+ATOM 257 C SER A 33 22.110 61.972 -6.953 1.00 8.43 C
+ATOM 258 O SER A 33 22.070 63.215 -6.846 1.00 7.20 O
+ATOM 259 CB SER A 33 21.403 60.628 -9.007 1.00 10.41 C
+ATOM 260 OG SER A 33 22.293 61.521 -9.675 1.00 10.51 O
+ATOM 261 N ALA A 34 23.177 61.302 -6.599 1.00 9.22 N
+ATOM 262 CA ALA A 34 24.351 61.885 -6.019 1.00 9.62 C
+ATOM 263 C ALA A 34 25.020 62.837 -7.012 1.00 10.11 C
+ATOM 264 O ALA A 34 25.658 63.792 -6.552 1.00 8.62 O
+ATOM 265 CB ALA A 34 25.363 60.804 -5.587 1.00 10.36 C
+ATOM 266 N ASP A 35 24.741 62.725 -8.306 1.00 10.17 N
+ATOM 267 CA ASP A 35 25.338 63.652 -9.285 1.00 10.79 C
+ATOM 268 C ASP A 35 24.786 65.055 -9.195 1.00 10.13 C
+ATOM 269 O ASP A 35 25.395 65.975 -9.752 1.00 10.35 O
+ATOM 270 CB ASP A 35 25.128 63.125 -10.716 1.00 10.95 C
+ATOM 271 CG ASP A 35 26.036 61.950 -10.989 1.00 13.32 C
+ATOM 272 OD1 ASP A 35 26.762 61.509 -10.074 1.00 13.54 O
+ATOM 273 OD2 ASP A 35 25.999 61.432 -12.143 1.00 15.25 O
+ATOM 274 N ASP A 36 23.653 65.296 -8.506 1.00 8.36 N
+ATOM 275 CA ASP A 36 23.147 66.659 -8.307 1.00 8.03 C
+ATOM 276 C ASP A 36 24.109 67.504 -7.475 1.00 9.21 C
+ATOM 277 O ASP A 36 23.956 68.727 -7.446 1.00 11.05 O
+ATOM 278 CB ASP A 36 21.751 66.553 -7.614 1.00 10.47 C
+ATOM 279 CG ASP A 36 20.924 67.813 -7.861 1.00 16.13 C
+ATOM 280 OD1 ASP A 36 20.773 68.227 -9.024 1.00 17.12 O
+ATOM 281 OD2 ASP A 36 20.439 68.471 -6.912 1.00 15.32 O
+ATOM 282 N TRP A 37 25.079 66.931 -6.753 1.00 10.46 N
+ATOM 283 CA TRP A 37 25.984 67.664 -5.858 1.00 7.76 C
+ATOM 284 C TRP A 37 27.297 68.042 -6.484 1.00 9.56 C
+ATOM 285 O TRP A 37 28.193 68.574 -5.791 1.00 11.85 O
+ATOM 286 CB TRP A 37 26.253 66.742 -4.622 1.00 7.60 C
+ATOM 287 CG TRP A 37 25.001 66.543 -3.784 1.00 9.11 C
+ATOM 288 CD1 TRP A 37 24.267 65.410 -3.597 1.00 8.67 C
+ATOM 289 CD2 TRP A 37 24.403 67.551 -2.961 1.00 8.08 C
+ATOM 290 NE1 TRP A 37 23.223 65.663 -2.717 1.00 10.07 N
+ATOM 291 CE2 TRP A 37 23.291 66.972 -2.332 1.00 10.35 C
+ATOM 292 CE3 TRP A 37 24.710 68.902 -2.760 1.00 7.63 C
+ATOM 293 CZ2 TRP A 37 22.447 67.674 -1.470 1.00 8.35 C
+ATOM 294 CZ3 TRP A 37 23.891 69.609 -1.890 1.00 11.31 C
+ATOM 295 CH2 TRP A 37 22.793 68.985 -1.258 1.00 10.30 C
+ATOM 296 N ASP A 38 27.525 67.787 -7.774 1.00 9.33 N
+ATOM 297 CA ASP A 38 28.799 68.073 -8.410 1.00 11.16 C
+ATOM 298 C ASP A 38 29.467 69.360 -7.886 1.00 12.35 C
+ATOM 299 O ASP A 38 30.620 69.352 -7.489 1.00 12.36 O
+ATOM 300 CB ASP A 38 28.729 68.134 -9.915 1.00 11.22 C
+ATOM 301 CG ASP A 38 28.618 66.748 -10.584 1.00 14.58 C
+ATOM 302 OD1 ASP A 38 28.801 65.679 -9.939 1.00 11.78 O
+ATOM 303 OD2 ASP A 38 28.316 66.810 -11.796 1.00 14.06 O
+ATOM 304 N ASN A 39 28.773 70.486 -7.986 1.00 11.87 N
+ATOM 305 CA ASN A 39 29.347 71.774 -7.620 1.00 13.12 C
+ATOM 306 C ASN A 39 29.858 71.808 -6.175 1.00 12.64 C
+ATOM 307 O ASN A 39 30.969 72.304 -5.934 1.00 12.56 O
+ATOM 308 CB ASN A 39 28.246 72.828 -7.881 1.00 12.86 C
+ATOM 309 CG ASN A 39 28.735 74.207 -7.488 1.00 16.95 C
+ATOM 310 OD1 ASN A 39 28.991 74.427 -6.302 1.00 17.51 O
+ATOM 311 ND2 ASN A 39 28.936 75.144 -8.422 1.00 13.94 N
+ATOM 312 N GLN A 40 29.005 71.401 -5.228 1.00 10.79 N
+ATOM 313 CA GLN A 40 29.310 71.388 -3.802 1.00 12.37 C
+ATOM 314 C GLN A 40 30.359 70.336 -3.532 1.00 13.56 C
+ATOM 315 O GLN A 40 31.222 70.596 -2.672 1.00 14.85 O
+ATOM 316 CB GLN A 40 28.073 71.098 -2.903 1.00 10.94 C
+ATOM 317 CG GLN A 40 27.177 72.304 -2.752 1.00 12.64 C
+ATOM 318 CD GLN A 40 26.363 72.654 -3.968 1.00 13.95 C
+ATOM 319 OE1 GLN A 40 25.892 71.692 -4.634 1.00 12.38 O
+ATOM 320 NE2 GLN A 40 26.198 73.969 -4.228 1.00 11.57 N
+ATOM 321 N MET A 41 30.361 69.216 -4.265 1.00 9.82 N
+ATOM 322 CA MET A 41 31.420 68.252 -3.999 1.00 12.73 C
+ATOM 323 C MET A 41 32.790 68.783 -4.357 1.00 14.38 C
+ATOM 324 O MET A 41 33.713 68.665 -3.538 1.00 15.37 O
+ATOM 325 CB MET A 41 31.096 66.887 -4.643 1.00 15.27 C
+ATOM 326 CG MET A 41 30.171 66.198 -3.570 1.00 19.95 C
+ATOM 327 SD MET A 41 29.527 64.729 -4.235 1.00 30.23 S
+ATOM 328 CE MET A 41 30.795 63.508 -3.872 1.00 20.16 C
+ATOM 329 N LEU A 42 32.919 69.481 -5.499 1.00 13.84 N
+ATOM 330 CA LEU A 42 34.198 70.049 -5.851 1.00 13.52 C
+ATOM 331 C LEU A 42 34.587 71.209 -4.916 1.00 14.94 C
+ATOM 332 O LEU A 42 35.767 71.348 -4.584 1.00 14.55 O
+ATOM 333 CB LEU A 42 34.098 70.552 -7.285 1.00 13.38 C
+ATOM 334 CG LEU A 42 33.957 69.466 -8.388 1.00 15.26 C
+ATOM 335 CD1 LEU A 42 34.392 70.007 -9.736 1.00 15.85 C
+ATOM 336 CD2 LEU A 42 34.821 68.241 -8.130 1.00 15.96 C
+ATOM 337 N PHE A 43 33.602 71.998 -4.533 1.00 13.32 N
+ATOM 338 CA PHE A 43 33.891 73.166 -3.644 1.00 15.81 C
+ATOM 339 C PHE A 43 34.440 72.729 -2.294 1.00 16.66 C
+ATOM 340 O PHE A 43 35.503 73.159 -1.864 1.00 17.10 O
+ATOM 341 CB PHE A 43 32.595 73.964 -3.487 1.00 15.51 C
+ATOM 342 CG PHE A 43 32.710 75.058 -2.429 1.00 17.53 C
+ATOM 343 CD1 PHE A 43 33.261 76.274 -2.776 1.00 19.11 C
+ATOM 344 CD2 PHE A 43 32.234 74.829 -1.149 1.00 19.38 C
+ATOM 345 CE1 PHE A 43 33.370 77.294 -1.822 1.00 20.88 C
+ATOM 346 CE2 PHE A 43 32.326 75.840 -0.194 1.00 18.55 C
+ATOM 347 CZ PHE A 43 32.873 77.056 -0.549 1.00 17.92 C
+ATOM 348 N PHE A 44 33.809 71.736 -1.660 1.00 15.71 N
+ATOM 349 CA PHE A 44 34.273 71.205 -0.385 1.00 15.06 C
+ATOM 350 C PHE A 44 35.601 70.485 -0.464 1.00 17.32 C
+ATOM 351 O PHE A 44 36.489 70.536 0.432 1.00 18.03 O
+ATOM 352 CB PHE A 44 33.145 70.346 0.225 1.00 14.43 C
+ATOM 353 CG PHE A 44 32.209 71.241 1.023 1.00 15.08 C
+ATOM 354 CD1 PHE A 44 32.585 71.597 2.326 1.00 16.70 C
+ATOM 355 CD2 PHE A 44 31.065 71.730 0.481 1.00 14.94 C
+ATOM 356 CE1 PHE A 44 31.741 72.407 3.075 1.00 17.78 C
+ATOM 357 CE2 PHE A 44 30.214 72.551 1.232 1.00 17.65 C
+ATOM 358 CZ PHE A 44 30.566 72.898 2.530 1.00 18.75 C
+ATOM 359 N LEU A 45 35.814 69.714 -1.516 1.00 14.91 N
+ATOM 360 CA LEU A 45 37.072 69.069 -1.820 1.00 18.79 C
+ATOM 361 C LEU A 45 38.202 70.104 -1.871 1.00 18.00 C
+ATOM 362 O LEU A 45 39.295 69.831 -1.389 1.00 19.90 O
+ATOM 363 CB LEU A 45 37.067 68.428 -3.221 1.00 17.38 C
+ATOM 364 CG LEU A 45 36.611 66.991 -3.302 1.00 19.50 C
+ATOM 365 CD1 LEU A 45 36.562 66.566 -4.776 1.00 17.84 C
+ATOM 366 CD2 LEU A 45 37.585 66.165 -2.472 1.00 21.51 C
+ATOM 367 N SER A 46 37.947 71.227 -2.524 1.00 19.84 N
+ATOM 368 CA SER A 46 38.955 72.267 -2.609 1.00 22.20 C
+ATOM 369 C SER A 46 39.293 72.862 -1.231 1.00 24.61 C
+ATOM 370 O SER A 46 40.319 73.529 -1.110 1.00 23.74 O
+ATOM 371 CB SER A 46 38.529 73.380 -3.552 1.00 22.83 C
+ATOM 372 OG SER A 46 37.650 74.268 -2.896 1.00 29.36 O
+ATOM 373 N HIS A 47 38.435 72.677 -0.217 1.00 22.29 N
+ATOM 374 CA HIS A 47 38.714 73.191 1.106 1.00 22.20 C
+ATOM 375 C HIS A 47 39.197 72.068 2.028 1.00 22.23 C
+ATOM 376 O HIS A 47 39.283 72.314 3.240 1.00 22.21 O
+ATOM 377 CB HIS A 47 37.510 73.910 1.714 1.00 19.45 C
+ATOM 378 CG HIS A 47 37.353 75.211 1.008 1.00 21.06 C
+ATOM 379 ND1 HIS A 47 38.075 76.309 1.399 1.00 21.99 N
+ATOM 380 CD2 HIS A 47 36.571 75.599 -0.040 1.00 21.66 C
+ATOM 381 CE1 HIS A 47 37.783 77.329 0.616 1.00 22.57 C
+ATOM 382 NE2 HIS A 47 36.881 76.923 -0.265 1.00 22.90 N
+ATOM 383 N GLY A 48 39.580 70.947 1.422 1.00 21.01 N
+ATOM 384 CA GLY A 48 40.180 69.832 2.096 1.00 20.70 C
+ATOM 385 C GLY A 48 39.247 68.872 2.804 1.00 21.71 C
+ATOM 386 O GLY A 48 39.735 68.092 3.647 1.00 22.39 O
+ATOM 387 N TYR A 49 37.965 68.836 2.460 1.00 19.45 N
+ATOM 388 CA TYR A 49 37.060 67.879 3.116 1.00 18.69 C
+ATOM 389 C TYR A 49 36.949 66.587 2.335 1.00 18.08 C
+ATOM 390 O TYR A 49 37.309 66.479 1.169 1.00 19.13 O
+ATOM 391 CB TYR A 49 35.657 68.503 3.299 1.00 18.85 C
+ATOM 392 CG TYR A 49 35.695 69.660 4.286 1.00 20.92 C
+ATOM 393 CD1 TYR A 49 35.571 69.406 5.649 1.00 22.05 C
+ATOM 394 CD2 TYR A 49 35.870 70.964 3.868 1.00 21.65 C
+ATOM 395 CE1 TYR A 49 35.623 70.443 6.578 1.00 23.11 C
+ATOM 396 CE2 TYR A 49 35.939 72.011 4.774 1.00 22.46 C
+ATOM 397 CZ TYR A 49 35.802 71.725 6.127 1.00 23.54 C
+ATOM 398 OH TYR A 49 35.844 72.792 7.013 1.00 24.88 O
+ATOM 399 N ARG A 50 36.557 65.521 3.016 1.00 16.04 N
+ATOM 400 CA ARG A 50 36.229 64.239 2.430 1.00 16.01 C
+ATOM 401 C ARG A 50 34.742 64.366 2.059 1.00 15.33 C
+ATOM 402 O ARG A 50 33.974 64.921 2.866 1.00 14.61 O
+ATOM 403 CB ARG A 50 36.459 63.081 3.351 1.00 14.64 C
+ATOM 404 CG ARG A 50 36.198 61.698 2.748 1.00 14.58 C
+ATOM 405 CD ARG A 50 36.284 60.686 3.911 1.00 14.44 C
+ATOM 406 NE ARG A 50 35.910 59.347 3.508 1.00 13.80 N
+ATOM 407 CZ ARG A 50 35.864 58.283 4.280 1.00 16.31 C
+ATOM 408 NH1 ARG A 50 36.284 58.411 5.553 1.00 18.83 N
+ATOM 409 NH2 ARG A 50 35.431 57.118 3.862 1.00 15.18 N
+ATOM 410 N VAL A 51 34.388 64.016 0.811 1.00 14.78 N
+ATOM 411 CA VAL A 51 33.006 64.310 0.374 1.00 13.11 C
+ATOM 412 C VAL A 51 32.385 63.009 -0.096 1.00 14.09 C
+ATOM 413 O VAL A 51 33.049 62.179 -0.759 1.00 12.81 O
+ATOM 414 CB VAL A 51 32.915 65.397 -0.724 1.00 14.40 C
+ATOM 415 CG1 VAL A 51 33.250 66.769 -0.120 1.00 12.81 C
+ATOM 416 CG2 VAL A 51 33.876 65.101 -1.892 1.00 12.06 C
+ATOM 417 N ILE A 52 31.222 62.741 0.547 1.00 13.24 N
+ATOM 418 CA ILE A 52 30.505 61.490 0.279 1.00 12.71 C
+ATOM 419 C ILE A 52 29.086 61.792 -0.194 1.00 12.59 C
+ATOM 420 O ILE A 52 28.398 62.678 0.330 1.00 12.28 O
+ATOM 421 CB ILE A 52 30.463 60.671 1.600 1.00 13.98 C
+ATOM 422 CG1 ILE A 52 31.922 60.262 1.942 1.00 16.07 C
+ATOM 423 CG2 ILE A 52 29.585 59.445 1.464 1.00 13.36 C
+ATOM 424 CD1 ILE A 52 32.153 60.127 3.447 1.00 17.69 C
+ATOM 425 N ALA A 53 28.601 60.985 -1.147 1.00 10.28 N
+ATOM 426 CA ALA A 53 27.216 61.184 -1.632 1.00 8.98 C
+ATOM 427 C ALA A 53 26.727 59.861 -2.201 1.00 10.37 C
+ATOM 428 O ALA A 53 27.502 59.254 -2.974 1.00 10.18 O
+ATOM 429 CB ALA A 53 27.159 62.271 -2.691 1.00 9.23 C
+ATOM 430 N HIS A 54 25.538 59.424 -1.835 1.00 9.75 N
+ATOM 431 CA HIS A 54 25.032 58.180 -2.300 1.00 10.49 C
+ATOM 432 C HIS A 54 23.820 58.433 -3.213 1.00 10.00 C
+ATOM 433 O HIS A 54 23.120 59.451 -3.072 1.00 12.24 O
+ATOM 434 CB HIS A 54 24.611 57.227 -1.152 1.00 10.17 C
+ATOM 435 CG HIS A 54 23.445 57.748 -0.360 1.00 15.03 C
+ATOM 436 ND1 HIS A 54 23.518 58.948 0.309 1.00 16.75 N
+ATOM 437 CD2 HIS A 54 22.190 57.271 -0.134 1.00 17.52 C
+ATOM 438 CE1 HIS A 54 22.394 59.226 0.914 1.00 17.95 C
+ATOM 439 NE2 HIS A 54 21.572 58.229 0.645 1.00 18.90 N
+ATOM 440 N ASP A 55 23.496 57.437 -4.036 1.00 9.81 N
+ATOM 441 CA ASP A 55 22.204 57.427 -4.751 1.00 8.89 C
+ATOM 442 C ASP A 55 21.190 56.723 -3.863 1.00 10.25 C
+ATOM 443 O ASP A 55 21.345 55.518 -3.493 1.00 9.90 O
+ATOM 444 CB ASP A 55 22.333 56.595 -6.057 1.00 9.35 C
+ATOM 445 CG ASP A 55 23.176 57.300 -7.110 1.00 10.41 C
+ATOM 446 OD1 ASP A 55 23.432 58.516 -7.031 1.00 11.07 O
+ATOM 447 OD2 ASP A 55 23.583 56.640 -8.101 1.00 13.40 O
+ATOM 448 N ARG A 56 20.081 57.388 -3.549 1.00 9.91 N
+ATOM 449 CA ARG A 56 18.999 56.735 -2.828 1.00 11.19 C
+ATOM 450 C ARG A 56 18.509 55.507 -3.574 1.00 12.76 C
+ATOM 451 O ARG A 56 18.561 55.394 -4.806 1.00 11.30 O
+ATOM 452 CB ARG A 56 17.870 57.727 -2.625 1.00 11.77 C
+ATOM 453 CG ARG A 56 16.705 57.275 -1.749 1.00 14.73 C
+ATOM 454 CD ARG A 56 15.812 58.475 -1.410 1.00 11.41 C
+ATOM 455 NE ARG A 56 16.636 59.407 -0.677 1.00 11.61 N
+ATOM 456 CZ ARG A 56 16.963 60.632 -1.020 1.00 12.74 C
+ATOM 457 NH1 ARG A 56 16.422 61.207 -2.128 1.00 11.30 N
+ATOM 458 NH2 ARG A 56 17.817 61.305 -0.288 1.00 9.77 N
+ATOM 459 N ARG A 57 18.034 54.489 -2.841 1.00 11.59 N
+ATOM 460 CA ARG A 57 17.554 53.270 -3.462 1.00 11.95 C
+ATOM 461 C ARG A 57 16.476 53.640 -4.511 1.00 11.10 C
+ATOM 462 O ARG A 57 15.688 54.546 -4.275 1.00 11.20 O
+ATOM 463 CB ARG A 57 16.901 52.256 -2.513 1.00 13.57 C
+ATOM 464 CG ARG A 57 15.752 52.707 -1.643 1.00 16.84 C
+ATOM 465 CD ARG A 57 15.027 51.450 -1.048 1.00 15.52 C
+ATOM 466 NE ARG A 57 15.916 50.739 -0.135 1.00 16.36 N
+ATOM 467 CZ ARG A 57 15.871 49.511 0.349 1.00 18.20 C
+ATOM 468 NH1 ARG A 57 14.931 48.652 -0.033 1.00 16.83 N
+ATOM 469 NH2 ARG A 57 16.809 49.053 1.218 1.00 14.46 N
+ATOM 470 N GLY A 58 16.570 52.946 -5.635 1.00 10.12 N
+ATOM 471 CA GLY A 58 15.677 53.236 -6.739 1.00 10.60 C
+ATOM 472 C GLY A 58 16.030 54.514 -7.501 1.00 12.64 C
+ATOM 473 O GLY A 58 15.229 55.037 -8.289 1.00 10.99 O
+ATOM 474 N HIS A 59 17.210 55.088 -7.279 1.00 10.50 N
+ATOM 475 CA HIS A 59 17.596 56.321 -7.908 1.00 12.35 C
+ATOM 476 C HIS A 59 19.013 56.112 -8.483 1.00 11.51 C
+ATOM 477 O HIS A 59 19.823 55.335 -7.953 1.00 12.39 O
+ATOM 478 CB HIS A 59 17.703 57.517 -6.933 1.00 10.93 C
+ATOM 479 CG HIS A 59 16.404 57.959 -6.334 1.00 11.57 C
+ATOM 480 ND1 HIS A 59 15.663 57.055 -5.561 1.00 11.08 N
+ATOM 481 CD2 HIS A 59 15.722 59.144 -6.363 1.00 10.20 C
+ATOM 482 CE1 HIS A 59 14.557 57.704 -5.174 1.00 10.17 C
+ATOM 483 NE2 HIS A 59 14.592 58.946 -5.616 1.00 9.32 N
+ATOM 484 N GLY A 60 19.320 56.942 -9.479 1.00 10.42 N
+ATOM 485 CA GLY A 60 20.652 56.902 -10.083 1.00 10.86 C
+ATOM 486 C GLY A 60 21.107 55.513 -10.457 1.00 12.19 C
+ATOM 487 O GLY A 60 20.488 54.778 -11.237 1.00 12.14 O
+ATOM 488 N ARG A 61 22.260 55.118 -9.880 1.00 11.29 N
+ATOM 489 CA ARG A 61 22.891 53.831 -10.138 1.00 11.62 C
+ATOM 490 C ARG A 61 22.610 52.796 -9.048 1.00 13.15 C
+ATOM 491 O ARG A 61 23.199 51.709 -9.085 1.00 13.99 O
+ATOM 492 CB ARG A 61 24.424 54.022 -10.215 1.00 13.31 C
+ATOM 493 CG ARG A 61 24.869 54.879 -11.400 1.00 14.55 C
+ATOM 494 CD ARG A 61 26.024 55.827 -11.120 1.00 17.01 C
+ATOM 495 NE ARG A 61 25.549 56.911 -10.209 1.00 17.03 N
+ATOM 496 CZ ARG A 61 25.917 58.162 -10.189 1.00 16.70 C
+ATOM 497 NH1 ARG A 61 26.861 58.590 -11.048 1.00 15.95 N
+ATOM 498 NH2 ARG A 61 25.412 59.028 -9.296 1.00 14.51 N
+ATOM 499 N SER A 62 21.828 53.136 -8.030 1.00 12.83 N
+ATOM 500 CA SER A 62 21.476 52.138 -7.014 1.00 11.39 C
+ATOM 501 C SER A 62 20.502 51.121 -7.582 1.00 14.15 C
+ATOM 502 O SER A 62 19.868 51.367 -8.630 1.00 15.29 O
+ATOM 503 CB SER A 62 20.891 52.847 -5.765 1.00 7.46 C
+ATOM 504 OG SER A 62 21.998 53.564 -5.200 1.00 10.03 O
+ATOM 505 N ASP A 63 20.282 50.006 -6.905 1.00 13.37 N
+ATOM 506 CA ASP A 63 19.352 48.989 -7.346 1.00 13.66 C
+ATOM 507 C ASP A 63 17.945 49.568 -7.386 1.00 13.82 C
+ATOM 508 O ASP A 63 17.725 50.578 -6.697 1.00 14.80 O
+ATOM 509 CB ASP A 63 19.307 47.844 -6.333 1.00 14.50 C
+ATOM 510 CG ASP A 63 20.470 46.874 -6.460 1.00 20.41 C
+ATOM 511 OD1 ASP A 63 21.342 47.019 -7.311 1.00 19.01 O
+ATOM 512 OD2 ASP A 63 20.551 45.974 -5.600 1.00 21.85 O
+ATOM 513 N GLN A 64 17.002 48.902 -8.037 1.00 10.61 N
+ATOM 514 CA GLN A 64 15.623 49.389 -8.075 1.00 14.00 C
+ATOM 515 C GLN A 64 14.743 48.255 -7.487 1.00 15.71 C
+ATOM 516 O GLN A 64 14.178 47.458 -8.232 1.00 14.95 O
+ATOM 517 CB GLN A 64 15.189 49.636 -9.520 1.00 15.19 C
+ATOM 518 CG GLN A 64 16.210 50.338 -10.413 1.00 16.24 C
+ATOM 519 CD GLN A 64 15.614 50.878 -11.703 1.00 16.57 C
+ATOM 520 OE1 GLN A 64 14.652 50.305 -12.262 1.00 14.89 O
+ATOM 521 NE2 GLN A 64 16.176 52.005 -12.176 1.00 13.26 N
+ATOM 522 N PRO A 65 14.705 48.137 -6.173 1.00 15.24 N
+ATOM 523 CA PRO A 65 13.975 47.093 -5.494 1.00 15.11 C
+ATOM 524 C PRO A 65 12.494 47.338 -5.537 1.00 14.85 C
+ATOM 525 O PRO A 65 12.042 48.417 -5.865 1.00 15.52 O
+ATOM 526 CB PRO A 65 14.471 47.185 -4.047 1.00 14.78 C
+ATOM 527 CG PRO A 65 14.822 48.628 -3.868 1.00 16.59 C
+ATOM 528 CD PRO A 65 15.331 49.113 -5.221 1.00 15.09 C
+ATOM 529 N SER A 66 11.713 46.308 -5.209 1.00 15.98 N
+ATOM 530 CA SER A 66 10.274 46.407 -5.248 1.00 18.01 C
+ATOM 531 C SER A 66 9.716 47.229 -4.103 1.00 17.99 C
+ATOM 532 O SER A 66 8.650 47.851 -4.183 1.00 18.04 O
+ATOM 533 CB SER A 66 9.746 44.948 -4.997 1.00 19.08 C
+ATOM 534 OG SER A 66 8.331 45.114 -5.016 1.00 24.82 O
+ATOM 535 N THR A 67 10.422 47.149 -2.963 1.00 17.08 N
+ATOM 536 CA THR A 67 9.934 47.775 -1.740 1.00 19.31 C
+ATOM 537 C THR A 67 10.996 48.608 -1.030 1.00 18.68 C
+ATOM 538 O THR A 67 12.126 48.750 -1.492 1.00 18.47 O
+ATOM 539 CB THR A 67 9.470 46.694 -0.712 1.00 22.72 C
+ATOM 540 OG1 THR A 67 10.568 45.822 -0.383 1.00 25.78 O
+ATOM 541 CG2 THR A 67 8.418 45.758 -1.272 1.00 24.64 C
+ATOM 542 N GLY A 68 10.544 49.264 0.050 1.00 18.44 N
+ATOM 543 CA GLY A 68 11.410 50.070 0.881 1.00 18.48 C
+ATOM 544 C GLY A 68 11.430 51.513 0.425 1.00 18.03 C
+ATOM 545 O GLY A 68 12.341 52.225 0.869 1.00 17.43 O
+ATOM 546 N HIS A 69 10.386 51.958 -0.298 1.00 15.63 N
+ATOM 547 CA HIS A 69 10.355 53.371 -0.688 1.00 14.93 C
+ATOM 548 C HIS A 69 9.757 54.226 0.416 1.00 17.11 C
+ATOM 549 O HIS A 69 8.638 54.710 0.233 1.00 17.45 O
+ATOM 550 CB HIS A 69 9.572 53.474 -2.035 1.00 15.52 C
+ATOM 551 CG HIS A 69 10.239 52.528 -2.995 1.00 17.07 C
+ATOM 552 ND1 HIS A 69 11.567 52.724 -3.352 1.00 16.36 N
+ATOM 553 CD2 HIS A 69 9.833 51.360 -3.537 1.00 17.57 C
+ATOM 554 CE1 HIS A 69 11.915 51.713 -4.163 1.00 17.29 C
+ATOM 555 NE2 HIS A 69 10.894 50.860 -4.272 1.00 15.49 N
+ATOM 556 N ASP A 70 10.401 54.382 1.579 1.00 17.34 N
+ATOM 557 CA ASP A 70 9.849 55.101 2.717 1.00 18.16 C
+ATOM 558 C ASP A 70 11.016 55.692 3.544 1.00 16.30 C
+ATOM 559 O ASP A 70 12.116 55.163 3.410 1.00 13.01 O
+ATOM 560 CB ASP A 70 8.928 54.178 3.541 1.00 20.28 C
+ATOM 561 CG ASP A 70 9.746 53.058 4.173 1.00 23.91 C
+ATOM 562 OD1 ASP A 70 10.450 53.230 5.194 1.00 24.82 O
+ATOM 563 OD2 ASP A 70 9.798 51.942 3.629 1.00 27.21 O
+ATOM 564 N MET A 71 10.727 56.674 4.374 1.00 16.04 N
+ATOM 565 CA MET A 71 11.751 57.382 5.138 1.00 17.42 C
+ATOM 566 C MET A 71 12.489 56.507 6.126 1.00 18.97 C
+ATOM 567 O MET A 71 13.668 56.733 6.391 1.00 19.57 O
+ATOM 568 CB MET A 71 11.113 58.595 5.817 1.00 17.57 C
+ATOM 569 CG MET A 71 10.799 59.737 4.828 1.00 19.70 C
+ATOM 570 SD MET A 71 12.346 60.497 4.262 1.00 23.19 S
+ATOM 571 CE MET A 71 11.642 61.291 2.798 1.00 21.28 C
+ATOM 572 N ASP A 72 11.775 55.560 6.792 1.00 18.86 N
+ATOM 573 CA ASP A 72 12.473 54.698 7.726 1.00 20.01 C
+ATOM 574 C ASP A 72 13.515 53.867 6.990 1.00 17.50 C
+ATOM 575 O ASP A 72 14.636 53.699 7.436 1.00 17.67 O
+ATOM 576 CB ASP A 72 11.540 53.702 8.440 1.00 21.15 C
+ATOM 577 CG ASP A 72 10.651 54.414 9.426 1.00 23.56 C
+ATOM 578 OD1 ASP A 72 11.007 55.456 9.999 1.00 25.29 O
+ATOM 579 OD2 ASP A 72 9.544 53.929 9.677 1.00 26.30 O
+ATOM 580 N THR A 73 13.175 53.274 5.861 1.00 17.67 N
+ATOM 581 CA THR A 73 14.185 52.520 5.103 1.00 16.73 C
+ATOM 582 C THR A 73 15.262 53.441 4.560 1.00 16.33 C
+ATOM 583 O THR A 73 16.445 53.092 4.560 1.00 15.98 O
+ATOM 584 CB THR A 73 13.467 51.793 3.952 1.00 19.40 C
+ATOM 585 OG1 THR A 73 12.385 51.035 4.527 1.00 19.44 O
+ATOM 586 CG2 THR A 73 14.438 50.906 3.183 1.00 20.03 C
+ATOM 587 N TYR A 74 14.901 54.643 4.086 1.00 14.43 N
+ATOM 588 CA TYR A 74 15.942 55.537 3.560 1.00 14.73 C
+ATOM 589 C TYR A 74 16.957 55.842 4.662 1.00 15.63 C
+ATOM 590 O TYR A 74 18.142 55.858 4.393 1.00 13.39 O
+ATOM 591 CB TYR A 74 15.344 56.863 3.076 1.00 12.85 C
+ATOM 592 CG TYR A 74 14.417 56.781 1.865 1.00 13.05 C
+ATOM 593 CD1 TYR A 74 14.461 55.725 0.994 1.00 13.06 C
+ATOM 594 CD2 TYR A 74 13.504 57.830 1.665 1.00 11.61 C
+ATOM 595 CE1 TYR A 74 13.591 55.676 -0.092 1.00 13.74 C
+ATOM 596 CE2 TYR A 74 12.613 57.756 0.570 1.00 13.06 C
+ATOM 597 CZ TYR A 74 12.688 56.699 -0.283 1.00 12.46 C
+ATOM 598 OH TYR A 74 11.843 56.599 -1.381 1.00 15.66 O
+ATOM 599 N ALA A 75 16.454 56.130 5.890 1.00 14.81 N
+ATOM 600 CA ALA A 75 17.414 56.440 6.971 1.00 15.93 C
+ATOM 601 C ALA A 75 18.205 55.188 7.368 1.00 17.41 C
+ATOM 602 O ALA A 75 19.366 55.333 7.761 1.00 19.66 O
+ATOM 603 CB ALA A 75 16.636 56.997 8.152 1.00 17.42 C
+ATOM 604 N ALA A 76 17.653 53.997 7.255 1.00 16.77 N
+ATOM 605 CA ALA A 76 18.407 52.784 7.602 1.00 18.34 C
+ATOM 606 C ALA A 76 19.466 52.475 6.548 1.00 17.45 C
+ATOM 607 O ALA A 76 20.572 51.981 6.804 1.00 15.95 O
+ATOM 608 CB ALA A 76 17.468 51.599 7.773 1.00 18.78 C
+ATOM 609 N ASP A 77 19.139 52.844 5.291 1.00 15.37 N
+ATOM 610 CA ASP A 77 20.136 52.652 4.211 1.00 13.81 C
+ATOM 611 C ASP A 77 21.277 53.630 4.498 1.00 13.34 C
+ATOM 612 O ASP A 77 22.424 53.249 4.306 1.00 16.53 O
+ATOM 613 CB ASP A 77 19.494 52.994 2.858 1.00 13.74 C
+ATOM 614 CG ASP A 77 18.513 51.988 2.327 1.00 17.10 C
+ATOM 615 OD1 ASP A 77 18.425 50.849 2.881 1.00 16.29 O
+ATOM 616 OD2 ASP A 77 17.788 52.307 1.343 1.00 15.78 O
+ATOM 617 N VAL A 78 21.051 54.844 4.975 1.00 13.30 N
+ATOM 618 CA VAL A 78 22.112 55.774 5.317 1.00 13.87 C
+ATOM 619 C VAL A 78 22.995 55.177 6.445 1.00 15.32 C
+ATOM 620 O VAL A 78 24.221 55.230 6.400 1.00 14.19 O
+ATOM 621 CB VAL A 78 21.571 57.143 5.763 1.00 14.43 C
+ATOM 622 CG1 VAL A 78 22.714 57.985 6.298 1.00 15.65 C
+ATOM 623 CG2 VAL A 78 20.904 57.852 4.554 1.00 14.95 C
+ATOM 624 N ALA A 79 22.342 54.591 7.449 1.00 14.95 N
+ATOM 625 CA ALA A 79 23.102 53.964 8.557 1.00 15.95 C
+ATOM 626 C ALA A 79 23.934 52.847 8.022 1.00 15.19 C
+ATOM 627 O ALA A 79 25.079 52.715 8.472 1.00 17.54 O
+ATOM 628 CB ALA A 79 22.124 53.500 9.656 1.00 16.85 C
+ATOM 629 N ALA A 80 23.456 52.027 7.093 1.00 14.80 N
+ATOM 630 CA ALA A 80 24.236 50.967 6.501 1.00 17.47 C
+ATOM 631 C ALA A 80 25.499 51.562 5.868 1.00 17.32 C
+ATOM 632 O ALA A 80 26.583 50.993 6.093 1.00 19.66 O
+ATOM 633 CB ALA A 80 23.454 50.067 5.575 1.00 17.72 C
+ATOM 634 N LEU A 81 25.450 52.649 5.130 1.00 15.51 N
+ATOM 635 CA LEU A 81 26.623 53.274 4.528 1.00 15.62 C
+ATOM 636 C LEU A 81 27.582 53.880 5.552 1.00 16.94 C
+ATOM 637 O LEU A 81 28.808 53.700 5.418 1.00 18.22 O
+ATOM 638 CB LEU A 81 26.102 54.456 3.671 1.00 16.49 C
+ATOM 639 CG LEU A 81 27.157 55.396 3.066 1.00 19.29 C
+ATOM 640 CD1 LEU A 81 27.932 54.622 2.007 1.00 21.95 C
+ATOM 641 CD2 LEU A 81 26.473 56.621 2.490 1.00 22.69 C
+ATOM 642 N THR A 82 27.065 54.575 6.550 1.00 14.71 N
+ATOM 643 CA THR A 82 27.980 55.227 7.505 1.00 18.33 C
+ATOM 644 C THR A 82 28.678 54.214 8.422 1.00 19.91 C
+ATOM 645 O THR A 82 29.841 54.412 8.805 1.00 19.40 O
+ATOM 646 CB THR A 82 27.335 56.325 8.359 1.00 16.68 C
+ATOM 647 OG1 THR A 82 26.292 55.847 9.185 1.00 18.54 O
+ATOM 648 CG2 THR A 82 26.849 57.480 7.498 1.00 16.27 C
+ATOM 649 N GLU A 83 28.048 53.063 8.588 1.00 21.58 N
+ATOM 650 CA GLU A 83 28.658 51.958 9.340 1.00 25.23 C
+ATOM 651 C GLU A 83 29.713 51.272 8.482 1.00 24.69 C
+ATOM 652 O GLU A 83 30.819 51.012 8.961 1.00 23.50 O
+ATOM 653 CB GLU A 83 27.568 50.963 9.751 1.00 27.95 C
+ATOM 654 CG GLU A 83 28.084 49.713 10.444 1.00 33.90 C
+ATOM 655 CD GLU A 83 26.905 48.776 10.709 1.00 38.78 C
+ATOM 656 OE1 GLU A 83 26.519 48.018 9.785 1.00 40.54 O
+ATOM 657 OE2 GLU A 83 26.371 48.884 11.836 1.00 41.13 O
+ATOM 658 N ALA A 84 29.419 50.976 7.208 1.00 20.78 N
+ATOM 659 CA ALA A 84 30.450 50.419 6.330 1.00 19.99 C
+ATOM 660 C ALA A 84 31.664 51.318 6.205 1.00 20.70 C
+ATOM 661 O ALA A 84 32.793 50.773 6.143 1.00 22.41 O
+ATOM 662 CB ALA A 84 29.839 50.024 4.963 1.00 18.65 C
+ATOM 663 N LEU A 85 31.571 52.650 6.272 1.00 18.54 N
+ATOM 664 CA LEU A 85 32.699 53.528 6.145 1.00 19.39 C
+ATOM 665 C LEU A 85 33.261 53.914 7.518 1.00 19.27 C
+ATOM 666 O LEU A 85 34.291 54.579 7.531 1.00 21.45 O
+ATOM 667 CB LEU A 85 32.306 54.856 5.426 1.00 20.66 C
+ATOM 668 CG LEU A 85 31.663 54.697 4.046 1.00 23.58 C
+ATOM 669 CD1 LEU A 85 31.411 56.053 3.395 1.00 24.14 C
+ATOM 670 CD2 LEU A 85 32.588 53.894 3.145 1.00 23.29 C
+ATOM 671 N ASP A 86 32.514 53.615 8.539 1.00 20.86 N
+ATOM 672 CA ASP A 86 32.806 53.988 9.929 1.00 23.39 C
+ATOM 673 C ASP A 86 33.019 55.472 10.098 1.00 22.50 C
+ATOM 674 O ASP A 86 34.055 55.964 10.581 1.00 20.76 O
+ATOM 675 CB ASP A 86 34.038 53.213 10.432 1.00 26.61 C
+ATOM 676 CG ASP A 86 34.220 53.280 11.931 1.00 31.20 C
+ATOM 677 OD1 ASP A 86 33.267 53.429 12.719 1.00 29.69 O
+ATOM 678 OD2 ASP A 86 35.409 53.170 12.353 1.00 33.56 O
+ATOM 679 N LEU A 87 32.008 56.260 9.689 1.00 19.97 N
+ATOM 680 CA LEU A 87 32.208 57.705 9.781 1.00 19.09 C
+ATOM 681 C LEU A 87 31.999 58.169 11.221 1.00 19.84 C
+ATOM 682 O LEU A 87 31.084 57.671 11.897 1.00 19.74 O
+ATOM 683 CB LEU A 87 31.177 58.411 8.887 1.00 18.71 C
+ATOM 684 CG LEU A 87 31.249 58.071 7.387 1.00 19.32 C
+ATOM 685 CD1 LEU A 87 30.308 59.050 6.653 1.00 19.65 C
+ATOM 686 CD2 LEU A 87 32.639 58.230 6.800 1.00 19.00 C
+ATOM 687 N ARG A 88 32.733 59.164 11.620 1.00 19.63 N
+ATOM 688 CA ARG A 88 32.583 59.767 12.939 1.00 23.48 C
+ATOM 689 C ARG A 88 32.615 61.266 12.788 1.00 20.52 C
+ATOM 690 O ARG A 88 33.367 61.762 11.941 1.00 21.55 O
+ATOM 691 CB ARG A 88 33.748 59.318 13.859 1.00 25.09 C
+ATOM 692 CG ARG A 88 33.681 57.870 14.334 1.00 30.33 C
+ATOM 693 CD ARG A 88 32.394 57.510 15.074 1.00 34.04 C
+ATOM 694 NE ARG A 88 32.267 56.084 15.232 1.00 38.78 N
+ATOM 695 CZ ARG A 88 31.458 55.214 15.805 1.00 40.77 C
+ATOM 696 NH1 ARG A 88 30.364 55.549 16.484 1.00 40.44 N
+ATOM 697 NH2 ARG A 88 31.729 53.897 15.680 1.00 42.08 N
+ATOM 698 N GLY A 89 31.834 62.045 13.514 1.00 20.15 N
+ATOM 699 CA GLY A 89 31.858 63.465 13.455 1.00 17.54 C
+ATOM 700 C GLY A 89 31.500 64.049 12.081 1.00 18.79 C
+ATOM 701 O GLY A 89 32.003 65.107 11.684 1.00 16.87 O
+ATOM 702 N ALA A 90 30.643 63.348 11.355 1.00 17.83 N
+ATOM 703 CA ALA A 90 30.297 63.763 10.001 1.00 15.52 C
+ATOM 704 C ALA A 90 29.336 64.899 9.940 1.00 16.33 C
+ATOM 705 O ALA A 90 28.558 65.115 10.883 1.00 16.82 O
+ATOM 706 CB ALA A 90 29.561 62.547 9.393 1.00 17.00 C
+ATOM 707 N VAL A 91 29.393 65.720 8.871 1.00 13.67 N
+ATOM 708 CA VAL A 91 28.366 66.742 8.683 1.00 13.22 C
+ATOM 709 C VAL A 91 27.402 66.248 7.590 1.00 15.06 C
+ATOM 710 O VAL A 91 27.920 65.809 6.536 1.00 16.66 O
+ATOM 711 CB VAL A 91 28.974 68.075 8.297 1.00 16.04 C
+ATOM 712 CG1 VAL A 91 27.865 69.095 8.026 1.00 17.56 C
+ATOM 713 CG2 VAL A 91 29.861 68.570 9.447 1.00 16.48 C
+ATOM 714 N HIS A 92 26.113 66.229 7.807 1.00 11.63 N
+ATOM 715 CA HIS A 92 25.144 65.719 6.845 1.00 12.18 C
+ATOM 716 C HIS A 92 24.390 66.886 6.224 1.00 14.67 C
+ATOM 717 O HIS A 92 23.679 67.641 6.923 1.00 16.35 O
+ATOM 718 CB HIS A 92 24.212 64.719 7.527 1.00 12.33 C
+ATOM 719 CG HIS A 92 24.897 63.407 7.758 1.00 12.93 C
+ATOM 720 ND1 HIS A 92 24.708 62.309 6.964 1.00 12.24 N
+ATOM 721 CD2 HIS A 92 25.856 63.057 8.714 1.00 12.63 C
+ATOM 722 CE1 HIS A 92 25.485 61.284 7.376 1.00 13.63 C
+ATOM 723 NE2 HIS A 92 26.187 61.759 8.423 1.00 13.06 N
+ATOM 724 N ILE A 93 24.414 66.994 4.881 1.00 11.18 N
+ATOM 725 CA ILE A 93 23.709 68.114 4.203 1.00 9.98 C
+ATOM 726 C ILE A 93 22.616 67.515 3.326 1.00 11.23 C
+ATOM 727 O ILE A 93 22.892 66.634 2.469 1.00 10.49 O
+ATOM 728 CB ILE A 93 24.745 68.932 3.406 1.00 13.14 C
+ATOM 729 CG1 ILE A 93 25.852 69.482 4.320 1.00 14.06 C
+ATOM 730 CG2 ILE A 93 24.042 70.097 2.677 1.00 14.50 C
+ATOM 731 CD1 ILE A 93 26.903 70.365 3.678 1.00 15.40 C
+ATOM 732 N GLY A 94 21.366 67.912 3.536 1.00 10.62 N
+ATOM 733 CA GLY A 94 20.292 67.240 2.765 1.00 12.88 C
+ATOM 734 C GLY A 94 19.501 68.350 2.052 1.00 16.16 C
+ATOM 735 O GLY A 94 19.190 69.361 2.686 1.00 15.14 O
+ATOM 736 N HIS A 95 19.136 68.044 0.795 1.00 13.09 N
+ATOM 737 CA HIS A 95 18.354 69.000 0.020 1.00 13.32 C
+ATOM 738 C HIS A 95 17.014 68.337 -0.282 1.00 12.35 C
+ATOM 739 O HIS A 95 16.868 67.134 -0.584 1.00 11.34 O
+ATOM 740 CB HIS A 95 19.055 69.391 -1.297 1.00 15.02 C
+ATOM 741 CG HIS A 95 18.167 70.144 -2.238 1.00 16.82 C
+ATOM 742 ND1 HIS A 95 17.703 69.564 -3.414 1.00 17.88 N
+ATOM 743 CD2 HIS A 95 17.651 71.394 -2.174 1.00 14.59 C
+ATOM 744 CE1 HIS A 95 16.917 70.432 -4.040 1.00 18.81 C
+ATOM 745 NE2 HIS A 95 16.871 71.550 -3.318 1.00 17.88 N
+ATOM 746 N SER A 96 15.998 69.172 -0.067 1.00 14.04 N
+ATOM 747 CA SER A 96 14.618 68.802 -0.390 1.00 15.68 C
+ATOM 748 C SER A 96 14.201 67.538 0.301 1.00 14.88 C
+ATOM 749 O SER A 96 14.305 67.430 1.548 1.00 15.16 O
+ATOM 750 CB SER A 96 14.612 68.763 -1.957 1.00 15.50 C
+ATOM 751 OG SER A 96 13.280 68.544 -2.353 1.00 18.71 O
+ATOM 752 N THR A 97 13.778 66.487 -0.386 1.00 15.07 N
+ATOM 753 CA THR A 97 13.509 65.168 0.216 1.00 14.67 C
+ATOM 754 C THR A 97 14.711 64.635 0.982 1.00 15.48 C
+ATOM 755 O THR A 97 14.515 63.911 1.974 1.00 13.67 O
+ATOM 756 CB THR A 97 13.245 64.127 -0.904 1.00 15.45 C
+ATOM 757 OG1 THR A 97 11.997 64.541 -1.527 1.00 18.38 O
+ATOM 758 CG2 THR A 97 13.111 62.695 -0.449 1.00 15.51 C
+ATOM 759 N GLY A 98 15.948 64.972 0.540 1.00 12.55 N
+ATOM 760 CA GLY A 98 17.127 64.504 1.268 1.00 13.01 C
+ATOM 761 C GLY A 98 17.175 65.171 2.668 1.00 13.48 C
+ATOM 762 O GLY A 98 17.769 64.575 3.564 1.00 13.47 O
+ATOM 763 N GLY A 99 16.551 66.331 2.823 1.00 11.31 N
+ATOM 764 CA GLY A 99 16.509 66.993 4.126 1.00 12.15 C
+ATOM 765 C GLY A 99 15.628 66.175 5.084 1.00 14.00 C
+ATOM 766 O GLY A 99 16.046 66.003 6.243 1.00 17.52 O
+ATOM 767 N GLY A 100 14.603 65.494 4.591 1.00 12.96 N
+ATOM 768 CA GLY A 100 13.783 64.630 5.428 1.00 13.74 C
+ATOM 769 C GLY A 100 14.562 63.397 5.850 1.00 16.67 C
+ATOM 770 O GLY A 100 14.514 62.950 7.015 1.00 12.89 O
+ATOM 771 N GLU A 101 15.294 62.790 4.888 1.00 11.79 N
+ATOM 772 CA GLU A 101 16.136 61.641 5.177 1.00 12.41 C
+ATOM 773 C GLU A 101 17.190 62.010 6.223 1.00 11.59 C
+ATOM 774 O GLU A 101 17.465 61.163 7.080 1.00 13.66 O
+ATOM 775 CB GLU A 101 16.845 61.224 3.872 1.00 11.32 C
+ATOM 776 CG GLU A 101 17.903 60.135 3.989 1.00 12.29 C
+ATOM 777 CD GLU A 101 18.353 59.709 2.596 1.00 11.09 C
+ATOM 778 OE1 GLU A 101 17.684 58.906 1.932 1.00 12.25 O
+ATOM 779 OE2 GLU A 101 19.368 60.280 2.164 1.00 11.73 O
+ATOM 780 N VAL A 102 17.798 63.183 6.104 1.00 12.63 N
+ATOM 781 CA VAL A 102 18.799 63.629 7.065 1.00 14.35 C
+ATOM 782 C VAL A 102 18.122 63.741 8.461 1.00 16.40 C
+ATOM 783 O VAL A 102 18.707 63.289 9.448 1.00 17.06 O
+ATOM 784 CB VAL A 102 19.464 64.953 6.700 1.00 13.42 C
+ATOM 785 CG1 VAL A 102 20.226 65.622 7.859 1.00 14.21 C
+ATOM 786 CG2 VAL A 102 20.515 64.672 5.568 1.00 13.88 C
+ATOM 787 N ALA A 103 16.983 64.407 8.540 1.00 14.66 N
+ATOM 788 CA ALA A 103 16.350 64.567 9.878 1.00 16.92 C
+ATOM 789 C ALA A 103 16.100 63.217 10.552 1.00 18.96 C
+ATOM 790 O ALA A 103 16.526 63.086 11.728 1.00 19.92 O
+ATOM 791 CB ALA A 103 15.035 65.312 9.745 1.00 13.74 C
+ATOM 792 N ARG A 104 15.546 62.223 9.872 1.00 16.46 N
+ATOM 793 CA ARG A 104 15.300 60.914 10.427 1.00 18.30 C
+ATOM 794 C ARG A 104 16.570 60.126 10.722 1.00 20.67 C
+ATOM 795 O ARG A 104 16.637 59.523 11.812 1.00 21.85 O
+ATOM 796 CB ARG A 104 14.374 60.048 9.567 1.00 18.66 C
+ATOM 797 CG ARG A 104 14.049 58.698 10.193 1.00 20.98 C
+ATOM 798 CD ARG A 104 12.603 58.316 10.017 1.00 21.99 C
+ATOM 799 NE ARG A 104 11.671 59.387 10.338 1.00 22.40 N
+ATOM 800 CZ ARG A 104 10.379 59.279 10.084 1.00 22.61 C
+ATOM 801 NH1 ARG A 104 9.932 58.170 9.524 1.00 24.41 N
+ATOM 802 NH2 ARG A 104 9.556 60.253 10.423 1.00 21.87 N
+ATOM 803 N TYR A 105 17.603 60.158 9.873 1.00 16.74 N
+ATOM 804 CA TYR A 105 18.826 59.467 10.174 1.00 17.07 C
+ATOM 805 C TYR A 105 19.526 60.064 11.388 1.00 17.78 C
+ATOM 806 O TYR A 105 20.034 59.322 12.264 1.00 19.08 O
+ATOM 807 CB TYR A 105 19.799 59.508 8.959 1.00 15.36 C
+ATOM 808 CG TYR A 105 21.215 59.137 9.390 1.00 15.12 C
+ATOM 809 CD1 TYR A 105 21.508 57.825 9.719 1.00 16.22 C
+ATOM 810 CD2 TYR A 105 22.214 60.067 9.473 1.00 15.78 C
+ATOM 811 CE1 TYR A 105 22.791 57.475 10.150 1.00 16.69 C
+ATOM 812 CE2 TYR A 105 23.511 59.756 9.850 1.00 13.42 C
+ATOM 813 CZ TYR A 105 23.779 58.438 10.170 1.00 16.63 C
+ATOM 814 OH TYR A 105 25.049 58.067 10.566 1.00 17.46 O
+ATOM 815 N VAL A 106 19.649 61.371 11.449 1.00 18.18 N
+ATOM 816 CA VAL A 106 20.361 62.081 12.506 1.00 20.66 C
+ATOM 817 C VAL A 106 19.665 61.827 13.838 1.00 22.94 C
+ATOM 818 O VAL A 106 20.336 61.536 14.817 1.00 23.69 O
+ATOM 819 CB VAL A 106 20.542 63.579 12.280 1.00 20.43 C
+ATOM 820 CG1 VAL A 106 21.154 64.247 13.510 1.00 21.56 C
+ATOM 821 CG2 VAL A 106 21.526 63.775 11.094 1.00 19.15 C
+ATOM 822 N ALA A 107 18.351 61.806 13.873 1.00 22.13 N
+ATOM 823 CA ALA A 107 17.619 61.540 15.127 1.00 24.16 C
+ATOM 824 C ALA A 107 17.904 60.150 15.661 1.00 24.09 C
+ATOM 825 O ALA A 107 17.879 59.949 16.878 1.00 26.11 O
+ATOM 826 CB ALA A 107 16.135 61.723 14.786 1.00 21.13 C
+ATOM 827 N ARG A 108 18.181 59.164 14.827 1.00 24.23 N
+ATOM 828 CA ARG A 108 18.403 57.793 15.229 1.00 27.39 C
+ATOM 829 C ARG A 108 19.857 57.319 15.183 1.00 24.90 C
+ATOM 830 O ARG A 108 20.095 56.113 15.363 1.00 23.81 O
+ATOM 831 CB ARG A 108 17.652 56.917 14.189 1.00 30.03 C
+ATOM 832 CG ARG A 108 16.143 56.892 14.376 1.00 35.83 C
+ATOM 833 CD ARG A 108 15.500 56.000 13.299 1.00 38.87 C
+ATOM 834 NE ARG A 108 14.064 56.229 13.238 1.00 41.87 N
+ATOM 835 CZ ARG A 108 13.112 55.774 12.436 1.00 43.22 C
+ATOM 836 NH1 ARG A 108 13.256 54.906 11.437 1.00 42.75 N
+ATOM 837 NH2 ARG A 108 11.866 56.217 12.661 1.00 44.61 N
+ATOM 838 N ALA A 109 20.781 58.196 14.821 1.00 21.52 N
+ATOM 839 CA ALA A 109 22.128 57.736 14.551 1.00 24.73 C
+ATOM 840 C ALA A 109 22.839 57.349 15.856 1.00 25.69 C
+ATOM 841 O ALA A 109 22.528 57.924 16.900 1.00 23.47 O
+ATOM 842 CB ALA A 109 22.905 58.824 13.831 1.00 23.45 C
+ATOM 843 N GLU A 110 23.769 56.423 15.755 1.00 28.23 N
+ATOM 844 CA GLU A 110 24.601 56.048 16.899 1.00 31.70 C
+ATOM 845 C GLU A 110 25.324 57.316 17.323 1.00 32.18 C
+ATOM 846 O GLU A 110 25.861 58.036 16.463 1.00 33.02 O
+ATOM 847 CB GLU A 110 25.691 55.061 16.459 1.00 35.35 C
+ATOM 848 CG GLU A 110 25.247 53.732 15.905 1.00 40.99 C
+ATOM 849 CD GLU A 110 26.474 52.906 15.518 1.00 45.41 C
+ATOM 850 OE1 GLU A 110 27.453 52.903 16.311 1.00 46.51 O
+ATOM 851 OE2 GLU A 110 26.437 52.312 14.415 1.00 47.09 O
+ATOM 852 N PRO A 111 25.385 57.628 18.593 1.00 32.76 N
+ATOM 853 CA PRO A 111 26.064 58.859 19.029 1.00 32.92 C
+ATOM 854 C PRO A 111 27.525 58.863 18.572 1.00 30.57 C
+ATOM 855 O PRO A 111 28.177 57.817 18.417 1.00 28.47 O
+ATOM 856 CB PRO A 111 25.832 58.843 20.542 1.00 35.07 C
+ATOM 857 CG PRO A 111 24.629 57.971 20.767 1.00 34.07 C
+ATOM 858 CD PRO A 111 24.754 56.872 19.718 1.00 33.77 C
+ATOM 859 N GLY A 112 28.067 60.009 18.191 1.00 30.19 N
+ATOM 860 CA GLY A 112 29.431 60.163 17.673 1.00 29.60 C
+ATOM 861 C GLY A 112 29.555 60.103 16.144 1.00 29.16 C
+ATOM 862 O GLY A 112 30.480 60.685 15.553 1.00 27.81 O
+ATOM 863 N ARG A 113 28.565 59.512 15.468 1.00 26.41 N
+ATOM 864 CA ARG A 113 28.576 59.431 14.025 1.00 26.06 C
+ATOM 865 C ARG A 113 28.300 60.801 13.383 1.00 23.47 C
+ATOM 866 O ARG A 113 28.790 61.008 12.289 1.00 21.34 O
+ATOM 867 CB ARG A 113 27.486 58.469 13.573 1.00 28.07 C
+ATOM 868 CG ARG A 113 27.700 57.000 13.894 1.00 28.06 C
+ATOM 869 CD ARG A 113 28.098 56.271 12.609 1.00 29.02 C
+ATOM 870 NE ARG A 113 28.332 54.847 12.862 1.00 30.94 N
+ATOM 871 CZ ARG A 113 29.542 54.292 12.942 1.00 31.35 C
+ATOM 872 NH1 ARG A 113 30.693 54.940 12.771 1.00 29.03 N
+ATOM 873 NH2 ARG A 113 29.575 52.980 13.180 1.00 31.95 N
+ATOM 874 N VAL A 114 27.489 61.652 14.010 1.00 19.46 N
+ATOM 875 CA VAL A 114 27.141 62.931 13.415 1.00 17.53 C
+ATOM 876 C VAL A 114 27.562 64.113 14.273 1.00 19.91 C
+ATOM 877 O VAL A 114 27.231 64.194 15.452 1.00 19.40 O
+ATOM 878 CB VAL A 114 25.604 63.059 13.247 1.00 15.39 C
+ATOM 879 CG1 VAL A 114 25.198 64.377 12.593 1.00 13.59 C
+ATOM 880 CG2 VAL A 114 25.068 61.889 12.413 1.00 14.34 C
+ATOM 881 N ALA A 115 28.163 65.123 13.644 1.00 16.23 N
+ATOM 882 CA ALA A 115 28.538 66.316 14.352 1.00 19.35 C
+ATOM 883 C ALA A 115 27.535 67.438 14.137 1.00 19.13 C
+ATOM 884 O ALA A 115 27.319 68.240 15.040 1.00 18.48 O
+ATOM 885 CB ALA A 115 29.903 66.879 13.936 1.00 19.47 C
+ATOM 886 N LYS A 116 27.083 67.657 12.889 1.00 19.00 N
+ATOM 887 CA LYS A 116 26.223 68.787 12.568 1.00 16.04 C
+ATOM 888 C LYS A 116 25.330 68.354 11.382 1.00 16.14 C
+ATOM 889 O LYS A 116 25.719 67.411 10.678 1.00 16.69 O
+ATOM 890 CB LYS A 116 27.043 69.958 12.040 1.00 20.65 C
+ATOM 891 CG LYS A 116 28.035 70.656 12.936 1.00 22.85 C
+ATOM 892 CD LYS A 116 28.758 71.804 12.264 1.00 25.09 C
+ATOM 893 CE LYS A 116 29.914 72.284 13.163 1.00 28.02 C
+ATOM 894 NZ LYS A 116 29.929 73.775 13.090 1.00 31.95 N
+ATOM 895 N ALA A 117 24.262 69.074 11.152 1.00 16.05 N
+ATOM 896 CA ALA A 117 23.399 68.717 10.002 1.00 15.76 C
+ATOM 897 C ALA A 117 22.900 69.977 9.336 1.00 16.26 C
+ATOM 898 O ALA A 117 22.890 71.045 9.959 1.00 15.86 O
+ATOM 899 CB ALA A 117 22.293 67.767 10.424 1.00 16.07 C
+ATOM 900 N VAL A 118 22.578 69.919 8.026 1.00 15.13 N
+ATOM 901 CA VAL A 118 22.140 71.108 7.298 1.00 13.37 C
+ATOM 902 C VAL A 118 20.890 70.657 6.530 1.00 15.18 C
+ATOM 903 O VAL A 118 20.919 69.584 5.885 1.00 15.17 O
+ATOM 904 CB VAL A 118 23.178 71.662 6.304 1.00 15.05 C
+ATOM 905 CG1 VAL A 118 22.614 72.842 5.495 1.00 14.19 C
+ATOM 906 CG2 VAL A 118 24.502 72.078 6.932 1.00 13.64 C
+ATOM 907 N LEU A 119 19.783 71.328 6.638 1.00 14.09 N
+ATOM 908 CA LEU A 119 18.560 71.101 5.910 1.00 15.14 C
+ATOM 909 C LEU A 119 18.329 72.253 4.919 1.00 15.74 C
+ATOM 910 O LEU A 119 18.074 73.387 5.312 1.00 19.06 O
+ATOM 911 CB LEU A 119 17.300 71.025 6.790 1.00 17.15 C
+ATOM 912 CG LEU A 119 17.423 70.088 8.009 1.00 21.07 C
+ATOM 913 CD1 LEU A 119 16.113 70.093 8.796 1.00 23.48 C
+ATOM 914 CD2 LEU A 119 17.921 68.706 7.682 1.00 19.76 C
+ATOM 915 N VAL A 120 18.545 71.997 3.640 1.00 16.09 N
+ATOM 916 CA VAL A 120 18.399 73.007 2.601 1.00 13.95 C
+ATOM 917 C VAL A 120 17.109 72.766 1.821 1.00 14.28 C
+ATOM 918 O VAL A 120 16.913 71.663 1.282 1.00 12.45 O
+ATOM 919 CB VAL A 120 19.578 72.966 1.595 1.00 16.45 C
+ATOM 920 CG1 VAL A 120 19.431 74.146 0.623 1.00 14.13 C
+ATOM 921 CG2 VAL A 120 20.958 72.961 2.231 1.00 14.24 C
+ATOM 922 N SER A 121 16.233 73.785 1.746 1.00 13.51 N
+ATOM 923 CA SER A 121 14.986 73.663 1.007 1.00 16.25 C
+ATOM 924 C SER A 121 14.283 72.381 1.389 1.00 15.98 C
+ATOM 925 O SER A 121 13.751 71.670 0.532 1.00 16.42 O
+ATOM 926 CB SER A 121 15.274 73.688 -0.529 1.00 15.59 C
+ATOM 927 OG SER A 121 16.228 74.729 -0.787 1.00 17.82 O
+ATOM 928 N ALA A 122 14.306 71.993 2.677 1.00 15.58 N
+ATOM 929 CA ALA A 122 13.901 70.673 3.083 1.00 13.61 C
+ATOM 930 C ALA A 122 12.438 70.544 3.422 1.00 15.75 C
+ATOM 931 O ALA A 122 11.781 71.492 3.836 1.00 15.81 O
+ATOM 932 CB ALA A 122 14.791 70.273 4.278 1.00 14.14 C
+ATOM 933 N VAL A 123 11.924 69.312 3.284 1.00 15.36 N
+ATOM 934 CA VAL A 123 10.527 69.027 3.512 1.00 18.14 C
+ATOM 935 C VAL A 123 9.974 69.164 4.923 1.00 19.99 C
+ATOM 936 O VAL A 123 8.776 69.479 5.035 1.00 21.14 O
+ATOM 937 CB VAL A 123 10.062 67.644 2.940 1.00 18.42 C
+ATOM 938 CG1 VAL A 123 10.238 67.646 1.421 1.00 19.16 C
+ATOM 939 CG2 VAL A 123 10.861 66.474 3.520 1.00 18.69 C
+ATOM 940 N PRO A 124 10.721 68.892 5.987 1.00 19.16 N
+ATOM 941 CA PRO A 124 10.182 69.032 7.342 1.00 20.59 C
+ATOM 942 C PRO A 124 9.628 70.397 7.654 1.00 20.01 C
+ATOM 943 O PRO A 124 10.109 71.434 7.171 1.00 22.48 O
+ATOM 944 CB PRO A 124 11.392 68.800 8.286 1.00 19.48 C
+ATOM 945 CG PRO A 124 12.323 67.936 7.435 1.00 19.07 C
+ATOM 946 CD PRO A 124 12.128 68.471 6.025 1.00 18.32 C
+ATOM 947 N PRO A 125 8.721 70.443 8.644 1.00 21.76 N
+ATOM 948 CA PRO A 125 8.219 69.310 9.380 1.00 20.46 C
+ATOM 949 C PRO A 125 7.308 68.302 8.697 1.00 20.38 C
+ATOM 950 O PRO A 125 7.375 67.082 8.880 1.00 18.46 O
+ATOM 951 CB PRO A 125 7.324 69.985 10.466 1.00 20.66 C
+ATOM 952 CG PRO A 125 7.877 71.352 10.605 1.00 22.04 C
+ATOM 953 CD PRO A 125 8.255 71.757 9.197 1.00 20.22 C
+ATOM 954 N VAL A 126 6.316 68.801 7.967 1.00 19.98 N
+ATOM 955 CA VAL A 126 5.353 68.009 7.227 1.00 21.55 C
+ATOM 956 C VAL A 126 4.727 68.878 6.123 1.00 22.41 C
+ATOM 957 O VAL A 126 4.335 70.045 6.330 1.00 22.55 O
+ATOM 958 CB VAL A 126 4.230 67.380 8.073 1.00 24.15 C
+ATOM 959 CG1 VAL A 126 3.540 68.441 8.942 1.00 24.05 C
+ATOM 960 CG2 VAL A 126 3.210 66.654 7.208 1.00 24.22 C
+ATOM 961 N MET A 127 4.625 68.324 4.915 1.00 20.38 N
+ATOM 962 CA MET A 127 4.112 69.139 3.815 1.00 21.43 C
+ATOM 963 C MET A 127 2.597 69.118 3.663 1.00 23.72 C
+ATOM 964 O MET A 127 2.009 70.163 3.364 1.00 25.21 O
+ATOM 965 CB MET A 127 4.718 68.684 2.467 1.00 22.06 C
+ATOM 966 CG MET A 127 6.210 69.033 2.339 1.00 23.44 C
+ATOM 967 SD MET A 127 6.785 68.631 0.633 1.00 23.31 S
+ATOM 968 CE MET A 127 6.062 69.979 -0.273 1.00 22.99 C
+ATOM 969 N VAL A 128 2.000 67.948 3.707 1.00 24.76 N
+ATOM 970 CA VAL A 128 0.589 67.847 3.367 1.00 26.65 C
+ATOM 971 C VAL A 128 -0.316 68.452 4.443 1.00 30.56 C
+ATOM 972 O VAL A 128 -0.016 68.420 5.630 1.00 28.24 O
+ATOM 973 CB VAL A 128 0.229 66.380 3.125 1.00 26.19 C
+ATOM 974 CG1 VAL A 128 0.157 65.553 4.402 1.00 25.58 C
+ATOM 975 CG2 VAL A 128 -1.079 66.284 2.332 1.00 26.20 C
+ATOM 976 N LYS A 129 -1.455 68.930 3.955 1.00 33.75 N
+ATOM 977 CA LYS A 129 -2.528 69.410 4.811 1.00 37.76 C
+ATOM 978 C LYS A 129 -3.114 68.230 5.578 1.00 38.61 C
+ATOM 979 O LYS A 129 -3.401 67.151 5.056 1.00 39.57 O
+ATOM 980 CB LYS A 129 -3.606 70.087 3.961 1.00 39.66 C
+ATOM 981 CG LYS A 129 -4.822 70.488 4.789 1.00 42.50 C
+ATOM 982 CD LYS A 129 -5.900 71.086 3.899 1.00 43.45 C
+ATOM 983 CE LYS A 129 -5.819 72.598 3.876 1.00 44.88 C
+ATOM 984 NZ LYS A 129 -5.178 73.126 2.641 1.00 45.64 N
+ATOM 985 N SER A 130 -3.283 68.410 6.883 1.00 38.84 N
+ATOM 986 CA SER A 130 -3.854 67.425 7.778 1.00 38.69 C
+ATOM 987 C SER A 130 -4.493 68.142 8.982 1.00 39.55 C
+ATOM 988 O SER A 130 -4.423 69.362 9.058 1.00 38.38 O
+ATOM 989 CB SER A 130 -2.760 66.504 8.347 1.00 37.38 C
+ATOM 990 OG SER A 130 -1.819 67.347 9.027 1.00 37.20 O
+ATOM 991 N ASP A 131 -4.953 67.365 9.948 1.00 43.09 N
+ATOM 992 CA ASP A 131 -5.550 67.875 11.165 1.00 47.90 C
+ATOM 993 C ASP A 131 -4.518 68.671 11.989 1.00 48.15 C
+ATOM 994 O ASP A 131 -4.889 69.577 12.705 1.00 47.07 O
+ATOM 995 CB ASP A 131 -6.077 66.856 12.146 1.00 49.76 C
+ATOM 996 CG ASP A 131 -6.898 65.680 11.761 1.00 53.37 C
+ATOM 997 OD1 ASP A 131 -8.018 65.812 11.202 1.00 54.42 O
+ATOM 998 OD2 ASP A 131 -6.379 64.566 12.083 1.00 55.34 O
+ATOM 999 N THR A 132 -3.268 68.235 11.891 1.00 50.01 N
+ATOM 1000 CA THR A 132 -2.186 68.888 12.615 1.00 50.68 C
+ATOM 1001 C THR A 132 -1.449 69.908 11.776 1.00 50.61 C
+ATOM 1002 O THR A 132 -0.586 70.594 12.349 1.00 52.20 O
+ATOM 1003 CB THR A 132 -1.238 67.812 13.162 1.00 52.11 C
+ATOM 1004 OG1 THR A 132 -0.694 67.033 12.076 1.00 54.39 O
+ATOM 1005 CG2 THR A 132 -1.995 66.843 14.062 1.00 52.04 C
+ATOM 1006 N ASN A 133 -1.786 70.083 10.503 1.00 48.26 N
+ATOM 1007 CA ASN A 133 -1.122 71.040 9.629 1.00 47.55 C
+ATOM 1008 C ASN A 133 -2.042 71.671 8.597 1.00 49.07 C
+ATOM 1009 O ASN A 133 -2.045 71.329 7.408 1.00 48.16 O
+ATOM 1010 CB ASN A 133 0.037 70.296 8.925 1.00 45.68 C
+ATOM 1011 CG ASN A 133 0.818 71.178 7.974 1.00 44.93 C
+ATOM 1012 OD1 ASN A 133 1.060 72.351 8.252 1.00 44.22 O
+ATOM 1013 ND2 ASN A 133 1.215 70.634 6.821 1.00 43.36 N
+ATOM 1014 N PRO A 134 -2.842 72.662 8.992 1.00 50.69 N
+ATOM 1015 CA PRO A 134 -3.792 73.363 8.147 1.00 50.45 C
+ATOM 1016 C PRO A 134 -3.214 74.285 7.093 1.00 50.20 C
+ATOM 1017 O PRO A 134 -3.880 74.595 6.098 1.00 50.56 O
+ATOM 1018 CB PRO A 134 -4.600 74.225 9.144 1.00 51.82 C
+ATOM 1019 CG PRO A 134 -3.567 74.517 10.205 1.00 52.01 C
+ATOM 1020 CD PRO A 134 -2.897 73.167 10.405 1.00 51.50 C
+ATOM 1021 N ASP A 135 -1.986 74.767 7.250 1.00 49.38 N
+ATOM 1022 CA ASP A 135 -1.376 75.621 6.231 1.00 49.28 C
+ATOM 1023 C ASP A 135 -0.669 74.792 5.163 1.00 46.05 C
+ATOM 1024 O ASP A 135 -0.143 75.332 4.189 1.00 46.07 O
+ATOM 1025 CB ASP A 135 -0.421 76.614 6.892 1.00 52.19 C
+ATOM 1026 CG ASP A 135 -1.096 77.685 7.735 1.00 55.03 C
+ATOM 1027 OD1 ASP A 135 -2.344 77.641 7.906 1.00 56.45 O
+ATOM 1028 OD2 ASP A 135 -0.377 78.592 8.231 1.00 55.00 O
+ATOM 1029 N GLY A 136 -0.638 73.472 5.304 1.00 43.89 N
+ATOM 1030 CA GLY A 136 0.011 72.587 4.340 1.00 40.79 C
+ATOM 1031 C GLY A 136 -0.607 72.638 2.949 1.00 39.43 C
+ATOM 1032 O GLY A 136 -1.544 73.385 2.650 1.00 39.15 O
+ATOM 1033 N LEU A 137 -0.041 71.877 2.008 1.00 35.97 N
+ATOM 1034 CA LEU A 137 -0.546 71.797 0.644 1.00 32.66 C
+ATOM 1035 C LEU A 137 -1.582 70.678 0.590 1.00 29.24 C
+ATOM 1036 O LEU A 137 -1.435 69.663 1.243 1.00 26.74 O
+ATOM 1037 CB LEU A 137 0.577 71.474 -0.348 1.00 32.81 C
+ATOM 1038 CG LEU A 137 1.599 72.592 -0.555 1.00 35.09 C
+ATOM 1039 CD1 LEU A 137 2.843 72.066 -1.253 1.00 34.97 C
+ATOM 1040 CD2 LEU A 137 0.972 73.766 -1.309 1.00 35.67 C
+ATOM 1041 N PRO A 138 -2.652 70.861 -0.170 1.00 29.45 N
+ATOM 1042 CA PRO A 138 -3.675 69.844 -0.304 1.00 30.23 C
+ATOM 1043 C PRO A 138 -3.107 68.606 -0.990 1.00 31.36 C
+ATOM 1044 O PRO A 138 -2.182 68.693 -1.822 1.00 32.13 O
+ATOM 1045 CB PRO A 138 -4.783 70.503 -1.102 1.00 29.06 C
+ATOM 1046 CG PRO A 138 -4.217 71.741 -1.663 1.00 30.42 C
+ATOM 1047 CD PRO A 138 -2.923 72.077 -0.982 1.00 29.28 C
+ATOM 1048 N LEU A 139 -3.672 67.458 -0.684 1.00 31.51 N
+ATOM 1049 CA LEU A 139 -3.265 66.176 -1.216 1.00 32.88 C
+ATOM 1050 C LEU A 139 -3.340 66.131 -2.741 1.00 31.99 C
+ATOM 1051 O LEU A 139 -2.504 65.504 -3.406 1.00 28.55 O
+ATOM 1052 CB LEU A 139 -4.092 65.037 -0.623 1.00 33.94 C
+ATOM 1053 CG LEU A 139 -3.372 63.699 -0.466 1.00 37.35 C
+ATOM 1054 CD1 LEU A 139 -3.117 63.063 -1.822 1.00 39.86 C
+ATOM 1055 CD2 LEU A 139 -2.017 63.789 0.231 1.00 37.96 C
+ATOM 1056 N GLU A 140 -4.318 66.831 -3.302 1.00 31.28 N
+ATOM 1057 CA GLU A 140 -4.527 66.920 -4.732 1.00 34.12 C
+ATOM 1058 C GLU A 140 -3.313 67.462 -5.475 1.00 31.45 C
+ATOM 1059 O GLU A 140 -3.031 67.028 -6.610 1.00 30.08 O
+ATOM 1060 CB GLU A 140 -5.794 67.732 -5.049 1.00 37.68 C
+ATOM 1061 CG GLU A 140 -6.040 68.878 -4.111 1.00 43.67 C
+ATOM 1062 CD GLU A 140 -7.019 68.713 -2.958 1.00 45.80 C
+ATOM 1063 OE1 GLU A 140 -7.115 67.641 -2.311 1.00 45.98 O
+ATOM 1064 OE2 GLU A 140 -7.718 69.740 -2.683 1.00 47.17 O
+ATOM 1065 N VAL A 141 -2.523 68.339 -4.866 1.00 28.37 N
+ATOM 1066 CA VAL A 141 -1.286 68.790 -5.493 1.00 27.33 C
+ATOM 1067 C VAL A 141 -0.410 67.546 -5.757 1.00 25.57 C
+ATOM 1068 O VAL A 141 0.194 67.413 -6.827 1.00 25.43 O
+ATOM 1069 CB VAL A 141 -0.540 69.789 -4.610 1.00 29.32 C
+ATOM 1070 CG1 VAL A 141 0.888 70.082 -5.057 1.00 29.44 C
+ATOM 1071 CG2 VAL A 141 -1.302 71.127 -4.543 1.00 31.16 C
+ATOM 1072 N PHE A 142 -0.337 66.631 -4.805 1.00 21.76 N
+ATOM 1073 CA PHE A 142 0.516 65.463 -4.882 1.00 21.71 C
+ATOM 1074 C PHE A 142 -0.097 64.394 -5.767 1.00 20.83 C
+ATOM 1075 O PHE A 142 0.623 63.660 -6.423 1.00 19.11 O
+ATOM 1076 CB PHE A 142 0.877 64.900 -3.471 1.00 20.89 C
+ATOM 1077 CG PHE A 142 1.543 66.015 -2.693 1.00 20.73 C
+ATOM 1078 CD1 PHE A 142 2.757 66.537 -3.093 1.00 20.49 C
+ATOM 1079 CD2 PHE A 142 0.877 66.575 -1.607 1.00 20.60 C
+ATOM 1080 CE1 PHE A 142 3.325 67.590 -2.410 1.00 22.14 C
+ATOM 1081 CE2 PHE A 142 1.453 67.642 -0.942 1.00 22.34 C
+ATOM 1082 CZ PHE A 142 2.686 68.155 -1.324 1.00 20.93 C
+ATOM 1083 N ASP A 143 -1.417 64.311 -5.833 1.00 22.05 N
+ATOM 1084 CA ASP A 143 -2.112 63.389 -6.697 1.00 22.94 C
+ATOM 1085 C ASP A 143 -1.835 63.782 -8.163 1.00 22.41 C
+ATOM 1086 O ASP A 143 -1.703 62.840 -8.927 1.00 23.26 O
+ATOM 1087 CB ASP A 143 -3.619 63.441 -6.447 1.00 27.10 C
+ATOM 1088 CG ASP A 143 -4.051 62.727 -5.176 1.00 29.44 C
+ATOM 1089 OD1 ASP A 143 -3.371 61.870 -4.594 1.00 29.15 O
+ATOM 1090 OD2 ASP A 143 -5.176 63.078 -4.763 1.00 31.30 O
+ATOM 1091 N GLU A 144 -1.766 65.045 -8.493 1.00 21.73 N
+ATOM 1092 CA GLU A 144 -1.374 65.485 -9.837 1.00 25.52 C
+ATOM 1093 C GLU A 144 0.040 65.073 -10.232 1.00 24.13 C
+ATOM 1094 O GLU A 144 0.208 64.690 -11.388 1.00 22.40 O
+ATOM 1095 CB GLU A 144 -1.421 67.006 -10.030 1.00 28.14 C
+ATOM 1096 CG GLU A 144 -2.869 67.480 -10.020 1.00 36.33 C
+ATOM 1097 CD GLU A 144 -3.033 68.985 -10.091 1.00 40.88 C
+ATOM 1098 OE1 GLU A 144 -2.047 69.768 -9.974 1.00 42.24 O
+ATOM 1099 OE2 GLU A 144 -4.217 69.376 -10.273 1.00 44.88 O
+ATOM 1100 N PHE A 145 1.036 65.242 -9.360 1.00 22.28 N
+ATOM 1101 CA PHE A 145 2.390 64.743 -9.629 1.00 20.58 C
+ATOM 1102 C PHE A 145 2.385 63.240 -9.889 1.00 18.51 C
+ATOM 1103 O PHE A 145 2.992 62.744 -10.867 1.00 19.78 O
+ATOM 1104 CB PHE A 145 3.316 64.959 -8.436 1.00 22.71 C
+ATOM 1105 CG PHE A 145 3.666 66.343 -8.007 1.00 26.44 C
+ATOM 1106 CD1 PHE A 145 3.575 67.430 -8.857 1.00 27.94 C
+ATOM 1107 CD2 PHE A 145 4.064 66.546 -6.686 1.00 28.67 C
+ATOM 1108 CE1 PHE A 145 3.895 68.699 -8.438 1.00 30.51 C
+ATOM 1109 CE2 PHE A 145 4.391 67.832 -6.253 1.00 31.78 C
+ATOM 1110 CZ PHE A 145 4.318 68.909 -7.123 1.00 31.64 C
+ATOM 1111 N ARG A 146 1.749 62.471 -8.993 1.00 14.95 N
+ATOM 1112 CA ARG A 146 1.594 61.053 -9.210 1.00 16.50 C
+ATOM 1113 C ARG A 146 1.000 60.747 -10.594 1.00 16.19 C
+ATOM 1114 O ARG A 146 1.537 59.853 -11.263 1.00 16.94 O
+ATOM 1115 CB ARG A 146 0.712 60.363 -8.159 1.00 15.44 C
+ATOM 1116 CG ARG A 146 1.448 59.903 -6.913 1.00 18.49 C
+ATOM 1117 CD ARG A 146 0.522 59.214 -5.904 1.00 19.25 C
+ATOM 1118 NE ARG A 146 -0.263 60.147 -5.116 1.00 18.99 N
+ATOM 1119 CZ ARG A 146 0.162 60.845 -4.055 1.00 22.00 C
+ATOM 1120 NH1 ARG A 146 1.417 60.708 -3.589 1.00 20.74 N
+ATOM 1121 NH2 ARG A 146 -0.666 61.682 -3.424 1.00 19.74 N
+ATOM 1122 N ALA A 147 -0.108 61.405 -10.930 1.00 15.41 N
+ATOM 1123 CA ALA A 147 -0.742 61.068 -12.224 1.00 16.02 C
+ATOM 1124 C ALA A 147 0.098 61.494 -13.424 1.00 15.60 C
+ATOM 1125 O ALA A 147 0.205 60.731 -14.389 1.00 15.55 O
+ATOM 1126 CB ALA A 147 -2.112 61.756 -12.317 1.00 17.78 C
+ATOM 1127 N ALA A 148 0.745 62.663 -13.374 1.00 13.66 N
+ATOM 1128 CA ALA A 148 1.608 63.038 -14.492 1.00 13.34 C
+ATOM 1129 C ALA A 148 2.797 62.104 -14.625 1.00 15.15 C
+ATOM 1130 O ALA A 148 3.231 61.756 -15.756 1.00 14.91 O
+ATOM 1131 CB ALA A 148 2.058 64.486 -14.318 1.00 14.20 C
+ATOM 1132 N LEU A 149 3.391 61.691 -13.481 1.00 14.37 N
+ATOM 1133 CA LEU A 149 4.554 60.815 -13.474 1.00 15.07 C
+ATOM 1134 C LEU A 149 4.182 59.482 -14.107 1.00 16.23 C
+ATOM 1135 O LEU A 149 4.885 58.970 -14.955 1.00 15.81 O
+ATOM 1136 CB LEU A 149 5.075 60.558 -12.059 1.00 16.20 C
+ATOM 1137 CG LEU A 149 6.412 59.846 -11.889 1.00 18.76 C
+ATOM 1138 CD1 LEU A 149 7.086 60.354 -10.615 1.00 17.72 C
+ATOM 1139 CD2 LEU A 149 6.246 58.348 -11.940 1.00 17.67 C
+ATOM 1140 N ALA A 150 3.075 58.893 -13.651 1.00 15.42 N
+ATOM 1141 CA ALA A 150 2.615 57.620 -14.189 1.00 15.16 C
+ATOM 1142 C ALA A 150 2.230 57.738 -15.673 1.00 13.78 C
+ATOM 1143 O ALA A 150 2.514 56.789 -16.397 1.00 19.26 O
+ATOM 1144 CB ALA A 150 1.364 57.251 -13.386 1.00 16.42 C
+ATOM 1145 N ALA A 151 1.636 58.823 -16.125 1.00 13.40 N
+ATOM 1146 CA ALA A 151 1.186 58.908 -17.525 1.00 15.13 C
+ATOM 1147 C ALA A 151 2.360 59.061 -18.521 1.00 15.01 C
+ATOM 1148 O ALA A 151 2.327 58.380 -19.543 1.00 17.01 O
+ATOM 1149 CB ALA A 151 0.202 60.066 -17.659 1.00 16.40 C
+ATOM 1150 N ASN A 152 3.331 59.915 -18.248 1.00 12.29 N
+ATOM 1151 CA ASN A 152 4.439 60.148 -19.182 1.00 13.18 C
+ATOM 1152 C ASN A 152 5.573 60.722 -18.357 1.00 10.57 C
+ATOM 1153 O ASN A 152 5.726 61.921 -18.232 1.00 11.29 O
+ATOM 1154 CB ASN A 152 3.982 61.130 -20.277 1.00 14.78 C
+ATOM 1155 CG ASN A 152 5.036 61.288 -21.358 1.00 16.16 C
+ATOM 1156 OD1 ASN A 152 6.178 60.853 -21.145 1.00 12.66 O
+ATOM 1157 ND2 ASN A 152 4.588 61.815 -22.497 1.00 15.63 N
+ATOM 1158 N ARG A 153 6.332 59.814 -17.706 1.00 9.65 N
+ATOM 1159 CA ARG A 153 7.398 60.294 -16.812 1.00 9.45 C
+ATOM 1160 C ARG A 153 8.406 61.123 -17.576 1.00 10.07 C
+ATOM 1161 O ARG A 153 8.902 62.130 -17.059 1.00 9.84 O
+ATOM 1162 CB ARG A 153 8.047 59.062 -16.122 1.00 9.95 C
+ATOM 1163 CG ARG A 153 9.129 59.432 -15.113 1.00 11.95 C
+ATOM 1164 CD ARG A 153 9.551 58.224 -14.256 1.00 13.02 C
+ATOM 1165 NE ARG A 153 10.347 57.245 -14.983 1.00 10.42 N
+ATOM 1166 CZ ARG A 153 11.605 56.976 -14.698 1.00 12.00 C
+ATOM 1167 NH1 ARG A 153 12.210 57.583 -13.658 1.00 11.11 N
+ATOM 1168 NH2 ARG A 153 12.259 56.076 -15.418 1.00 11.45 N
+ATOM 1169 N ALA A 154 8.807 60.640 -18.788 1.00 9.44 N
+ATOM 1170 CA ALA A 154 9.789 61.415 -19.576 1.00 9.28 C
+ATOM 1171 C ALA A 154 9.390 62.843 -19.851 1.00 8.79 C
+ATOM 1172 O ALA A 154 10.271 63.686 -19.920 1.00 9.13 O
+ATOM 1173 CB ALA A 154 10.040 60.700 -20.903 1.00 9.50 C
+ATOM 1174 N GLN A 155 8.137 63.191 -20.063 1.00 9.37 N
+ATOM 1175 CA GLN A 155 7.712 64.565 -20.311 1.00 10.37 C
+ATOM 1176 C GLN A 155 7.519 65.339 -19.000 1.00 9.78 C
+ATOM 1177 O GLN A 155 7.921 66.483 -18.873 1.00 11.62 O
+ATOM 1178 CB GLN A 155 6.341 64.590 -21.027 1.00 10.74 C
+ATOM 1179 CG GLN A 155 5.909 66.003 -21.439 1.00 9.94 C
+ATOM 1180 CD GLN A 155 6.902 66.609 -22.400 1.00 11.90 C
+ATOM 1181 OE1 GLN A 155 7.337 65.974 -23.381 1.00 14.39 O
+ATOM 1182 NE2 GLN A 155 7.351 67.806 -22.090 1.00 12.98 N
+ATOM 1183 N PHE A 156 7.013 64.634 -17.972 1.00 10.53 N
+ATOM 1184 CA PHE A 156 6.839 65.277 -16.659 1.00 11.74 C
+ATOM 1185 C PHE A 156 8.203 65.727 -16.154 1.00 9.48 C
+ATOM 1186 O PHE A 156 8.397 66.768 -15.554 1.00 10.94 O
+ATOM 1187 CB PHE A 156 6.256 64.245 -15.646 1.00 12.12 C
+ATOM 1188 CG PHE A 156 6.000 64.794 -14.241 1.00 13.48 C
+ATOM 1189 CD1 PHE A 156 5.211 65.908 -14.082 1.00 13.11 C
+ATOM 1190 CD2 PHE A 156 6.477 64.155 -13.111 1.00 15.50 C
+ATOM 1191 CE1 PHE A 156 4.970 66.445 -12.813 1.00 15.16 C
+ATOM 1192 CE2 PHE A 156 6.204 64.647 -11.834 1.00 13.39 C
+ATOM 1193 CZ PHE A 156 5.465 65.796 -11.690 1.00 13.21 C
+ATOM 1194 N TYR A 157 9.294 64.964 -16.487 1.00 9.39 N
+ATOM 1195 CA TYR A 157 10.626 65.323 -15.969 1.00 8.62 C
+ATOM 1196 C TYR A 157 11.296 66.373 -16.831 1.00 10.81 C
+ATOM 1197 O TYR A 157 12.368 66.844 -16.467 1.00 9.98 O
+ATOM 1198 CB TYR A 157 11.523 64.093 -15.831 1.00 8.88 C
+ATOM 1199 CG TYR A 157 11.170 63.193 -14.660 1.00 10.44 C
+ATOM 1200 CD1 TYR A 157 10.110 63.418 -13.807 1.00 11.47 C
+ATOM 1201 CD2 TYR A 157 12.026 62.108 -14.415 1.00 11.17 C
+ATOM 1202 CE1 TYR A 157 9.883 62.572 -12.727 1.00 12.14 C
+ATOM 1203 CE2 TYR A 157 11.781 61.252 -13.378 1.00 12.49 C
+ATOM 1204 CZ TYR A 157 10.724 61.517 -12.513 1.00 13.38 C
+ATOM 1205 OH TYR A 157 10.501 60.602 -11.501 1.00 13.61 O
+ATOM 1206 N ILE A 158 10.671 66.837 -17.923 1.00 11.10 N
+ATOM 1207 CA ILE A 158 11.089 68.071 -18.598 1.00 12.31 C
+ATOM 1208 C ILE A 158 10.292 69.254 -17.938 1.00 11.59 C
+ATOM 1209 O ILE A 158 10.835 70.306 -17.575 1.00 11.49 O
+ATOM 1210 CB ILE A 158 10.750 68.081 -20.098 1.00 14.66 C
+ATOM 1211 CG1 ILE A 158 11.572 66.972 -20.802 1.00 15.74 C
+ATOM 1212 CG2 ILE A 158 10.961 69.479 -20.712 1.00 14.05 C
+ATOM 1213 CD1 ILE A 158 11.294 66.947 -22.300 1.00 13.62 C
+ATOM 1214 N ASP A 159 9.015 69.001 -17.726 1.00 11.12 N
+ATOM 1215 CA ASP A 159 8.133 70.029 -17.174 1.00 14.77 C
+ATOM 1216 C ASP A 159 8.546 70.562 -15.812 1.00 14.63 C
+ATOM 1217 O ASP A 159 8.522 71.789 -15.625 1.00 14.25 O
+ATOM 1218 CB ASP A 159 6.680 69.568 -17.124 1.00 16.02 C
+ATOM 1219 CG ASP A 159 6.089 69.272 -18.514 1.00 18.51 C
+ATOM 1220 OD1 ASP A 159 6.635 69.648 -19.554 1.00 16.93 O
+ATOM 1221 OD2 ASP A 159 5.053 68.602 -18.482 1.00 21.22 O
+ATOM 1222 N VAL A 160 8.925 69.692 -14.850 1.00 12.85 N
+ATOM 1223 CA VAL A 160 9.310 70.214 -13.540 1.00 11.22 C
+ATOM 1224 C VAL A 160 10.503 71.122 -13.472 1.00 12.66 C
+ATOM 1225 O VAL A 160 10.469 72.246 -12.937 1.00 13.19 O
+ATOM 1226 CB VAL A 160 9.428 68.997 -12.593 1.00 11.11 C
+ATOM 1227 CG1 VAL A 160 9.929 69.425 -11.226 1.00 11.13 C
+ATOM 1228 CG2 VAL A 160 8.091 68.302 -12.477 1.00 11.30 C
+ATOM 1229 N PRO A 161 11.685 70.742 -14.006 1.00 12.43 N
+ATOM 1230 CA PRO A 161 12.865 71.568 -14.015 1.00 9.91 C
+ATOM 1231 C PRO A 161 12.738 72.752 -14.967 1.00 11.78 C
+ATOM 1232 O PRO A 161 13.416 73.744 -14.772 1.00 12.50 O
+ATOM 1233 CB PRO A 161 13.986 70.622 -14.404 1.00 11.67 C
+ATOM 1234 CG PRO A 161 13.286 69.625 -15.276 1.00 11.08 C
+ATOM 1235 CD PRO A 161 11.920 69.391 -14.600 1.00 11.57 C
+ATOM 1236 N SER A 162 11.928 72.722 -16.013 1.00 14.47 N
+ATOM 1237 CA SER A 162 11.728 73.853 -16.910 1.00 15.87 C
+ATOM 1238 C SER A 162 10.859 74.906 -16.214 1.00 16.10 C
+ATOM 1239 O SER A 162 10.962 76.062 -16.524 1.00 17.75 O
+ATOM 1240 CB SER A 162 10.907 73.440 -18.163 1.00 15.71 C
+ATOM 1241 OG SER A 162 11.778 72.620 -18.953 1.00 17.94 O
+ATOM 1242 N GLY A 163 10.051 74.517 -15.251 1.00 16.08 N
+ATOM 1243 CA GLY A 163 9.114 75.422 -14.610 1.00 15.70 C
+ATOM 1244 C GLY A 163 9.439 75.796 -13.184 1.00 13.60 C
+ATOM 1245 O GLY A 163 10.290 76.646 -12.907 1.00 17.17 O
+ATOM 1246 N PRO A 164 8.868 75.092 -12.239 1.00 13.87 N
+ATOM 1247 CA PRO A 164 9.008 75.470 -10.837 1.00 16.88 C
+ATOM 1248 C PRO A 164 10.303 75.134 -10.124 1.00 15.68 C
+ATOM 1249 O PRO A 164 10.732 75.912 -9.280 1.00 18.25 O
+ATOM 1250 CB PRO A 164 7.861 74.726 -10.159 1.00 15.51 C
+ATOM 1251 CG PRO A 164 7.482 73.607 -11.078 1.00 16.56 C
+ATOM 1252 CD PRO A 164 7.838 74.033 -12.470 1.00 13.98 C
+ATOM 1253 N PHE A 165 10.976 74.030 -10.462 1.00 12.34 N
+ATOM 1254 CA PHE A 165 12.148 73.659 -9.622 1.00 10.59 C
+ATOM 1255 C PHE A 165 13.198 74.691 -9.452 1.00 12.15 C
+ATOM 1256 O PHE A 165 13.771 74.818 -8.345 1.00 11.34 O
+ATOM 1257 CB PHE A 165 12.687 72.322 -10.141 1.00 10.42 C
+ATOM 1258 CG PHE A 165 13.442 71.439 -9.175 1.00 11.90 C
+ATOM 1259 CD1 PHE A 165 14.778 71.695 -8.921 1.00 10.94 C
+ATOM 1260 CD2 PHE A 165 12.765 70.417 -8.530 1.00 10.90 C
+ATOM 1261 CE1 PHE A 165 15.483 70.894 -8.028 1.00 10.77 C
+ATOM 1262 CE2 PHE A 165 13.485 69.589 -7.619 1.00 11.84 C
+ATOM 1263 CZ PHE A 165 14.809 69.854 -7.408 1.00 10.14 C
+ATOM 1264 N TYR A 166 13.663 75.363 -10.531 1.00 10.46 N
+ATOM 1265 CA TYR A 166 14.773 76.252 -10.531 1.00 10.78 C
+ATOM 1266 C TYR A 166 14.304 77.687 -10.721 1.00 12.77 C
+ATOM 1267 O TYR A 166 15.122 78.569 -10.885 1.00 12.36 O
+ATOM 1268 CB TYR A 166 15.787 75.939 -11.692 1.00 11.17 C
+ATOM 1269 CG TYR A 166 16.528 74.625 -11.458 1.00 11.96 C
+ATOM 1270 CD1 TYR A 166 17.380 74.452 -10.368 1.00 9.60 C
+ATOM 1271 CD2 TYR A 166 16.345 73.558 -12.345 1.00 11.53 C
+ATOM 1272 CE1 TYR A 166 18.063 73.266 -10.197 1.00 11.76 C
+ATOM 1273 CE2 TYR A 166 17.009 72.369 -12.141 1.00 10.68 C
+ATOM 1274 CZ TYR A 166 17.843 72.214 -11.080 1.00 12.29 C
+ATOM 1275 OH TYR A 166 18.480 71.014 -10.899 1.00 12.68 O
+ATOM 1276 N GLY A 167 12.999 77.909 -10.657 1.00 15.04 N
+ATOM 1277 CA GLY A 167 12.464 79.276 -10.833 1.00 15.35 C
+ATOM 1278 C GLY A 167 12.686 79.797 -12.233 1.00 18.42 C
+ATOM 1279 O GLY A 167 12.609 81.029 -12.452 1.00 18.56 O
+ATOM 1280 N PHE A 168 12.913 78.946 -13.257 1.00 16.77 N
+ATOM 1281 CA PHE A 168 13.139 79.499 -14.597 1.00 17.30 C
+ATOM 1282 C PHE A 168 11.827 80.019 -15.198 1.00 18.88 C
+ATOM 1283 O PHE A 168 11.829 80.544 -16.321 1.00 20.43 O
+ATOM 1284 CB PHE A 168 13.741 78.420 -15.516 1.00 13.57 C
+ATOM 1285 CG PHE A 168 15.090 77.911 -15.125 1.00 12.80 C
+ATOM 1286 CD1 PHE A 168 15.968 78.689 -14.402 1.00 12.39 C
+ATOM 1287 CD2 PHE A 168 15.496 76.641 -15.519 1.00 13.54 C
+ATOM 1288 CE1 PHE A 168 17.235 78.262 -14.064 1.00 13.46 C
+ATOM 1289 CE2 PHE A 168 16.756 76.190 -15.161 1.00 13.74 C
+ATOM 1290 CZ PHE A 168 17.634 77.005 -14.447 1.00 15.04 C
+ATOM 1291 N ASN A 169 10.683 79.833 -14.579 1.00 19.48 N
+ATOM 1292 CA ASN A 169 9.430 80.400 -15.026 1.00 19.75 C
+ATOM 1293 C ASN A 169 9.268 81.820 -14.475 1.00 22.95 C
+ATOM 1294 O ASN A 169 8.198 82.390 -14.727 1.00 25.06 O
+ATOM 1295 CB ASN A 169 8.225 79.540 -14.653 1.00 18.97 C
+ATOM 1296 CG ASN A 169 8.138 79.306 -13.144 1.00 19.69 C
+ATOM 1297 OD1 ASN A 169 8.983 79.792 -12.369 1.00 19.38 O
+ATOM 1298 ND2 ASN A 169 7.139 78.551 -12.712 1.00 20.25 N
+ATOM 1299 N ARG A 170 10.204 82.385 -13.737 1.00 23.31 N
+ATOM 1300 CA ARG A 170 10.128 83.741 -13.239 1.00 26.22 C
+ATOM 1301 C ARG A 170 10.757 84.695 -14.256 1.00 29.13 C
+ATOM 1302 O ARG A 170 11.840 84.460 -14.818 1.00 28.21 O
+ATOM 1303 CB ARG A 170 10.945 83.901 -11.942 1.00 26.41 C
+ATOM 1304 CG ARG A 170 10.421 83.225 -10.688 1.00 26.12 C
+ATOM 1305 CD ARG A 170 8.948 83.458 -10.439 1.00 27.65 C
+ATOM 1306 NE ARG A 170 8.461 82.948 -9.166 1.00 28.05 N
+ATOM 1307 CZ ARG A 170 7.304 82.334 -8.992 1.00 26.76 C
+ATOM 1308 NH1 ARG A 170 6.476 82.167 -10.018 1.00 28.15 N
+ATOM 1309 NH2 ARG A 170 6.945 81.890 -7.789 1.00 28.29 N
+ATOM 1310 N GLU A 171 10.145 85.866 -14.406 1.00 31.67 N
+ATOM 1311 CA GLU A 171 10.681 86.880 -15.319 1.00 34.31 C
+ATOM 1312 C GLU A 171 12.058 87.315 -14.869 1.00 32.61 C
+ATOM 1313 O GLU A 171 12.327 87.492 -13.675 1.00 32.62 O
+ATOM 1314 CB GLU A 171 9.723 88.065 -15.395 1.00 38.74 C
+ATOM 1315 CG GLU A 171 9.948 88.980 -16.605 1.00 44.51 C
+ATOM 1316 CD GLU A 171 9.069 90.213 -16.402 1.00 48.11 C
+ATOM 1317 OE1 GLU A 171 7.851 90.025 -16.152 1.00 49.29 O
+ATOM 1318 OE2 GLU A 171 9.609 91.345 -16.463 1.00 50.71 O
+ATOM 1319 N GLY A 172 12.982 87.400 -15.819 1.00 32.49 N
+ATOM 1320 CA GLY A 172 14.336 87.855 -15.516 1.00 32.07 C
+ATOM 1321 C GLY A 172 15.282 86.815 -14.974 1.00 31.91 C
+ATOM 1322 O GLY A 172 16.459 87.097 -14.734 1.00 33.27 O
+ATOM 1323 N ALA A 173 14.828 85.556 -14.816 1.00 30.17 N
+ATOM 1324 CA ALA A 173 15.752 84.549 -14.292 1.00 27.07 C
+ATOM 1325 C ALA A 173 16.775 84.203 -15.361 1.00 24.53 C
+ATOM 1326 O ALA A 173 16.487 84.219 -16.546 1.00 25.51 O
+ATOM 1327 CB ALA A 173 15.000 83.283 -13.904 1.00 25.63 C
+ATOM 1328 N THR A 174 17.932 83.752 -14.951 1.00 22.90 N
+ATOM 1329 CA THR A 174 18.928 83.202 -15.841 1.00 22.99 C
+ATOM 1330 C THR A 174 18.583 81.726 -16.073 1.00 23.99 C
+ATOM 1331 O THR A 174 18.592 80.919 -15.125 1.00 24.96 O
+ATOM 1332 CB THR A 174 20.312 83.282 -15.204 1.00 25.97 C
+ATOM 1333 OG1 THR A 174 20.521 84.676 -14.873 1.00 30.01 O
+ATOM 1334 CG2 THR A 174 21.319 82.728 -16.197 1.00 25.88 C
+ATOM 1335 N VAL A 175 18.273 81.328 -17.286 1.00 21.03 N
+ATOM 1336 CA VAL A 175 17.909 79.949 -17.552 1.00 20.73 C
+ATOM 1337 C VAL A 175 19.121 79.152 -18.014 1.00 22.27 C
+ATOM 1338 O VAL A 175 19.899 79.639 -18.845 1.00 24.88 O
+ATOM 1339 CB VAL A 175 16.759 79.908 -18.532 1.00 21.57 C
+ATOM 1340 CG1 VAL A 175 16.286 78.467 -18.747 1.00 22.84 C
+ATOM 1341 CG2 VAL A 175 15.576 80.732 -17.996 1.00 21.51 C
+ATOM 1342 N SER A 176 19.350 77.969 -17.430 1.00 18.64 N
+ATOM 1343 CA SER A 176 20.483 77.183 -17.964 1.00 16.78 C
+ATOM 1344 C SER A 176 19.890 75.925 -18.536 1.00 16.00 C
+ATOM 1345 O SER A 176 19.319 75.128 -17.780 1.00 14.12 O
+ATOM 1346 CB SER A 176 21.452 76.900 -16.810 1.00 19.20 C
+ATOM 1347 OG SER A 176 22.314 75.823 -17.131 1.00 21.14 O
+ATOM 1348 N GLN A 177 19.977 75.667 -19.843 1.00 14.92 N
+ATOM 1349 CA GLN A 177 19.442 74.434 -20.420 1.00 14.44 C
+ATOM 1350 C GLN A 177 20.191 73.241 -19.783 1.00 13.19 C
+ATOM 1351 O GLN A 177 19.582 72.186 -19.653 1.00 13.85 O
+ATOM 1352 CB GLN A 177 19.757 74.419 -21.930 1.00 16.12 C
+ATOM 1353 CG GLN A 177 19.085 73.308 -22.712 1.00 20.11 C
+ATOM 1354 CD GLN A 177 17.574 73.256 -22.528 1.00 22.45 C
+ATOM 1355 OE1 GLN A 177 16.935 74.312 -22.627 1.00 22.84 O
+ATOM 1356 NE2 GLN A 177 16.981 72.095 -22.254 1.00 20.44 N
+ATOM 1357 N GLY A 178 21.459 73.432 -19.453 1.00 10.51 N
+ATOM 1358 CA GLY A 178 22.223 72.341 -18.829 1.00 11.89 C
+ATOM 1359 C GLY A 178 21.577 71.808 -17.560 1.00 12.67 C
+ATOM 1360 O GLY A 178 21.528 70.599 -17.310 1.00 11.81 O
+ATOM 1361 N LEU A 179 21.088 72.738 -16.710 1.00 10.92 N
+ATOM 1362 CA LEU A 179 20.479 72.322 -15.433 1.00 13.02 C
+ATOM 1363 C LEU A 179 19.204 71.553 -15.733 1.00 11.34 C
+ATOM 1364 O LEU A 179 18.899 70.575 -15.080 1.00 11.30 O
+ATOM 1365 CB LEU A 179 20.235 73.531 -14.526 1.00 12.08 C
+ATOM 1366 CG LEU A 179 21.538 74.187 -13.986 1.00 12.17 C
+ATOM 1367 CD1 LEU A 179 21.116 75.288 -12.986 1.00 13.45 C
+ATOM 1368 CD2 LEU A 179 22.423 73.181 -13.302 1.00 12.26 C
+ATOM 1369 N ILE A 180 18.407 72.020 -16.673 1.00 9.92 N
+ATOM 1370 CA ILE A 180 17.211 71.274 -17.084 1.00 10.91 C
+ATOM 1371 C ILE A 180 17.512 69.852 -17.555 1.00 9.25 C
+ATOM 1372 O ILE A 180 16.937 68.845 -17.076 1.00 11.55 O
+ATOM 1373 CB ILE A 180 16.452 72.015 -18.204 1.00 12.44 C
+ATOM 1374 CG1 ILE A 180 16.020 73.421 -17.682 1.00 12.77 C
+ATOM 1375 CG2 ILE A 180 15.240 71.187 -18.595 1.00 12.48 C
+ATOM 1376 CD1 ILE A 180 15.408 74.297 -18.803 1.00 13.61 C
+ATOM 1377 N ASP A 181 18.442 69.744 -18.506 1.00 7.41 N
+ATOM 1378 CA ASP A 181 18.764 68.454 -19.090 1.00 8.73 C
+ATOM 1379 C ASP A 181 19.405 67.513 -18.048 1.00 8.90 C
+ATOM 1380 O ASP A 181 19.099 66.331 -18.061 1.00 9.63 O
+ATOM 1381 CB ASP A 181 19.726 68.557 -20.286 1.00 9.91 C
+ATOM 1382 CG ASP A 181 19.132 69.371 -21.466 1.00 14.59 C
+ATOM 1383 OD1 ASP A 181 17.919 69.647 -21.490 1.00 12.65 O
+ATOM 1384 OD2 ASP A 181 20.013 69.724 -22.304 1.00 15.86 O
+ATOM 1385 N HIS A 182 20.242 68.041 -17.182 1.00 9.27 N
+ATOM 1386 CA HIS A 182 20.826 67.163 -16.146 1.00 7.11 C
+ATOM 1387 C HIS A 182 19.775 66.675 -15.167 1.00 8.04 C
+ATOM 1388 O HIS A 182 19.841 65.538 -14.689 1.00 11.75 O
+ATOM 1389 CB HIS A 182 21.940 67.904 -15.391 1.00 6.65 C
+ATOM 1390 CG HIS A 182 22.826 66.915 -14.649 1.00 10.34 C
+ATOM 1391 ND1 HIS A 182 23.573 67.304 -13.582 1.00 10.88 N
+ATOM 1392 CD2 HIS A 182 23.079 65.590 -14.829 1.00 10.02 C
+ATOM 1393 CE1 HIS A 182 24.287 66.280 -13.134 1.00 10.72 C
+ATOM 1394 NE2 HIS A 182 23.991 65.223 -13.875 1.00 10.31 N
+ATOM 1395 N TRP A 183 18.799 67.492 -14.818 1.00 8.64 N
+ATOM 1396 CA TRP A 183 17.742 67.036 -13.890 1.00 9.94 C
+ATOM 1397 C TRP A 183 17.008 65.867 -14.517 1.00 9.97 C
+ATOM 1398 O TRP A 183 16.703 64.790 -13.960 1.00 8.51 O
+ATOM 1399 CB TRP A 183 16.859 68.266 -13.597 1.00 7.17 C
+ATOM 1400 CG TRP A 183 15.831 68.172 -12.524 1.00 8.96 C
+ATOM 1401 CD1 TRP A 183 15.894 68.916 -11.364 1.00 9.78 C
+ATOM 1402 CD2 TRP A 183 14.606 67.449 -12.427 1.00 9.64 C
+ATOM 1403 NE1 TRP A 183 14.791 68.653 -10.573 1.00 10.40 N
+ATOM 1404 CE2 TRP A 183 13.982 67.779 -11.201 1.00 9.11 C
+ATOM 1405 CE3 TRP A 183 13.925 66.582 -13.292 1.00 8.09 C
+ATOM 1406 CZ2 TRP A 183 12.738 67.272 -10.808 1.00 11.24 C
+ATOM 1407 CZ3 TRP A 183 12.737 66.018 -12.906 1.00 9.24 C
+ATOM 1408 CH2 TRP A 183 12.120 66.372 -11.665 1.00 12.29 C
+ATOM 1409 N TRP A 184 16.643 66.082 -15.783 1.00 8.52 N
+ATOM 1410 CA TRP A 184 15.920 65.065 -16.562 1.00 9.38 C
+ATOM 1411 C TRP A 184 16.713 63.754 -16.614 1.00 7.61 C
+ATOM 1412 O TRP A 184 16.143 62.696 -16.479 1.00 8.91 O
+ATOM 1413 CB TRP A 184 15.701 65.630 -18.008 1.00 9.25 C
+ATOM 1414 CG TRP A 184 14.886 64.663 -18.857 1.00 11.21 C
+ATOM 1415 CD1 TRP A 184 13.529 64.560 -18.972 1.00 11.89 C
+ATOM 1416 CD2 TRP A 184 15.424 63.658 -19.739 1.00 10.38 C
+ATOM 1417 NE1 TRP A 184 13.195 63.524 -19.839 1.00 9.26 N
+ATOM 1418 CE2 TRP A 184 14.352 62.989 -20.326 1.00 9.95 C
+ATOM 1419 CE3 TRP A 184 16.757 63.294 -20.054 1.00 12.74 C
+ATOM 1420 CZ2 TRP A 184 14.525 61.932 -21.241 1.00 11.15 C
+ATOM 1421 CZ3 TRP A 184 16.946 62.252 -20.973 1.00 11.45 C
+ATOM 1422 CH2 TRP A 184 15.819 61.608 -21.567 1.00 12.34 C
+ATOM 1423 N LEU A 185 17.999 63.833 -16.876 1.00 6.27 N
+ATOM 1424 CA LEU A 185 18.793 62.596 -17.049 1.00 10.24 C
+ATOM 1425 C LEU A 185 18.837 61.838 -15.719 1.00 10.43 C
+ATOM 1426 O LEU A 185 18.628 60.635 -15.698 1.00 10.91 O
+ATOM 1427 CB LEU A 185 20.218 62.983 -17.434 1.00 10.32 C
+ATOM 1428 CG LEU A 185 21.262 61.854 -17.427 1.00 11.18 C
+ATOM 1429 CD1 LEU A 185 20.894 60.860 -18.551 1.00 12.36 C
+ATOM 1430 CD2 LEU A 185 22.685 62.375 -17.666 1.00 10.10 C
+ATOM 1431 N GLN A 186 19.103 62.572 -14.626 1.00 8.89 N
+ATOM 1432 CA GLN A 186 19.199 61.907 -13.327 1.00 9.70 C
+ATOM 1433 C GLN A 186 17.846 61.266 -12.990 1.00 8.06 C
+ATOM 1434 O GLN A 186 17.798 60.153 -12.448 1.00 9.13 O
+ATOM 1435 CB GLN A 186 19.560 62.896 -12.199 1.00 9.42 C
+ATOM 1436 CG GLN A 186 20.957 63.535 -12.355 1.00 9.12 C
+ATOM 1437 CD GLN A 186 21.146 64.513 -11.195 1.00 11.83 C
+ATOM 1438 OE1 GLN A 186 21.292 64.093 -10.032 1.00 11.79 O
+ATOM 1439 NE2 GLN A 186 21.012 65.788 -11.535 1.00 10.13 N
+ATOM 1440 N GLY A 187 16.772 61.955 -13.267 1.00 8.35 N
+ATOM 1441 CA GLY A 187 15.461 61.414 -13.026 1.00 8.49 C
+ATOM 1442 C GLY A 187 15.194 60.162 -13.852 1.00 8.16 C
+ATOM 1443 O GLY A 187 14.716 59.112 -13.356 1.00 8.16 O
+ATOM 1444 N MET A 188 15.512 60.205 -15.135 1.00 9.94 N
+ATOM 1445 CA MET A 188 15.162 59.076 -16.026 1.00 12.01 C
+ATOM 1446 C MET A 188 16.050 57.871 -15.686 1.00 10.90 C
+ATOM 1447 O MET A 188 15.635 56.733 -15.965 1.00 13.40 O
+ATOM 1448 CB MET A 188 15.294 59.472 -17.494 1.00 12.71 C
+ATOM 1449 CG MET A 188 14.215 60.423 -18.048 1.00 13.39 C
+ATOM 1450 SD MET A 188 12.566 60.130 -17.425 1.00 15.53 S
+ATOM 1451 CE MET A 188 12.044 58.633 -18.268 1.00 14.29 C
+ATOM 1452 N MET A 189 17.237 58.080 -15.096 1.00 11.10 N
+ATOM 1453 CA MET A 189 18.030 56.919 -14.654 1.00 14.24 C
+ATOM 1454 C MET A 189 17.366 56.122 -13.534 1.00 12.37 C
+ATOM 1455 O MET A 189 17.601 54.901 -13.419 1.00 11.72 O
+ATOM 1456 CB MET A 189 19.440 57.310 -14.176 1.00 16.66 C
+ATOM 1457 CG MET A 189 20.245 58.044 -15.255 1.00 28.15 C
+ATOM 1458 SD MET A 189 21.010 56.974 -16.498 1.00 40.58 S
+ATOM 1459 CE MET A 189 19.638 56.414 -17.489 1.00 38.46 C
+ATOM 1460 N GLY A 190 16.678 56.814 -12.625 1.00 10.17 N
+ATOM 1461 CA GLY A 190 16.046 56.099 -11.531 1.00 9.20 C
+ATOM 1462 C GLY A 190 14.771 55.361 -11.921 1.00 11.93 C
+ATOM 1463 O GLY A 190 14.229 55.469 -13.014 1.00 10.60 O
+ATOM 1464 N ALA A 191 14.226 54.617 -10.962 1.00 11.31 N
+ATOM 1465 CA ALA A 191 13.091 53.725 -11.178 1.00 10.61 C
+ATOM 1466 C ALA A 191 11.760 54.417 -11.063 1.00 11.13 C
+ATOM 1467 O ALA A 191 11.487 55.155 -10.092 1.00 11.13 O
+ATOM 1468 CB ALA A 191 13.107 52.641 -10.089 1.00 11.42 C
+ATOM 1469 N ALA A 192 10.862 54.066 -11.979 1.00 9.45 N
+ATOM 1470 CA ALA A 192 9.531 54.735 -11.912 1.00 11.53 C
+ATOM 1471 C ALA A 192 8.732 54.395 -10.649 1.00 10.83 C
+ATOM 1472 O ALA A 192 8.132 55.314 -10.072 1.00 11.89 O
+ATOM 1473 CB ALA A 192 8.751 54.335 -13.177 1.00 9.77 C
+ATOM 1474 N ASN A 193 8.846 53.171 -10.144 1.00 10.66 N
+ATOM 1475 CA ASN A 193 8.076 52.841 -8.909 1.00 12.75 C
+ATOM 1476 C ASN A 193 8.661 53.572 -7.696 1.00 12.52 C
+ATOM 1477 O ASN A 193 7.890 54.174 -6.932 1.00 13.42 O
+ATOM 1478 CB ASN A 193 7.997 51.329 -8.712 1.00 11.36 C
+ATOM 1479 CG ASN A 193 9.355 50.722 -8.356 1.00 13.45 C
+ATOM 1480 OD1 ASN A 193 10.445 51.187 -8.706 1.00 11.68 O
+ATOM 1481 ND2 ASN A 193 9.298 49.706 -7.493 1.00 13.73 N
+ATOM 1482 N ALA A 194 9.985 53.589 -7.572 1.00 11.34 N
+ATOM 1483 CA ALA A 194 10.570 54.387 -6.453 1.00 13.24 C
+ATOM 1484 C ALA A 194 10.158 55.839 -6.484 1.00 13.82 C
+ATOM 1485 O ALA A 194 9.705 56.487 -5.504 1.00 13.38 O
+ATOM 1486 CB ALA A 194 12.096 54.295 -6.576 1.00 12.18 C
+ATOM 1487 N HIS A 195 10.275 56.465 -7.701 1.00 12.12 N
+ATOM 1488 CA HIS A 195 9.908 57.885 -7.768 1.00 10.89 C
+ATOM 1489 C HIS A 195 8.427 58.074 -7.444 1.00 12.44 C
+ATOM 1490 O HIS A 195 8.081 59.125 -6.923 1.00 12.87 O
+ATOM 1491 CB HIS A 195 10.263 58.461 -9.162 1.00 12.63 C
+ATOM 1492 CG HIS A 195 11.732 58.465 -9.437 1.00 11.63 C
+ATOM 1493 ND1 HIS A 195 12.300 58.796 -10.665 1.00 13.18 N
+ATOM 1494 CD2 HIS A 195 12.763 58.213 -8.578 1.00 12.01 C
+ATOM 1495 CE1 HIS A 195 13.608 58.700 -10.553 1.00 12.63 C
+ATOM 1496 NE2 HIS A 195 13.938 58.358 -9.290 1.00 11.68 N
+ATOM 1497 N TYR A 196 7.570 57.204 -7.923 1.00 11.14 N
+ATOM 1498 CA TYR A 196 6.138 57.326 -7.676 1.00 14.97 C
+ATOM 1499 C TYR A 196 5.817 57.247 -6.167 1.00 15.63 C
+ATOM 1500 O TYR A 196 5.234 58.169 -5.604 1.00 14.86 O
+ATOM 1501 CB TYR A 196 5.430 56.248 -8.482 1.00 15.46 C
+ATOM 1502 CG TYR A 196 3.910 56.330 -8.437 1.00 19.96 C
+ATOM 1503 CD1 TYR A 196 3.199 55.719 -7.404 1.00 21.21 C
+ATOM 1504 CD2 TYR A 196 3.208 57.050 -9.393 1.00 20.06 C
+ATOM 1505 CE1 TYR A 196 1.809 55.792 -7.362 1.00 21.13 C
+ATOM 1506 CE2 TYR A 196 1.824 57.104 -9.380 1.00 22.27 C
+ATOM 1507 CZ TYR A 196 1.145 56.479 -8.349 1.00 21.98 C
+ATOM 1508 OH TYR A 196 -0.227 56.565 -8.320 1.00 23.99 O
+ATOM 1509 N GLU A 197 6.325 56.205 -5.494 1.00 17.04 N
+ATOM 1510 CA GLU A 197 6.104 55.965 -4.078 1.00 19.99 C
+ATOM 1511 C GLU A 197 6.719 57.005 -3.172 1.00 19.94 C
+ATOM 1512 O GLU A 197 6.137 57.375 -2.153 1.00 19.19 O
+ATOM 1513 CB GLU A 197 6.646 54.576 -3.734 1.00 23.97 C
+ATOM 1514 CG GLU A 197 5.943 53.559 -4.658 1.00 31.50 C
+ATOM 1515 CD GLU A 197 5.869 52.224 -3.953 1.00 38.58 C
+ATOM 1516 OE1 GLU A 197 5.731 52.243 -2.689 1.00 41.22 O
+ATOM 1517 OE2 GLU A 197 5.981 51.193 -4.678 1.00 42.93 O
+ATOM 1518 N CYS A 198 7.855 57.575 -3.585 1.00 15.64 N
+ATOM 1519 CA CYS A 198 8.530 58.598 -2.852 1.00 14.07 C
+ATOM 1520 C CYS A 198 7.701 59.847 -2.670 1.00 15.20 C
+ATOM 1521 O CYS A 198 7.983 60.665 -1.779 1.00 15.38 O
+ATOM 1522 CB CYS A 198 9.915 58.926 -3.486 1.00 14.77 C
+ATOM 1523 SG CYS A 198 10.965 59.847 -2.309 1.00 17.95 S
+ATOM 1524 N ILE A 199 6.788 60.118 -3.601 1.00 14.16 N
+ATOM 1525 CA ILE A 199 6.000 61.354 -3.458 1.00 15.06 C
+ATOM 1526 C ILE A 199 5.212 61.263 -2.133 1.00 15.89 C
+ATOM 1527 O ILE A 199 5.246 62.248 -1.393 1.00 17.25 O
+ATOM 1528 CB ILE A 199 5.058 61.589 -4.646 1.00 14.31 C
+ATOM 1529 CG1 ILE A 199 5.919 61.773 -5.926 1.00 13.62 C
+ATOM 1530 CG2 ILE A 199 4.225 62.869 -4.453 1.00 16.62 C
+ATOM 1531 CD1 ILE A 199 5.116 61.665 -7.217 1.00 15.90 C
+ATOM 1532 N ALA A 200 4.605 60.103 -1.867 1.00 16.81 N
+ATOM 1533 CA ALA A 200 3.911 60.065 -0.551 1.00 18.97 C
+ATOM 1534 C ALA A 200 4.919 60.148 0.604 1.00 20.23 C
+ATOM 1535 O ALA A 200 4.620 60.781 1.655 1.00 19.90 O
+ATOM 1536 CB ALA A 200 2.986 58.884 -0.446 1.00 15.52 C
+ATOM 1537 N ALA A 201 6.089 59.528 0.449 1.00 18.68 N
+ATOM 1538 CA ALA A 201 7.069 59.520 1.538 1.00 18.65 C
+ATOM 1539 C ALA A 201 7.542 60.914 1.842 1.00 17.85 C
+ATOM 1540 O ALA A 201 7.725 61.253 2.998 1.00 19.21 O
+ATOM 1541 CB ALA A 201 8.328 58.714 1.156 1.00 17.95 C
+ATOM 1542 N PHE A 202 7.837 61.775 0.840 1.00 16.49 N
+ATOM 1543 CA PHE A 202 8.342 63.085 1.191 1.00 16.50 C
+ATOM 1544 C PHE A 202 7.212 64.031 1.627 1.00 18.56 C
+ATOM 1545 O PHE A 202 7.519 65.003 2.339 1.00 17.49 O
+ATOM 1546 CB PHE A 202 9.217 63.700 0.113 1.00 16.52 C
+ATOM 1547 CG PHE A 202 8.613 64.267 -1.135 1.00 18.72 C
+ATOM 1548 CD1 PHE A 202 7.809 65.387 -1.130 1.00 19.52 C
+ATOM 1549 CD2 PHE A 202 8.916 63.675 -2.378 1.00 18.96 C
+ATOM 1550 CE1 PHE A 202 7.287 65.924 -2.309 1.00 20.55 C
+ATOM 1551 CE2 PHE A 202 8.361 64.171 -3.545 1.00 19.53 C
+ATOM 1552 CZ PHE A 202 7.551 65.294 -3.514 1.00 20.22 C
+ATOM 1553 N SER A 203 5.995 63.867 1.125 1.00 16.75 N
+ATOM 1554 CA SER A 203 4.977 64.881 1.393 1.00 17.39 C
+ATOM 1555 C SER A 203 4.041 64.542 2.557 1.00 19.14 C
+ATOM 1556 O SER A 203 3.414 65.490 3.079 1.00 21.16 O
+ATOM 1557 CB SER A 203 4.115 65.074 0.111 1.00 16.63 C
+ATOM 1558 OG SER A 203 3.448 63.857 -0.213 1.00 15.32 O
+ATOM 1559 N GLU A 204 3.866 63.303 2.951 1.00 17.78 N
+ATOM 1560 CA GLU A 204 3.010 62.913 4.038 1.00 20.17 C
+ATOM 1561 C GLU A 204 3.746 62.459 5.301 1.00 22.47 C
+ATOM 1562 O GLU A 204 3.081 62.265 6.313 1.00 24.51 O
+ATOM 1563 CB GLU A 204 2.106 61.750 3.610 1.00 21.28 C
+ATOM 1564 CG GLU A 204 1.217 62.227 2.443 1.00 23.76 C
+ATOM 1565 CD GLU A 204 0.472 61.046 1.858 1.00 28.74 C
+ATOM 1566 OE1 GLU A 204 0.197 60.125 2.643 1.00 32.02 O
+ATOM 1567 OE2 GLU A 204 0.188 60.952 0.650 1.00 29.09 O
+ATOM 1568 N THR A 205 5.045 62.199 5.255 1.00 20.01 N
+ATOM 1569 CA THR A 205 5.714 61.810 6.487 1.00 20.70 C
+ATOM 1570 C THR A 205 5.803 63.033 7.398 1.00 19.77 C
+ATOM 1571 O THR A 205 6.177 64.112 6.971 1.00 18.85 O
+ATOM 1572 CB THR A 205 7.119 61.252 6.191 1.00 20.73 C
+ATOM 1573 OG1 THR A 205 6.899 60.206 5.265 1.00 19.14 O
+ATOM 1574 CG2 THR A 205 7.746 60.699 7.483 1.00 20.93 C
+ATOM 1575 N ASP A 206 5.485 62.849 8.673 1.00 20.72 N
+ATOM 1576 CA ASP A 206 5.619 63.949 9.636 1.00 22.29 C
+ATOM 1577 C ASP A 206 6.961 63.824 10.331 1.00 19.79 C
+ATOM 1578 O ASP A 206 7.212 62.782 10.929 1.00 21.12 O
+ATOM 1579 CB ASP A 206 4.480 63.899 10.659 1.00 23.33 C
+ATOM 1580 CG ASP A 206 4.416 65.167 11.478 1.00 24.70 C
+ATOM 1581 OD1 ASP A 206 5.392 65.891 11.719 1.00 24.33 O
+ATOM 1582 OD2 ASP A 206 3.282 65.485 11.893 1.00 26.52 O
+ATOM 1583 N PHE A 207 7.851 64.807 10.225 1.00 19.16 N
+ATOM 1584 CA PHE A 207 9.167 64.664 10.842 1.00 17.15 C
+ATOM 1585 C PHE A 207 9.212 65.387 12.191 1.00 20.05 C
+ATOM 1586 O PHE A 207 10.278 65.633 12.760 1.00 18.32 O
+ATOM 1587 CB PHE A 207 10.223 65.340 9.892 1.00 18.67 C
+ATOM 1588 CG PHE A 207 10.313 64.565 8.587 1.00 18.91 C
+ATOM 1589 CD1 PHE A 207 11.097 63.443 8.484 1.00 17.68 C
+ATOM 1590 CD2 PHE A 207 9.585 65.002 7.473 1.00 18.47 C
+ATOM 1591 CE1 PHE A 207 11.199 62.735 7.297 1.00 18.48 C
+ATOM 1592 CE2 PHE A 207 9.685 64.289 6.277 1.00 16.55 C
+ATOM 1593 CZ PHE A 207 10.461 63.151 6.192 1.00 16.53 C
+ATOM 1594 N THR A 208 8.087 65.900 12.677 1.00 19.62 N
+ATOM 1595 CA THR A 208 8.056 66.672 13.920 1.00 22.75 C
+ATOM 1596 C THR A 208 8.816 66.008 15.047 1.00 22.23 C
+ATOM 1597 O THR A 208 9.692 66.602 15.680 1.00 20.08 O
+ATOM 1598 CB THR A 208 6.586 66.962 14.258 1.00 23.60 C
+ATOM 1599 OG1 THR A 208 6.151 67.888 13.207 1.00 23.98 O
+ATOM 1600 CG2 THR A 208 6.477 67.664 15.627 1.00 23.88 C
+ATOM 1601 N ASP A 209 8.565 64.731 15.297 1.00 24.26 N
+ATOM 1602 CA ASP A 209 9.232 63.981 16.348 1.00 25.53 C
+ATOM 1603 C ASP A 209 10.725 63.806 16.139 1.00 26.38 C
+ATOM 1604 O ASP A 209 11.527 63.827 17.113 1.00 26.69 O
+ATOM 1605 CB ASP A 209 8.544 62.629 16.529 1.00 27.20 C
+ATOM 1606 CG ASP A 209 7.183 62.737 17.206 1.00 30.81 C
+ATOM 1607 OD1 ASP A 209 6.811 63.836 17.684 1.00 32.11 O
+ATOM 1608 OD2 ASP A 209 6.451 61.720 17.257 1.00 31.40 O
+ATOM 1609 N ASP A 210 11.146 63.603 14.882 1.00 23.96 N
+ATOM 1610 CA ASP A 210 12.577 63.470 14.618 1.00 23.14 C
+ATOM 1611 C ASP A 210 13.291 64.772 15.006 1.00 22.91 C
+ATOM 1612 O ASP A 210 14.370 64.794 15.623 1.00 21.36 O
+ATOM 1613 CB ASP A 210 12.858 63.222 13.139 1.00 22.22 C
+ATOM 1614 CG ASP A 210 12.268 61.954 12.618 1.00 25.56 C
+ATOM 1615 OD1 ASP A 210 12.476 60.862 13.164 1.00 26.63 O
+ATOM 1616 OD2 ASP A 210 11.498 61.961 11.641 1.00 28.94 O
+ATOM 1617 N LEU A 211 12.707 65.883 14.528 1.00 19.62 N
+ATOM 1618 CA LEU A 211 13.282 67.186 14.785 1.00 20.91 C
+ATOM 1619 C LEU A 211 13.461 67.510 16.262 1.00 23.01 C
+ATOM 1620 O LEU A 211 14.404 68.220 16.657 1.00 23.21 O
+ATOM 1621 CB LEU A 211 12.413 68.269 14.135 1.00 21.39 C
+ATOM 1622 CG LEU A 211 12.443 68.358 12.605 1.00 22.37 C
+ATOM 1623 CD1 LEU A 211 11.574 69.523 12.148 1.00 22.52 C
+ATOM 1624 CD2 LEU A 211 13.851 68.493 12.035 1.00 20.52 C
+ATOM 1625 N LYS A 212 12.524 67.051 17.099 1.00 23.93 N
+ATOM 1626 CA LYS A 212 12.613 67.267 18.539 1.00 27.10 C
+ATOM 1627 C LYS A 212 13.701 66.420 19.158 1.00 26.94 C
+ATOM 1628 O LYS A 212 14.160 66.700 20.264 1.00 28.31 O
+ATOM 1629 CB LYS A 212 11.233 66.948 19.160 1.00 28.04 C
+ATOM 1630 CG LYS A 212 10.321 68.136 18.854 1.00 31.50 C
+ATOM 1631 CD LYS A 212 8.855 67.798 18.978 1.00 35.44 C
+ATOM 1632 CE LYS A 212 8.312 68.047 20.379 1.00 37.51 C
+ATOM 1633 NZ LYS A 212 6.847 67.714 20.444 1.00 39.24 N
+ATOM 1634 N ARG A 213 14.109 65.349 18.509 1.00 26.06 N
+ATOM 1635 CA ARG A 213 15.149 64.474 18.985 1.00 28.52 C
+ATOM 1636 C ARG A 213 16.556 64.907 18.603 1.00 27.90 C
+ATOM 1637 O ARG A 213 17.500 64.329 19.120 1.00 27.40 O
+ATOM 1638 CB ARG A 213 14.945 63.046 18.442 1.00 31.62 C
+ATOM 1639 CG ARG A 213 13.654 62.428 18.982 1.00 36.82 C
+ATOM 1640 CD ARG A 213 13.496 61.001 18.446 1.00 38.77 C
+ATOM 1641 NE ARG A 213 14.651 60.228 18.815 1.00 42.52 N
+ATOM 1642 CZ ARG A 213 15.115 59.056 18.444 1.00 45.13 C
+ATOM 1643 NH1 ARG A 213 14.517 58.275 17.549 1.00 46.98 N
+ATOM 1644 NH2 ARG A 213 16.243 58.629 19.024 1.00 46.27 N
+ATOM 1645 N ILE A 214 16.726 65.834 17.666 1.00 26.80 N
+ATOM 1646 CA ILE A 214 18.081 66.162 17.254 1.00 26.11 C
+ATOM 1647 C ILE A 214 18.776 67.087 18.237 1.00 26.77 C
+ATOM 1648 O ILE A 214 18.273 68.191 18.442 1.00 28.67 O
+ATOM 1649 CB ILE A 214 18.013 66.777 15.827 1.00 23.81 C
+ATOM 1650 CG1 ILE A 214 17.546 65.680 14.869 1.00 23.81 C
+ATOM 1651 CG2 ILE A 214 19.367 67.329 15.454 1.00 23.71 C
+ATOM 1652 CD1 ILE A 214 17.282 66.138 13.453 1.00 22.80 C
+ATOM 1653 N ASP A 215 19.967 66.753 18.704 1.00 28.08 N
+ATOM 1654 CA ASP A 215 20.649 67.692 19.592 1.00 34.14 C
+ATOM 1655 C ASP A 215 21.857 68.372 18.962 1.00 32.68 C
+ATOM 1656 O ASP A 215 22.214 69.432 19.497 1.00 34.56 O
+ATOM 1657 CB ASP A 215 21.048 67.039 20.910 1.00 39.14 C
+ATOM 1658 CG ASP A 215 21.559 65.631 20.746 1.00 43.79 C
+ATOM 1659 OD1 ASP A 215 22.287 65.301 19.779 1.00 47.08 O
+ATOM 1660 OD2 ASP A 215 21.221 64.817 21.638 1.00 47.43 O
+ATOM 1661 N VAL A 216 22.436 67.867 17.873 1.00 27.40 N
+ATOM 1662 CA VAL A 216 23.567 68.627 17.293 1.00 23.33 C
+ATOM 1663 C VAL A 216 23.080 69.924 16.670 1.00 21.01 C
+ATOM 1664 O VAL A 216 21.882 70.069 16.381 1.00 21.10 O
+ATOM 1665 CB VAL A 216 24.142 67.722 16.184 1.00 25.27 C
+ATOM 1666 CG1 VAL A 216 24.665 66.398 16.740 1.00 24.58 C
+ATOM 1667 CG2 VAL A 216 23.061 67.457 15.116 1.00 22.61 C
+ATOM 1668 N PRO A 217 23.973 70.851 16.354 1.00 20.43 N
+ATOM 1669 CA PRO A 217 23.672 72.070 15.656 1.00 20.74 C
+ATOM 1670 C PRO A 217 23.181 71.759 14.217 1.00 20.77 C
+ATOM 1671 O PRO A 217 23.725 70.875 13.568 1.00 19.36 O
+ATOM 1672 CB PRO A 217 24.924 72.901 15.625 1.00 19.85 C
+ATOM 1673 CG PRO A 217 25.907 72.179 16.491 1.00 22.91 C
+ATOM 1674 CD PRO A 217 25.431 70.750 16.658 1.00 20.14 C
+ATOM 1675 N VAL A 218 22.165 72.504 13.838 1.00 20.18 N
+ATOM 1676 CA VAL A 218 21.468 72.332 12.571 1.00 20.06 C
+ATOM 1677 C VAL A 218 21.296 73.694 11.916 1.00 20.90 C
+ATOM 1678 O VAL A 218 20.879 74.704 12.497 1.00 21.77 O
+ATOM 1679 CB VAL A 218 20.110 71.636 12.636 1.00 18.64 C
+ATOM 1680 CG1 VAL A 218 19.455 71.501 11.244 1.00 19.81 C
+ATOM 1681 CG2 VAL A 218 20.143 70.267 13.292 1.00 16.52 C
+ATOM 1682 N LEU A 219 21.783 73.761 10.678 1.00 17.40 N
+ATOM 1683 CA LEU A 219 21.580 74.953 9.843 1.00 16.12 C
+ATOM 1684 C LEU A 219 20.366 74.734 8.974 1.00 14.45 C
+ATOM 1685 O LEU A 219 20.321 73.694 8.302 1.00 16.29 O
+ATOM 1686 CB LEU A 219 22.806 75.277 8.987 1.00 16.77 C
+ATOM 1687 CG LEU A 219 22.575 76.259 7.809 1.00 18.95 C
+ATOM 1688 CD1 LEU A 219 22.229 77.646 8.285 1.00 18.80 C
+ATOM 1689 CD2 LEU A 219 23.814 76.317 6.895 1.00 19.30 C
+ATOM 1690 N VAL A 220 19.356 75.585 8.970 1.00 14.90 N
+ATOM 1691 CA VAL A 220 18.137 75.427 8.176 1.00 16.15 C
+ATOM 1692 C VAL A 220 18.140 76.521 7.115 1.00 17.44 C
+ATOM 1693 O VAL A 220 18.195 77.698 7.480 1.00 19.42 O
+ATOM 1694 CB VAL A 220 16.835 75.526 8.989 1.00 15.89 C
+ATOM 1695 CG1 VAL A 220 15.593 75.365 8.113 1.00 17.38 C
+ATOM 1696 CG2 VAL A 220 16.838 74.463 10.070 1.00 16.33 C
+ATOM 1697 N ALA A 221 18.324 76.183 5.845 1.00 16.87 N
+ATOM 1698 CA ALA A 221 18.462 77.213 4.779 1.00 15.60 C
+ATOM 1699 C ALA A 221 17.278 77.086 3.838 1.00 16.91 C
+ATOM 1700 O ALA A 221 16.898 75.929 3.533 1.00 17.96 O
+ATOM 1701 CB ALA A 221 19.803 76.978 4.073 1.00 15.92 C
+ATOM 1702 N HIS A 222 16.754 78.167 3.270 1.00 17.41 N
+ATOM 1703 CA HIS A 222 15.587 78.015 2.391 1.00 17.26 C
+ATOM 1704 C HIS A 222 15.350 79.268 1.565 1.00 17.59 C
+ATOM 1705 O HIS A 222 15.612 80.387 2.021 1.00 19.47 O
+ATOM 1706 CB HIS A 222 14.387 77.681 3.244 1.00 15.92 C
+ATOM 1707 CG HIS A 222 13.331 76.813 2.640 1.00 15.70 C
+ATOM 1708 ND1 HIS A 222 13.013 75.584 3.175 1.00 13.82 N
+ATOM 1709 CD2 HIS A 222 12.483 77.019 1.588 1.00 13.84 C
+ATOM 1710 CE1 HIS A 222 12.021 75.044 2.500 1.00 13.64 C
+ATOM 1711 NE2 HIS A 222 11.686 75.892 1.528 1.00 14.68 N
+ATOM 1712 N GLY A 223 14.955 79.085 0.312 1.00 17.02 N
+ATOM 1713 CA GLY A 223 14.750 80.290 -0.538 1.00 17.05 C
+ATOM 1714 C GLY A 223 13.318 80.748 -0.316 1.00 18.82 C
+ATOM 1715 O GLY A 223 12.430 79.913 -0.190 1.00 18.60 O
+ATOM 1716 N THR A 224 13.092 82.064 -0.281 1.00 22.61 N
+ATOM 1717 CA THR A 224 11.712 82.541 -0.038 1.00 22.98 C
+ATOM 1718 C THR A 224 10.868 82.456 -1.297 1.00 24.29 C
+ATOM 1719 O THR A 224 9.629 82.546 -1.130 1.00 26.26 O
+ATOM 1720 CB THR A 224 11.687 83.980 0.522 1.00 22.43 C
+ATOM 1721 OG1 THR A 224 12.117 84.891 -0.469 1.00 21.09 O
+ATOM 1722 CG2 THR A 224 12.670 84.100 1.695 1.00 21.74 C
+ATOM 1723 N ASP A 225 11.419 82.183 -2.496 1.00 20.64 N
+ATOM 1724 CA ASP A 225 10.481 82.007 -3.621 1.00 22.70 C
+ATOM 1725 C ASP A 225 10.459 80.542 -4.053 1.00 22.61 C
+ATOM 1726 O ASP A 225 10.432 80.190 -5.232 1.00 22.64 O
+ATOM 1727 CB ASP A 225 10.839 82.992 -4.744 1.00 23.76 C
+ATOM 1728 CG ASP A 225 9.896 82.985 -5.926 1.00 26.05 C
+ATOM 1729 OD1 ASP A 225 8.713 82.638 -5.765 1.00 26.68 O
+ATOM 1730 OD2 ASP A 225 10.289 83.242 -7.083 1.00 27.90 O
+ATOM 1731 N ASP A 226 10.516 79.616 -3.099 1.00 21.34 N
+ATOM 1732 CA ASP A 226 10.518 78.186 -3.310 1.00 20.81 C
+ATOM 1733 C ASP A 226 9.157 77.729 -3.782 1.00 20.97 C
+ATOM 1734 O ASP A 226 8.183 77.809 -3.007 1.00 19.82 O
+ATOM 1735 CB ASP A 226 10.911 77.417 -2.032 1.00 17.80 C
+ATOM 1736 CG ASP A 226 11.235 75.974 -2.382 1.00 16.53 C
+ATOM 1737 OD1 ASP A 226 10.518 75.353 -3.189 1.00 16.31 O
+ATOM 1738 OD2 ASP A 226 12.232 75.442 -1.848 1.00 17.08 O
+ATOM 1739 N GLN A 227 9.075 77.263 -5.030 1.00 19.72 N
+ATOM 1740 CA GLN A 227 7.785 76.850 -5.564 1.00 17.43 C
+ATOM 1741 C GLN A 227 7.505 75.380 -5.385 1.00 19.38 C
+ATOM 1742 O GLN A 227 6.431 74.932 -5.805 1.00 21.65 O
+ATOM 1743 CB GLN A 227 7.668 77.195 -7.047 1.00 18.59 C
+ATOM 1744 CG GLN A 227 7.836 78.671 -7.388 1.00 20.16 C
+ATOM 1745 CD GLN A 227 7.893 78.869 -8.911 1.00 20.26 C
+ATOM 1746 OE1 GLN A 227 6.994 78.356 -9.582 1.00 23.64 O
+ATOM 1747 NE2 GLN A 227 8.911 79.538 -9.409 1.00 18.19 N
+ATOM 1748 N VAL A 228 8.395 74.601 -4.748 1.00 17.76 N
+ATOM 1749 CA VAL A 228 8.167 73.180 -4.567 1.00 17.48 C
+ATOM 1750 C VAL A 228 7.865 72.850 -3.117 1.00 19.55 C
+ATOM 1751 O VAL A 228 6.905 72.159 -2.817 1.00 21.20 O
+ATOM 1752 CB VAL A 228 9.446 72.393 -5.009 1.00 18.09 C
+ATOM 1753 CG1 VAL A 228 9.275 70.900 -4.720 1.00 17.92 C
+ATOM 1754 CG2 VAL A 228 9.678 72.682 -6.492 1.00 19.09 C
+ATOM 1755 N VAL A 229 8.722 73.353 -2.202 1.00 20.35 N
+ATOM 1756 CA VAL A 229 8.526 73.211 -0.766 1.00 19.77 C
+ATOM 1757 C VAL A 229 8.364 74.614 -0.207 1.00 19.13 C
+ATOM 1758 O VAL A 229 9.286 75.422 -0.083 1.00 16.92 O
+ATOM 1759 CB VAL A 229 9.679 72.480 -0.061 1.00 22.29 C
+ATOM 1760 CG1 VAL A 229 9.441 72.421 1.457 1.00 22.21 C
+ATOM 1761 CG2 VAL A 229 9.800 71.058 -0.573 1.00 21.99 C
+ATOM 1762 N PRO A 230 7.100 74.997 0.009 1.00 21.14 N
+ATOM 1763 CA PRO A 230 6.756 76.361 0.405 1.00 20.29 C
+ATOM 1764 C PRO A 230 7.479 76.816 1.653 1.00 22.08 C
+ATOM 1765 O PRO A 230 7.510 76.087 2.666 1.00 22.87 O
+ATOM 1766 CB PRO A 230 5.237 76.341 0.552 1.00 21.98 C
+ATOM 1767 CG PRO A 230 4.818 75.235 -0.360 1.00 21.77 C
+ATOM 1768 CD PRO A 230 5.889 74.148 -0.143 1.00 20.68 C
+ATOM 1769 N TYR A 231 8.106 77.969 1.560 1.00 21.53 N
+ATOM 1770 CA TYR A 231 8.970 78.480 2.591 1.00 23.86 C
+ATOM 1771 C TYR A 231 8.346 78.584 3.990 1.00 25.63 C
+ATOM 1772 O TYR A 231 8.976 78.174 4.966 1.00 23.52 O
+ATOM 1773 CB TYR A 231 9.527 79.834 2.156 1.00 25.37 C
+ATOM 1774 CG TYR A 231 10.300 80.493 3.290 1.00 27.01 C
+ATOM 1775 CD1 TYR A 231 11.633 80.262 3.478 1.00 26.19 C
+ATOM 1776 CD2 TYR A 231 9.634 81.343 4.191 1.00 28.75 C
+ATOM 1777 CE1 TYR A 231 12.331 80.823 4.524 1.00 27.73 C
+ATOM 1778 CE2 TYR A 231 10.312 81.938 5.239 1.00 28.59 C
+ATOM 1779 CZ TYR A 231 11.656 81.663 5.404 1.00 29.48 C
+ATOM 1780 OH TYR A 231 12.368 82.236 6.428 1.00 27.33 O
+ATOM 1781 N ALA A 232 7.177 79.208 4.086 1.00 26.31 N
+ATOM 1782 CA ALA A 232 6.561 79.498 5.381 1.00 27.61 C
+ATOM 1783 C ALA A 232 6.117 78.272 6.150 1.00 28.15 C
+ATOM 1784 O ALA A 232 6.191 78.309 7.380 1.00 29.95 O
+ATOM 1785 CB ALA A 232 5.453 80.529 5.171 1.00 25.94 C
+ATOM 1786 N ASP A 233 5.737 77.169 5.571 1.00 27.74 N
+ATOM 1787 CA ASP A 233 5.364 75.918 6.194 1.00 27.18 C
+ATOM 1788 C ASP A 233 6.568 75.006 6.432 1.00 23.34 C
+ATOM 1789 O ASP A 233 6.367 73.902 6.944 1.00 23.91 O
+ATOM 1790 CB ASP A 233 4.375 75.149 5.313 1.00 32.20 C
+ATOM 1791 CG ASP A 233 3.469 74.115 5.938 1.00 36.48 C
+ATOM 1792 OD1 ASP A 233 2.840 74.379 7.012 1.00 39.35 O
+ATOM 1793 OD2 ASP A 233 3.271 72.985 5.390 1.00 35.48 O
+ATOM 1794 N ALA A 234 7.783 75.418 6.056 1.00 20.43 N
+ATOM 1795 CA ALA A 234 8.892 74.518 6.269 1.00 20.37 C
+ATOM 1796 C ALA A 234 9.945 75.097 7.206 1.00 20.01 C
+ATOM 1797 O ALA A 234 9.884 74.815 8.408 1.00 22.38 O
+ATOM 1798 CB ALA A 234 9.489 74.028 4.954 1.00 18.32 C
+ATOM 1799 N ALA A 235 10.784 75.971 6.739 1.00 19.94 N
+ATOM 1800 CA ALA A 235 11.981 76.454 7.358 1.00 20.45 C
+ATOM 1801 C ALA A 235 11.815 77.097 8.726 1.00 22.59 C
+ATOM 1802 O ALA A 235 12.446 76.666 9.671 1.00 21.74 O
+ATOM 1803 CB ALA A 235 12.772 77.317 6.381 1.00 18.56 C
+ATOM 1804 N PRO A 236 10.991 78.124 8.872 1.00 25.79 N
+ATOM 1805 CA PRO A 236 10.774 78.725 10.197 1.00 26.29 C
+ATOM 1806 C PRO A 236 10.154 77.698 11.127 1.00 25.86 C
+ATOM 1807 O PRO A 236 10.560 77.668 12.294 1.00 27.68 O
+ATOM 1808 CB PRO A 236 9.968 79.968 9.867 1.00 26.42 C
+ATOM 1809 CG PRO A 236 9.187 79.572 8.664 1.00 27.90 C
+ATOM 1810 CD PRO A 236 10.167 78.759 7.825 1.00 25.69 C
+ATOM 1811 N LYS A 237 9.305 76.781 10.710 1.00 25.66 N
+ATOM 1812 CA LYS A 237 8.752 75.776 11.616 1.00 28.08 C
+ATOM 1813 C LYS A 237 9.768 74.746 12.073 1.00 28.23 C
+ATOM 1814 O LYS A 237 9.786 74.279 13.216 1.00 28.93 O
+ATOM 1815 CB LYS A 237 7.560 75.056 10.981 1.00 29.41 C
+ATOM 1816 CG LYS A 237 6.466 76.080 10.627 1.00 32.45 C
+ATOM 1817 CD LYS A 237 5.347 75.394 9.862 1.00 35.79 C
+ATOM 1818 CE LYS A 237 3.979 75.773 10.406 1.00 39.66 C
+ATOM 1819 NZ LYS A 237 3.130 76.428 9.378 1.00 42.19 N
+ATOM 1820 N SER A 238 10.634 74.344 11.128 1.00 26.02 N
+ATOM 1821 CA SER A 238 11.696 73.423 11.495 1.00 25.28 C
+ATOM 1822 C SER A 238 12.590 74.049 12.553 1.00 24.86 C
+ATOM 1823 O SER A 238 12.950 73.380 13.527 1.00 26.05 O
+ATOM 1824 CB SER A 238 12.539 73.182 10.214 1.00 23.43 C
+ATOM 1825 OG SER A 238 11.722 72.238 9.514 1.00 25.88 O
+ATOM 1826 N ALA A 239 13.000 75.289 12.296 1.00 24.46 N
+ATOM 1827 CA ALA A 239 13.920 75.973 13.201 1.00 26.21 C
+ATOM 1828 C ALA A 239 13.348 76.141 14.620 1.00 28.34 C
+ATOM 1829 O ALA A 239 14.106 76.104 15.585 1.00 29.57 O
+ATOM 1830 CB ALA A 239 14.251 77.333 12.615 1.00 24.77 C
+ATOM 1831 N GLU A 240 12.040 76.346 14.744 1.00 29.85 N
+ATOM 1832 CA GLU A 240 11.423 76.478 16.055 1.00 33.55 C
+ATOM 1833 C GLU A 240 11.382 75.163 16.800 1.00 31.62 C
+ATOM 1834 O GLU A 240 11.478 75.200 18.033 1.00 32.58 O
+ATOM 1835 CB GLU A 240 9.994 77.027 15.941 1.00 37.55 C
+ATOM 1836 CG GLU A 240 10.071 78.411 15.290 1.00 44.40 C
+ATOM 1837 CD GLU A 240 8.681 78.951 14.996 1.00 48.88 C
+ATOM 1838 OE1 GLU A 240 7.726 78.534 15.707 1.00 51.76 O
+ATOM 1839 OE2 GLU A 240 8.590 79.779 14.061 1.00 51.05 O
+ATOM 1840 N LEU A 241 11.307 74.030 16.123 1.00 29.85 N
+ATOM 1841 CA LEU A 241 11.293 72.736 16.794 1.00 27.12 C
+ATOM 1842 C LEU A 241 12.664 72.197 17.170 1.00 26.32 C
+ATOM 1843 O LEU A 241 12.793 71.336 18.043 1.00 26.70 O
+ATOM 1844 CB LEU A 241 10.623 71.704 15.872 1.00 27.11 C
+ATOM 1845 CG LEU A 241 9.154 71.997 15.538 1.00 28.57 C
+ATOM 1846 CD1 LEU A 241 8.699 71.181 14.356 1.00 27.01 C
+ATOM 1847 CD2 LEU A 241 8.301 71.633 16.763 1.00 29.28 C
+ATOM 1848 N LEU A 242 13.728 72.610 16.505 1.00 25.02 N
+ATOM 1849 CA LEU A 242 15.072 72.115 16.741 1.00 25.16 C
+ATOM 1850 C LEU A 242 15.682 72.868 17.923 1.00 25.16 C
+ATOM 1851 O LEU A 242 15.564 74.081 18.002 1.00 25.47 O
+ATOM 1852 CB LEU A 242 15.975 72.336 15.503 1.00 23.76 C
+ATOM 1853 CG LEU A 242 15.680 71.383 14.324 1.00 22.60 C
+ATOM 1854 CD1 LEU A 242 16.075 72.060 13.028 1.00 22.79 C
+ATOM 1855 CD2 LEU A 242 16.458 70.080 14.491 1.00 23.27 C
+ATOM 1856 N ALA A 243 16.354 72.138 18.778 1.00 26.16 N
+ATOM 1857 CA ALA A 243 17.012 72.689 19.958 1.00 27.21 C
+ATOM 1858 C ALA A 243 18.095 73.671 19.605 1.00 28.66 C
+ATOM 1859 O ALA A 243 18.093 74.829 20.062 1.00 29.92 O
+ATOM 1860 CB ALA A 243 17.585 71.499 20.730 1.00 28.40 C
+ATOM 1861 N ASN A 244 19.031 73.308 18.738 1.00 27.94 N
+ATOM 1862 CA ASN A 244 20.100 74.236 18.336 1.00 28.85 C
+ATOM 1863 C ASN A 244 20.052 74.542 16.846 1.00 28.46 C
+ATOM 1864 O ASN A 244 20.878 73.998 16.089 1.00 29.05 O
+ATOM 1865 CB ASN A 244 21.424 73.581 18.753 1.00 31.44 C
+ATOM 1866 CG ASN A 244 22.640 74.463 18.612 1.00 35.35 C
+ATOM 1867 OD1 ASN A 244 22.605 75.645 18.228 1.00 36.23 O
+ATOM 1868 ND2 ASN A 244 23.809 73.896 18.949 1.00 37.56 N
+ATOM 1869 N ALA A 245 19.116 75.361 16.359 1.00 27.26 N
+ATOM 1870 CA ALA A 245 19.108 75.601 14.914 1.00 26.46 C
+ATOM 1871 C ALA A 245 19.525 77.010 14.554 1.00 26.33 C
+ATOM 1872 O ALA A 245 19.373 77.925 15.365 1.00 27.04 O
+ATOM 1873 CB ALA A 245 17.716 75.331 14.367 1.00 28.39 C
+ATOM 1874 N THR A 246 20.056 77.231 13.378 1.00 23.76 N
+ATOM 1875 CA THR A 246 20.350 78.548 12.815 1.00 24.23 C
+ATOM 1876 C THR A 246 19.524 78.650 11.517 1.00 25.52 C
+ATOM 1877 O THR A 246 19.521 77.708 10.675 1.00 24.33 O
+ATOM 1878 CB THR A 246 21.835 78.733 12.507 1.00 24.82 C
+ATOM 1879 OG1 THR A 246 22.629 78.586 13.716 1.00 26.36 O
+ATOM 1880 CG2 THR A 246 22.118 80.075 11.868 1.00 22.82 C
+ATOM 1881 N LEU A 247 18.752 79.692 11.359 1.00 25.04 N
+ATOM 1882 CA LEU A 247 17.856 79.853 10.218 1.00 26.55 C
+ATOM 1883 C LEU A 247 18.430 80.853 9.231 1.00 28.97 C
+ATOM 1884 O LEU A 247 18.684 82.007 9.614 1.00 27.62 O
+ATOM 1885 CB LEU A 247 16.472 80.337 10.659 1.00 27.65 C
+ATOM 1886 CG LEU A 247 15.395 80.538 9.618 1.00 30.51 C
+ATOM 1887 CD1 LEU A 247 15.056 79.219 8.944 1.00 29.55 C
+ATOM 1888 CD2 LEU A 247 14.078 81.117 10.172 1.00 30.17 C
+ATOM 1889 N LYS A 248 18.620 80.426 7.981 1.00 25.07 N
+ATOM 1890 CA LYS A 248 19.107 81.324 6.944 1.00 26.55 C
+ATOM 1891 C LYS A 248 18.056 81.357 5.835 1.00 26.74 C
+ATOM 1892 O LYS A 248 17.672 80.324 5.277 1.00 22.68 O
+ATOM 1893 CB LYS A 248 20.474 80.925 6.404 1.00 28.26 C
+ATOM 1894 CG LYS A 248 21.616 81.357 7.307 1.00 33.64 C
+ATOM 1895 CD LYS A 248 22.960 81.381 6.603 1.00 36.94 C
+ATOM 1896 CE LYS A 248 23.573 82.783 6.755 1.00 39.86 C
+ATOM 1897 NZ LYS A 248 23.723 83.031 8.233 1.00 42.16 N
+ATOM 1898 N SER A 249 17.600 82.556 5.535 1.00 24.84 N
+ATOM 1899 CA SER A 249 16.586 82.837 4.546 1.00 24.86 C
+ATOM 1900 C SER A 249 17.204 83.500 3.310 1.00 23.82 C
+ATOM 1901 O SER A 249 18.019 84.403 3.566 1.00 21.16 O
+ATOM 1902 CB SER A 249 15.691 83.977 5.146 1.00 26.60 C
+ATOM 1903 OG SER A 249 14.521 83.315 5.573 1.00 31.36 O
+ATOM 1904 N TYR A 250 16.859 83.057 2.099 1.00 19.26 N
+ATOM 1905 CA TYR A 250 17.531 83.687 0.935 1.00 21.04 C
+ATOM 1906 C TYR A 250 16.448 84.307 0.075 1.00 21.32 C
+ATOM 1907 O TYR A 250 15.632 83.593 -0.538 1.00 19.98 O
+ATOM 1908 CB TYR A 250 18.336 82.649 0.129 1.00 19.11 C
+ATOM 1909 CG TYR A 250 19.527 82.131 0.907 1.00 19.35 C
+ATOM 1910 CD1 TYR A 250 19.341 81.030 1.729 1.00 19.89 C
+ATOM 1911 CD2 TYR A 250 20.775 82.733 0.882 1.00 20.02 C
+ATOM 1912 CE1 TYR A 250 20.384 80.505 2.480 1.00 19.18 C
+ATOM 1913 CE2 TYR A 250 21.816 82.237 1.641 1.00 20.59 C
+ATOM 1914 CZ TYR A 250 21.603 81.116 2.425 1.00 20.45 C
+ATOM 1915 OH TYR A 250 22.620 80.577 3.198 1.00 21.79 O
+ATOM 1916 N GLU A 251 16.357 85.626 0.123 1.00 23.34 N
+ATOM 1917 CA GLU A 251 15.334 86.351 -0.583 1.00 25.33 C
+ATOM 1918 C GLU A 251 15.278 86.023 -2.080 1.00 24.07 C
+ATOM 1919 O GLU A 251 16.288 86.165 -2.754 1.00 23.97 O
+ATOM 1920 CB GLU A 251 15.540 87.890 -0.477 1.00 29.45 C
+ATOM 1921 CG GLU A 251 14.167 88.574 -0.563 1.00 36.84 C
+ATOM 1922 CD GLU A 251 13.311 88.131 0.630 1.00 41.39 C
+ATOM 1923 OE1 GLU A 251 13.936 88.024 1.723 1.00 43.88 O
+ATOM 1924 OE2 GLU A 251 12.092 87.869 0.480 1.00 43.37 O
+ATOM 1925 N GLY A 252 14.103 85.637 -2.533 1.00 23.71 N
+ATOM 1926 CA GLY A 252 13.797 85.384 -3.929 1.00 22.29 C
+ATOM 1927 C GLY A 252 14.442 84.138 -4.539 1.00 22.08 C
+ATOM 1928 O GLY A 252 14.311 84.005 -5.774 1.00 17.92 O
+ATOM 1929 N LEU A 253 15.113 83.276 -3.746 1.00 18.87 N
+ATOM 1930 CA LEU A 253 15.782 82.129 -4.429 1.00 16.86 C
+ATOM 1931 C LEU A 253 14.840 80.969 -4.577 1.00 15.26 C
+ATOM 1932 O LEU A 253 13.916 80.801 -3.793 1.00 13.98 O
+ATOM 1933 CB LEU A 253 17.073 81.807 -3.678 1.00 17.62 C
+ATOM 1934 CG LEU A 253 18.170 82.874 -3.713 1.00 18.37 C
+ATOM 1935 CD1 LEU A 253 19.495 82.262 -3.294 1.00 17.40 C
+ATOM 1936 CD2 LEU A 253 18.181 83.594 -5.069 1.00 18.65 C
+ATOM 1937 N PRO A 254 15.091 80.055 -5.527 1.00 14.37 N
+ATOM 1938 CA PRO A 254 14.214 78.972 -5.827 1.00 13.57 C
+ATOM 1939 C PRO A 254 14.480 77.679 -5.056 1.00 13.95 C
+ATOM 1940 O PRO A 254 15.412 77.616 -4.256 1.00 13.92 O
+ATOM 1941 CB PRO A 254 14.532 78.682 -7.310 1.00 12.53 C
+ATOM 1942 CG PRO A 254 15.982 78.940 -7.381 1.00 13.12 C
+ATOM 1943 CD PRO A 254 16.215 80.175 -6.505 1.00 13.32 C
+ATOM 1944 N HIS A 255 13.705 76.654 -5.425 1.00 11.11 N
+ATOM 1945 CA HIS A 255 13.911 75.361 -4.770 1.00 14.52 C
+ATOM 1946 C HIS A 255 15.279 74.772 -5.064 1.00 13.83 C
+ATOM 1947 O HIS A 255 15.953 74.248 -4.166 1.00 13.63 O
+ATOM 1948 CB HIS A 255 12.793 74.411 -5.215 1.00 14.63 C
+ATOM 1949 CG HIS A 255 12.841 73.123 -4.440 1.00 15.65 C
+ATOM 1950 ND1 HIS A 255 12.661 73.118 -3.063 1.00 14.47 N
+ATOM 1951 CD2 HIS A 255 12.982 71.841 -4.821 1.00 14.90 C
+ATOM 1952 CE1 HIS A 255 12.728 71.871 -2.635 1.00 16.38 C
+ATOM 1953 NE2 HIS A 255 12.914 71.059 -3.672 1.00 16.38 N
+ATOM 1954 N GLY A 256 15.738 74.913 -6.317 1.00 12.47 N
+ATOM 1955 CA GLY A 256 17.052 74.301 -6.642 1.00 12.60 C
+ATOM 1956 C GLY A 256 18.140 75.335 -6.530 1.00 13.71 C
+ATOM 1957 O GLY A 256 19.067 75.356 -7.331 1.00 12.53 O
+ATOM 1958 N MET A 257 18.102 76.205 -5.467 1.00 11.47 N
+ATOM 1959 CA MET A 257 19.094 77.264 -5.378 1.00 11.88 C
+ATOM 1960 C MET A 257 20.504 76.798 -5.196 1.00 10.29 C
+ATOM 1961 O MET A 257 21.404 77.594 -5.462 1.00 11.06 O
+ATOM 1962 CB MET A 257 18.801 78.260 -4.206 1.00 14.18 C
+ATOM 1963 CG MET A 257 18.670 77.500 -2.869 1.00 15.11 C
+ATOM 1964 SD MET A 257 18.139 78.639 -1.535 1.00 15.54 S
+ATOM 1965 CE MET A 257 18.290 77.519 -0.105 1.00 15.63 C
+ATOM 1966 N LEU A 258 20.784 75.563 -4.755 1.00 11.32 N
+ATOM 1967 CA LEU A 258 22.186 75.150 -4.629 1.00 13.70 C
+ATOM 1968 C LEU A 258 22.841 75.027 -6.032 1.00 14.34 C
+ATOM 1969 O LEU A 258 24.087 74.955 -6.072 1.00 12.79 O
+ATOM 1970 CB LEU A 258 22.253 73.770 -3.966 1.00 14.69 C
+ATOM 1971 CG LEU A 258 21.924 73.823 -2.455 1.00 15.37 C
+ATOM 1972 CD1 LEU A 258 21.534 72.409 -2.065 1.00 16.20 C
+ATOM 1973 CD2 LEU A 258 23.103 74.332 -1.659 1.00 13.34 C
+ATOM 1974 N SER A 259 22.008 74.873 -7.055 1.00 12.71 N
+ATOM 1975 CA SER A 259 22.566 74.797 -8.418 1.00 14.13 C
+ATOM 1976 C SER A 259 22.454 76.123 -9.176 1.00 13.04 C
+ATOM 1977 O SER A 259 23.329 76.391 -10.009 1.00 13.89 O
+ATOM 1978 CB SER A 259 21.768 73.704 -9.173 1.00 14.12 C
+ATOM 1979 OG SER A 259 22.209 72.459 -8.637 1.00 15.46 O
+ATOM 1980 N THR A 260 21.486 76.988 -8.825 1.00 12.37 N
+ATOM 1981 CA THR A 260 21.375 78.240 -9.592 1.00 14.17 C
+ATOM 1982 C THR A 260 22.195 79.340 -8.927 1.00 16.88 C
+ATOM 1983 O THR A 260 22.782 80.222 -9.554 1.00 14.34 O
+ATOM 1984 CB THR A 260 19.914 78.694 -9.696 1.00 15.13 C
+ATOM 1985 OG1 THR A 260 19.341 78.786 -8.389 1.00 12.51 O
+ATOM 1986 CG2 THR A 260 19.047 77.700 -10.495 1.00 15.43 C
+ATOM 1987 N HIS A 261 22.357 79.243 -7.588 1.00 14.37 N
+ATOM 1988 CA HIS A 261 23.126 80.290 -6.900 1.00 14.38 C
+ATOM 1989 C HIS A 261 24.158 79.717 -5.953 1.00 14.70 C
+ATOM 1990 O HIS A 261 24.202 80.098 -4.757 1.00 14.22 O
+ATOM 1991 CB HIS A 261 22.090 81.091 -6.044 1.00 12.97 C
+ATOM 1992 CG HIS A 261 21.129 81.840 -6.895 1.00 14.62 C
+ATOM 1993 ND1 HIS A 261 19.997 81.283 -7.428 1.00 13.83 N
+ATOM 1994 CD2 HIS A 261 21.196 83.114 -7.399 1.00 16.52 C
+ATOM 1995 CE1 HIS A 261 19.356 82.163 -8.187 1.00 16.22 C
+ATOM 1996 NE2 HIS A 261 20.075 83.273 -8.173 1.00 16.57 N
+ATOM 1997 N PRO A 262 25.021 78.803 -6.384 1.00 12.56 N
+ATOM 1998 CA PRO A 262 26.010 78.176 -5.529 1.00 12.94 C
+ATOM 1999 C PRO A 262 26.982 79.194 -4.950 1.00 14.51 C
+ATOM 2000 O PRO A 262 27.566 79.026 -3.890 1.00 14.12 O
+ATOM 2001 CB PRO A 262 26.774 77.198 -6.471 1.00 11.50 C
+ATOM 2002 CG PRO A 262 26.644 77.927 -7.814 1.00 13.49 C
+ATOM 2003 CD PRO A 262 25.174 78.297 -7.767 1.00 13.60 C
+ATOM 2004 N GLU A 263 27.333 80.261 -5.684 1.00 14.87 N
+ATOM 2005 CA GLU A 263 28.260 81.269 -5.183 1.00 17.68 C
+ATOM 2006 C GLU A 263 27.686 81.975 -3.936 1.00 18.93 C
+ATOM 2007 O GLU A 263 28.471 82.408 -3.044 1.00 19.21 O
+ATOM 2008 CB GLU A 263 28.615 82.273 -6.296 1.00 17.10 C
+ATOM 2009 CG GLU A 263 27.452 83.187 -6.605 1.00 22.08 C
+ATOM 2010 CD GLU A 263 26.362 82.535 -7.472 1.00 26.54 C
+ATOM 2011 OE1 GLU A 263 26.613 81.423 -8.032 1.00 27.63 O
+ATOM 2012 OE2 GLU A 263 25.257 83.132 -7.613 1.00 27.42 O
+ATOM 2013 N VAL A 264 26.380 82.049 -3.779 1.00 17.24 N
+ATOM 2014 CA VAL A 264 25.798 82.618 -2.556 1.00 18.73 C
+ATOM 2015 C VAL A 264 25.769 81.586 -1.433 1.00 20.06 C
+ATOM 2016 O VAL A 264 26.226 81.820 -0.309 1.00 17.96 O
+ATOM 2017 CB VAL A 264 24.345 83.086 -2.827 1.00 19.60 C
+ATOM 2018 CG1 VAL A 264 23.656 83.555 -1.540 1.00 20.68 C
+ATOM 2019 CG2 VAL A 264 24.328 84.231 -3.829 1.00 20.42 C
+ATOM 2020 N LEU A 265 25.302 80.367 -1.716 1.00 17.50 N
+ATOM 2021 CA LEU A 265 25.102 79.334 -0.718 1.00 17.19 C
+ATOM 2022 C LEU A 265 26.328 78.624 -0.173 1.00 16.22 C
+ATOM 2023 O LEU A 265 26.385 78.374 1.046 1.00 16.14 O
+ATOM 2024 CB LEU A 265 24.179 78.257 -1.345 1.00 17.49 C
+ATOM 2025 CG LEU A 265 22.683 78.258 -1.058 1.00 21.30 C
+ATOM 2026 CD1 LEU A 265 22.400 78.031 0.427 1.00 23.41 C
+ATOM 2027 CD2 LEU A 265 22.010 79.539 -1.517 1.00 21.84 C
+ATOM 2028 N ASN A 266 27.319 78.338 -1.027 1.00 14.29 N
+ATOM 2029 CA ASN A 266 28.483 77.567 -0.680 1.00 14.50 C
+ATOM 2030 C ASN A 266 29.285 78.175 0.477 1.00 15.93 C
+ATOM 2031 O ASN A 266 29.642 77.462 1.405 1.00 13.70 O
+ATOM 2032 CB ASN A 266 29.387 77.283 -1.882 1.00 15.15 C
+ATOM 2033 CG ASN A 266 28.839 76.233 -2.856 1.00 16.40 C
+ATOM 2034 OD1 ASN A 266 27.768 75.674 -2.595 1.00 16.53 O
+ATOM 2035 ND2 ASN A 266 29.496 76.035 -3.987 1.00 17.41 N
+ATOM 2036 N PRO A 267 29.535 79.477 0.435 1.00 16.09 N
+ATOM 2037 CA PRO A 267 30.301 80.112 1.521 1.00 17.58 C
+ATOM 2038 C PRO A 267 29.577 79.998 2.862 1.00 16.92 C
+ATOM 2039 O PRO A 267 30.183 79.818 3.928 1.00 18.06 O
+ATOM 2040 CB PRO A 267 30.362 81.581 1.073 1.00 18.07 C
+ATOM 2041 CG PRO A 267 30.253 81.514 -0.437 1.00 17.37 C
+ATOM 2042 CD PRO A 267 29.220 80.411 -0.664 1.00 16.05 C
+ATOM 2043 N ASP A 268 28.261 80.080 2.895 1.00 16.99 N
+ATOM 2044 CA ASP A 268 27.429 79.945 4.080 1.00 17.51 C
+ATOM 2045 C ASP A 268 27.431 78.498 4.566 1.00 19.19 C
+ATOM 2046 O ASP A 268 27.490 78.286 5.791 1.00 18.17 O
+ATOM 2047 CB ASP A 268 25.958 80.324 3.878 1.00 18.39 C
+ATOM 2048 CG ASP A 268 25.819 81.826 3.658 1.00 21.89 C
+ATOM 2049 OD1 ASP A 268 26.795 82.562 3.864 1.00 23.14 O
+ATOM 2050 OD2 ASP A 268 24.732 82.256 3.232 1.00 22.88 O
+ATOM 2051 N LEU A 269 27.413 77.519 3.602 1.00 15.58 N
+ATOM 2052 CA LEU A 269 27.545 76.143 4.099 1.00 16.81 C
+ATOM 2053 C LEU A 269 28.913 75.931 4.741 1.00 16.08 C
+ATOM 2054 O LEU A 269 29.055 75.220 5.747 1.00 15.61 O
+ATOM 2055 CB LEU A 269 27.332 75.119 2.960 1.00 15.57 C
+ATOM 2056 CG LEU A 269 26.015 75.252 2.182 1.00 17.03 C
+ATOM 2057 CD1 LEU A 269 25.956 74.223 1.028 1.00 16.82 C
+ATOM 2058 CD2 LEU A 269 24.860 74.857 3.129 1.00 19.95 C
+ATOM 2059 N LEU A 270 29.963 76.462 4.113 1.00 13.05 N
+ATOM 2060 CA LEU A 270 31.321 76.362 4.554 1.00 15.60 C
+ATOM 2061 C LEU A 270 31.523 76.975 5.951 1.00 16.88 C
+ATOM 2062 O LEU A 270 32.149 76.339 6.808 1.00 18.26 O
+ATOM 2063 CB LEU A 270 32.313 77.096 3.612 1.00 17.08 C
+ATOM 2064 CG LEU A 270 33.794 76.980 3.956 1.00 17.88 C
+ATOM 2065 CD1 LEU A 270 34.284 75.540 4.059 1.00 17.42 C
+ATOM 2066 CD2 LEU A 270 34.647 77.758 2.938 1.00 18.93 C
+ATOM 2067 N ALA A 271 30.972 78.148 6.154 1.00 16.94 N
+ATOM 2068 CA ALA A 271 31.078 78.853 7.444 1.00 18.93 C
+ATOM 2069 C ALA A 271 30.507 78.005 8.584 1.00 21.00 C
+ATOM 2070 O ALA A 271 31.103 77.781 9.646 1.00 18.11 O
+ATOM 2071 CB ALA A 271 30.241 80.146 7.263 1.00 18.68 C
+ATOM 2072 N PHE A 272 29.367 77.364 8.278 1.00 20.97 N
+ATOM 2073 CA PHE A 272 28.690 76.486 9.230 1.00 21.95 C
+ATOM 2074 C PHE A 272 29.514 75.254 9.516 1.00 24.01 C
+ATOM 2075 O PHE A 272 29.686 74.851 10.663 1.00 25.21 O
+ATOM 2076 CB PHE A 272 27.276 76.155 8.733 1.00 21.93 C
+ATOM 2077 CG PHE A 272 26.507 75.280 9.698 1.00 22.54 C
+ATOM 2078 CD1 PHE A 272 25.909 75.842 10.827 1.00 23.69 C
+ATOM 2079 CD2 PHE A 272 26.407 73.925 9.494 1.00 21.33 C
+ATOM 2080 CE1 PHE A 272 25.211 75.033 11.713 1.00 22.50 C
+ATOM 2081 CE2 PHE A 272 25.695 73.113 10.359 1.00 22.51 C
+ATOM 2082 CZ PHE A 272 25.113 73.681 11.487 1.00 22.56 C
+ATOM 2083 N VAL A 273 30.092 74.614 8.488 1.00 22.45 N
+ATOM 2084 CA VAL A 273 30.925 73.452 8.729 1.00 23.66 C
+ATOM 2085 C VAL A 273 32.178 73.821 9.517 1.00 26.23 C
+ATOM 2086 O VAL A 273 32.595 72.962 10.320 1.00 25.36 O
+ATOM 2087 CB VAL A 273 31.223 72.725 7.427 1.00 21.42 C
+ATOM 2088 CG1 VAL A 273 32.125 71.532 7.647 1.00 22.68 C
+ATOM 2089 CG2 VAL A 273 29.877 72.277 6.838 1.00 19.99 C
+ATOM 2090 N LYS A 274 32.729 75.022 9.328 1.00 27.59 N
+ATOM 2091 CA LYS A 274 33.900 75.418 10.106 1.00 32.61 C
+ATOM 2092 C LYS A 274 33.630 75.908 11.526 1.00 35.38 C
+ATOM 2093 O LYS A 274 34.520 75.919 12.383 1.00 37.25 O
+ATOM 2094 CB LYS A 274 34.529 76.619 9.393 1.00 31.85 C
+ATOM 2095 CG LYS A 274 35.297 76.340 8.119 1.00 32.44 C
+ATOM 2096 CD LYS A 274 36.012 77.641 7.763 1.00 33.40 C
+ATOM 2097 CE LYS A 274 37.391 77.436 7.167 1.00 35.22 C
+ATOM 2098 NZ LYS A 274 37.759 78.681 6.408 1.00 36.95 N
+ATOM 2099 N SER A 275 32.469 76.450 11.830 1.00 37.38 N
+ATOM 2100 CA SER A 275 32.096 76.962 13.128 1.00 39.67 C
+ATOM 2101 C SER A 275 32.157 75.977 14.288 1.00 40.91 C
+ATOM 2102 O SER A 275 31.980 76.499 15.432 1.00 43.49 O
+ATOM 2103 CB SER A 275 30.648 77.488 13.091 1.00 39.47 C
+ATOM 2104 OG SER A 275 29.849 76.295 12.959 1.00 41.94 O
+ATOM 2105 OXT SER A 275 32.192 74.734 14.203 1.00 41.57 O
+TER 2106 SER A 275
+END
diff --git a/loop/tests/test_all_atom_positions.cc b/loop/tests/test_all_atom_positions.cc
index bdecca598bd2d86da16db22ec0d2c440f6c818a8..14a21edaf8b21eb69c372bec36a20722c8880a6a 100644
--- a/loop/tests/test_all_atom_positions.cc
+++ b/loop/tests/test_all_atom_positions.cc
@@ -224,7 +224,7 @@ BOOST_AUTO_TEST_CASE(test_aap_indexing) {
BOOST_CHECK_THROW(atoms.GetIndex(1, "XX"), promod3::Error);
BOOST_CHECK_THROW(atoms.GetIndex(2, "BA"), promod3::Error);
BOOST_CHECK_THROW(atoms.GetIndex(3, "ND1"), promod3::Error);
- BOOST_CHECK_THROW(atoms.GetIndex(4, "NE2"), promod3::Error)
+ BOOST_CHECK_THROW(atoms.GetIndex(4, "NE2"), promod3::Error);
BOOST_CHECK_THROW(atoms.GetIndex(6, "CG"), promod3::Error);
}
diff --git a/loop/tests/test_ss_assignment.cc b/loop/tests/test_ss_assignment.cc
deleted file mode 100644
index 3a922811e06e00d5342c43759646cfdc1c717d1c..0000000000000000000000000000000000000000
--- a/loop/tests/test_ss_assignment.cc
+++ /dev/null
@@ -1,50 +0,0 @@
-#include <promod3/loop/sec_struct.hh>
-#include <promod3/core/message.hh>
-#define BOOST_TEST_DYN_LINK
-#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
-
-#include <ost/io/mol/pdb_reader.hh>
-#include <ost/conop/heuristic.hh>
-#include <ost/mol/builder.hh>
-
-BOOST_AUTO_TEST_SUITE( loop );
-
-using namespace promod3::loop;
-
-BOOST_AUTO_TEST_CASE(test_ss_assignment){
-
- //load an entity to test...
- String pdb_name = "data/3DEFA.pdb";
-
- ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
- ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
- reader.Import(test_ent);
-
- ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor(false,true,true,true,ost::conop::CONOP_SILENT));
- processor->Process(test_ent);
-
- ost::mol::ResidueHandleList res_list = test_ent.GetResidueList();
-
- String sequence(res_list.size(),'X');
-
- for(uint i = 0; i < res_list.size(); ++i){
- sequence[i] = res_list[i].GetOneLetterCode();
- }
-
- BackboneList bb_list(sequence,res_list);
-
- String ss_estimate;
- EstimateSS(bb_list,ss_estimate);
-
- String expected_output = "CBCHHHHTSCHHHHHHHHHHHHHHHHTTCCEEEEEEEECTTSSHHHHHHH";
- expected_output += "HHTSCCSCCCSSCCSCCCEEEEEBETTEEEEEEECCCSEETTEECHHHHHHHHHHT";
- expected_output += "TTCEECEEEEEEESSCSCCCHHHHHHHHHHHHHHCGGGGGGEEEEEECTTCCCSTT";
- expected_output += "CCHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHCCEEEECCCCTTCCBCTTSCEECT";
- expected_output += "TSCBHHHHHHHHHHHHHTSCSCCEEC";
-
- BOOST_CHECK(ss_estimate == expected_output);
-}
-
-
-BOOST_AUTO_TEST_SUITE_END();
diff --git a/loop/tests/test_structuredb.cc b/loop/tests/test_structuredb.cc
new file mode 100644
index 0000000000000000000000000000000000000000..01cf26055402ab8a89363d2426287329d48a3dff
--- /dev/null
+++ b/loop/tests/test_structuredb.cc
@@ -0,0 +1,423 @@
+
+#include <promod3/loop/structure_db.hh>
+#include <promod3/core/message.hh>
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+
+#include <ost/io/mol/pdb_reader.hh>
+#include <ost/conop/heuristic.hh>
+#include <ost/io/seq/load.hh>
+#include <ost/mol/entity_view.hh>
+#include <ost/mol/alg/accessibility.hh>
+#include <ost/mol/alg/sec_struct.hh>
+
+BOOST_AUTO_TEST_SUITE( loop );
+
+namespace {
+
+ost::mol::EntityView LoadTestStructure(const String& path) {
+ ost::io::PDBReader reader(path, ost::io::IOProfile());
+ ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
+ reader.Import(test_ent);
+ ost::conop::HeuristicProcessor heu_proc;
+ heu_proc.Process(test_ent);
+ return test_ent.CreateFullView();
+}
+
+ost::seq::ProfileHandlePtr LoadTestProfile(const String& path) {
+ return ost::io::LoadSequenceProfile(path);
+}
+
+}
+
+using namespace promod3::loop;
+
+BOOST_AUTO_TEST_CASE(test_structuredb_initialization) {
+
+ // default initialization is supposed to contain all data
+ StructureDB db_one;
+
+ BOOST_CHECK(db_one.HasData(StructureDB::Dihedrals));
+ BOOST_CHECK(db_one.HasData(StructureDB::SolventAccessibilities));
+ BOOST_CHECK(db_one.HasData(StructureDB::ResidueDepths));
+ BOOST_CHECK(db_one.HasData(StructureDB::DSSP));
+ BOOST_CHECK(db_one.HasData(StructureDB::AAFrequencies));
+ BOOST_CHECK(db_one.HasData(StructureDB::AAFrequenciesStruct));
+
+
+ // test of bitwise or operation
+ StructureDB db_two(StructureDB::Dihedrals | StructureDB::DSSP);
+
+ BOOST_CHECK(db_two.HasData(StructureDB::Dihedrals));
+ BOOST_CHECK(!db_two.HasData(StructureDB::SolventAccessibilities));
+ BOOST_CHECK(!db_two.HasData(StructureDB::ResidueDepths));
+ BOOST_CHECK(db_two.HasData(StructureDB::DSSP));
+ BOOST_CHECK(!db_two.HasData(StructureDB::AAFrequencies));
+ BOOST_CHECK(!db_two.HasData(StructureDB::AAFrequenciesStruct));
+}
+
+
+BOOST_AUTO_TEST_CASE(test_structuredb_errors_when_adding_coordinates) {
+
+ ost::mol::EntityView test_ent =
+ LoadTestStructure("data/1A88A.pdb");
+
+ ost::seq::ProfileHandlePtr profile = LoadTestProfile("data/1A88A.hhm");
+ ost::seq::ProfileHandlePtr fake_profile = LoadTestProfile("data/1A88A.hhm");
+
+ String raw_seqres = profile->GetSequence();
+ String raw_seqres_fake = raw_seqres;
+ raw_seqres_fake[5] = 'Q';
+ fake_profile->SetSequence(raw_seqres_fake);
+
+ ost::seq::SequenceHandle seqres = ost::seq::CreateSequence("seqres",
+ raw_seqres);
+ ost::seq::SequenceHandle fake_seqres = ost::seq::CreateSequence("fake_seqres",
+ raw_seqres_fake);
+
+ // some StructureDBs to play around with
+ StructureDB db_full;
+ StructureDB db_no_aa_frequencies(StructureDB::Dihedrals |
+ StructureDB::SolventAccessibilities |
+ StructureDB::ResidueDepths |
+ StructureDB::DSSP);
+
+ // try to add chain that is not present
+ BOOST_CHECK_THROW(db_full.AddCoordinates("1a88", "X", test_ent,
+ seqres, profile),
+ promod3::Error);
+
+ // try to provide no valid profile
+ BOOST_CHECK_THROW(db_full.AddCoordinates("1a88", "A", test_ent,
+ seqres), promod3::Error);
+
+
+ // db_full has AAFrequencies, it therefore checks consistency between
+ // seqres and profile... lets trigger that error
+ BOOST_CHECK_THROW(db_full.AddCoordinates("1a88", "A", test_ent,
+ seqres, fake_profile),
+ promod3::Error);
+
+ // the above should work if we provide the right profile
+ BOOST_CHECK_NO_THROW(db_full.AddCoordinates("1a88", "A", test_ent,
+ seqres, profile));
+
+ // we check, whether we can add coordinates without valid profile
+ // in the DB without AAFrequencies
+ BOOST_CHECK_NO_THROW(db_no_aa_frequencies.AddCoordinates("1a88", "A",
+ test_ent, seqres));
+
+ // BUT an error is thrown if the seqres does not match with seqres!
+ BOOST_CHECK_THROW(db_no_aa_frequencies.AddCoordinates("1a88", "A",
+ test_ent, fake_seqres),
+ promod3::Error);
+
+
+ // also check whether size is properly checked when adding structure profile
+ ost::seq::ProfileHandlePtr short_profile = profile->Extract(10, 50);
+ BOOST_CHECK_THROW(db_full.SetStructureProfile(0, short_profile), promod3::Error);
+ BOOST_CHECK_NO_THROW(db_full.SetStructureProfile(0, profile));
+}
+
+BOOST_AUTO_TEST_CASE(test_structuredb_longest_stretch_flag) {
+
+ ost::mol::EntityView test_ent_with_gap =
+ LoadTestStructure("data/1A88A_with_gap.pdb");
+ ost::seq::ProfileHandlePtr profile = LoadTestProfile("data/1A88A.hhm");
+ String raw_seqres = profile->GetSequence();
+ ost::seq::SequenceHandle seqres = ost::seq::CreateSequence("seqres",
+ raw_seqres);
+
+
+ StructureDB db;
+
+ // we add coordinates with longest stretch flag set to true
+ db.AddCoordinates("1a88", "A", test_ent_with_gap,
+ seqres, profile, true);
+
+ // we expect exactly one entry
+ BOOST_CHECK(db.GetNumCoords() == 1);
+
+ // with length 255
+ BOOST_CHECK(db.GetCoordInfo(0).size == 255);
+
+ // we add coordinates with longest stretch flag set to false
+ db.AddCoordinates("1a88", "A", test_ent_with_gap,
+ seqres, profile, false);
+
+ // we expect two more entries
+ BOOST_CHECK(db.GetNumCoords() == 3);
+
+ // with lengths 17 and 255
+ BOOST_CHECK(db.GetCoordInfo(1).size == 17);
+ BOOST_CHECK(db.GetCoordInfo(2).size == 255);
+}
+
+BOOST_AUTO_TEST_CASE(test_fragment_validity) {
+
+ ost::mol::EntityView test_ent = LoadTestStructure("data/1A88A.pdb");
+ ost::seq::ProfileHandlePtr profile = LoadTestProfile("data/1A88A.hhm");
+ String raw_seqres = profile->GetSequence();
+ ost::seq::SequenceHandle seqres = ost::seq::CreateSequence("seqres",
+ raw_seqres);
+
+ StructureDB db;
+
+ // lets add some stuff
+ db.AddCoordinates("1a88", "A", test_ent, seqres, profile, true);
+
+ FragmentInfo valid_frag_info(0, 5, 12);
+ FragmentInfo invalid_coord_idx(1, 5, 12);
+ FragmentInfo invalid_offset(0, 1000, 12);
+ FragmentInfo invalid_length(0, 5, 1000);
+
+ BOOST_CHECK_NO_THROW(db.GetSequence(valid_frag_info));
+ BOOST_CHECK_THROW(db.GetSequence(invalid_coord_idx), promod3::Error);
+ BOOST_CHECK_THROW(db.GetSequence(invalid_offset), promod3::Error);
+ BOOST_CHECK_THROW(db.GetSequence(invalid_length), promod3::Error);
+}
+
+BOOST_AUTO_TEST_CASE(test_data_extraction) {
+
+ ost::mol::EntityView test_ent = LoadTestStructure("data/1A88A.pdb");
+ ost::seq::ProfileHandlePtr profile = LoadTestProfile("data/1A88A.hhm");
+ String raw_seqres = profile->GetSequence();
+ ost::seq::SequenceHandle seqres = ost::seq::CreateSequence("seqres",
+ raw_seqres);
+
+ StructureDB db;
+
+ // we add coordinates with longest stretch flag set to true,
+ // the first entry therefore corresponds to residue with resnum 21
+ db.AddCoordinates("1a88", "A", test_ent, seqres, profile, true);
+
+ // we reload an entity in order to forget all generic properties that have
+ // been set in AddCoordinates
+ test_ent = LoadTestStructure("data/1A88A.pdb");
+
+ // we test the data for the residues in a range 25-50
+ ost::mol::EntityView sel = test_ent.Select("rnum=25:50");
+ ost::mol::ResidueViewList residues = sel.GetResidueList();
+ ost::mol::ResidueHandleList residue_handles;
+ for(ost::mol::ResidueViewList::iterator it = residues.begin();
+ it != residues.end(); ++it) {
+ residue_handles.push_back(it->GetHandle());
+ }
+
+ // lets assign secondary structures and solvent accessibilities
+ ost::mol::alg::AssignSecStruct(test_ent);
+ ost::mol::alg::Accessibility(test_ent);
+
+ // lets extract data directly from the structure
+
+ String expected_sequence(residues.size(), 'X');
+ for(uint i = 0; i < residues.size(); ++i) {
+ expected_sequence[i] = residues[i].GetOneLetterCode();
+ }
+
+ BackboneList expected_bb_list(expected_sequence, residue_handles);
+
+ std::vector<Real> expected_sol_acc;
+ for(ost::mol::ResidueViewList::iterator it = residues.begin();
+ it != residues.end(); ++it) {
+ expected_sol_acc.push_back(it->GetFloatProp("asaAbs"));
+ }
+
+ std::vector<char> expected_sec_struct;
+ for(ost::mol::ResidueViewList::iterator it = residues.begin();
+ it != residues.end(); ++it) {
+ expected_sec_struct.push_back(char(it->GetSecStructure()));
+ }
+
+ std::vector<Real> expected_phi_torsions;
+ std::vector<Real> expected_psi_torsions;
+ for(ost::mol::ResidueViewList::iterator it = residues.begin();
+ it != residues.end(); ++it) {
+ expected_phi_torsions.push_back(it->GetPhiTorsion().GetAngle());
+ expected_psi_torsions.push_back(it->GetPsiTorsion().GetAngle());
+ }
+
+ ost::seq::ProfileHandlePtr expected_prof = profile->Extract(24, 50);
+
+ // and compare it with the data from the StructureDB
+ FragmentInfo frag_info(0, 24, 26);
+
+ String sequence = db.GetSequence(frag_info);
+ BOOST_CHECK(sequence.size() == expected_sequence.size());
+ for(uint i = 0; i < sequence.size(); ++i) {
+ BOOST_CHECK(sequence[i] == expected_sequence[i]);
+ }
+
+ BackboneList bb_list;
+ db.FillBackbone(bb_list, frag_info, sequence);
+ BOOST_CHECK(bb_list.GetSequence() == expected_bb_list.GetSequence());
+ BOOST_CHECK(bb_list.RMSD(expected_bb_list, true) < 0.1);
+
+ // if we reverse the shift that has been applied in AddCoordinates,
+ // the superposition flag in RMSD() should not be necessary anymore
+ geom::Vec3 shift = db.GetCoordInfo(0).shift;
+ geom::Mat4 transform;
+ transform(0,3) = -shift[0];
+ transform(1,3) = -shift[1];
+ transform(2,3) = -shift[2];
+ bb_list.ApplyTransform(transform);
+ BOOST_CHECK(bb_list.RMSD(expected_bb_list, false) < 0.1);
+
+ std::vector<int> sol_acc = db.GetSolventAccessibilities(frag_info);
+ BOOST_CHECK(sol_acc.size() == expected_sol_acc.size());
+ for(uint i = 0; i < sol_acc.size(); ++i) {
+ BOOST_CHECK(static_cast<unsigned short>(expected_sol_acc[i]) == sol_acc[i]);
+ }
+
+ String sec_struct = db.GetDSSPStates(frag_info);
+ BOOST_CHECK(sec_struct.size() == expected_sec_struct.size());
+ for(uint i = 0; i < sec_struct.size(); ++i) {
+ BOOST_CHECK(sec_struct[i] == expected_sec_struct[i]);
+ }
+
+ std::vector<std::pair<Real, Real> > torsion_angles =
+ db.GetDihedralAngles(frag_info);
+ BOOST_CHECK(torsion_angles.size() == expected_phi_torsions.size());
+ BOOST_CHECK(torsion_angles.size() == expected_psi_torsions.size());
+ for(uint i = 0; i < torsion_angles.size(); ++i) {
+ Real phi_d = std::abs(torsion_angles[i].first - expected_phi_torsions[i]);
+ Real psi_d = std::abs(torsion_angles[i].second - expected_psi_torsions[i]);
+ BOOST_CHECK(phi_d < 0.001);
+ BOOST_CHECK(psi_d < 0.001);
+ }
+
+ ost::seq::ProfileHandlePtr prof = db.GetSequenceProfile(frag_info);
+ BOOST_CHECK(prof->size() == expected_prof->size());
+ BOOST_CHECK(prof->GetSequence() == expected_prof->GetSequence());
+
+ for(uint i = 0; i < prof->size(); ++i) {
+ const ost::seq::ProfileColumn& col = (*prof)[i];
+ const ost::seq::ProfileColumn& expected_col = (*expected_prof)[i];
+
+ const Real* freqs = col.freqs_begin();
+ const Real* expected_freqs = expected_col.freqs_begin();
+
+ for(uint j = 0; j < 20; ++j) {
+ Real diff = std::abs(freqs[j] - expected_freqs[j]);
+ BOOST_CHECK(diff < 0.001);
+ }
+ }
+
+ // the structure profile is expected to contain only zeros for now
+ ost::seq::ProfileHandlePtr structure_prof = db.GetStructureProfile(frag_info);
+ for(uint i = 0; i < structure_prof->size(); ++i) {
+ const ost::seq::ProfileColumn& col = (*structure_prof)[i];
+ const Real* freqs = col.freqs_begin();
+ for(uint j = 0; j < 20; ++j) {
+ BOOST_CHECK(freqs[j] == 0.0);
+ }
+ }
+
+ // we set the sequence profile as structure profile
+ db.SetStructureProfile(0, profile);
+ structure_prof = db.GetStructureProfile(frag_info);
+
+ // now it should be the same as expected_prof...
+ BOOST_CHECK(structure_prof->size() == expected_prof->size());
+ BOOST_CHECK(structure_prof->GetSequence() == expected_prof->GetSequence());
+
+ for(uint i = 0; i < structure_prof->size(); ++i) {
+ const ost::seq::ProfileColumn& col = (*structure_prof)[i];
+ const ost::seq::ProfileColumn& expected_col = (*expected_prof)[i];
+
+ const Real* freqs = col.freqs_begin();
+ const Real* expected_freqs = expected_col.freqs_begin();
+
+ for(uint j = 0; j < 20; ++j) {
+ Real diff = std::abs(freqs[j] - expected_freqs[j]);
+ BOOST_CHECK(diff < 0.001);
+ }
+ }
+}
+
+BOOST_AUTO_TEST_CASE(test_coordinate_removal) {
+
+ ost::mol::EntityView test_ent_with_gap =
+ LoadTestStructure("data/1A88A_with_gap.pdb");
+ ost::seq::ProfileHandlePtr profile = LoadTestProfile("data/1A88A.hhm");
+ String raw_seqres = profile->GetSequence();
+ ost::seq::SequenceHandle seqres = ost::seq::CreateSequence("seqres",
+ raw_seqres);
+
+
+ StructureDB db_one;
+ StructureDB db_two;
+
+ // we add coordinates with longest stretch flag set to false
+ db_one.AddCoordinates("1a88", "A", test_ent_with_gap,
+ seqres, profile, false);
+
+ db_two.AddCoordinates("1a88", "A", test_ent_with_gap,
+ seqres, profile, false);
+
+ // we're expecting two entries in the database
+ BOOST_CHECK(db_one.GetNumCoords() == 2);
+ BOOST_CHECK(db_two.GetNumCoords() == 2);
+
+ db_two.RemoveCoordinates(0);
+
+ // now its one...
+ BOOST_CHECK(db_two.GetNumCoords() == 1);
+
+ // check the CoordInfoObjects
+ BOOST_CHECK(db_one.GetCoordInfo(1).id ==
+ db_two.GetCoordInfo(0).id);
+ BOOST_CHECK(db_one.GetCoordInfo(1).chain_name ==
+ db_two.GetCoordInfo(0).chain_name);
+ // offset requires some special treatment
+ BOOST_CHECK(db_one.GetCoordInfo(1).offset - db_one.GetCoordInfo(0).size ==
+ db_two.GetCoordInfo(0).offset);
+ BOOST_CHECK(db_one.GetCoordInfo(1).size ==
+ db_two.GetCoordInfo(0).size);
+ BOOST_CHECK(db_one.GetCoordInfo(1).start_resnum ==
+ db_two.GetCoordInfo(0).start_resnum);
+ BOOST_CHECK(db_one.GetCoordInfo(1).shift ==
+ db_two.GetCoordInfo(0).shift);
+
+ // the FragmentInfo objects defined here should point at the same information
+ // in their corresponding databases
+ FragmentInfo frag_info_one(1, 24, 10);
+ FragmentInfo frag_info_two(0, 24, 10);
+
+ BOOST_CHECK(db_one.GetSequence(frag_info_one) ==
+ db_two.GetSequence(frag_info_two));
+
+ BackboneList bb_list_one;
+ db_one.FillBackbone(bb_list_one, frag_info_one,
+ db_one.GetSequence(frag_info_one));
+
+ BackboneList bb_list_two;
+ db_two.FillBackbone(bb_list_two, frag_info_two,
+ db_two.GetSequence(frag_info_two));
+
+ BOOST_CHECK(bb_list_one.RMSD(bb_list_two) < 0.001);
+
+ BOOST_CHECK(db_one.GetDSSPStates(frag_info_one) ==
+ db_two.GetDSSPStates(frag_info_two));
+
+ BOOST_CHECK(db_one.GetDihedralAngles(frag_info_one) ==
+ db_two.GetDihedralAngles(frag_info_two));
+
+ BOOST_CHECK(db_one.GetResidueDepths(frag_info_one) ==
+ db_two.GetResidueDepths(frag_info_two));
+
+ BOOST_CHECK(db_one.GetSolventAccessibilities(frag_info_one) ==
+ db_two.GetSolventAccessibilities(frag_info_two));
+
+ BOOST_CHECK((*db_one.GetSequenceProfile(frag_info_one)) ==
+ (*db_two.GetSequenceProfile(frag_info_two)));
+
+ BOOST_CHECK((*db_one.GetStructureProfile(frag_info_one)) ==
+ (*db_two.GetStructureProfile(frag_info_two)));
+}
+
+
+
+
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/modelling/doc/algorithms.rst b/modelling/doc/algorithms.rst
index 439fd2d9009650a24933a6ccaebb0a6d567c8528..7ff5ae3a33e08ccccdf6d98f87abe2748e1d0d19 100644
--- a/modelling/doc/algorithms.rst
+++ b/modelling/doc/algorithms.rst
@@ -24,11 +24,9 @@ iterative superposition multiple times by using a sliding window to select the
initial subset and gathers all unique results. These results can be very
similar and only differ by single positions. The algorithm therefore reduces
the amount of solutions by merging them based on a threshold of similarity.
-If the sum of matching positions within the distance threshold divided by
-the maximum length of the two solutions is above a cluster thresh, the two
-solutions get merged by producing a common solution containing the shared
-positions. As a final result, the algorithm therefore detects common rigid
-subsets of positions.
+The similarity is defined by the fraction of positions in solution A that are
+also present in solution B. As a final result, the algorithm therefore detects
+common rigid subsets of positions.
.. method:: RigidBlocks(bb_list_one, bb_list_two, [window_length = 12, max_iterations=20, distance_thresh=3.0, cluster_thresh=0.9])
diff --git a/modelling/doc/loop_candidates.rst b/modelling/doc/loop_candidates.rst
index dc3b5c96a28b7320d2fbb4dbdf47fe2492b49ff1..d0711c5a7c89292a61e3f1547ed28af62841382b 100644
--- a/modelling/doc/loop_candidates.rst
+++ b/modelling/doc/loop_candidates.rst
@@ -67,6 +67,12 @@ The LoopCandidates class
Uses Monte Carlo simulated annealing to sample the loop to be modelled.
If *initial_bb* is given, every Monte Carlo run starts from that configuration.
+
+ .. warning:: The :class:`~promod3.scoring.BackboneScoreEnv`
+ attached to *scorer* will be altered in the specified stretch.
+ You might consider the Stash / Pop mechanism of the
+ :class:`~promod3.scoring.BackboneScoreEnv` to restore to the
+ original state once the sampling is done.
:param initial_bb: Initial configuration used for the sampling
:param seq: The sequence of residues to be sampled
@@ -181,10 +187,14 @@ The LoopCandidates class
useful to keep track of scores and other data extracted before.
:rtype: :class:`list` of :class:`int`
- .. method:: CalculateBackboneScores(score_container, scorer, \
+ .. method:: CalculateBackboneScores(score_container, scorer, scorer_env,\
start_resnum, chain_idx=0)
- CalculateBackboneScores(score_container, scorer, keys, \
+ CalculateBackboneScores(score_container, scorer, scorer_env,\
+ keys, start_resnum, chain_idx=0)
+ CalculateBackboneScores(score_container, mhandle,\
start_resnum, chain_idx=0)
+ CalculateBackboneScores(score_container, mhandle,\
+ keys, start_resnum, chain_idx=0)
CalculateAllAtomScores(score_container, mhandle, \
start_resnum, chain_idx=0)
CalculateAllAtomScores(score_container, mhandle, keys, \
@@ -201,7 +211,10 @@ The LoopCandidates class
:param scorer: Backbone scoring object with set environment for the
particular loop modelling problem.
:type scorer: :class:`~promod3.scoring.BackboneOverallScorer`
- :param mhandle: Modelling handle set up for all atom scoring (see
+ :param scorer_env: The scoring environment attached to *scorer*
+ :type scorer_env: :class:`~promod3.scoring.BackboneScoreEnv`
+ :param mhandle: Modelling handle set up scoring (see
+ :func:`SetupDefaultBackboneScoring`
:func:`SetupDefaultAllAtomScoring`).
:type mhandle: :class:`ModellingHandle`
:param keys: Keys of the desired scorers. If not given, we use the set of
@@ -484,15 +497,25 @@ on loop candidates.
a consistent naming of keys used for backbone and all atom scorers as set up
by :func:`SetupDefaultBackboneScoring` and :func:`SetupDefaultAllAtomScoring`.
+ Different sets of weights are available. You can get general weights
+ that have been optimized for a non redundant set of loops with lengths [3,14]
+ (including stem residues). The alternative is to get weights that have only
+ been optimized on a length specific subset of loops. By default you get
+ different weights for following lengths: [0,1,2,3,4], [5,6], [7,8], [9,10],
+ [11,12], [13,14].
+
If you choose to modify the weights, please ensure to set consistently named
keys in here and to use consistently named scorers and scoring computations!
- .. staticmethod:: GetWeights(with_db=False, with_aa=False)
+ .. staticmethod:: GetWeights(with_db=False, with_aa=False,\
+ length_dependent=False, loop_length=-1)
:return: Named weights to be used when scoring loop candidates. The default
weights were optimized to give the best performance when choosing
the loop candidate with the lowest combined score. Each set of
- weights includes (different) backbone scoring weights.
+ weights includes (different) backbone scoring weights, that are
+ optionally only trained on a subset of loops with corresponding
+ loop length.
:rtype: :class:`dict` (keys: :class:`str`, values: :class:`float`)
:param with_db: True to choose a set of weights including DB specific scores
@@ -500,12 +523,21 @@ on loop candidates.
:type with_db: :class:`bool`
:param with_aa: True to choose a set of weights including all atom scores
:type with_aa: :class:`bool`
+ :param length_dependent: Whether to use general weights or their length
+ length dependent counterparts.
+ :type length_dependent: :class:`bool`
+ :param loop_length: Length of full loop. If no weights are available for
+ this length or when *loop_length* is -1, the general
+ weights are returned.
+ :type loop_length: :class:`int`
- .. staticmethod:: SetWeights(with_db, with_aa, weights)
+ .. staticmethod:: SetWeights(with_db, with_aa, weights,\
+ length_dependent=False, loop_length=-1)
Overwrite a set of weights as returned by :meth:`GetWeights`.
- .. staticmethod:: GetBackboneWeights(with_db=False, with_aa=False)
+ .. staticmethod:: GetBackboneWeights(with_db=False, with_aa=False,\
+ length_dependent=False, loop_length=-1)
:return: Subset of :meth:`GetWeights` for backbone scoring as in
:meth:`scoring.BackboneOverallScorer.CalculateLinearCombination`.
@@ -515,8 +547,13 @@ on loop candidates.
:type with_db: :class:`bool`
:param with_aa: As in :meth:`GetWeights`
:type with_aa: :class:`bool`
+ :param length_dependent: As in :meth:`GetWeights`
+ :type length_dependent: :class:`bool`
+ :param loop_length: As in :meth:`GetWeights`
+ :type loop_length: :class:`int`
- .. staticmethod:: GetAllAtomWeights(with_db=False)
+ .. staticmethod:: GetAllAtomWeights(with_db=False, length_dependent=False,\
+ loop_length=-1)
:return: Subset of :meth:`GetWeights` for all atom scoring as in
:meth:`scoring.AllAtomOverallScorer.CalculateLinearCombination`.
@@ -524,6 +561,10 @@ on loop candidates.
:param with_db: As in :meth:`GetWeights`
:type with_db: :class:`bool`
+ :param length_dependent: As in :meth:`GetWeights`
+ :type length_dependent: :class:`bool`
+ :param loop_length: As in :meth:`GetWeights`
+ :type loop_length: :class:`int`
.. staticmethod:: GetStemRMSDsKey()
diff --git a/modelling/doc/loop_closing.rst b/modelling/doc/loop_closing.rst
index 386458ba39abdf80e0b2289a35c5eb25b7cb6463..7ec7230b20a4e32fd9cc1f15a9e84ea7b549c113 100644
--- a/modelling/doc/loop_closing.rst
+++ b/modelling/doc/loop_closing.rst
@@ -197,7 +197,11 @@ the relaxer.
.. method:: Run(bb_list, steps=100, stop_criterion=0.01)
- Performs steepest descent on given BackboneList.
+ Performs steepest descent on given BackboneList. The function possibly fails
+ if there are particles (almost) on top of each other, resulting in NaN
+ positions in the OpenMM system. The positions of **bb_list** are not touched
+ in this case and the function returns an infinit potential energy.
+ In Python you can check for that with float("inf").
:param bb_list: To be relaxed
:param steps: number of steepest descent steps
@@ -209,7 +213,7 @@ the relaxer.
:type steps: :class:`int`
:type stop_criterion: :class:`float`
- :return: Forcefield energy upon relaxation
+ :return: Forcefield energy upon relaxation, infinity in case of OpenMM Error
:rtype: :class:`float`
:raises: :exc:`~exceptions.RuntimeError` if *bb_list* has not the same
@@ -332,7 +336,11 @@ Example usage:
.. method:: Run(sc_data, steps=100, stop_criterion=0.01)
Performs steepest descent for this system and writes updated positions into
- *sc_data.env_pos.all_pos*.
+ *sc_data.env_pos.all_pos*. The function possibly fails
+ if there are particles (almost) on top of each other, resulting in NaN
+ positions in the OpenMM system. The positions of *sc_data.env_pos.all_pos*
+ are not touched in this case and the function returns an infinit potential
+ energy. In Python you can check for that with float("inf").
:param sc_data: Sidechain reconstruction result to be updated
:type sc_data: :class:`~promod3.modelling.SidechainReconstructionData`
@@ -342,7 +350,7 @@ Example usage:
that threshold, the relaxation aborts.
:type stop_criterion: :class:`float`
- :return: Potential energy after relaxation
+ :return: Potential energy after relaxation, infinity in case of OpenMM Error
:rtype: :class:`float`
:raises: :exc:`~exceptions.RuntimeError` if *sc_data* is incompatible with
diff --git a/modelling/doc/monte_carlo.rst b/modelling/doc/monte_carlo.rst
index 328b73d366cf8ce5a6affe7cce3d27a1d6325036..56e572a8788749bde35c415893a964126c5e67b9 100644
--- a/modelling/doc/monte_carlo.rst
+++ b/modelling/doc/monte_carlo.rst
@@ -402,18 +402,29 @@ The scorer asses a proposed conformation and are intended to return a pseudo
energy, the lower the better.
-.. class:: LinearScorer(scorer, start_resnum, chain_idx, linear_weights)
+.. class:: LinearScorer(scorer, scorer_env, start_resnum, num_residues,
+ chain_idx, linear_weights)
The LinearScorer allows to combine the scores available from
:class:`~promod3.scoring.BackboneOverallScorer` in a linear manner. See
:meth:`~promod3.scoring.BackboneOverallScorer.CalculateLinearCombination` for a
detailed description of the arguments.
+ .. warning:: The provided *scorer_env* will be altered in every
+ :func:`GetScore` call.
+ You might consider the Stash / Pop mechanism of the
+ :class:`~promod3.scoring.BackboneScoreEnv` to restore to the
+ original state once the sampling is done.
+
:param scorer: Scorer Object with set environment for the particular loop
modelling problem.
:type scorer: :class:`~promod3.scoring.BackboneOverallScorer`
+ :param scorer_env: The environment that is linked to the *scorer*
+ :type scorer_env: :class:`~promod3.scoring.BackboneScoreEnv`
:param start_resnum: Res. number defining the position in the SEQRES.
:type start_resnum: :class:`int`
+ :param num_residues: Number of residues to score
+ :type num_residues: :class:`int`
:param chain_idx: Index of chain the loop(s) belong to.
:type chain_idx: :class:`int`
:param linear_weights: Weights for each desired scorer.
diff --git a/modelling/doc/pipeline.rst b/modelling/doc/pipeline.rst
index db7dc9d5bf060bf81fcca1e3b918b9824d6d145d..175b65c5d6554d15f76076e3bd3c530595a7cf64 100644
--- a/modelling/doc/pipeline.rst
+++ b/modelling/doc/pipeline.rst
@@ -236,10 +236,8 @@ Modelling Steps
- "reduced": :class:`~promod3.scoring.ReducedScorer`
- "clash": :class:`~promod3.scoring.ClashScorer`
- "hbond": :class:`~promod3.scoring.HBondScorer`
- - "ss_agreement": :class:`~promod3.scoring.SSAgreementScorer`
- "torsion": :class:`~promod3.scoring.TorsionScorer`
- "pairwise": :class:`~promod3.scoring.PairwiseScorer`
- - "density": :class:`~promod3.scoring.DensityScorer`
:param mhandle: The modelling handle. This will set the properties
:attr:`~ModellingHandle.backbone_scorer` and
diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py
index 96b5f819145b8c3fbd48d8b05127ba4d95e8a5c2..aa857023be8b7543a56670d0b8db6e340a4edcf1 100644
--- a/modelling/pymod/_closegaps.py
+++ b/modelling/pymod/_closegaps.py
@@ -15,7 +15,7 @@ import sys
###############################################################################
# loop candidate selection setup
def _GetBestLC(mhandle, loop_candidates, start_resnum, chain_idx,
- db_scores, max_num_all_atom=0):
+ db_scores, max_num_all_atom=0, length_dep_weights=False):
# returns (min_idx, min_score)
# dummy check
@@ -25,19 +25,24 @@ def _GetBestLC(mhandle, loop_candidates, start_resnum, chain_idx,
# setup weights
with_db = (not db_scores.IsEmpty())
with_aa = (max_num_all_atom > 0)
- weights = ScoringWeights.GetWeights(with_db, with_aa)
+ weights = ScoringWeights.GetWeights(with_db, with_aa,
+ length_dep_weights,
+ len(loop_candidates[0]))
# setup all scores object (we collect needed scores there)
all_scores = db_scores.Copy() # copy to avoid changing db_scores
# add backbone scores
- loop_candidates.CalculateBackboneScores(all_scores, mhandle.backbone_scorer,
+ loop_candidates.CalculateBackboneScores(all_scores, mhandle,
start_resnum, chain_idx)
# add all atom scores?
if with_aa:
# get best ones based on previous scores
- non_aa_weights = ScoringWeights.GetWeights(with_db, False)
+ non_aa_weights = ScoringWeights.GetWeights(with_db, False,
+ length_dep_weights,
+ len(loop_candidates[0]))
+
non_aa_scores = all_scores.LinearCombine(non_aa_weights)
arg_sorted_scores = sorted([(v,i) for i,v in enumerate(non_aa_scores)])
min_indices = [i for v,i in arg_sorted_scores[:max_num_all_atom]]
@@ -102,7 +107,8 @@ def _ResolveLogInfo(gap_orig, optimal_gap, n_candidates, with_db, with_aa):
(str(gap_orig), str(optimal_gap), n_candidates, scor_str))
def _CloseLoopFrame(mhandle, gap_orig, actual_candidates, actual_extended_gaps,
- actual_db_scores=[], max_num_all_atom=0):
+ actual_db_scores=[], max_num_all_atom=0,
+ length_dep_weights=False):
'''Rank candidates with "frame-approach".
All found candidates are extended prior to scoring so they match in size.
'''
@@ -153,7 +159,8 @@ def _CloseLoopFrame(mhandle, gap_orig, actual_candidates, actual_extended_gaps,
# get best
min_idx, min_score = _GetBestLC(mhandle, final_loop_candidates,
min_before_resnum, actual_chain_idx,
- db_scores, max_num_all_atom)
+ db_scores, max_num_all_atom,
+ length_dep_weights)
ost.LogVerbose("Gap %s - %d candidates, best (min) score %g" %
(str(gap_orig), len(final_loop_candidates), min_score))
# resolve loop
@@ -174,7 +181,7 @@ def _CloseLoopFrame(mhandle, gap_orig, actual_candidates, actual_extended_gaps,
def _CloseLoopBare(mhandle, gap_orig, actual_candidates, actual_extended_gaps,
actual_db_scores=[], penalize_length=True,
- max_num_all_atom=0):
+ max_num_all_atom=0, length_dep_weights=False):
'''Rank candidates directly.
All candidates are scored directly and optionally penalized for gap length.
'''
@@ -196,7 +203,7 @@ def _CloseLoopBare(mhandle, gap_orig, actual_candidates, actual_extended_gaps,
db_scores = actual_db_scores[i]
best_idx, score = _GetBestLC(mhandle, loop_candidates, before_resnum,
actual_chain_idx, db_scores,
- max_num_all_atom)
+ max_num_all_atom, length_dep_weights)
# compare with others
if penalize_length:
# penalized by gap length
@@ -224,7 +231,7 @@ def _CloseLoopBare(mhandle, gap_orig, actual_candidates, actual_extended_gaps,
def _CloseLoop(mhandle, gap_orig, actual_candidates,
actual_extended_gaps, variant=0, actual_db_scores=[],
- max_num_all_atom=0):
+ max_num_all_atom=0, length_dep_weights=False):
'''Choose best scoring loop candidate and close loop in mhandle.
:param gap_orig: Gap we actually wanted to close
:param actual_candidates: List of LoopCandidates
@@ -250,11 +257,12 @@ def _CloseLoop(mhandle, gap_orig, actual_candidates,
if variant == 0:
return _CloseLoopFrame(mhandle, gap_orig, actual_candidates,
actual_extended_gaps, actual_db_scores,
- max_num_all_atom)
+ max_num_all_atom, length_dep_weights)
elif variant in [1,2]:
return _CloseLoopBare(mhandle, gap_orig, actual_candidates,
actual_extended_gaps, actual_db_scores,
- variant == 2, max_num_all_atom)
+ variant == 2, max_num_all_atom,
+ length_dep_weights)
else:
raise RuntimeError("Unknown variant %d" % variant);
@@ -290,11 +298,14 @@ def _InRange(gap, chain_idx, resnum_range):
return True
def _GetMCWeights():
- # get weights for Monte Carlo sampling (BB only)
- return {"reduced": 3.0,
- "cb_packing": 2.0,
- "hbond": 1.0,
- "clash": 0.05}
+ # get weights for Monte Carlo sampling (subset of BB only scores for super
+ # fast sampling)
+ bb_weights = ScoringWeights.GetWeights()
+ return_weights = dict()
+ return_weights["reduced"] = bb_weights["reduced"]
+ return_weights["cb_packing"] = bb_weights["cb_packing"]
+ return_weights["clash"] = bb_weights["clash"]
+ return return_weights
###############################################################################
@@ -335,7 +346,8 @@ def CloseSmallDeletions(mhandle, max_extension=9, clash_thresh=1.0,
For the scondary-structure-penalty to work,
the model-template must have the appropriate
information before :func:`BuildRawModel` is
- called (e.g. with :mod:`ost.bindings.dssp`).
+ called (e.g. with
+ :meth:`ost.mol.alg.AssignSecStruct`).
:type use_scoring_extender: :class:`bool`
:param use_full_extender: True = use :class:`FullGapExtender` instead of
@@ -374,7 +386,12 @@ def CloseSmallDeletions(mhandle, max_extension=9, clash_thresh=1.0,
# check/setup scoring
if not IsBackboneScoringSetUp(mhandle):
SetupDefaultBackboneScoring(mhandle)
- clash_scorer = mhandle.backbone_scorer.Get("clash")
+
+ # we're only calculating clash scores here, so we copy the default
+ # env and only attach a clash scorer.
+ clash_scorer_env = mhandle.backbone_scorer_env.Copy()
+ clash_scorer = scoring.ClashScorer()
+ clash_scorer.AttachEnvironment(clash_scorer_env)
if ff_lookup == None:
ff_lookup = loop.ForcefieldLookup.GetDefault()
@@ -433,9 +450,18 @@ def CloseSmallDeletions(mhandle, max_extension=9, clash_thresh=1.0,
bb_relaxer = BackboneRelaxer(bb_list, ff_lookup)
potential_e = bb_relaxer.Run(bb_list, 300, 0.1)
# check for clashes
- score = clash_scorer.CalculateScore(bb_list,
- n_stem_resnum.GetNum(),
+
+ # its a bit problematic since we score loops that are shifting
+ # around... so we perform a stash operation for each scoring step
+
+ clash_scorer_env.Stash(n_stem_resnum.GetNum(),
+ len(bb_list), current_chain_index)
+ clash_scorer_env.SetEnvironment(bb_list, n_stem_resnum.GetNum(),
+ current_chain_index)
+ score = clash_scorer.CalculateScore(n_stem_resnum.GetNum(),
+ len(bb_list),
current_chain_index)
+ clash_scorer_env.Pop()
# if there is no clash and potential energy is low enough we
# just solved a gap, delete it and update the scorer for the
@@ -446,9 +472,13 @@ def CloseSmallDeletions(mhandle, max_extension=9, clash_thresh=1.0,
ost.LogInfo("Closed: %s by relaxing %s" % \
(mhandle.gaps[current_gap_index], current_gap))
InsertLoopClearGaps(mhandle, bb_list, current_gap)
+ clash_scorer_env.SetEnvironment(bb_list,
+ n_stem_resnum.GetNum(),
+ current_chain_index)
success = True
break
+
# On closed gap, it is removed so the no. of gaps goes down by itself.
# In case of no success, counter needs to be increased to jump to the
# next gap.
@@ -539,7 +569,7 @@ def FillLoopsByDatabase(mhandle, fragment_db, structure_db,
use_full_extender=True, score_variant=0,
ring_punch_detection=1, chain_idx=None,
resnum_range=None, max_num_all_atom=0,
- clash_thresh=-1):
+ clash_thresh=-1, length_dep_weights=False):
'''Try to fill up loops from a structural database.
Usually this will extend the gaps a bit to match candidates from the
@@ -637,6 +667,13 @@ def FillLoopsByDatabase(mhandle, fragment_db, structure_db,
:param clash_thresh: If > 0, we only keep loop candidates which have a
backbone clash score lower than this.
:type clash_thresh: :class:`float`
+
+ :param length_dep_weights: :class:`ScoringWeights` provides different sets
+ of weights that have been trained on different
+ loop subsets. If this flag is true, the length
+ dependent weights are used to select the final
+ loops.
+ :type length_dep_weights: :class:`bool`
'''
prof_name = 'closegaps::FillLoopsByDatabase'
@@ -757,13 +794,15 @@ def FillLoopsByDatabase(mhandle, fragment_db, structure_db,
# remove clashing ones if desired
if clash_thresh > 0:
- scorer = mhandle.backbone_scorer.Get("clash")
+ clash_score_container = ScoreContainer()
+ candidates.CalculateBackboneScores(clash_score_container,
+ mhandle, ["clash"],
+ n_stem.GetNumber().GetNum(),
+ actual_gap.GetChainIndex())
+ clash_scores = clash_score_container.Get("clash")
to_keep = []
for i, bb_list in enumerate(candidates):
- score = scorer.CalculateScore(bb_list,
- n_stem.GetNumber().GetNum(),
- actual_gap.GetChainIndex())
- if score < clash_thresh:
+ if clash_scores[i] < clash_thresh:
to_keep.append(i)
candidates = candidates.Extract(to_keep)
orig_indices = [orig_indices[i] for i in to_keep]
@@ -815,7 +854,8 @@ def FillLoopsByDatabase(mhandle, fragment_db, structure_db,
##################################
new_idx = _CloseLoop(mhandle, gap_orig, actual_candidates,
actual_extended_gaps, score_variant,
- actual_db_scores, max_num_all_atom)
+ actual_db_scores, max_num_all_atom,
+ length_dep_weights)
if new_idx == -2:
# try next one if we failed
gap_idx += 1
@@ -831,7 +871,7 @@ def FillLoopsByMonteCarlo(mhandle, torsion_sampler, max_loops_to_search=6,
use_scoring_extender=True, use_full_extender=True,
score_variant=0, ring_punch_detection=1,
fragger_handles=None, chain_idx=None,
- resnum_range=None):
+ resnum_range=None, length_dep_weights=False):
'''Try to fill up loops with Monte Carlo sampling.
This is meant as a "last-resort" approach when it is not possible to fill
@@ -898,6 +938,13 @@ def FillLoopsByMonteCarlo(mhandle, torsion_sampler, max_loops_to_search=6,
:param resnum_range: If not None, only gaps within this resnum range get
processed
:type resnum_range: :class:`tuple` containing two :class:`int`
+
+ :param length_dep_weights: :class:`ScoringWeights` provides different sets
+ of weights that have been trained on different
+ loop subsets. If this flag is true, the length
+ dependent weights are used to select the final
+ loops.
+ :type length_dep_weights: :class:`bool`
'''
prof_name = 'closegaps::FillLoopsByMonteCarlo'
@@ -999,7 +1046,9 @@ def FillLoopsByMonteCarlo(mhandle, torsion_sampler, max_loops_to_search=6,
weights = _GetMCWeights()
mc_scorer = LinearScorer(mhandle.backbone_scorer,
+ mhandle.backbone_scorer_env,
actual_gap.before.GetNumber().GetNum(),
+ len(actual_gap.full_seq),
actual_chain_idx, weights)
start_temperature = 100
@@ -1045,7 +1094,8 @@ def FillLoopsByMonteCarlo(mhandle, torsion_sampler, max_loops_to_search=6,
# close loop
##################################
new_idx = _CloseLoop(mhandle, gap_orig, actual_candidates,
- actual_extended_gaps, score_variant)
+ actual_extended_gaps, score_variant,
+ length_dep_weights=length_dep_weights)
if new_idx == -2:
# try next one if we failed
gap_idx += 1
@@ -1058,7 +1108,7 @@ def FillLoopsByMonteCarlo(mhandle, torsion_sampler, max_loops_to_search=6,
def CloseGaps(mhandle, merge_distance=4, fragment_db=None, structure_db=None,
torsion_sampler=None, fragger_handles=None, chain_idx=None,
- resnum_range=None):
+ resnum_range=None, length_dep_weights=False):
'''
Tries to close all gaps in a model, except termini. It will go through
following steps:
@@ -1104,6 +1154,13 @@ def CloseGaps(mhandle, merge_distance=4, fragment_db=None, structure_db=None,
:param resnum_range: If not None, only gaps within this resnum range get
processed.
:type resnum_range: :class:`tuple` containing two :class:`int`
+
+ :param length_dep_weights: :class:`ScoringWeights` provides different sets
+ of weights that have been trained on different
+ loop subsets. If this flag is true, the length
+ dependent weights are used to close loops with
+ database / Monte Carlo.
+ :type length_dep_weights: :class:`bool`
'''
# load stuff if needed
@@ -1125,22 +1182,26 @@ def CloseGaps(mhandle, merge_distance=4, fragment_db=None, structure_db=None,
FillLoopsByDatabase(mhandle, fragment_db, structure_db,
torsion_sampler, min_loops_required=-1,
max_res_extension=6, chain_idx=chain_idx,
- resnum_range=resnum_range, clash_thresh=10)
+ resnum_range=resnum_range, clash_thresh=10,
+ length_dep_weights=length_dep_weights)
# if above fails, try DB-fill with less restrictions
FillLoopsByDatabase(mhandle, fragment_db, structure_db,
torsion_sampler, min_loops_required=-1,
chain_idx=chain_idx, resnum_range=resnum_range,
- clash_thresh=10)
+ clash_thresh=10,
+ length_dep_weights=length_dep_weights)
FillLoopsByDatabase(mhandle, fragment_db, structure_db,
torsion_sampler, chain_idx=chain_idx,
- resnum_range=resnum_range)
+ resnum_range=resnum_range,
+ length_dep_weights=length_dep_weights)
# close remaining gaps by Monte Carlo
FillLoopsByMonteCarlo(mhandle, torsion_sampler,
fragger_handles=fragger_handles,
chain_idx=chain_idx,
- resnum_range=resnum_range)
+ resnum_range=resnum_range,
+ length_dep_weights=length_dep_weights)
# last resort approach to close large deletions
CloseLargeDeletions(mhandle, structure_db, chain_idx=chain_idx,
@@ -1236,7 +1297,9 @@ def ModelTermini(mhandle, torsion_sampler, fragger_handles=None,
# setup scorer
weights = _GetMCWeights()
- mc_scorer = LinearScorer(mhandle.backbone_scorer, start_resnum,
+ mc_scorer = LinearScorer(mhandle.backbone_scorer,
+ mhandle.backbone_scorer_env,
+ start_resnum, len(actual_gap.full_seq),
actual_chain_idx, weights)
# setup cooler
@@ -1257,8 +1320,7 @@ def ModelTermini(mhandle, torsion_sampler, fragger_handles=None,
if len(candidates) > 0:
# score candidates
bb_scores = ScoreContainer()
- candidates.CalculateBackboneScores(bb_scores,
- mhandle.backbone_scorer,
+ candidates.CalculateBackboneScores(bb_scores, mhandle,
start_resnum, actual_chain_idx)
scores = bb_scores.LinearCombine(ScoringWeights.GetWeights())
min_score = min(scores)
@@ -1442,8 +1504,10 @@ def CloseLargeDeletions(mhandle, structure_db, linker_length=8,
closer.Close(bb_list, bb_list)
# a simple score gets calculated and best chosen
+ mhandle.backbone_scorer_env.SetEnvironment(bb_list, first_num,
+ actual_chain_idx)
score = mhandle.backbone_scorer.CalculateLinearCombination(\
- scorer_weights, bb_list, first_num, actual_chain_idx)
+ scorer_weights, first_num, len(bb_list), actual_chain_idx)
if score < best_score:
best_score = score
diff --git a/modelling/pymod/_denovo.py b/modelling/pymod/_denovo.py
index 94a06c8ca623df214a99c9f88e3cf8ab474a2292..51dd26d0ca0b540c9b6523c66337f5aa0a96fa52 100644
--- a/modelling/pymod/_denovo.py
+++ b/modelling/pymod/_denovo.py
@@ -8,6 +8,7 @@ def GenerateDeNovoTrajectories(sequence,
psipred_prediction = None,
fragment_handler = None,
scorer = None,
+ scorer_env = None,
scoring_weights = None):
'''Example de novo modelling pipeline based on Fragment sampling and
backbone scoring. Take this as a starting point for more advanced
@@ -47,6 +48,10 @@ def GenerateDeNovoTrajectories(sequence,
torsion and pairwise
:type scorer: :class:`promod3.scoring.BackboneOverallScorer`
+ :param scorer_env: The scoring env that relates to **scorer**
+ This environment will be changed!
+ :type scorer_env: :class:`promod3.scoring.BackboneScoreEnv`
+
:param scoring_weights: Linear weights for different scores. If not provided,
the output of ScoringWeights.GetWeights() is used.
Please note, that the weights must be consistent
@@ -71,6 +76,9 @@ def GenerateDeNovoTrajectories(sequence,
err = "psipred_prediction must be consistent with the input sequence!"
raise RuntimeError(err)
+ if scorer != None and scorer_env == None:
+ raise RuntimeError("Must provide an environment when you provide a scorer!")
+
if fragment_handler == None:
# we first have to build our own handler
fragment_handler = modelling.FraggerHandle(sequence,
@@ -104,7 +112,8 @@ def GenerateDeNovoTrajectories(sequence,
mc_sampler = FragmentSampler(sequence, fragger_list,
init_fragments = 5)
mc_closer = DeNovoCloser()
- mc_scorer = LinearScorer(scorer, 1, 0, scoring_weights)
+ mc_scorer = LinearScorer(scorer, scorer_env, 1, len(sequence), 0,
+ scoring_weights)
mc_cooler = ExponentialCooler(start_temperature,
cooling_interval,
cooling_factor)
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index 6f149369b31259b54dada119733bac167d7da50f..fdea48505c30f4bb49832cd1182c89babe04acd0 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -386,7 +386,9 @@ def CheckFinalModel(mhandle):
ost.PopVerbosityLevel()
# set bool props in model-residues
atoms = [e.GetFirstAtom() for e in clash_info.GetClashList()]\
+ + [e.GetSecondAtom() for e in clash_info.GetClashList()]\
+ [e.GetFirstAtom() for e in stereo_info.GetBondViolationList()]\
+ + [e.GetSecondAtom() for e in stereo_info.GetBondViolationList()]\
+ [e.GetSecondAtom() for e in stereo_info.GetAngleViolationList()]
for atomui in atoms:
res = model_src.FindResidue(atomui.GetChainName(), atomui.GetResNum())
diff --git a/modelling/pymod/_reconstruct_sidechains.py b/modelling/pymod/_reconstruct_sidechains.py
index 26d31567bb76a95dd5703e3da840a77b937e70f5..cc465d832149d465348823cbfc67db6386235b93 100644
--- a/modelling/pymod/_reconstruct_sidechains.py
+++ b/modelling/pymod/_reconstruct_sidechains.py
@@ -1,5 +1,6 @@
from ost import geom, mol, conop
from promod3 import core, sidechain
+import traceback
###############################################################################
# helper functions
@@ -10,7 +11,6 @@ def _GetRotamerIDs(res_list):
rot_id = sidechain.TLCToRotID(r.GetName())
if rot_id == sidechain.XXX:
continue # no idea what it is, so we stick with ALA
- # => don't model sidechain
rotamer_ids[i] = rot_id
return rotamer_ids
@@ -105,12 +105,11 @@ def _AddLigandFrameResidues(frame_residues, ent_lig, rotamer_constructor, offset
fr1 = rotamer_constructor.ConstructBackboneFrameResidue(\
res.handle, rot_id, res_idx,
phi, n_ter, c_ter)
- if rot_id != sidechain.ALA and rot_id != sidechain.GLY:
- fr2 = rotamer_constructor.ConstructSidechainFrameResidue(\
- res.handle, rot_id, res_idx)
- frame_residues.extend([fr1,fr2])
- else:
- frame_residues.append(fr1)
+
+ fr2 = rotamer_constructor.ConstructSidechainFrameResidue(\
+ res.handle, rot_id, res_idx)
+
+ frame_residues.extend([fr1,fr2])
except:
pass # ignore peptide treatment and treat below
else:
@@ -148,9 +147,6 @@ def _AddSidechainFrameResidues(frame_residues, incomplete_sidechains,
cystein_indices.append(i)
continue
- if rotamer_ids[i] == sidechain.ALA or rotamer_ids[i] == sidechain.GLY:
- continue # no sidechain to model
-
try:
frame_residue = rotamer_constructor.ConstructSidechainFrameResidue(\
r.handle, rotamer_ids[i], i)
@@ -166,9 +162,6 @@ def _AddSidechainFrameResidues(frame_residues, incomplete_sidechains,
cystein_indices.append(i)
continue
- if rotamer_ids[i] == sidechain.ALA or rotamer_ids[i] == sidechain.GLY:
- continue # no sidechain to model
-
incomplete_sidechains.append(i)
def _AddCysteinFrameResidues(frame_residues, incomplete_sidechains,
@@ -231,7 +224,7 @@ def _GetRotamerGroups(res_list, rot_ids, indices, rot_lib, rot_constructor,
phi_angles, psi_angles, use_frm, bbdep, frame_residues):
'''Get list of rotamer groups from subset of res_list.
Residues are chosen as res_list[i] for i in indices and only if a rotamer
- group can be created (e.g. no ALA, GLY).
+ group can be created.
Rotamer groups are filtered to keep only best ones (given frame).
Returns list of rotamer groups and list of res. indices they belong to.
'''
@@ -249,9 +242,6 @@ def _GetRotamerGroups(res_list, rot_ids, indices, rot_lib, rot_constructor,
# get rotamer ID
r = res_list[i]
rot_id = rot_ids[i]
-
- if rot_id == sidechain.ALA or rot_id == sidechain.GLY:
- continue
if rot_id == sidechain.CYS:
rot_id = sidechain.CYH
@@ -442,7 +432,7 @@ def ReconstructSidechains(ent, keep_sidechains=False, build_disulfids=True,
if type(rotamer_library) is sidechain.BBDepRotamerLib:
bbdep = True
- rotamer_constructor = sidechain.SCWRLRotamerConstructor()
+ rotamer_constructor = sidechain.SCWRLRotamerConstructor(False)
# take out ligand chain and any non-peptides
prot = ent.Select("peptide=true and cname!='_'")
diff --git a/modelling/pymod/export_loop_candidate.cc b/modelling/pymod/export_loop_candidate.cc
index 3ef94b937e1d04c803c0b87c1edac864dd69e1a5..7bb657db9d310ff2319217e054fa184b6f2df44d 100644
--- a/modelling/pymod/export_loop_candidate.cc
+++ b/modelling/pymod/export_loop_candidate.cc
@@ -133,21 +133,40 @@ boost::python::list WrapGetClusteredCandidates(LoopCandidatesPtr p,
return return_list;
}
+void WrapCalculateBackboneScoresMH(LoopCandidatesPtr p,
+ ScoreContainer& score_container,
+ const ModellingHandle& mhandle,
+ uint start_resnum, uint chain_idx) {
+ p->CalculateBackboneScores(score_container, mhandle, start_resnum, chain_idx);
+}
+void WrapCalculateBackboneScoresMH_K(LoopCandidatesPtr p,
+ ScoreContainer& score_container,
+ const ModellingHandle& mhandle,
+ const boost::python::list& keys,
+ uint start_resnum, uint chain_idx) {
+ std::vector<String> v_keys;
+ core::ConvertListToVector(keys, v_keys);
+ p->CalculateBackboneScores(score_container, mhandle, v_keys, start_resnum,
+ chain_idx);
+}
void WrapCalculateBackboneScores(LoopCandidatesPtr p,
ScoreContainer& score_container,
scoring::BackboneOverallScorerPtr scorer,
+ scoring::BackboneScoreEnvPtr scorer_env,
uint start_resnum, uint chain_idx) {
- p->CalculateBackboneScores(score_container, scorer, start_resnum, chain_idx);
+ p->CalculateBackboneScores(score_container, scorer, scorer_env, start_resnum,
+ chain_idx);
}
void WrapCalculateBackboneScoresK(LoopCandidatesPtr p,
ScoreContainer& score_container,
scoring::BackboneOverallScorerPtr scorer,
+ scoring::BackboneScoreEnvPtr scorer_env,
const boost::python::list& keys,
uint start_resnum, uint chain_idx) {
std::vector<String> v_keys;
core::ConvertListToVector(keys, v_keys);
- p->CalculateBackboneScores(score_container, scorer, v_keys, start_resnum,
- chain_idx);
+ p->CalculateBackboneScores(score_container, scorer, scorer_env, v_keys,
+ start_resnum, chain_idx);
}
void WrapCalculateAllAtomScores(LoopCandidatesPtr p,
ScoreContainer& score_container,
@@ -267,12 +286,18 @@ void export_loop_candidate() {
.def("ApplyKIC", &WrapApplyKIC,
(arg("n_stem"), arg("c_stem"), arg("pivot_one"), arg("pivot_two"),
arg("pivot_three")))
+ .def("CalculateBackboneScores", &WrapCalculateBackboneScoresMH,
+ (arg("score_container"), arg("mhandle"),
+ arg("start_resnum"), arg("chain_idx")=0))
+ .def("CalculateBackboneScores", &WrapCalculateBackboneScoresMH_K,
+ (arg("score_container"), arg("mhandle"), arg("keys"),
+ arg("start_resnum"), arg("chain_idx")=0))
.def("CalculateBackboneScores", &WrapCalculateBackboneScores,
- (arg("score_container"), arg("scorer"),
+ (arg("score_container"), arg("scorer"), arg("scorer_env"),
arg("start_resnum"), arg("chain_idx")=0))
.def("CalculateBackboneScores", &WrapCalculateBackboneScoresK,
- (arg("score_container"), arg("scorer"), arg("keys"),
- arg("start_resnum"), arg("chain_idx")=0))
+ (arg("score_container"), arg("scorer"), arg("scorer_env"),
+ arg("keys"), arg("start_resnum"), arg("chain_idx")=0))
.def("CalculateAllAtomScores", &WrapCalculateAllAtomScores,
(arg("score_container"), arg("mhandle"),
arg("start_resnum"), arg("chain_idx")=0))
diff --git a/modelling/pymod/export_monte_carlo.cc b/modelling/pymod/export_monte_carlo.cc
index 84d614fd599d31afc8f58e7cfda948e06168aae6..7d296ccf9550ec7db9ebf53c06aa4e4792370e0f 100644
--- a/modelling/pymod/export_monte_carlo.cc
+++ b/modelling/pymod/export_monte_carlo.cc
@@ -225,12 +225,14 @@ CCDCloserPtr CCDCloserWrapperList(const ost::mol::ResidueHandle& n_stem,
}
LinearScorerPtr LinearScorerInitWrapper(scoring::BackboneOverallScorerPtr scorer,
- uint start_resnum, uint chain_index,
+ scoring::BackboneScoreEnvPtr scorer_env,
+ uint start_resnum, uint num_residues,
+ uint chain_index,
const boost::python::dict& weights) {
std::map<String,Real> m_weights;
core::ConvertDictToMap(weights, m_weights);
- LinearScorerPtr p(new LinearScorer(scorer, start_resnum, chain_index,
- m_weights));
+ LinearScorerPtr p(new LinearScorer(scorer, scorer_env, start_resnum,
+ num_residues, chain_index, m_weights));
return p;
}
diff --git a/modelling/pymod/export_scoring_weights.cc b/modelling/pymod/export_scoring_weights.cc
index f6243ef7a97ccc9fd1ae835b6dc6f2641e8e98d3..11e3c18eb54a48f5162e88bab3c0286d4f8aca55 100644
--- a/modelling/pymod/export_scoring_weights.cc
+++ b/modelling/pymod/export_scoring_weights.cc
@@ -11,28 +11,40 @@ using namespace boost::python;
// WRAPPERS
namespace {
-boost::python::dict WrapGetWeights(bool with_db, bool with_aa) {
+boost::python::dict WrapGetWeights(bool with_db, bool with_aa,
+ bool length_dependent, int loop_length) {
boost::python::dict result;
core::ConvertMapToDict(
- ScoringWeights::GetInstance().GetWeights(with_db, with_aa), result);
+ ScoringWeights::GetInstance().GetWeights(with_db, with_aa,
+ length_dependent,
+ loop_length), result);
return result;
}
-void WrapSetWeights(bool with_db, bool with_aa, const boost::python::dict& wd) {
+void WrapSetWeights(bool with_db, bool with_aa, const boost::python::dict& wd,
+ bool length_dependent, int loop_length) {
std::map<String, Real> weights;
core::ConvertDictToMap(wd, weights);
- ScoringWeights::GetInstance().SetWeights(with_db, with_aa, weights);
+ ScoringWeights::GetInstance().SetWeights(with_db, with_aa, weights,
+ length_dependent, loop_length);
}
-boost::python::dict WrapGetBackboneWeights(bool with_db, bool with_aa) {
+boost::python::dict WrapGetBackboneWeights(bool with_db, bool with_aa,
+ bool length_dependent,
+ int loop_length) {
boost::python::dict result;
core::ConvertMapToDict(
- ScoringWeights::GetInstance().GetBackboneWeights(with_db, with_aa),
+ ScoringWeights::GetInstance().GetBackboneWeights(with_db, with_aa,
+ length_dependent,
+ loop_length),
result);
return result;
}
-boost::python::dict WrapGetAllAtomWeights(bool with_db) {
+boost::python::dict WrapGetAllAtomWeights(bool with_db, bool length_dependent,
+ int loop_length) {
boost::python::dict result;
core::ConvertMapToDict(
- ScoringWeights::GetInstance().GetAllAtomWeights(with_db), result);
+ ScoringWeights::GetInstance().GetAllAtomWeights(with_db,
+ length_dependent,
+ loop_length), result);
return result;
}
@@ -85,15 +97,20 @@ void export_scoring_weights() {
class_<ScoringWeights>("ScoringWeights", no_init)
.def("GetWeights", WrapGetWeights,
- (arg("with_db")=false, arg("with_aa")=false))
+ (arg("with_db")=false, arg("with_aa")=false,
+ arg("length_dependent")=false, arg("loop_length")=-1))
.staticmethod("GetWeights")
.def("SetWeights", WrapSetWeights,
- (arg("with_db"), arg("with_aa"), arg("weights")))
+ (arg("with_db"), arg("with_aa"), arg("weights"),
+ arg("length_dependent")=false, arg("loop_length")=-1))
.staticmethod("SetWeights")
.def("GetBackboneWeights", WrapGetBackboneWeights,
- (arg("with_db")=false, arg("with_aa")=false))
+ (arg("with_db")=false, arg("with_aa")=false,
+ arg("length_dependent")=false, arg("loop_length")=-1))
.staticmethod("GetBackboneWeights")
- .def("GetAllAtomWeights", WrapGetAllAtomWeights, (arg("with_db")=false))
+ .def("GetAllAtomWeights", WrapGetAllAtomWeights,
+ (arg("with_db")=false, arg("length_dependent")=false,
+ arg("loop_length")=-1))
.staticmethod("GetAllAtomWeights")
.def("GetStemRMSDsKey", WrapGetStemRMSDsKey)
.staticmethod("GetStemRMSDsKey")
diff --git a/modelling/src/all_atom_relaxer.cc b/modelling/src/all_atom_relaxer.cc
index 3f99edbf13851294773042c9fc4d4b98c388efe5..9fe1dc51136b70c71d5b4945978375c06f00d0e5 100644
--- a/modelling/src/all_atom_relaxer.cc
+++ b/modelling/src/all_atom_relaxer.cc
@@ -1,6 +1,8 @@
#include <promod3/modelling/all_atom_relaxer.hh>
#include <promod3/loop/hydrogen_constructor.hh>
#include <promod3/core/runtime_profiling.hh>
+#include <exception>
+#include <limits>
namespace promod3 { namespace modelling {
@@ -52,7 +54,14 @@ Real AllAtomRelaxer::Run(ScRecDataPtr sc_data, int steps, Real stop_criterion) {
// run it
ost::mol::mm::SimulationPtr sim = mm_system_creator_->GetSimulation();
- sim->ApplySD(stop_criterion, steps);
+
+ // guard against OpenMM error that is thrown when positions become NaN
+ // => typically when you particles are (almost) on top of each other
+ try {
+ sim->ApplySD(stop_criterion, steps);
+ } catch(std::exception& e) {
+ return std::numeric_limits<Real>::infinity();
+ }
// update positions in sc_data
loop::AllAtomPositionsPtr out_pos = sc_data_->env_pos->all_pos;
diff --git a/modelling/src/backbone_relaxer.cc b/modelling/src/backbone_relaxer.cc
index 9db1825f8507f62ac3fd9dfc82b3ab8c67fd0011..ded52f6a222d2cf2135de02027563fdc94ce9a13 100644
--- a/modelling/src/backbone_relaxer.cc
+++ b/modelling/src/backbone_relaxer.cc
@@ -6,6 +6,8 @@
#include <ost/mol/mm/system_creator.hh>
#include <ost/mol/mm/steep.hh>
#include <set>
+#include <exception>
+#include <limits>
namespace{
@@ -307,7 +309,15 @@ Real BackboneRelaxer::Run(loop::BackboneList& bb_list, int steps,
if (!simulation_) this->Init();
this->SetSimulationPositions(bb_list);
- simulation_->ApplySD(stop_criterion, steps);
+
+ // guard against OpenMM error that is thrown when positions become NaN
+ // => typicall when you particles are (almost) on top of each other
+ try {
+ simulation_->ApplySD(stop_criterion, steps);
+ } catch(std::exception& e) {
+ return std::numeric_limits<Real>::infinity();
+ }
+
this->ExtractSimulationPositions(bb_list);
return simulation_->GetPotentialEnergy();
diff --git a/modelling/src/kic.cc b/modelling/src/kic.cc
index a3ecaeca05bd5c475dafb9cda1fd87d5ab2a1145..fb7005aedd659dd59c21dbb7513657945e62726a 100644
--- a/modelling/src/kic.cc
+++ b/modelling/src/kic.cc
@@ -1,4 +1,5 @@
#include <promod3/modelling/kic.hh>
+#include <promod3/core/eigen_types.hh>
#include <promod3/core/message.hh>
#include <promod3/core/runtime_profiling.hh>
#include <Eigen/Dense>
@@ -23,10 +24,6 @@ struct KICParameters {
geom::Mat4 F2_initial_transform;
};
-typedef Eigen::Matrix<double,8,8> EMat8;
-typedef Eigen::Matrix<double,16,16> EMat16;
-typedef Eigen::Matrix<double,16,3> EMat16_3;
-
void BuildFragmentBase(const geom::Vec3& pos1, const geom::Vec3& pos2, const geom::Vec3& pos3, geom::Mat3& base){
geom::Vec3 a,b,c;
@@ -133,7 +130,8 @@ bool FillKICParameters(const promod3::loop::BackboneList& bb_list,
return true;
}
-void FillDixonMatrices(KICParameters& parameters,EMat8& R0, EMat8& R1, EMat8& R2){
+void FillDixonMatrices(KICParameters& parameters, promod3::core::EMat8& R0,
+ promod3::core::EMat8& R1, promod3::core::EMat8& R2){
Real p[3][3][3];
Real c_theta[3]; //c:cosine, s:sine, naming more or less as in the Coutsias paper
Real s_delta[3];
@@ -202,9 +200,9 @@ void FillDixonMatrices(KICParameters& parameters,EMat8& R0, EMat8& R1, EMat8& R2
}
}
- EMat8* RArray[3] = {&R0, &R1, &R2};
+ promod3::core::EMat8* RArray[3] = {&R0, &R1, &R2};
for(int i = 0; i < 3; ++i){
- EMat8& Ri = *RArray[i];
+ promod3::core::EMat8& Ri = *RArray[i];
Ri(0,1) = A[0][i]; Ri(0,2) = A[1][i]; Ri(0,3) = A[2][i];
Ri(0,5) = B[0][i]; Ri(0,6) = B[1][i]; Ri(0,7) = B[2][i];
@@ -228,9 +226,11 @@ void FillDixonMatrices(KICParameters& parameters,EMat8& R0, EMat8& R1, EMat8& R2
}
}
-void ResolveEigenProblem(EMat8& R0, EMat8& R1, EMat8& R2, std::vector<std::vector<Real> >& taus){
- EMat16 E0 = EMat16::Zero();
- EMat16 E1 = EMat16::Zero();
+void ResolveEigenProblem(promod3::core::EMat8& R0, promod3::core::EMat8& R1,
+ promod3::core::EMat8& R2,
+ std::vector<std::vector<Real> >& taus){
+ promod3::core::EMat16 E0 = promod3::core::EMat16::Zero();
+ promod3::core::EMat16 E1 = promod3::core::EMat16::Zero();
E0.topRightCorner(8,8).setIdentity();
E0.bottomLeftCorner(8,8) = -R0;
@@ -239,7 +239,7 @@ void ResolveEigenProblem(EMat8& R0, EMat8& R1, EMat8& R2, std::vector<std::vecto
E1.topLeftCorner(8,8).setIdentity();
E1.bottomRightCorner(8,8) = R2;
- typedef Eigen::GeneralizedEigenSolver<EMat16> EigenSolver;
+ typedef Eigen::GeneralizedEigenSolver<promod3::core::EMat16> EigenSolver;
EigenSolver solver(E0, E1, true);
const EigenSolver::ComplexVectorType& alpha = solver.alphas();
const EigenSolver::VectorType& beta = solver.betas();
@@ -417,9 +417,9 @@ void KIC::Close(const loop::BackboneList& bb_list, uint pivot_one,
KICParameters parameters;
// initialize Dixon Matrices directly with zeros
- EMat8 R0 = EMat8::Zero();
- EMat8 R1 = EMat8::Zero();
- EMat8 R2 = EMat8::Zero();
+ promod3::core::EMat8 R0 = promod3::core::EMat8::Zero();
+ promod3::core::EMat8 R1 = promod3::core::EMat8::Zero();
+ promod3::core::EMat8 R2 = promod3::core::EMat8::Zero();
// solutions will be stored in here
std::vector<std::vector<Real> > taus;
if (!FillKICParameters(bb_list, n_stem_, c_stem_, pivot_one, pivot_two,
diff --git a/modelling/src/loop_candidate.cc b/modelling/src/loop_candidate.cc
index 82fda8923c1cab9c909f45903756889f6de2f577..5aa7cccee59836bc3589f851f741bf1e158c6a4e 100644
--- a/modelling/src/loop_candidate.cc
+++ b/modelling/src/loop_candidate.cc
@@ -412,25 +412,64 @@ LoopCandidatesPtr LoopCandidates::GetLargestCluster(Real max_dist,
}
}
+void LoopCandidates::CalculateBackboneScores(
+ ScoreContainer& score_container,
+ scoring::BackboneOverallScorerPtr scorer,
+ scoring::BackboneScoreEnvPtr scorer_env,
+ const std::vector<String>& keys,
+ uint start_resnum, uint chain_idx) const {
+
+ uint N = candidates_.size();
+ uint L = sequence_.size();
+
+ scorer_env->Stash(start_resnum, L, chain_idx);
+
+ for (uint i = 0; i < keys.size(); ++i) {
+ std::vector<Real> scores(N);
+ for(uint j = 0; j < N; ++j) {
+ scorer_env->SetEnvironment(candidates_[j], start_resnum, chain_idx);
+ scores[j] = scorer->Calculate(keys[i], start_resnum, L, chain_idx);
+ }
+ score_container.Set(keys[i], scores);
+ }
+ scorer_env->Pop();
+}
+
+void LoopCandidates::CalculateBackboneScores(
+ ScoreContainer& score_container,
+ scoring::BackboneOverallScorerPtr scorer,
+ scoring::BackboneScoreEnvPtr scorer_env,
+ uint start_resnum, uint chain_idx) const {
+
+ const std::vector<String>&
+ keys = ScoringWeights::GetInstance().GetBackboneScoringKeys();
+ CalculateBackboneScores(score_container, scorer, scorer_env, keys,
+ start_resnum, chain_idx);
+}
+
void LoopCandidates::CalculateBackboneScores(
ScoreContainer& score_container,
- scoring::BackboneOverallScorerPtr scorer,
+ const ModellingHandle& mhandle,
uint start_resnum, uint chain_idx) const {
+
const std::vector<String>&
keys = ScoringWeights::GetInstance().GetBackboneScoringKeys();
- CalculateBackboneScores(score_container, scorer, keys, start_resnum,
+ scoring::BackboneOverallScorerPtr scorer = mhandle.backbone_scorer;
+ scoring::BackboneScoreEnvPtr env = mhandle.backbone_scorer_env;
+ CalculateBackboneScores(score_container, scorer, env, keys, start_resnum,
chain_idx);
}
+
void LoopCandidates::CalculateBackboneScores(
ScoreContainer& score_container,
- scoring::BackboneOverallScorerPtr scorer,
+ const ModellingHandle& mhandle,
const std::vector<String>& keys,
uint start_resnum, uint chain_idx) const {
- for (uint i = 0; i < keys.size(); ++i) {
- std::vector<Real> scores;
- scores = scorer->Calculate(keys[i], candidates_, start_resnum, chain_idx);
- score_container.Set(keys[i], scores);
- }
+
+ scoring::BackboneOverallScorerPtr scorer = mhandle.backbone_scorer;
+ scoring::BackboneScoreEnvPtr env = mhandle.backbone_scorer_env;
+ CalculateBackboneScores(score_container, scorer, env, keys, start_resnum,
+ chain_idx);
}
void LoopCandidates::CalculateAllAtomScores(
diff --git a/modelling/src/loop_candidate.hh b/modelling/src/loop_candidate.hh
index 39b47b8a53663ab18dd47b177e813849ca075737..0b30ecf4bf2b51c2422ca0b26ec7607d805be3e0 100644
--- a/modelling/src/loop_candidate.hh
+++ b/modelling/src/loop_candidate.hh
@@ -89,9 +89,18 @@ public:
void CalculateBackboneScores(ScoreContainer& score_container,
scoring::BackboneOverallScorerPtr scorer,
+ scoring::BackboneScoreEnvPtr scorer_env,
uint start_resnum, uint chain_idx = 0) const;
void CalculateBackboneScores(ScoreContainer& score_container,
scoring::BackboneOverallScorerPtr scorer,
+ scoring::BackboneScoreEnvPtr scorer_env,
+ const std::vector<String>& keys,
+ uint start_resnum, uint chain_idx = 0) const;
+ void CalculateBackboneScores(ScoreContainer& score_container,
+ const ModellingHandle& mhandle,
+ uint start_resnum, uint chain_idx = 0) const;
+ void CalculateBackboneScores(ScoreContainer& score_container,
+ const ModellingHandle& mhandle,
const std::vector<String>& keys,
uint start_resnum, uint chain_idx = 0) const;
void CalculateAllAtomScores(ScoreContainer& score_container,
diff --git a/modelling/src/monte_carlo_scorer.cc b/modelling/src/monte_carlo_scorer.cc
index f8dd0ac6cfe01f7e72a1aedbcdbb1c3f84132dd4..ba536e7d772fc8b8d506c8375269e4d9fb528da1 100644
--- a/modelling/src/monte_carlo_scorer.cc
+++ b/modelling/src/monte_carlo_scorer.cc
@@ -5,21 +5,34 @@ namespace promod3 { namespace modelling {
MonteCarloScorer::~MonteCarloScorer() { }
LinearScorer::LinearScorer(scoring::BackboneOverallScorerPtr scorer,
- uint start_resnum, uint chain_index,
- const std::map<String,Real>& weights)
- : scorer_(scorer)
- , chain_index_(chain_index)
- , start_resnum_(start_resnum)
+ scoring::BackboneScoreEnvPtr scorer_env,
+ uint start_resnum, uint num_residues,
+ uint chain_index,
+ const std::map<String,Real>& weights):
+ scorer_(scorer),
+ scorer_env_(scorer_env),
+ start_resnum_(start_resnum),
+ num_residues_(num_residues),
+ chain_index_(chain_index)
{
w_scorers_ = scorer->GetWeightedScorers(weights);
}
Real LinearScorer::GetScore(const loop::BackboneList& positions) {
- Real score = 0;
+
+ if(positions.size() != num_residues_) {
+ throw promod3::Error("Input BackboneList is inconsistent with loop length "
+ "that you defined at initialization of the "
+ "LinearScorer");
+ }
+
+ scorer_env_->SetEnvironment(positions, start_resnum_, chain_index_);
+ Real score = 0.0;
for (uint i = 0; i < w_scorers_.size(); ++i) {
const Real weight = w_scorers_[i].first;
scoring::BackboneScorerPtr one_scorer = w_scorers_[i].second;
- score += weight * one_scorer->CalculateScore(positions, start_resnum_,
+ score += weight * one_scorer->CalculateScore(start_resnum_,
+ num_residues_,
chain_index_);
}
return score;
diff --git a/modelling/src/monte_carlo_scorer.hh b/modelling/src/monte_carlo_scorer.hh
index 6bd3e47b34675df0578affed4ccc289ea294a47b..a6707b359e0a138f296120815e524bfd9f4488b8 100644
--- a/modelling/src/monte_carlo_scorer.hh
+++ b/modelling/src/monte_carlo_scorer.hh
@@ -25,15 +25,24 @@ public:
class LinearScorer : public MonteCarloScorer {
public:
- LinearScorer(scoring::BackboneOverallScorerPtr scorer, uint start_resnum,
+ LinearScorer(scoring::BackboneOverallScorerPtr scorer,
+ scoring::BackboneScoreEnvPtr scorer_env,
+ uint start_resnum, uint num_residues,
uint chain_index, const std::map<String,Real>& weights);
Real GetScore(const loop::BackboneList& positions);
+ void StashScoringEnv() { scorer_env_->Stash(start_resnum_, num_residues_,
+ chain_index_); }
+
+ void PopScoringEnv() { scorer_env_->Pop(); }
+
private:
scoring::BackboneOverallScorerPtr scorer_;
- uint chain_index_;
+ scoring::BackboneScoreEnvPtr scorer_env_;
uint start_resnum_;
+ uint num_residues_;
+ uint chain_index_;
std::vector<std::pair<Real, scoring::BackboneScorerPtr> > w_scorers_;
};
diff --git a/modelling/src/rigid_blocks.cc b/modelling/src/rigid_blocks.cc
index ef24abeb7a846f4039e1fd5331a5fc13b954691b..df46c90fc4195cf3c47b6f4bb09a2b9ec5301e7f 100644
--- a/modelling/src/rigid_blocks.cc
+++ b/modelling/src/rigid_blocks.cc
@@ -30,7 +30,7 @@ inline Real IndexListSimilarity(const std::vector<uint>& v1,
sum += complete_v1[i] * complete_v2[i];
}
- return static_cast<Real>(sum) / std::max(v1.size(),v2.size());
+ return static_cast<Real>(sum) / std::min(v1.size(),v2.size());
}
void DoIt(promod3::core::EMatX3& pos_mat_one,
@@ -76,18 +76,15 @@ void DoIt(promod3::core::EMatX3& pos_mat_one,
for(uint j = 1; j < clusters[i].size(); ++j){
- uint size = std::max(current_indices.size(),
- initial_indices[clusters[i][j]].size());
+ std::vector<uint> union_result;
- std::vector<uint> intersection_result(size, 0);
+ std::set_union(current_indices.begin(),
+ current_indices.end(),
+ initial_indices[clusters[i][j]].begin(),
+ initial_indices[clusters[i][j]].end(),
+ std::back_inserter(union_result));
- it = std::set_intersection(current_indices.begin(),
- current_indices.end(),
- initial_indices[clusters[i][j]].begin(),
- initial_indices[clusters[i][j]].end(),
- intersection_result.begin());
-
- current_indices.assign(intersection_result.begin(),it);
+ current_indices = union_result;
}
indices.push_back(current_indices);
}
diff --git a/modelling/src/scoring_weights.cc b/modelling/src/scoring_weights.cc
index d4c58e122f32b378b2deba056c1b7214d2d35cc4..ac8ad4f8fd8408a604842f5c54744ed6a1e50f05 100644
--- a/modelling/src/scoring_weights.cc
+++ b/modelling/src/scoring_weights.cc
@@ -30,50 +30,366 @@ ScoringWeights::ScoringWeights() {
// weights trained with scripts in extras/scoring_weight_training
// BB_DB_AANR
- weights_bb_db_aa_["aa_clash"] = 0.16219;
- weights_bb_db_aa_["aa_interaction"] = 21.7161;
- weights_bb_db_aa_["aa_packing"] = 0.914035;
- weights_bb_db_aa_["cb_packing"] = 1.19015;
- weights_bb_db_aa_["cbeta"] = 3.12139;
- weights_bb_db_aa_["clash"] = 0.00675967;
+ weights_bb_db_aa_["aa_clash"] = 0.0171401;
+ weights_bb_db_aa_["aa_interaction"] = 0.00256632;
+ weights_bb_db_aa_["aa_packing"] = 0.0383423;
+ weights_bb_db_aa_["cb_packing"] = 1.15539;
+ weights_bb_db_aa_["cbeta"] = 0.262183;
+ weights_bb_db_aa_["clash"] = 0.0134694;
weights_bb_db_aa_["hbond"] = 1;
+ weights_bb_db_aa_["reduced"] = 0.201682;
+ weights_bb_db_aa_["seq_prof_score"] = -0.338147;
+ weights_bb_db_aa_["stem_rmsd"] = 0.0814165;
+ weights_bb_db_aa_["str_prof_score"] = -1.75976;
+ weights_bb_db_aa_["torsion"] = 0.809906;
weights_bb_db_aa_["pairwise"] = -0.7;
- weights_bb_db_aa_["reduced"] = 1.83614;
- weights_bb_db_aa_["seq_prof_score"] = -0.325626;
- weights_bb_db_aa_["stem_rmsd"] = 0.0832467;
- weights_bb_db_aa_["str_prof_score"] = -1.5734;
- weights_bb_db_aa_["torsion"] = 0.761249;
// BB_DB
- weights_bb_db_["cb_packing"] = 0.791056;
- weights_bb_db_["cbeta"] = 3.40341;
- weights_bb_db_["clash"] = 0.0320885;
+ weights_bb_db_["cb_packing"] = 0.843167;
+ weights_bb_db_["cbeta"] = 0.371329;
+ weights_bb_db_["clash"] = 0.0319755;
weights_bb_db_["hbond"] = 1;
+ weights_bb_db_["reduced"] = 0.229909;
+ weights_bb_db_["seq_prof_score"] = -0.313212;
+ weights_bb_db_["stem_rmsd"] = 0.0580353;
+ weights_bb_db_["str_prof_score"] = -1.32155;
+ weights_bb_db_["torsion"] = 0.602527;
weights_bb_db_["pairwise"] = -0.7;
- weights_bb_db_["reduced"] = 1.95437;
- weights_bb_db_["seq_prof_score"] = -0.264727;
- weights_bb_db_["stem_rmsd"] = 0.0598802;
- weights_bb_db_["str_prof_score"] = -0.941646;
- weights_bb_db_["torsion"] = 0.50904;
// BB_AANR
- weights_bb_aa_["aa_clash"] = 0.107664;
- weights_bb_aa_["aa_interaction"] = 26.4636;
- weights_bb_aa_["aa_packing"] = 0.860152;
- weights_bb_aa_["cb_packing"] = 1.25946;
- weights_bb_aa_["cbeta"] = 2.67089;
- weights_bb_aa_["clash"] = 0.0147412;
+ weights_bb_aa_["aa_clash"] = 0.0268085;
+ weights_bb_aa_["aa_interaction"] = 0.00464609;
+ weights_bb_aa_["aa_packing"] = 0.0890843;
+ weights_bb_aa_["cb_packing"] = 1.13975;
+ weights_bb_aa_["cbeta"] = 0.383702;
+ weights_bb_aa_["clash"] = 0.0320327;
weights_bb_aa_["hbond"] = 1;
+ weights_bb_aa_["reduced"] = 0.229512;
+ weights_bb_aa_["torsion"] = 0.839257;
weights_bb_aa_["pairwise"] = -0.7;
- weights_bb_aa_["reduced"] = 1.87516;
- weights_bb_aa_["torsion"] = 0.707425;
// BB
- weights_bb_["cb_packing"] = 0.753716;
- weights_bb_["cbeta"] = 3.62385;
- weights_bb_["clash"] = 0.119614;
+ weights_bb_["cb_packing"] = 0.793275;
+ weights_bb_["cbeta"] = 0.500879;
+ weights_bb_["clash"] = 0.0801205;
weights_bb_["hbond"] = 1;
+ weights_bb_["reduced"] = 0.238478;
+ weights_bb_["torsion"] = 0.729424;
weights_bb_["pairwise"] = -0.7;
- weights_bb_["reduced"] = 1.82769;
- weights_bb_["torsion"] = 0.555789;
+
+
+
+ // BB_DB_AANR length dependent
+ std::map<String, Real> weight_map;
+ weight_map["aa_clash"] = 0.0120408;
+ weight_map["aa_interaction"] = 0.0114092;
+ weight_map["aa_packing"] = 0.000125384;
+ weight_map["cb_packing"] = 0.040684;
+ weight_map["cbeta"] = 0.356074;
+ weight_map["clash"] = 0.848652;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.0470799;
+ weight_map["seq_prof_score"] = -0.036081;
+ weight_map["stem_rmsd"] = 0.144414;
+ weight_map["str_prof_score"] = -0.302214;
+ weight_map["torsion"] = 0.32667;
+ length_dependent_weights_bb_db_aa_[0] = weight_map;
+ length_dependent_weights_bb_db_aa_[1] = weight_map;
+ length_dependent_weights_bb_db_aa_[2] = weight_map;
+ length_dependent_weights_bb_db_aa_[3] = weight_map;
+ length_dependent_weights_bb_db_aa_[4] = weight_map;
+
+ weight_map["aa_clash"] = 0.0301478;
+ weight_map["aa_interaction"] = 0.00839642;
+ weight_map["aa_packing"] = 0.038416;
+ weight_map["cb_packing"] = 0.250168;
+ weight_map["cbeta"] = 0.1976;
+ weight_map["clash"] = 0.0756704;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.135068;
+ weight_map["seq_prof_score"] = -0.111772;
+ weight_map["stem_rmsd"] = 0.0624659;
+ weight_map["str_prof_score"] = -0.856625;
+ weight_map["torsion"] = 0.443652;
+ length_dependent_weights_bb_db_aa_[5] = weight_map;
+ length_dependent_weights_bb_db_aa_[6] = weight_map;
+
+ weight_map["aa_clash"] = 0.0266467;
+ weight_map["aa_interaction"] = 0.00495266;
+ weight_map["aa_packing"] = 0.0570628;
+ weight_map["cb_packing"] = 0.55212;
+ weight_map["cbeta"] = 0.331541;
+ weight_map["clash"] = 0.0341554;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.189735;
+ weight_map["seq_prof_score"] = -0.293038;
+ weight_map["stem_rmsd"] = 0.0809159;
+ weight_map["str_prof_score"] = -0.851421;
+ weight_map["torsion"] = 0.548451;
+ length_dependent_weights_bb_db_aa_[7] = weight_map;
+ length_dependent_weights_bb_db_aa_[8] = weight_map;
+
+ weight_map["aa_clash"] = 0.012002;
+ weight_map["aa_interaction"] = 0.00860129;
+ weight_map["aa_packing"] = 0.0903933;
+ weight_map["cb_packing"] = 1.63694;
+ weight_map["cbeta"] = 0.171588;
+ weight_map["clash"] = 4.51029e-05;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.299024;
+ weight_map["seq_prof_score"] = -0.368841;
+ weight_map["stem_rmsd"] = 0.103716;
+ weight_map["str_prof_score"] = -2.17521;
+ weight_map["torsion"] = 1.12767;
+ length_dependent_weights_bb_db_aa_[9] = weight_map;
+ length_dependent_weights_bb_db_aa_[10] = weight_map;
+
+ weight_map["aa_clash"] = 0.0025594;
+ weight_map["aa_interaction"] = 0.00290232;
+ weight_map["aa_packing"] = 0.0819373;
+ weight_map["cb_packing"] = 1.52471;
+ weight_map["cbeta"] = 0.274828;
+ weight_map["clash"] = 0.0161732;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.124048;
+ weight_map["seq_prof_score"] = -0.407456;
+ weight_map["stem_rmsd"] = 0.074869;
+ weight_map["str_prof_score"] = -2.70179;
+ weight_map["torsion"] = 0.972806;
+ length_dependent_weights_bb_db_aa_[11] = weight_map;
+ length_dependent_weights_bb_db_aa_[12] = weight_map;
+
+ weight_map["aa_clash"] = 0.000384705;
+ weight_map["aa_interaction"] = 0.00239001;
+ weight_map["aa_packing"] = 0.0020213;
+ weight_map["cb_packing"] = 2.16407;
+ weight_map["cbeta"] = 0.288299;
+ weight_map["clash"] = 0.00155468;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.238341;
+ weight_map["seq_prof_score"] = -0.1732;
+ weight_map["stem_rmsd"] = 0.0975998;
+ weight_map["str_prof_score"] = -3.22575;
+ weight_map["torsion"] = 1.06902;
+ length_dependent_weights_bb_db_aa_[13] = weight_map;
+ length_dependent_weights_bb_db_aa_[14] = weight_map;
+ length_dependent_weights_bb_db_aa_[-1] = weights_bb_db_aa_;
+
+ // BB_DB length dependent
+ weight_map.clear();
+ weight_map["cb_packing"] = 0.426734;
+ weight_map["cbeta"] = 0.116532;
+ weight_map["clash"] = 0.963033;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.173565;
+ weight_map["seq_prof_score"] = -0.0381537;
+ weight_map["stem_rmsd"] = 0.150966;
+ weight_map["str_prof_score"] = -0.219757;
+ weight_map["torsion"] = 0.338468;
+ length_dependent_weights_bb_db_[0] = weight_map;
+ length_dependent_weights_bb_db_[1] = weight_map;
+ length_dependent_weights_bb_db_[2] = weight_map;
+ length_dependent_weights_bb_db_[3] = weight_map;
+ length_dependent_weights_bb_db_[4] = weight_map;
+
+ weight_map["cb_packing"] = 0.102926;
+ weight_map["cbeta"] = 0.32014;
+ weight_map["clash"] = 0.15599;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.228402;
+ weight_map["seq_prof_score"] = -0.173496;
+ weight_map["stem_rmsd"] = 0.0571533;
+ weight_map["str_prof_score"] = -0.622599;
+ weight_map["torsion"] = 0.356714;
+ length_dependent_weights_bb_db_[5] = weight_map;
+ length_dependent_weights_bb_db_[6] = weight_map;
+
+ weight_map["cb_packing"] = 0.448069;
+ weight_map["cbeta"] = 0.525517;
+ weight_map["clash"] = 0.0448608;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.192292;
+ weight_map["seq_prof_score"] = -0.332023;
+ weight_map["stem_rmsd"] = 0.0882085;
+ weight_map["str_prof_score"] = -0.645988;
+ weight_map["torsion"] = 0.493079;
+ length_dependent_weights_bb_db_[7] = weight_map;
+ length_dependent_weights_bb_db_[8] = weight_map;
+
+ weight_map["cb_packing"] = 1.07076;
+ weight_map["cbeta"] = 0.531162;
+ weight_map["clash"] = 0.079354;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.503881;
+ weight_map["seq_prof_score"] = -0.49335;
+ weight_map["stem_rmsd"] = 0.110282;
+ weight_map["str_prof_score"] = -2.06894;
+ weight_map["torsion"] = 0.897905;
+ length_dependent_weights_bb_db_[9] = weight_map;
+ length_dependent_weights_bb_db_[10] = weight_map;
+
+ weight_map["cb_packing"] = 1.99384;
+ weight_map["cbeta"] = 0.713817;
+ weight_map["clash"] = 0.046714;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.500903;
+ weight_map["seq_prof_score"] = -0.761715;
+ weight_map["stem_rmsd"] = 0.102398;
+ weight_map["str_prof_score"] = -2.71036;
+ weight_map["torsion"] = 1.03345;
+ length_dependent_weights_bb_db_[11] = weight_map;
+ length_dependent_weights_bb_db_[12] = weight_map;
+
+ weight_map["cb_packing"] = 1.99907;
+ weight_map["cbeta"] = 0.278163;
+ weight_map["clash"] = 0.0423564;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.20795;
+ weight_map["seq_prof_score"] = -0.106216;
+ weight_map["stem_rmsd"] = 0.0810602;
+ weight_map["str_prof_score"] = -2.98924;
+ weight_map["torsion"] = 1.06368;
+ length_dependent_weights_bb_db_[13] = weight_map;
+ length_dependent_weights_bb_db_[14] = weight_map;
+ length_dependent_weights_bb_db_[-1] = weights_bb_db_;
+
+ // BB_AANR length dependent
+ weight_map.clear();
+ weight_map["aa_clash"] = 0.283751;
+ weight_map["aa_interaction"] = 0.017465;
+ weight_map["aa_packing"] = 0.241799;
+ weight_map["cb_packing"] = 0.127742;
+ weight_map["cbeta"] = 0.352376;
+ weight_map["clash"] = 0.704888;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.149259;
+ weight_map["torsion"] = 0.490918;
+ length_dependent_weights_bb_aa_[0] = weight_map;
+ length_dependent_weights_bb_aa_[1] = weight_map;
+ length_dependent_weights_bb_aa_[2] = weight_map;
+ length_dependent_weights_bb_aa_[3] = weight_map;
+ length_dependent_weights_bb_aa_[4] = weight_map;
+
+ weight_map["aa_clash"] = 0.036239;
+ weight_map["aa_interaction"] = 0.00620728;
+ weight_map["aa_packing"] = 0.0614946;
+ weight_map["cb_packing"] = 0.288402;
+ weight_map["cbeta"] = 0.272684;
+ weight_map["clash"] = 0.0750436;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.0720939;
+ weight_map["torsion"] = 0.348388;
+ length_dependent_weights_bb_aa_[5] = weight_map;
+ length_dependent_weights_bb_aa_[6] = weight_map;
+
+ weight_map["aa_clash"] = 0.0616729;
+ weight_map["aa_interaction"] = 0.00672076;
+ weight_map["aa_packing"] = 0.0850889;
+ weight_map["cb_packing"] = 0.617773;
+ weight_map["cbeta"] = 0.252535;
+ weight_map["clash"] = 0.0521921;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.244583;
+ weight_map["torsion"] = 0.760732;
+ length_dependent_weights_bb_aa_[7] = weight_map;
+ length_dependent_weights_bb_aa_[8] = weight_map;
+
+ weight_map["aa_clash"] = 0.0171586;
+ weight_map["aa_interaction"] = 0.0057374;
+ weight_map["aa_packing"] = 0.132462;
+ weight_map["cb_packing"] = 1.05146;
+ weight_map["cbeta"] = 0.0751599;
+ weight_map["clash"] = 0.0412901;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.233706;
+ weight_map["torsion"] = 0.932057;
+ length_dependent_weights_bb_aa_[9] = weight_map;
+ length_dependent_weights_bb_aa_[10] = weight_map;
+
+ weight_map["aa_clash"] = 0.015698;
+ weight_map["aa_interaction"] = 0.0080754;
+ weight_map["aa_packing"] = 0.0604609;
+ weight_map["cb_packing"] = 2.82079;
+ weight_map["cbeta"] = 0.289487;
+ weight_map["clash"] = 0.0174437;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.367916;
+ weight_map["torsion"] = 1.84005;
+ length_dependent_weights_bb_aa_[11] = weight_map;
+ length_dependent_weights_bb_aa_[12] = weight_map;
+
+ weight_map["aa_clash_no_relax"] = 0.00320302;
+ weight_map["aa_interaction_no_relax"] = 0.00431749;
+ weight_map["aa_packing_no_relax"] = 0.0794247;
+ weight_map["cb_packing"] = 2.55054;
+ weight_map["cbeta"] = 0.0981701;
+ weight_map["clash"] = 0.0181231;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.243598;
+ weight_map["torsion"] = 1.72607;
+ length_dependent_weights_bb_aa_[13] = weight_map;
+ length_dependent_weights_bb_aa_[14] = weight_map;
+ length_dependent_weights_bb_aa_[-1] = weights_bb_aa_;
+
+ // BB
+ weight_map.clear();
+ weight_map["cb_packing"] = 0.224327;
+ weight_map["cbeta"] = 0.226355;
+ weight_map["clash"] = 0.424003;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.076963;
+ weight_map["torsion"] = 0.253095;
+ length_dependent_weights_bb_[0] = weight_map;
+ length_dependent_weights_bb_[1] = weight_map;
+ length_dependent_weights_bb_[2] = weight_map;
+ length_dependent_weights_bb_[3] = weight_map;
+ length_dependent_weights_bb_[4] = weight_map;
+
+ weight_map["cb_packing"] = 0.137013;
+ weight_map["cbeta"] = 0.194254;
+ weight_map["clash"] = 0.283518;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.12837;
+ weight_map["torsion"] = 0.318854;
+ length_dependent_weights_bb_[5] = weight_map;
+ length_dependent_weights_bb_[6] = weight_map;
+
+ weight_map["cb_packing"] = 0.618752;
+ weight_map["cbeta"] = 0.50412;
+ weight_map["clash"] = 0.108268;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.183393;
+ weight_map["torsion"] = 0.636929;
+ length_dependent_weights_bb_[7] = weight_map;
+ length_dependent_weights_bb_[8] = weight_map;
+
+ weight_map["cb_packing"] = 0.943519;
+ weight_map["cbeta"] = 0.946992;
+ weight_map["clash"] = 0.0956615;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.251022;
+ weight_map["torsion"] = 0.921721;
+ length_dependent_weights_bb_[9] = weight_map;
+ length_dependent_weights_bb_[10] = weight_map;
+
+ weight_map["cb_packing"] = 1.06123;
+ weight_map["cbeta"] = 0.469593;
+ weight_map["clash"] = 0.0831533;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.268347;
+ weight_map["torsion"] = 0.88921;
+ length_dependent_weights_bb_[11] = weight_map;
+ length_dependent_weights_bb_[12] = weight_map;
+
+
+ weight_map["cb_packing"] = 2.05415;
+ weight_map["cbeta"] = 0.604888;
+ weight_map["clash"] = 0.024504;
+ weight_map["hbond"] = 1;
+ weight_map["reduced"] = 0.367079;
+ weight_map["torsion"] = 1.34862;
+ length_dependent_weights_bb_[13] = weight_map;
+ length_dependent_weights_bb_[14] = weight_map;
+ length_dependent_weights_bb_[-1] = weights_bb_;
+
// key naming consistent with default scorers and weights above
stem_rmsd_key_ = "stem_rmsd";
seq_prof_score_key_ = "seq_prof_score";
@@ -90,19 +406,127 @@ ScoringWeights::ScoringWeights() {
aa_scoring_keys_.push_back("aa_packing");
}
+const std::map<String, Real>& ScoringWeights::GetWeights(bool with_db,
+ bool with_aa,
+ bool length_dependent,
+ int loop_length) const {
+
+ if(!length_dependent) {
+ // its not length dependent, so lets return the length agnostic weights!
+ if (with_db) {
+ if (with_aa) {
+ return weights_bb_db_aa_;
+ }
+ else {
+ return weights_bb_db_;
+ }
+ } else {
+ if (with_aa) {
+ return weights_bb_aa_;
+ }
+ else {
+ return weights_bb_;
+ }
+ }
+ } else {
+ // its length dependent!
+ std::map<int, std::map<String, Real> >::const_iterator it;
+ if (with_db) {
+ if (with_aa) {
+ it = length_dependent_weights_bb_db_aa_.find(loop_length);
+ if(it == length_dependent_weights_bb_db_aa_.end()) {
+ it = length_dependent_weights_bb_db_aa_.find(-1);
+ }
+ return it->second;
+ }
+ else {
+ it = length_dependent_weights_bb_db_.find(loop_length);
+ if(it == length_dependent_weights_bb_db_.end()) {
+ it = length_dependent_weights_bb_db_.find(-1);
+ }
+ return it->second;
+ }
+ } else {
+ if (with_aa) {
+ it = length_dependent_weights_bb_aa_.find(loop_length);
+ if(it == length_dependent_weights_bb_aa_.end()) {
+ it = length_dependent_weights_bb_aa_.find(-1);
+ }
+ return it->second;
+ }
+ else {
+ it = length_dependent_weights_bb_.find(loop_length);
+ if(it == length_dependent_weights_bb_.end()) {
+ it = length_dependent_weights_bb_.find(-1);
+ }
+ return it->second;
+ }
+ }
+ }
+}
+
+void ScoringWeights::SetWeights(bool with_db, bool with_aa,
+ const std::map<String, Real>& weights,
+ bool length_dependent, int loop_length) {
+
+ if(!length_dependent){
+ // its not length dependent, so lets set the length agnostic weights!
+ if (with_db) {
+ if (with_aa) {
+ weights_bb_db_aa_ = weights;
+ }
+ else {
+ weights_bb_db_ = weights;
+ }
+ } else {
+ if (with_aa) {
+ weights_bb_aa_ = weights;
+ }
+ else {
+ weights_bb_ = weights;
+ }
+ }
+ } else {
+ // its length dependent!
+ if (with_db) {
+ if (with_aa) {
+ length_dependent_weights_bb_db_aa_[loop_length] = weights;
+ }
+ else {
+ length_dependent_weights_bb_db_[loop_length] = weights;
+ }
+ } else {
+ if (with_aa) {
+ length_dependent_weights_bb_aa_[loop_length] = weights;
+ }
+ else {
+ length_dependent_weights_bb_[loop_length] = weights;
+ }
+ }
+ }
+}
+
std::map<String, Real> ScoringWeights::GetBackboneWeights(bool with_db,
- bool with_aa) const {
+ bool with_aa,
+ bool length_dependent,
+ int loop_length) const {
std::map<String, Real> result;
- const std::map<String, Real>& all_weights = GetWeights(with_db, with_aa);
+ const std::map<String, Real>& all_weights = GetWeights(with_db, with_aa,
+ length_dependent,
+ loop_length);
for (uint i = 0; i < bb_scoring_keys_.size(); ++i) {
result[bb_scoring_keys_[i]] = GetWeight(all_weights, bb_scoring_keys_[i]);
}
return result;
}
-std::map<String, Real> ScoringWeights::GetAllAtomWeights(bool with_db) const {
+std::map<String, Real> ScoringWeights::GetAllAtomWeights(bool with_db,
+ bool length_dependent,
+ int loop_length) const {
std::map<String, Real> result;
- const std::map<String, Real>& all_weights = GetWeights(with_db, true);
+ const std::map<String, Real>& all_weights = GetWeights(with_db, true,
+ length_dependent,
+ loop_length);
for (uint i = 0; i < aa_scoring_keys_.size(); ++i) {
result[aa_scoring_keys_[i]] = GetWeight(all_weights, aa_scoring_keys_[i]);
}
diff --git a/modelling/src/scoring_weights.hh b/modelling/src/scoring_weights.hh
index 1e48d783b32e6fd1a5456b5abd755530ff4be7ee..b51158e330ef1f476c266751f4cdbf9a9f872406 100644
--- a/modelling/src/scoring_weights.hh
+++ b/modelling/src/scoring_weights.hh
@@ -17,29 +17,21 @@ public:
}
// Weight access
const std::map<String, Real>& GetWeights(bool with_db = false,
- bool with_aa = false) const {
- if (with_db) {
- if (with_aa) return weights_bb_db_aa_;
- else return weights_bb_db_;
- } else {
- if (with_aa) return weights_bb_aa_;
- else return weights_bb_;
- }
- }
+ bool with_aa = false,
+ bool length_dependent=false,
+ int loop_length = -1) const;
void SetWeights(bool with_db, bool with_aa,
- const std::map<String, Real>& weights) {
- if (with_db) {
- if (with_aa) weights_bb_db_aa_ = weights;
- else weights_bb_db_ = weights;
- } else {
- if (with_aa) weights_bb_aa_ = weights;
- else weights_bb_ = weights;
- }
- }
+ const std::map<String, Real>& weights,
+ bool length_dependent = false,
+ int loop_length = -1);
// get subsets (as copy for further editing/use)
std::map<String, Real> GetBackboneWeights(bool with_db = false,
- bool with_aa = false) const;
- std::map<String, Real> GetAllAtomWeights(bool with_db = false) const;
+ bool with_aa = false,
+ bool length_dependent=false,
+ int loop_length = -1) const;
+ std::map<String, Real> GetAllAtomWeights(bool with_db = false,
+ bool length_dependent=false,
+ int loop_length = -1) const;
// Key access
const String& GetStemRMSDsKey() const { return stem_rmsd_key_; }
void SetStemRMSDsKey(const String& key) { stem_rmsd_key_ = key; }
@@ -71,11 +63,19 @@ private:
// construction only inside here
ScoringWeights();
- // weights for all combinations
+ // weights for all combinations, length agnostic
std::map<String, Real> weights_bb_;
std::map<String, Real> weights_bb_db_;
std::map<String, Real> weights_bb_aa_;
std::map<String, Real> weights_bb_db_aa_;
+
+ // weights for all combinations, length dependent. The length key of -1
+ // represents the fallback for not covered input lengths (e.g. long loops)
+ std::map<int, std::map<String, Real> > length_dependent_weights_bb_;
+ std::map<int, std::map<String, Real> > length_dependent_weights_bb_db_;
+ std::map<int, std::map<String, Real> > length_dependent_weights_bb_aa_;
+ std::map<int, std::map<String, Real> > length_dependent_weights_bb_db_aa_;
+
// key names
String stem_rmsd_key_;
String seq_prof_score_key_;
diff --git a/modelling/src/sidechain_env_listener.cc b/modelling/src/sidechain_env_listener.cc
index 18a1297eef220f6b2aa55227a17038b918216282..d72e09f30a9c918c87d1569aabe9be055c6de17f 100644
--- a/modelling/src/sidechain_env_listener.cc
+++ b/modelling/src/sidechain_env_listener.cc
@@ -150,10 +150,7 @@ void SidechainEnvListener::SetResidue_(loop::ConstAllAtomPositionsPtr all_pos,
// we only add data if BB is set
if (bb_set) {
// get positions
- const geom::Vec3& n_pos = all_pos->GetPos(idx_N);
const geom::Vec3& ca_pos = all_pos->GetPos(idx_CA);
- const geom::Vec3& c_pos = all_pos->GetPos(idx_C);
- const geom::Vec3& o_pos = all_pos->GetPos(idx_O);
geom::Vec3 cb_pos;
if (r_id != sidechain::GLY) cb_pos = all_pos->GetPos(idx_CB);
@@ -177,36 +174,33 @@ void SidechainEnvListener::SetResidue_(loop::ConstAllAtomPositionsPtr all_pos,
// set backbone frame res.
bb_frame_residue_[res_idx]
- = rot_constructor_.ConstructBackboneFrameResidue(n_pos, ca_pos, c_pos,
- o_pos, cb_pos,
+ = rot_constructor_.ConstructBackboneFrameResidue(*all_pos, res_idx,
r_id, res_idx,
phi_angle_[res_idx],
n_ter_[res_idx],
c_ter_[res_idx]);
- // do we have a sidechain?
- if (r_id != sidechain::ALA && r_id != sidechain::GLY) {
- // set sidechain frame res. if all set
- if (all_set) {
- sc_frame_residue_[res_idx]
- = rot_constructor_.ConstructSidechainFrameResidue(*all_pos, res_idx,
- r_id, res_idx);
- } else {
- sc_frame_residue_[res_idx].reset();
- }
- // set rotamer if needed
- if (all_rotamers_ || !all_set) {
- SetRotamer_(all_pos, n_pos, ca_pos, cb_pos, r_id, res_idx);
- } else {
- if (use_frm_) frm_rotamer_group_[res_idx].reset();
- else rrm_rotamer_group_[res_idx].reset();
- }
- // set extra cystein rotamer if needed
- if (add_cyd_rotamers_ && r_id == sidechain::CYS) {
- CreateRotamerGroup(cyd_frm_rotamer_group_[res_idx], n_pos, ca_pos,
- cb_pos, sidechain::CYD, res_idx);
- }
+ // set sidechain frame res. if all set
+ if (all_set) {
+ sc_frame_residue_[res_idx]
+ = rot_constructor_.ConstructSidechainFrameResidue(*all_pos, res_idx,
+ r_id, res_idx);
+ } else {
+ sc_frame_residue_[res_idx].reset();
+ }
+ // set rotamer if needed
+ if (all_rotamers_ || !all_set) {
+ SetRotamer_(all_pos, r_id, res_idx);
+ } else {
+ if (use_frm_) frm_rotamer_group_[res_idx].reset();
+ else rrm_rotamer_group_[res_idx].reset();
}
+ // set extra cystein rotamer if needed
+ if (add_cyd_rotamers_ && r_id == sidechain::CYS) {
+ CreateRotamerGroup(cyd_frm_rotamer_group_[res_idx], all_pos,
+ sidechain::CYD, res_idx);
+ }
+
} else {
// clear stuff
if (bb_frame_residue_[res_idx]) {
@@ -224,9 +218,6 @@ void SidechainEnvListener::SetResidue_(loop::ConstAllAtomPositionsPtr all_pos,
}
void SidechainEnvListener::SetRotamer_(loop::ConstAllAtomPositionsPtr all_pos,
- const geom::Vec3& n_pos,
- const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
const sidechain::RotamerID r_id,
const uint res_idx) {
// add rotamer anyways -> potentially need to change ID
@@ -245,10 +236,10 @@ void SidechainEnvListener::SetRotamer_(loop::ConstAllAtomPositionsPtr all_pos,
// -> same with RRM: 0.30s
// -> RRM w/o BBdep: 0.23s
if (use_frm_) {
- CreateRotamerGroup(frm_rotamer_group_[res_idx], n_pos, ca_pos, cb_pos,
+ CreateRotamerGroup(frm_rotamer_group_[res_idx], all_pos,
rg_r_id, res_idx);
} else {
- CreateRotamerGroup(rrm_rotamer_group_[res_idx], n_pos, ca_pos, cb_pos,
+ CreateRotamerGroup(rrm_rotamer_group_[res_idx], all_pos,
rg_r_id, res_idx);
}
}
diff --git a/modelling/src/sidechain_env_listener.hh b/modelling/src/sidechain_env_listener.hh
index a35a0b36b8f18f7a497ec8c27f70739fda4576bf..2f8c14a1349f80b6d36464debc298b7aa3161d01 100644
--- a/modelling/src/sidechain_env_listener.hh
+++ b/modelling/src/sidechain_env_listener.hh
@@ -119,40 +119,33 @@ public:
// create a rotamer group based on internal settings (no use_frm_ check!)
void CreateRotamerGroup(sidechain::FRMRotamerGroupPtr& rot_group,
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
+ loop::ConstAllAtomPositionsPtr all_pos,
const sidechain::RotamerID r_id, const uint res_idx) {
if (use_bbdep_lib_) {
- rot_group = rot_constructor_.ConstructFRMRotamerGroup(n_pos, ca_pos,
- cb_pos, r_id,
- res_idx,
+ rot_group = rot_constructor_.ConstructFRMRotamerGroup(*all_pos, res_idx,
+ r_id, res_idx,
bbdep_library_,
phi_angle_[res_idx],
psi_angle_[res_idx]);
} else {
- rot_group = rot_constructor_.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
+ rot_group = rot_constructor_.ConstructFRMRotamerGroup(*all_pos, res_idx,
r_id, res_idx,
library_);
}
rot_constructor_.AssignInternalEnergies(rot_group);
}
void CreateRotamerGroup(sidechain::RRMRotamerGroupPtr& rot_group,
- const geom::Vec3& n_pos,
- const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- const sidechain::RotamerID r_id,
- const uint res_idx) {
+ loop::ConstAllAtomPositionsPtr all_pos,
+ const sidechain::RotamerID r_id, const uint res_idx) {
if (use_bbdep_lib_) {
- rot_group = rot_constructor_.ConstructRRMRotamerGroup(n_pos, ca_pos,
- cb_pos, r_id,
- res_idx,
+ rot_group = rot_constructor_.ConstructRRMRotamerGroup(*all_pos, res_idx,
+ r_id, res_idx,
bbdep_library_,
phi_angle_[res_idx],
psi_angle_[res_idx]);
} else {
- rot_group = rot_constructor_.ConstructRRMRotamerGroup(n_pos, ca_pos,
- cb_pos, r_id,
- res_idx,
+ rot_group = rot_constructor_.ConstructRRMRotamerGroup(*all_pos, res_idx,
+ r_id, res_idx,
library_);
}
rot_constructor_.AssignInternalEnergies(rot_group);
@@ -163,9 +156,7 @@ private:
// set stuff for one residue
void SetResidue_(loop::ConstAllAtomPositionsPtr all_pos, const uint res_idx);
void SetRotamer_(loop::ConstAllAtomPositionsPtr all_pos,
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, const sidechain::RotamerID r_id,
- const uint res_idx);
+ const sidechain::RotamerID r_id, const uint res_idx);
// global data
bool all_rotamers_; // construct rotamers for all res. with BB instead of
@@ -185,8 +176,8 @@ private:
// dynamic data per residue
// -> any data only set if BB set ("if (bb_frame_residue_[res_idx]) ...")
- // -> sc_frame_residue set if not ALA/GLY and all pos. available
- // -> xxx_rotamer_group set if not ALA/GLY and atoms missing or all_rotamers_
+ // -> sc_frame_residue set if not GLY and all pos. available
+ // -> xxx_rotamer_group set if no atoms are missing or all_rotamers_
// -> if use_frm_, only xxx = frm valid, else, only xxx = rrm
// -> CalculateInternalEnergies done for all rotamer groups
ScCBetaSpatialOrganizerItem* env_data_;
diff --git a/modelling/tests/data/port_frag_db.dat b/modelling/tests/data/port_frag_db.dat
index 1cc848360e16ec2840bc6c540fa6c7eda9e4fb95..167582ab4c931037fc88519a53f8a6d841a67e1c 100644
Binary files a/modelling/tests/data/port_frag_db.dat and b/modelling/tests/data/port_frag_db.dat differ
diff --git a/modelling/tests/data/port_str_db.dat b/modelling/tests/data/port_str_db.dat
index 5c183190ce902c88a35cc99fb5e4fd69a71ef62f..a861977c6a974dd2a15929b9f5c71415d57901d3 100644
Binary files a/modelling/tests/data/port_str_db.dat and b/modelling/tests/data/port_str_db.dat differ
diff --git a/modelling/tests/test_loop_candidates.cc b/modelling/tests/test_loop_candidates.cc
index fe902a579d7de55cad3a2a06026aa325b765847b..70c92d55fb35c002c0d3077aaaa1c334b9df29b5 100644
--- a/modelling/tests/test_loop_candidates.cc
+++ b/modelling/tests/test_loop_candidates.cc
@@ -303,7 +303,7 @@ BOOST_AUTO_TEST_CASE(test_loop_candidates_from_db) {
ost::mol::EntityHandle ent = LoadTestStructure("data/1CRN.pdb");
ost::seq::ProfileHandlePtr prof;
prof = ost::io::LoadSequenceProfile("data/1CRNA.hhm");
- const uint loop_length = 5;
+ const uint loop_length = 7;
const uint start_idx = 10;
// get dbs (small DBs created as in example codes using crambin)
@@ -311,15 +311,15 @@ BOOST_AUTO_TEST_CASE(test_loop_candidates_from_db) {
structure_db = loop::StructureDB::LoadPortable("data/port_str_db.dat");
// get known fragments to put in here
std::vector<loop::FragmentInfo> fragments;
- fragments.push_back(loop::FragmentInfo(1, 108, 5));
- fragments.push_back(loop::FragmentInfo(1, 24, 5));
- fragments.push_back(loop::FragmentInfo(1, 93, 5));
- fragments.push_back(loop::FragmentInfo(0, 10, 5));
- fragments.push_back(loop::FragmentInfo(0, 9, 5));
- fragments.push_back(loop::FragmentInfo(1, 90, 5));
- fragments.push_back(loop::FragmentInfo(0, 7, 5));
- fragments.push_back(loop::FragmentInfo(1, 28, 5));
- fragments.push_back(loop::FragmentInfo(1, 4, 5));
+ fragments.push_back(loop::FragmentInfo(1, 108, loop_length));
+ fragments.push_back(loop::FragmentInfo(1, 24, loop_length));
+ fragments.push_back(loop::FragmentInfo(1, 93, loop_length));
+ fragments.push_back(loop::FragmentInfo(0, 10, loop_length));
+ fragments.push_back(loop::FragmentInfo(0, 9, loop_length));
+ fragments.push_back(loop::FragmentInfo(1, 90, loop_length));
+ fragments.push_back(loop::FragmentInfo(0, 7, loop_length));
+ fragments.push_back(loop::FragmentInfo(1, 28, loop_length));
+ fragments.push_back(loop::FragmentInfo(1, 4, loop_length));
// manually fill loop candidates
String loop_seq = "";
@@ -343,9 +343,9 @@ BOOST_AUTO_TEST_CASE(test_loop_candidates_from_db) {
structure_db, *prof, start_idx);
stem_rmsds = loop_candidates->CalculateStemRMSDs(n_stem, c_stem);
// check scores
- CheckScore(seq_prof_scores, N_cand, -2.12749, 2.07746, -0.484273);
- CheckScore(str_prof_scores, N_cand, 0.149246, 0.426513, 0.282906);
- CheckScore(stem_rmsds, N_cand, 0.00893292, 1.66355, 0.691202);
+ CheckScore(seq_prof_scores, N_cand, -2.73226428, 2.37290597, -1.04137301);
+ CheckScore(str_prof_scores, N_cand, 0.0652512088, 0.749628067, 0.391301066);
+ CheckScore(stem_rmsds, N_cand, 0.0314558744, 2.9163394, 1.22806919);
// check ApplyXXX
// -> expected ApplyCCD: 0, 2, .., 8 converging
@@ -354,41 +354,51 @@ BOOST_AUTO_TEST_CASE(test_loop_candidates_from_db) {
orig_indices = lc.ApplyCCD(n_stem, c_stem);
CheckOrigIndices(lc, orig_indices, fragments);
// ShowIndices(orig_indices);
- BOOST_CHECK_EQUAL(orig_indices.size(), uint(8));
+ BOOST_CHECK_EQUAL(orig_indices.size(), uint(9));
BOOST_CHECK_EQUAL(orig_indices[0], uint(0));
- BOOST_CHECK_EQUAL(orig_indices[1], uint(2));
- BOOST_CHECK_EQUAL(orig_indices[7], uint(8));
+ BOOST_CHECK_EQUAL(orig_indices[1], uint(1));
+ BOOST_CHECK_EQUAL(orig_indices[8], uint(8));
CheckProfScores(lc, orig_indices, structure_db, prof, start_idx,
seq_prof_scores, str_prof_scores);
// -> expected ApplyKIC: 0 converging with 2 LC
lc = *loop_candidates; // COPY
- orig_indices = lc.ApplyKIC(n_stem, c_stem, 1, 2, 3);
+ orig_indices = lc.ApplyKIC(n_stem, c_stem, 1, 3, 5);
CheckOrigIndices(lc, orig_indices, fragments);
// ShowIndices(orig_indices);
- BOOST_CHECK_EQUAL(orig_indices.size(), uint(2));
- BOOST_CHECK_EQUAL(orig_indices[0], uint(3));
- BOOST_CHECK_EQUAL(orig_indices[1], uint(3));
+ BOOST_CHECK_EQUAL(orig_indices.size(), uint(50));
+
+
+ BOOST_CHECK_EQUAL(orig_indices[0], uint(0));
+ BOOST_CHECK_EQUAL(orig_indices[1], uint(0));
+ BOOST_CHECK_EQUAL(orig_indices[2], uint(0));
+ BOOST_CHECK_EQUAL(orig_indices[3], uint(0));
+ BOOST_CHECK_EQUAL(orig_indices[4], uint(1));
+ BOOST_CHECK_EQUAL(orig_indices[5], uint(1));
+ BOOST_CHECK_EQUAL(orig_indices[6], uint(1));
+ BOOST_CHECK_EQUAL(orig_indices[49], uint(8));
+
CheckProfScores(lc, orig_indices, structure_db, prof, start_idx,
seq_prof_scores, str_prof_scores);
// cluster them
std::vector< std::vector<uint> > clusters;
- const Real max_dist = 0.23;
+ const Real max_dist = 0.35;
loop_candidates->GetClusters(max_dist, clusters);
// ShowClusters(clusters);
- BOOST_CHECK_EQUAL(clusters.size(), uint(4));
+ BOOST_CHECK_EQUAL(clusters.size(), uint(5));
std::vector<uint> cluster_sizes;
- for(int i = 0; i < 4; ++i){
+ for(uint i = 0; i < clusters.size(); ++i){
cluster_sizes.push_back(clusters[i].size());
}
std::sort(cluster_sizes.begin(), cluster_sizes.end());
BOOST_CHECK_EQUAL(cluster_sizes[0], uint(1));
BOOST_CHECK_EQUAL(cluster_sizes[1], uint(1));
- BOOST_CHECK_EQUAL(cluster_sizes[2], uint(3));
- BOOST_CHECK_EQUAL(cluster_sizes[3], uint(4));
+ BOOST_CHECK_EQUAL(cluster_sizes[2], uint(1));
+ BOOST_CHECK_EQUAL(cluster_sizes[3], uint(3));
+ BOOST_CHECK_EQUAL(cluster_sizes[4], uint(3));
CheckClusters(clusters, N_cand);
// get filtered variant to check neglect_size_one below
diff --git a/scoring/doc/CMakeLists.txt b/scoring/doc/CMakeLists.txt
index c9d338020d208177bad785892b3e9aaa84f90d4a..a33e0d61b2c2ac4907e423be78ad9c31c4a08c79 100644
--- a/scoring/doc/CMakeLists.txt
+++ b/scoring/doc/CMakeLists.txt
@@ -3,6 +3,7 @@ set(SCORING_RST
backbone_score_env.rst
backbone_scorers.rst
all_atom_scorers.rst
+ other_scoring_functions.rst
)
add_doc_source(NAME scoring RST ${SCORING_RST})
diff --git a/scoring/doc/all_atom_scorers.rst b/scoring/doc/all_atom_scorers.rst
index 5637039287244c727e7e700670d182e2b64bacec..0a1b39b1613522dd671df0b73b32e98dcaac55eb 100644
--- a/scoring/doc/all_atom_scorers.rst
+++ b/scoring/doc/all_atom_scorers.rst
@@ -37,10 +37,10 @@ AllAtomOverallScorer class
:type env: :class:`~promod3.loop.AllAtomEnv`
.. method:: CalculateLinearCombination(linear_weights, start_resnum, \
- num_residues, chain_idx=0)
+ num_residues, chain_idx)
- Calculate linear combination of scores for the desired loop (extracted from
- environment) against the set environment (see
+ Calculate linear combination of scores for the desired loop(s) (extracted
+ from environment) against the set environment (see
:meth:`AllAtomScorer.CalculateScore`).
:param linear_weights: Weights for each desired scorer. You can add a
@@ -48,14 +48,14 @@ AllAtomOverallScorer class
with key "intercept".
:type linear_weights: :class:`dict` (keys: :class:`str`,
values: :class:`float`)
- :param start_resnum: Res. number defining the position in the SEQRES
+ :param start_resnum: Res. number(s) defining the position(s) in the SEQRES
(see :class:`~promod3.loop.AllAtomEnv` for indexing)
- :type start_resnum: :class:`int` / :class:`ost.mol.ResNum`
- :param num_residues: Length of loop.
- :type num_residues: :class:`int`
- :param chain_idx: Index of chain the loop belongs to
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Length of loop(s).
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :param chain_idx: Index of chain the loop(s) belongs to
(see :class:`~promod3.loop.AllAtomEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
:return: Score for the given set of atoms.
:rtype: :class:`float`
@@ -91,25 +91,20 @@ AllAtomScorer base class
:param env: Link scorer to this score environment.
:type env: :class:`~promod3.loop.AllAtomEnv`
- .. method:: CalculateScore(start_resnum, num_residues, chain_idx=0)
+ .. method:: CalculateScore(start_resnum, num_residues, chain_idx)
- Calculates score for the desired loop (extracted from environment) against
+ Calculates score for the desired loop(s) (extracted from environment) against
the set environment. Unless otherwise noted in the scorer, a lower "score"
is better!
- Note that the structural data of the loop is expected to be in the linked
- environment before calling this! This behavior is different from the
- corresponding function in :class:`BackboneScorer` as, for performance
- reasons, we require all the comparisons to be done against the environment.
-
- :param start_resnum: Res. number defining the position in the SEQRES
+ :param start_resnum: Res. number(s) defining the position(s) in the SEQRES
(see :class:`~promod3.loop.AllAtomEnv` for indexing)
- :type start_resnum: :class:`int` / :class:`ost.mol.ResNum`
- :param num_residues: Length of loop.
- :type num_residues: :class:`int`
- :param chain_idx: Index of chain the loop belongs to
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Length of loop(s).
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :param chain_idx: Index of chain the loop(s) belongs to
(see :class:`~promod3.loop.AllAtomEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
:return: Score for the given set of atoms.
:rtype: :class:`float`
@@ -121,25 +116,21 @@ AllAtomScorer base class
.. method:: CalculateScoreProfile(start_resnum, num_residues, chain_idx=0)
- Calculates per residue scores for the desired loop (extracted from
+ Calculates per residue scores for the desired loop(s) (extracted from
environment) against the set environment.
- Note that the structural data of the loop is expected to be in the linked
- environment before calling this! This behavior is different from the
- corresponding function in :class:`BackboneScorer` as, for performance
- reasons, we require all the comparisons to be done against the environment.
-
- :param start_resnum: Res. number defining the position in the SEQRES
+ :param start_resnum: Res. number(s) defining the position(s) in the SEQRES
(see :class:`~promod3.loop.AllAtomEnv` for indexing)
- :type start_resnum: :class:`int` / :class:`ost.mol.ResNum`
- :param num_residues: Length of loop.
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Length of loop(s).
:type num_residues: :class:`int`
- :param chain_idx: Index of chain the loop belongs to
+ :param chain_idx: Index of chain the loop(s) belongs to
(see :class:`~promod3.loop.AllAtomEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
- :return: Scores for the given loop, one for each residue.
- :rtype: :class:`list` of :class:`float`
+ :return: Scores for the given loop(s), one for each residue.
+ :rtype: :class:`list` of :class:`float` / :class:`list` of :class:`list`
+ of :class:`float`
:raises: same :exc:`~exceptions.RuntimeError` as :meth:`CalculateScore`.
@@ -154,8 +145,11 @@ AllAtomInteractionScorer class
*cutoff* and which are at least *seq_sep* residues apart. An energy is
assigned to each distance using equally sized bins and distinguishing all
possible pairs of atoms (usually the energy only differs for chemically
- distinguishable heavy atoms). The calculated score is normalized by the number
- of interacting atom pairs.
+ distinguishable heavy atoms).
+ By default, the scorer calculates the scores by
+ including everything, the stuff set in the environment and the coordinates
+ in the input loops. You can change this behaviour with the according
+ functions.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadAllAtomInteractionScorer`) or by setting all energies (see :meth:`SetEnergy`).
@@ -204,6 +198,10 @@ AllAtomInteractionScorer class
Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every pair of heavy atom types and for every *bin* < *bins*.
+ Internal symmetry is enforced => Calling SetEnergy(aaa1, aaa2, bin, energy) is
+ equivalent to calling SetEnergy(aaa1, aaa2, bin, energy) AND
+ SetEnergy(aaa2, aaa1, bin, energy).
+
:param aaa1: Heavy atom type for first interaction partner.
:type aaa1: :class:`~promod3.loop.AminoAcidAtom`
@@ -216,6 +214,24 @@ AllAtomInteractionScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoInternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions within the
+ loop. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoExternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions towards the
+ environment. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues in the input loop. True by default.
+ :type do_it: :class:`bool`
+
.. function:: LoadAllAtomInteractionScorer()
@@ -230,8 +246,7 @@ AllAtomPackingScorer class
Inherits all functionality of :class:`AllAtomScorer`. Evaluates pseudo
energies by counting surrounding atoms within a certain *cutoff* radius around
- all heavy atoms not belonging to the assessed residue itself. The calculated
- score is normalized by the number of atoms being assessed.
+ all heavy atoms not belonging to the assessed residue itself.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadAllAtomPackingScorer`) or by setting all energies (see
@@ -287,6 +302,12 @@ AllAtomPackingScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues in the input loop. True by default.
+ :type do_it: :class:`bool`
+
.. function:: LoadAllAtomPackingScorer()
@@ -302,5 +323,25 @@ AllAtomClashScorer class
Inherits all functionality of :class:`AllAtomScorer`. Calculates a simple
clash score of all atoms against the environment. There is no need to define
any parameters here as all interaction energies are fixed (see Eq. (11) in
- [canutescu2003b]_). The calculated score is normalized by the number of atoms
- being assessed.
+ [canutescu2003b]_). By default, the scorer calculates the scores by
+ including everything, the stuff set in the environment and the coordinates
+ in the input loops. You can change this behaviour with the according
+ functions.
+
+ .. method:: DoInternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions within the
+ loop. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoExternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions towards the
+ environment. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues in the input loop. True by default.
+ :type do_it: :class:`bool`
diff --git a/scoring/doc/backbone_score_env.rst b/scoring/doc/backbone_score_env.rst
index f9c1e18ce2d2537df02f053e2932ab28d24b7712..25980a4d34ba90890e7686c87838fa8dcd0f1679 100644
--- a/scoring/doc/backbone_score_env.rst
+++ b/scoring/doc/backbone_score_env.rst
@@ -12,10 +12,18 @@ BackboneScoreEnv class
used by the scorers. It is linked to a (list of) seqres (one per chain) at
construction. The idea is to initialize it at the beginning of the modelling
process with all known data (positions extracted from template, psipred
- prediction, density map, etc) and then update the environment whenever a new
- loop is being added. Note that, depending on the used scorers, some
- information must be provided for the score to make sense and any env. data can
- be set at any time before actually calculating a score.
+ prediction, etc). All scorers attached to that environment will see that data
+ and can calculate scores accordingly.
+ Scoring with this setup is a two step process:
+
+ * Set the positions you want to score in the environment to make it available
+ to all attached scorers
+ * Call the scorers to get the desired scores
+
+ One problem that might occur is that you mess around with the environment and
+ at some point you want to restore the original state. The
+ :class:`BackboneScoreEnv` provides a Stash / Pop mechanism to perform this
+ task.
:param seqres: Internal SEQRES to be set (single chain or list with one per
chain). Whenever setting structural data, consistency with this SEQRES is enforced.
@@ -94,17 +102,6 @@ BackboneScoreEnv class
inconsistent with the number of internal chains or when one of the
predictions' sizes is inconsistent with the internal SEQRES size.
- .. method:: SetMap(map, resolution, all_atom=False)
-
- Sets an internal density map, which is necessary to calculate some scores.
-
- :param map: The density map
- :type map: :class:`ost.img.ImageHandle`
- :param resolution: Expected resolution of the density map.
- :type resolution: :class:`float`
- :param all_atom: Whether the map is accurate enough to resolve all atoms.
- :type all_atom: :class:`bool`
-
.. method:: AddPairwiseFunction(function, function_type)
Adds a pairwise function that can be used in :meth:`ApplyPairwiseFunction`.
@@ -139,6 +136,26 @@ BackboneScoreEnv class
res. numbers is invalid, the interaction partners are the same
residue or when *f_idx* is an invalid index.
+ .. method:: Stash(start_rnum, num_residues, chain_idx)
+
+ FILO style stashing. You can perform up to 100 stash operations to save
+ the current state of certain stretches in the environment. This state can
+ be restored by calling :func:`Pop`. In one stash operation you can either
+ stash one stretch by providing integers as input or several stretches by
+ providing lists of integers.
+
+ :param start_rnum: start rnum of stretch to stash
+ :param num_residues: length of stretch to stash
+ :param chain_idx: chain idx of stretch to stash
+
+ :type start_rnum: :class:`int` / :class:`list` of :class:`int`
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
+
+ .. method:: Pop()
+
+ Remove and apply the the last stash operation.
+
.. method:: GetSeqres()
:return: SEQRES that was set in constructor (one sequence per chain).
diff --git a/scoring/doc/backbone_scorers.rst b/scoring/doc/backbone_scorers.rst
index ebb0bc300bd52033bb4a020ac0a5a63c390d3617..55a07ec77cc2e0ebc0b619c90c4ebaf824e9531a 100644
--- a/scoring/doc/backbone_scorers.rst
+++ b/scoring/doc/backbone_scorers.rst
@@ -36,55 +36,51 @@ BackboneOverallScorer class
:param env: Link all scorers to this score environment.
:type env: :class:`BackboneScoreEnv`
- .. method:: Calculate(key, bb_list, start_resnum, chain_idx=0)
+ .. method:: Calculate(key, start_resnum, num_residues, chain_idx=0)
- Calculate score(s) for one or many loop(s) with
- :meth:`BackboneScorer.CalculateScore`.
+ Calculate score for one or several stretches of amino acids given the
+ current scoring environment.
:param key: Key for desired scorer.
:type key: :class:`str`
- :param bb_list: Loop(s) for which to calculate the given score
- :type bb_list: :class:`~promod3.loop.BackboneList` / :class:`list` of
- :class:`~promod3.loop.BackboneList`
:param start_resnum: Res. number defining the position in the SEQRES
(see :class:`BackboneScoreEnv` for indexing)
- :type start_resnum: :class:`int`
- :param chain_idx: Index of chain the loop(s) belong to
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Number of residues in the stretch(es) to score
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :param chain_idx: Index of chain the stretch(es) belongs to
(see :class:`BackboneScoreEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
- :return: Score(s) calculated with the desired scorer for the given loop(s).
- In the case of multiple loops, the returned list has the same
- order as the input.
- :rtype: :class:`float` / :class:`list` of :class:`float`
+ :return: Score calculated with the desired scorer for the given stretch(es).
+ :rtype: :class:`float`
:raises: :exc:`~exceptions.RuntimeError` if there is no scorer with that
*key* or anything raised in :meth:`BackboneScorer.CalculateScore`.
- .. method:: CalculateLinearCombination(linear_weights, bb_list, start_resnum,\
- chain_idx=0)
+ .. method:: CalculateLinearCombination(linear_weights, start_resnum,\
+ num_residues, chain_idx=0)
- Calculate linear combination(s) of scores for one or many loop(s).
+ Calculate linear combination of scores for one or several stretches of
+ amino acids given the current scoring environment.
:param linear_weights: Weights for each desired scorer. You can add a
constant value to each score by defining a weight
with key "intercept".
:type linear_weights: :class:`dict` (keys: :class:`str`,
values: :class:`float`)
- :param bb_list: Loop(s) for which to calculate the given score
- :type bb_list: :class:`~promod3.loop.BackboneList` / :class:`list` of
- :class:`~promod3.loop.BackboneList`
:param start_resnum: Res. number defining the position in the SEQRES
(see :class:`BackboneScoreEnv` for indexing)
- :type start_resnum: :class:`int`
- :param chain_idx: Index of chain the loop(s) belong to
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Number of residues in the stretch(es) to score
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :param chain_idx: Index of chain the stretch(es) belongs to
(see :class:`BackboneScoreEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
- :return: Linear combination(s) of the scores calculated with the desired
- scorers for the given loop(s). In the case of multiple loops, the
- returned list has the same order as the input.
- :rtype: :class:`float` / :class:`list` of :class:`float`
+ :return: Linear combination of the scores calculated with the desired
+ scorers for the given stretch(es)
+ :rtype: :class:`float`
:raises: :exc:`~exceptions.RuntimeError` if *linear_weights* has a *key* for
which no scorer exists or anything raised in
@@ -103,7 +99,7 @@ BackboneOverallScorer class
:returns: Loads or creates the default scorers accessible through
following keys:
"cb_packing", "cbeta", "reduced", "clash", "hbond", "ss_agreement",\
- "torsion", "pairwise", "density"
+ "torsion", "pairwise"
:rtype: :class:`BackboneOverallScorer`
@@ -119,47 +115,46 @@ BackboneScorer base class
:param env: Link scorer to this score environment.
:type env: :class:`BackboneScoreEnv`
- .. method:: CalculateScore(bb_list, start_resnum, chain_idx=0)
+ .. method:: CalculateScore(start_resnum, num_residues, chain_idx=0)
- Calculates score for the given loop internally and against the set
- environment. Data in the environment, which overlaps with the given
- *bb_list* is ignored. Unless otherwise noted in the scorer, a lower "score"
- is better!
+ Calculates score for one or several stretches given the structural
+ information in the attached environment. Unless otherwise noted in the
+ scorer, a lower "score" is better!
- :param bb_list: Loop for which to calculate the given score
- :type bb_list: :class:`~promod3.loop.BackboneList`
:param start_resnum: Res. number defining the position in the SEQRES
(see :class:`BackboneScoreEnv` for indexing)
- :type start_resnum: :class:`int`
- :param chain_idx: Index of chain the loop belongs to
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Number of residues in the stretch(es) to score
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :param chain_idx: Index of chain the stretch(es) belongs to
(see :class:`BackboneScoreEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
- :return: Score for the given loop.
+ :return: Score for the given stretch(es).
:rtype: :class:`float`
:raises: (for most scorers) :exc:`~exceptions.RuntimeError` if scorer was
never attached to a score environment, if scorer has never been
- properly initialized or if *chain_index* / *start_resnum* lead to
- invalid positions.
+ properly initialized or if *start_resnum* / *num_residues* /
+ *chain_idx* lead to invalid positions.
- .. method:: CalculateScoreProfile(bb_list, start_resnum, chain_idx=0)
+ .. method:: CalculateScoreProfile(start_resnum, num_residues, chain_idx=0)
- Calculates per residue scores for the given loop internally and against the
- set environment. Data in the environment, which overlaps with the given
- *bb_list* is ignored.
+ Calculates per residue scores for one or several stretches given the
+ structural information in the attached environment.
- :param bb_list: Loop for which to calculate the given scores
- :type bb_list: :class:`~promod3.loop.BackboneList`
:param start_resnum: Res. number defining the position in the SEQRES
(see :class:`BackboneScoreEnv` for indexing)
- :type start_resnum: :class:`int`
- :param chain_idx: Index of chain the loop belongs to
+ :type start_resnum: :class:`int` / :class:`list` of :class:`int`
+ :param num_residues: Number of residues in the stretch(es) to score
+ :type num_residues: :class:`int` / :class:`list` of :class:`int`
+ :param chain_idx: Index of chain the stretch(es) belongs to
(see :class:`BackboneScoreEnv` for indexing)
- :type chain_idx: :class:`int`
+ :type chain_idx: :class:`int` / :class:`list` of :class:`int`
- :return: Scores for the given loop, one for each residue.
- :rtype: :class:`list` of :class:`float`
+ :return: Scores for the given stretch(es), one for each residue.
+ :rtype: :class:`list` of :class:`float` or :class:`list` of :class:`list`
+ of :class:`float`
:raises: same :exc:`~exceptions.RuntimeError` as :meth:`CalculateScore`.
@@ -171,25 +166,7 @@ CBPackingScorer class
Inherits all functionality of :class:`BackboneScorer`. Evaluates pseudo
energies by counting the number of other CB positions within a certain
- *cutoff* radius of the CB position of the residue to be evaluated. The
- calculated score is normalized by the number of residues in the loop.
- In the default mode, the scorer scores a :class:`promod3.loop.BackboneList`
- given the defined environment. By placing this
- :class:`promod3.loop.BackboneList`, the score of the residues in the
- environment also change. It is possible to honour this effect by using the
- "IncludeEnv" mode. In this alternative mode, every environment residue close
- to the input :class:`promod3.loop.BackboneList` also contributes
- to the final score by adding the difference in score when the environment
- residue sees the original environment and the score when the environment would
- be modified by the :class:`promod3.loop.BackboneList`. You choose the mode
- by specifically calling the according CalculateEnergy functions.
- If you call the CalculateScore function from the parent class
- (e.g. when the scorer is part of the :class:`BackboneOverallScorer`), it
- gets checked what mode is currently active. You can toggle the mode by calling
- the appropriate functions in this class. By default (when you load a scorer or
- when you create a new scorer) the classic version gets called. If you want to
- get per residue scores, the "IncludeEnv" mode makes not much sense and the
- scorer throws an error if a profile is requeset in this mode.
+ *cutoff* radius of the CB position of the residue to be evaluated.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadCBPackingScorer`) or by setting all energies (see
@@ -245,16 +222,12 @@ CBPackingScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
- .. method:: UseClassicMode()
+ .. method:: DoNormalize(do_it)
- If you call this function, the default mode is set to classic if the
- CalculateScore function from the parent class gets called.
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
- .. method:: UseIncludeEnvMode()
-
- If you call this function, the default mode is set to the
- described alternative mode if the CalculateScore function from the parent
- class gets called.
.. function:: LoadCBPackingScorer()
@@ -270,9 +243,8 @@ CBetaScorer class
Inherits all functionality of :class:`BackboneScorer`. Evaluates a pairwise
pseudo interaction energy between CB atoms which are located within a *cutoff*
and which are at least *seq_sep* residues apart. An energy is assigned to each
- distance using *bins* equally sized bins and distinguishing all possible pairs
- of amino acids. The calculated score is normalized by the number of
- interacting CB pairs.
+ distance using equally sized bins and distinguishing all possible pairs
+ of amino acids.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadCBetaScorer`) or by setting all energies (see :meth:`SetEnergy`).
@@ -321,6 +293,9 @@ CBetaScorer class
Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every pair of amino acids and for every *bin* < *bins*.
+ Internal symmetry is enforced => Calling SetEnergy(aa1, aa2, bin, energy) is
+ equivalent to calling SetEnergy(aa1, aa2, bin, energy) AND
+ SetEnergy(aa2, aa1, bin, energy).
:param aa1: Amino acid for first interaction partner.
:type aa1: :class:`ost.conop.AminoAcid`
@@ -333,6 +308,25 @@ CBetaScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoInternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions between
+ the scored residues. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoExternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions of the scored
+ residues towards the surrounding environment.
+ True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
+
.. function:: LoadCBetaScorer()
@@ -348,7 +342,7 @@ ReducedScorer class
Inherits all functionality of :class:`BackboneScorer`. Evaluates a pairwise
pseudo interaction energy between the reduced representation of residues.
Every residue gets represented by its CA position p and a directional
- component ``v = norm(ca_pos-n_pos) + norm (ca_pos-c_pos)``. Residues with CA
+ component ``v = norm(p-n_pos) + norm(p-c_pos)``. Residues with CA
distance < *cutoff* and which are at least *seq_sep* residues apart are
considered to be interacting. For interacting residues r1 and r2, we can
define a line l between p1 and p2. The potential then considers:
@@ -358,10 +352,6 @@ ReducedScorer class
* beta => angle between v2 and l
* gamma => dihedral between (p1+v1,p1,p2,p2+v2)
- Every pairwise interaction within the loop and to the environment gets
- evaluated according to the given parametrization, summed up and finally
- normalized by the number of total interactions.
-
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadReducedScorer`) or by setting all energies (see :meth:`SetEnergy`).
@@ -418,6 +408,11 @@ ReducedScorer class
called for every pair of amino acids, every *dist_bin* < *dist_bins*, every
*alpha_bin* < *angle_bins*, every *beta_bin* < *angle_bins* and every
*gamma_bin* < *dihedral_bins*.
+ Internal symmetry is enforced => Calling
+ SetEnergy(aa1, aa2, dist_bin, alpha_bin, beta_bin, energy) is
+ equivalent to calling
+ SetEnergy(aa1, aa2, dist_bin, alpha_bin, beta_bin, energy) AND
+ SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).
:param aa1: Amino acid for first interaction partner.
:type aa1: :class:`ost.conop.AminoAcid`
@@ -436,6 +431,24 @@ ReducedScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoInternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions between
+ the scored residues. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoExternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions of the scored
+ residues towards the surrounding environment.
+ True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
.. function:: LoadReducedScorer()
@@ -450,29 +463,27 @@ ClashScorer class
Inherits all functionality of :class:`BackboneScorer`. Calculates a simple
clash score of a loop itself and with the set environment. There is no need to
- define any parameters here as all interaction energies are fixed. The
- calculated score is normalized by the number of residues in the loop.
+ define any parameters here as all interaction energies are fixed (see Eq. (11)
+ in [canutescu2003b]_).
+ .. method:: DoInternalScores(do_it)
-DensityScorer class
---------------------------------------------------------------------------------
+ :param do_it: Whether to include pairwise interactions between
+ the scored residues. True by default.
+ :type do_it: :class:`bool`
-.. class:: DensityScorer
+ .. method:: DoExternalScores(do_it)
- Inherits all functionality of :class:`BackboneScorer`. Calculates the
- normalized cross correlation between a density generated from the input
- :class:`~promod3.loop.BackboneList` and a set map.
+ :param do_it: Whether to include pairwise interactions of the scored
+ residues towards the surrounding environment.
+ True by default.
+ :type do_it: :class:`bool`
- This scorer requires that the attached environment has a density map defined
- (see :meth:`BackboneScoreEnv.SetMap`) as soon as a score is to be calculated.
- The *resolution* and *all_atom* flags that were specified in SetMap determine
- how the backbone list is translated into an artificial density map. If
- *all_atom* is set to False (which is recommended for low resolution maps), the
- artificial map gets constructed by only using CA positions instead of all
- atoms.
+ .. method:: DoNormalize(do_it)
- Note that for this scorer a higher "score" is better! So take care when
- combining this to other scores, where it is commonly the other way around.
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
HBondScorer class
@@ -499,10 +510,6 @@ HBondScorer class
thats the one from which the energy is extracted. In all other cases, the
energy is extracted from the 0 state.
- Every pairwise interaction within the loop and to the environment gets
- evaluated according to the given parametrization, summed up and finally
- normalized by the number of residues in the loop.
-
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadHBondScorer`) or by setting all energies (see :meth:`SetEnergy`).
@@ -589,6 +596,25 @@ HBondScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoInternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions between
+ the scored residues. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoExternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions of the scored
+ residues towards the surrounding environment.
+ True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
+
.. function:: LoadHBondScorer()
@@ -607,8 +633,7 @@ SSAgreementScorer class
structure in the model. In every score evaluation, the secondary structure of
the loop is estimated by searching for hydrogen bonds leading to a secondary
structure as defined by dssp. The hbonds are searched internally in the loop
- as well as in the environment. The final score gets summed up over all
- residues in the loop and normalized by the number of residues.
+ as well as in the environment.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
:func:`LoadSSAgreementScorer`) or by setting scores for all possible states
@@ -665,6 +690,11 @@ SSAgreementScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
.. function:: LoadSSAgreementScorer()
@@ -679,9 +709,7 @@ TorsionScorer class
Inherits all functionality of :class:`BackboneScorer`. Evaluates pseudo
energies based on the identity of three consecutive residues and the phi/psi
- dihedral angles of the central residue. Every residue gets evaluated according
- to the set parametrization and the final score gets normalized by the total
- number of summed pseudo energies. The first phi and last psi angle get
+ dihedral angles of the central residue. The first phi and last psi angle get
determined with the help of the environment if set.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
@@ -746,6 +774,11 @@ TorsionScorer class
:raises: :exc:`~exceptions.RuntimeError` if inputs are invalid
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
.. function:: LoadTorsionScorer()
@@ -759,14 +792,28 @@ PairwiseScorer class
.. class:: PairwiseScorer
Inherits all functionality of :class:`BackboneScorer`. Evaluates a list of
- generic pairwise functions (see :class:`PairwiseFunction`). When evaluating a
- loop, the scores of all pairwise functions which involve a residue in the loop
- are summed up (the other residue can be either in the loop or in the env.) and
- normalized by the number of residues in the loop.
-
- This scorer assumes that the attached environment has pairwise functions
- defined (see :meth:`BackboneScoreEnv.ApplyPairwiseFunction`) as soon as a
- score is to be calculated.
+ generic pairwise functions (see :class:`PairwiseFunction`).
+ That are set in the attached scoring environment
+ (see :meth:`BackboneScoreEnv.ApplyPairwiseFunction`).
Note that for this scorer a higher "score" is better! So take care when
combining this to other scores, where it is commonly the other way around.
+
+ .. method:: DoInternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions between
+ the scored residues. True by default.
+ :type do_it: :class:`bool`
+
+ .. method:: DoExternalScores(do_it)
+
+ :param do_it: Whether to include pairwise interactions of the scored
+ residues towards the surrounding environment.
+ True by default.
+ :type do_it: :class:`bool`, true by default.
+
+ .. method:: DoNormalize(do_it)
+
+ :param do_it: Whether to normalize the calculated scores by the number
+ of residues to be scored. True by default.
+ :type do_it: :class:`bool`
diff --git a/scoring/doc/index.rst b/scoring/doc/index.rst
index 9b9a97882cf52c828b6d48133c6b721a34cb66b8..983d6b5587c5f70fc9088e6bdac386567fef16c3 100644
--- a/scoring/doc/index.rst
+++ b/scoring/doc/index.rst
@@ -9,8 +9,8 @@
Tools and algorithms to score loops. The scoring system is split between an
environment which contains model-specific data and scorers which evaluate loops.
-In this example, we load a structure, setup a score environment and a few
-scorers and finally score some loops:
+In this example, we load a structure, setup a score environment, link a few
+scorers to it and finally score some loops:
.. literalinclude:: ../../../tests/doc/scripts/scoring_main.py
@@ -22,3 +22,4 @@ Contents:
backbone_score_env
backbone_scorers
all_atom_scorers
+ other_scoring_functions
diff --git a/scoring/doc/other_scoring_functions.rst b/scoring/doc/other_scoring_functions.rst
new file mode 100644
index 0000000000000000000000000000000000000000..f505232e026655cdebf83d068269e805eb99fedd
--- /dev/null
+++ b/scoring/doc/other_scoring_functions.rst
@@ -0,0 +1,56 @@
+Other Scoring Functions
+================================================================================
+
+.. currentmodule:: promod3.scoring
+
+
+Scoring Functions from SCWRL3
+--------------------------------------------------------------------------------
+
+.. method:: SCWRL3PairwiseScore(d, Rij)
+
+ Pairwise score from the SCWRL3 sidechain construction algorithm
+ [canutescu2003b]_.
+
+ :param d: Distance between the two interacting particles
+ :param Rij: Summed hard-sphere radii of the interacting particles.
+ Suggestions from the paper:
+
+ - carbon: 1.6
+ - oxygen: 1.3
+ - nitrogen: 1.3
+ - sulfur: 1.7
+
+ :type d: :class:`float`
+ :type Rij: :class:`float`
+
+ :returns: The score
+ :rtype: :class:`float`
+
+
+.. method:: SCWRL3DisulfidScore(ca_pos_one, cb_pos_one, sg_pos_one\
+ ca_pos_two, cb_pos_two, sg_pos_two)
+
+ Implements the empirically derived disulfid score from the SCWRL3 sidechain
+ construction algorithm [canutescu2003b]_.
+
+ :param ca_pos_one: CA carbon position of first amino acid
+ :param cb_pos_one: CB carbon position of first amino acid
+ :param sg_pos_one: SG sulfur position of first amino acid
+ :param ca_pos_two: CA carbon position of second amino acid
+ :param cb_pos_two: CB carbon position of second amino acid
+ :param sg_pos_two: SG sulfur position of second amino acid
+
+ :type ca_pos_one: :class:`ost.geoom.Vec3`
+ :type cb_pos_one: :class:`ost.geoom.Vec3`
+ :type sg_pos_one: :class:`ost.geoom.Vec3`
+ :type ca_pos_two: :class:`ost.geoom.Vec3`
+ :type cb_pos_two: :class:`ost.geoom.Vec3`
+ :type sg_pos_two: :class:`ost.geoom.Vec3`
+
+ :returns: The score
+ :rtype: :class:`float`
+
+
+
+.. [canutescu2003b] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).
diff --git a/scoring/pymod/CMakeLists.txt b/scoring/pymod/CMakeLists.txt
index 5ab970484bfd5417bb6dab9677e8e29e8a3a0cad..204b23c99faca4e12550be667881f6bf5e3cb867 100644
--- a/scoring/pymod/CMakeLists.txt
+++ b/scoring/pymod/CMakeLists.txt
@@ -4,6 +4,8 @@ export_all_atom_score.cc
export_object_loader.cc
export_pairwise_functions.cc
export_constraint_constructor.cc
+export_scwrl3_energy_functions.cc
+export_density_scorer.cc
wrap_scoring.cc
)
diff --git a/scoring/pymod/export_all_atom_score.cc b/scoring/pymod/export_all_atom_score.cc
index c2d0f3da72a497c1830266da8207b7a77d87952b..ddaa3f50594fadf0dad1e71ee833d26e1d970777 100644
--- a/scoring/pymod/export_all_atom_score.cc
+++ b/scoring/pymod/export_all_atom_score.cc
@@ -28,26 +28,44 @@ Real WrapCalculateLinearCombination(AllAtomOverallScorer& s,
core::ConvertDictToMap(weights, w);
return s.CalculateLinearCombination(w, start_resnum, num_residues, chain_idx);
}
-Real WrapCalculateLinearCombinationRN(AllAtomOverallScorer& s,
- const boost::python::dict& weights,
- const ost::mol::ResNum& start_resnum,
- uint num_residues, uint chain_idx) {
- uint num = start_resnum.GetNum();
- return WrapCalculateLinearCombination(s, weights, num, num_residues,
- chain_idx);
-}
+Real WrapCalculateLinearCombinationList(AllAtomOverallScorer& s,
+ const boost::python::dict& weights,
+ const boost::python::list& start_resnum,
+ const boost::python::list& num_residues,
+ const boost::python::list& chain_idx) {
+ std::map<String, Real> w;
+ core::ConvertDictToMap(weights, w);
+
+ std::vector<uint> v_start_resnum;
+ std::vector<uint> v_num_residues;
+ std::vector<uint> v_chain_idx;
+
+ core::ConvertListToVector(start_resnum, v_start_resnum);
+ core::ConvertListToVector(num_residues, v_num_residues);
+ core::ConvertListToVector(chain_idx, v_chain_idx);
+ return s.CalculateLinearCombination(w, v_start_resnum, v_num_residues,
+ v_chain_idx);
+}
Real WrapAACalculateScore(const AllAtomScorer& scorer, uint start_resnum,
uint num_residues, uint chain_idx) {
return scorer.CalculateScore(start_resnum, num_residues, chain_idx);
-}
-Real WrapAACalculateScoreRN(const AllAtomScorer& scorer,
- const ost::mol::ResNum& start_resnum,
- uint num_residues, uint chain_idx) {
- uint num = start_resnum.GetNum();
- return scorer.CalculateScore(num, num_residues, chain_idx);
-}
+}
+Real WrapAACalculateScoreList(AllAtomScorer& scorer,
+ boost::python::list& start_resnum,
+ boost::python::list& num_residues,
+ boost::python::list& chain_idx) {
+
+ std::vector<uint> v_start_resnum;
+ std::vector<uint> v_num_residues;
+ std::vector<uint> v_chain_idx;
+
+ core::ConvertListToVector(start_resnum, v_start_resnum);
+ core::ConvertListToVector(num_residues, v_num_residues);
+ core::ConvertListToVector(chain_idx, v_chain_idx);
+ return scorer.CalculateScore(v_start_resnum, v_num_residues, v_chain_idx);
+}
boost::python::list
WrapAACalculateScoreProfile(const AllAtomScorer& scorer, uint start_resnum,
uint num_residues, uint chain_idx) {
@@ -57,21 +75,48 @@ WrapAACalculateScoreProfile(const AllAtomScorer& scorer, uint start_resnum,
core::AppendVectorToList(profile, return_list);
return return_list;
}
-boost::python::list
-WrapAACalculateScoreProfileRN(const AllAtomScorer& scorer,
- const ost::mol::ResNum& start_resnum,
- uint num_residues, uint chain_idx) {
- uint num = start_resnum.GetNum();
- return WrapAACalculateScoreProfile(scorer, num, num_residues, chain_idx);
-}
+boost::python::list
+WrapAACalculateScoreProfileList(const AllAtomScorer& scorer,
+ boost::python::list& start_resnum,
+ boost::python::list& num_residues,
+ boost::python::list& chain_idx) {
+
+ std::vector<uint> v_start_resnum;
+ std::vector<uint> v_num_residues;
+ std::vector<uint> v_chain_idx;
+
+ core::ConvertListToVector(start_resnum, v_start_resnum);
+ core::ConvertListToVector(num_residues, v_num_residues);
+ core::ConvertListToVector(chain_idx, v_chain_idx);
+
+ std::vector<std::vector<Real> > profile;
+ scorer.CalculateScoreProfile(v_start_resnum, v_num_residues, v_chain_idx,
+ profile);
+ boost::python::list return_list;
+ for(uint i = 0; i < profile.size(); ++i) {
+ boost::python::list l;
+ core::AppendVectorToList(profile[i], l);
+ return_list.append(l);
+ }
+ return return_list;
+}
} // anon wrapper ns
void export_AllAtomScore() {
// base scorer
class_<AllAtomScorer, boost::noncopyable, AllAtomScorerPtr>
- ("AllAtomScorer", no_init);
+ ("AllAtomScorer", no_init)
+ .def("CalculateScore", WrapAACalculateScore,
+ (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
+ .def("CalculateScore", WrapAACalculateScoreList,
+ (arg("start_resnum"), arg("num_residues"), arg("chain_idx")))
+ .def("CalculateScoreProfile", WrapAACalculateScoreProfile,
+ (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
+ .def("CalculateScoreProfile", WrapAACalculateScoreProfileList,
+ (arg("start_resnum"), arg("num_residues"), arg("chain_idx")))
+ ;
// overall scorer
class_<AllAtomOverallScorer, AllAtomOverallScorerPtr>
@@ -85,9 +130,9 @@ void export_AllAtomScore() {
.def("CalculateLinearCombination", &WrapCalculateLinearCombination,
(arg("linear_weights"), arg("start_resnum"), arg("num_residues"),
arg("chain_idx")=0))
- .def("CalculateLinearCombination", &WrapCalculateLinearCombinationRN,
+ .def("CalculateLinearCombination", &WrapCalculateLinearCombinationList,
(arg("linear_weights"), arg("start_resnum"), arg("num_residues"),
- arg("chain_idx")=0))
+ arg("chain_idx")))
;
class_<AllAtomInteractionScorer, AllAtomInteractionScorerPtr,
@@ -103,16 +148,11 @@ void export_AllAtomScore() {
(arg("filename")))
.def("SetEnergy", &AllAtomInteractionScorer::SetEnergy,
(arg("aaa1"), arg("aaa2"), arg("bin"), arg("energy")))
- .def("CalculateScore", WrapAACalculateScore,
- (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
- .def("CalculateScore", WrapAACalculateScoreRN,
- (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
- .def("CalculateScoreProfile", WrapAACalculateScoreProfile,
- (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
- .def("CalculateScoreProfile", WrapAACalculateScoreProfileRN,
- (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
.def("AttachEnvironment", &AllAtomInteractionScorer::AttachEnvironment,
(arg("env")))
+ .def("DoInternalScores", &AllAtomInteractionScorer::DoInternalScores)
+ .def("DoExternalScores", &AllAtomInteractionScorer::DoExternalScores)
+ .def("DoNormalize", &AllAtomInteractionScorer::DoNormalize)
;
class_<AllAtomPackingScorer, AllAtomPackingScorerPtr,
@@ -128,31 +168,19 @@ void export_AllAtomScore() {
(arg("filename")))
.def("SetEnergy", &AllAtomPackingScorer::SetEnergy,
(arg("aaa"), arg("count"), arg("energy")))
- .def("CalculateScore", WrapAACalculateScore,
- (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
- .def("CalculateScore", WrapAACalculateScoreRN,
- (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
- .def("CalculateScoreProfile", WrapAACalculateScoreProfile,
- (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
- .def("CalculateScoreProfile", WrapAACalculateScoreProfileRN,
- (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
.def("AttachEnvironment", &AllAtomPackingScorer::AttachEnvironment,
(arg("env")))
+ .def("DoNormalize", &AllAtomPackingScorer::DoNormalize)
;
class_<AllAtomClashScorer, AllAtomClashScorerPtr,
bases<AllAtomScorer> >
("AllAtomClashScorer",init<>())
- .def("CalculateScore", WrapAACalculateScore,
- (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
- .def("CalculateScore", WrapAACalculateScoreRN,
- (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
- .def("CalculateScoreProfile", WrapAACalculateScoreProfile,
- (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
- .def("CalculateScoreProfile", WrapAACalculateScoreProfileRN,
- (arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
.def("AttachEnvironment", &AllAtomClashScorer::AttachEnvironment,
(arg("env")))
+ .def("DoInternalScores", &AllAtomClashScorer::DoInternalScores)
+ .def("DoExternalScores", &AllAtomClashScorer::DoExternalScores)
+ .def("DoNormalize", &AllAtomClashScorer::DoNormalize)
;
}
diff --git a/scoring/pymod/export_backbone_score.cc b/scoring/pymod/export_backbone_score.cc
index 2d405b074bdec64c3d04e226808fb3f3e2836e53..8bc2b5800aac45118768dc14f9f0a44427bf0b36 100644
--- a/scoring/pymod/export_backbone_score.cc
+++ b/scoring/pymod/export_backbone_score.cc
@@ -8,7 +8,6 @@
#include <promod3/scoring/clash_score.hh>
#include <promod3/scoring/hbond_score.hh>
#include <promod3/scoring/ss_agreement_score.hh>
-#include <promod3/scoring/density_score.hh>
#include <promod3/scoring/torsion_score.hh>
#include <promod3/scoring/pairwise_score.hh>
@@ -68,6 +67,27 @@ namespace {
env->SetPsipredPrediction(pp_v);
}
+ void WrapStashSingle(BackboneScoreEnvPtr env, uint rnum, uint num_residues,
+ uint chain_idx) {
+ env->Stash(rnum, num_residues, chain_idx);
+ }
+
+
+ void WrapStashList(BackboneScoreEnvPtr env, const boost::python::list& rnum,
+ const boost::python::list& num_residues,
+ const boost::python::list& chain_idx) {
+
+ std::vector<uint> v_rnum;
+ std::vector<uint> v_num_residues;
+ std::vector<uint> v_chain_idx;
+
+ core::ConvertListToVector(rnum, v_rnum);
+ core::ConvertListToVector(num_residues, v_num_residues);
+ core::ConvertListToVector(chain_idx, v_chain_idx);
+
+ env->Stash(v_rnum, v_num_residues, v_chain_idx);
+ }
+
BackboneScorerPtr bos_getitem(BackboneOverallScorer& s, const String& key) {
return s[key];
}
@@ -76,52 +96,53 @@ namespace {
s[key] = item;
}
Real WrapCalculate(BackboneOverallScorer& s, const String& key,
- const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) {
- return s.Calculate(key, bb_list, start_resnum, chain_idx);
+ uint start_resnum, uint num_residues, uint chain_idx) {
+ return s.Calculate(key, start_resnum, num_residues, chain_idx);
}
- boost::python::list WrapCalculateList(
- BackboneOverallScorer& s, const String& key,
- const boost::python::list& py_list,
- uint start_resnum, uint chain_idx) {
- // get bb_lists
- std::vector<loop::BackboneList> bb_lists;
- core::ConvertListToVector(py_list, bb_lists);
- // get scores
- std::vector<Real> scores = s.Calculate(key, bb_lists, start_resnum,
- chain_idx);
- // convert and return
- boost::python::list return_list;
- core::AppendVectorToList(scores, return_list);
- return return_list;
+ Real WrapCalculateList(BackboneOverallScorer& s, const String& key,
+ const boost::python::list& start_resnum,
+ const boost::python::list& num_residues,
+ const boost::python::list& chain_idx) {
+
+ std::vector<uint> v_start_resnum;
+ std::vector<uint> v_num_residues;
+ std::vector<uint> v_chain_idx;
+
+ core::ConvertListToVector(start_resnum, v_start_resnum);
+ core::ConvertListToVector(num_residues, v_num_residues);
+ core::ConvertListToVector(chain_idx, v_chain_idx);
+
+ return s.Calculate(key, v_start_resnum, v_num_residues, v_chain_idx);
}
Real WrapCalculateLinearCombination(BackboneOverallScorer& s,
const boost::python::dict& weights,
- const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) {
+ uint start_resnum,
+ uint num_residues,
+ uint chain_idx) {
std::map<String, Real> w;
core::ConvertDictToMap(weights, w);
- return s.CalculateLinearCombination(w, bb_list, start_resnum, chain_idx);
+ return s.CalculateLinearCombination(w, start_resnum, num_residues,
+ chain_idx);
}
- boost::python::list WrapCalculateLinearCombinationList(
- BackboneOverallScorer& s,
- const boost::python::dict& weights,
- const boost::python::list& py_list,
- uint start_resnum, uint chain_idx) {
- // get bb_lists
- std::vector<loop::BackboneList> bb_lists;
- core::ConvertListToVector(py_list, bb_lists);
- // get scores
+ Real WrapCalculateLinearCombinationList(BackboneOverallScorer& s,
+ const boost::python::dict& weights,
+ const boost::python::list& start_resnum,
+ const boost::python::list& num_residues,
+ const boost::python::list& chain_idx) {
std::map<String, Real> w;
core::ConvertDictToMap(weights, w);
- std::vector<Real> scores =
- s.CalculateLinearCombination(w, bb_lists, start_resnum, chain_idx);
- // convert and return
- boost::python::list return_list;
- core::AppendVectorToList(scores, return_list);
- return return_list;
- }
+ std::vector<uint> v_start_resnum;
+ std::vector<uint> v_num_residues;
+ std::vector<uint> v_chain_idx;
+
+ core::ConvertListToVector(start_resnum, v_start_resnum);
+ core::ConvertListToVector(num_residues, v_num_residues);
+ core::ConvertListToVector(chain_idx, v_chain_idx);
+
+ return s.CalculateLinearCombination(w, v_start_resnum, v_num_residues,
+ v_chain_idx);
+ }
TorsionScorerPtr WrapTorsionScorerInit(
const boost::python::list& group_identifier,
uint bins_per_dimension) {
@@ -131,15 +152,60 @@ namespace {
return p;
}
- boost::python::list WrapScoreProfile(BackboneScorerPtr scorer,
- const promod3::loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx){
+ Real WrapScoreSingle(BackboneScorerPtr scorer, uint start_resnum,
+ uint num_residues, uint chain_idx){
+
+ return scorer->CalculateScore(start_resnum, num_residues, chain_idx);
+ }
+ boost::python::list WrapScoreProfileSingle(BackboneScorerPtr scorer,
+ uint start_resnum, uint num_residues,
+ uint chain_idx){
std::vector<Real> profile;
- scorer->CalculateScoreProfile(bb_list, start_resnum, chain_idx, profile);
+ scorer->CalculateScoreProfile(start_resnum, num_residues, chain_idx, profile);
boost::python::list return_list;
core::AppendVectorToList(profile, return_list);
return return_list;
}
+ Real WrapScoreList(BackboneScorerPtr scorer,
+ boost::python::list& start_resnum,
+ boost::python::list& num_residues,
+ boost::python::list& chain_idx) {
+
+ std::vector<uint> v_start_resnum;
+ std::vector<uint> v_num_residues;
+ std::vector<uint> v_chain_idx;
+
+ core::ConvertListToVector(start_resnum, v_start_resnum);
+ core::ConvertListToVector(num_residues, v_num_residues);
+ core::ConvertListToVector(chain_idx, v_chain_idx);
+
+ return scorer->CalculateScore(v_start_resnum, v_num_residues, v_chain_idx);
+ }
+ boost::python::list WrapScoreProfileList(BackboneScorerPtr scorer,
+ boost::python::list& start_resnum,
+ boost::python::list& num_residues,
+ boost::python::list& chain_idx){
+
+ std::vector<uint> v_start_resnum;
+ std::vector<uint> v_num_residues;
+ std::vector<uint> v_chain_idx;
+
+ core::ConvertListToVector(start_resnum, v_start_resnum);
+ core::ConvertListToVector(num_residues, v_num_residues);
+ core::ConvertListToVector(chain_idx, v_chain_idx);
+
+ std::vector<std::vector<Real> > profile;
+ scorer->CalculateScoreProfile(v_start_resnum, v_num_residues, v_chain_idx,
+ profile);
+
+ boost::python::list return_list;
+ for(uint i = 0; i < profile.size(); ++i) {
+ boost::python::list l;
+ core::AppendVectorToList(profile[i], l);
+ return_list.append(l);
+ }
+ return return_list;
+ }
}
void export_BackboneScore() {
@@ -166,19 +232,28 @@ void export_BackboneScore() {
(arg("start_resnum"), arg("num_residues"), arg("chain_idx") = 0))
.def("SetPsipredPrediction", &WrapSetPsipredPrediction, (arg("pred")))
.def("SetPsipredPrediction", &WrapSetPsipredPredictionList, (arg("pred")))
- .def("SetMap", &BackboneScoreEnv::SetMap,
- (arg("map"), arg("resolution"), arg("all_atom")=false))
.def("AddPairwiseFunction", &BackboneScoreEnv::AddPairwiseFunction,
(arg("function"), arg("function_type")))
.def("ApplyPairwiseFunction", &BackboneScoreEnv::ApplyPairwiseFunction,
(arg("chain_idx_one"), arg("resnum_one"), arg("chain_idx_two"),
arg("resnum_two"), arg("f_idx")))
+ .def("Stash", &WrapStashSingle, (arg("start_rnum"), arg("num_residues"),
+ arg("chain_idx")=0))
+ .def("Stash", &WrapStashList, (arg("start_rnums"), arg("num_residues"),
+ arg("chain_indices")=0))
+ .def("Pop", &BackboneScoreEnv::Pop)
.def("GetSeqres", &BackboneScoreEnv::GetSeqres)
;
// base scorer
class_<BackboneScorer, boost::noncopyable, BackboneScorerPtr>
- ("BackboneScorer", no_init);
+ ("BackboneScorer", no_init)
+ .def("CalculateScore", &WrapScoreSingle,(arg("start_resnum"), arg("num_residues"), arg("chain_idx") = 0))
+ .def("CalculateScoreProfile", &WrapScoreProfileSingle,(arg("start_resnum"), arg("num_residues"), arg("chain_idx") = 0))
+ .def("CalculateScore", &WrapScoreList,(arg("start_resnum"), arg("num_residues"), arg("chain_idx") = 0))
+ .def("CalculateScoreProfile", &WrapScoreProfileList,(arg("start_resnum"), arg("num_residues"), arg("chain_idx") = 0))
+
+ ;
// overall scorer
class_<BackboneOverallScorer, BackboneOverallScorerPtr>
@@ -190,15 +265,15 @@ void export_BackboneScore() {
.def("AttachEnvironment", &BackboneOverallScorer::AttachEnvironment,
(arg("env")))
.def("Calculate", &WrapCalculate,
- (arg("key"), arg("bb_list"), arg("start_resnum"), arg("chain_idx")=0))
- .def("Calculate", &WrapCalculateList,
- (arg("key"), arg("bb_lists"), arg("start_resnum"), arg("chain_idx")=0))
+ (arg("key"), arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
.def("CalculateLinearCombination", &WrapCalculateLinearCombination,
- (arg("linear_weights"), arg("bb_list"), arg("start_resnum"),
+ (arg("linear_weights"), arg("start_resnum"), arg("num_residues"),
arg("chain_idx")=0))
+ .def("Calculate", &WrapCalculateList,
+ (arg("key"), arg("start_resnum"), arg("num_residues"), arg("chain_idx")=0))
.def("CalculateLinearCombination", &WrapCalculateLinearCombinationList,
- (arg("linear_weights"), arg("bb_lists"), arg("start_resnum"),
- arg("chain_idx")=0))
+ (arg("linear_weights"), arg("start_resnum"), arg("num_residues"),
+ arg("chain_idx")))
;
// individual scorers
@@ -209,10 +284,7 @@ void export_BackboneScore() {
.def("LoadPortable", &CBPackingScorer::LoadPortable,(arg("filename"))).staticmethod("LoadPortable")
.def("SavePortable", &CBPackingScorer::SavePortable,(arg("filename")))
.def("SetEnergy", &CBPackingScorer::SetEnergy,(arg("aa"),arg("count"),arg("energy")))
- .def("CalculateScore", &CBPackingScorer::CalculateScore,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
- .def("CalculateScoreProfile", &WrapScoreProfile,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
- .def("UseClassicMode", &CBPackingScorer::UseClassicMode)
- .def("UseIncludeEnvMode",&CBPackingScorer::UseIncludeEnvMode)
+ .def("DoNormalize", &CBPackingScorer::DoNormalize)
.def("AttachEnvironment", &CBPackingScorer::AttachEnvironment,(arg("env")))
;
@@ -223,8 +295,9 @@ void export_BackboneScore() {
.def("LoadPortable", &CBetaScorer::LoadPortable,(arg("filename"))).staticmethod("LoadPortable")
.def("SavePortable", &CBetaScorer::SavePortable,(arg("filename")))
.def("SetEnergy", &CBetaScorer::SetEnergy,(arg("aa1"),arg("aa2"),arg("bin"),arg("energy")))
- .def("CalculateScore", &CBetaScorer::CalculateScore,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
- .def("CalculateScoreProfile", &WrapScoreProfile,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
+ .def("DoInternalScores", &CBetaScorer::DoInternalScores)
+ .def("DoExternalScores", &CBetaScorer::DoExternalScores)
+ .def("DoNormalize", &CBetaScorer::DoNormalize)
.def("AttachEnvironment", &CBetaScorer::AttachEnvironment,(arg("env")))
;
@@ -235,23 +308,18 @@ void export_BackboneScore() {
.def("LoadPortable", &ReducedScorer::LoadPortable,(arg("filename"))).staticmethod("LoadPortable")
.def("SavePortable", &ReducedScorer::SavePortable,(arg("filename")))
.def("SetEnergy", &ReducedScorer::SetEnergy,(arg("aa1"),arg("aa2"),arg("dist_bin"),arg("alpha_bin"),arg("beta_bin"),arg("gamma_bin"),arg("energy")))
- .def("CalculateScore", &ReducedScorer::CalculateScore,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
- .def("CalculateScoreProfile", &WrapScoreProfile,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
+ .def("DoInternalScores", &ReducedScorer::DoInternalScores)
+ .def("DoExternalScores", &ReducedScorer::DoExternalScores)
+ .def("DoNormalize", &ReducedScorer::DoNormalize)
.def("AttachEnvironment", &ReducedScorer::AttachEnvironment,(arg("env")))
;
class_<ClashScorer, ClashScorerPtr, bases<BackboneScorer> >
("ClashScorer",init<>())
- .def("CalculateScore", &ClashScorer::CalculateScore,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
- .def("CalculateScoreProfile", &WrapScoreProfile,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
.def("AttachEnvironment", &ClashScorer::AttachEnvironment,(arg("env")))
- ;
-
- class_<DensityScorer, DensityScorerPtr, bases<BackboneScorer> >
- ("DensityScorer", init<>())
- .def("CalculateScore", &DensityScorer::CalculateScore,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
- .def("CalculateScoreProfile", &WrapScoreProfile,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
- .def("AttachEnvironment", &DensityScorer::AttachEnvironment,(arg("env")))
+ .def("DoInternalScores", &ClashScorer::DoInternalScores)
+ .def("DoExternalScores", &ClashScorer::DoExternalScores)
+ .def("DoNormalize", &ClashScorer::DoNormalize)
;
class_<HBondScorer, HBondScorerPtr, bases<BackboneScorer> >
@@ -261,8 +329,9 @@ void export_BackboneScore() {
.def("LoadPortable", &HBondScorer::LoadPortable,(arg("filename"))).staticmethod("LoadPortable")
.def("SavePortable", &HBondScorer::SavePortable,(arg("filename")))
.def("SetEnergy", &HBondScorer::SetEnergy,(arg("state"),arg("d_bin"),arg("alpha_bin"),arg("beta_bin"),arg("gamma_bin"),arg("energy")))
- .def("CalculateScore", &HBondScorer::CalculateScore,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
- .def("CalculateScoreProfile", &WrapScoreProfile,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
+ .def("DoInternalScores", &HBondScorer::DoInternalScores)
+ .def("DoExternalScores", &HBondScorer::DoExternalScores)
+ .def("DoNormalize", &HBondScorer::DoNormalize)
.def("AttachEnvironment", &HBondScorer::AttachEnvironment,(arg("env")))
;
@@ -273,8 +342,7 @@ void export_BackboneScore() {
.def("LoadPortable", &SSAgreementScorer::LoadPortable,(arg("filename"))).staticmethod("LoadPortable")
.def("SavePortable", &SSAgreementScorer::SavePortable,(arg("filename")))
.def("SetScore", &SSAgreementScorer::SetScore,(arg("psipred_state"),arg("psipred_cfi"),arg("dssp_state"),arg("score")))
- .def("CalculateScore", &SSAgreementScorer::CalculateScore,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
- .def("CalculateScoreProfile", &WrapScoreProfile,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
+ .def("DoNormalize", &SSAgreementScorer::DoNormalize)
.def("AttachEnvironment", &SSAgreementScorer::AttachEnvironment,(arg("env")))
;
@@ -286,16 +354,16 @@ void export_BackboneScore() {
.def("LoadPortable", &TorsionScorer::LoadPortable,(arg("filename"))).staticmethod("LoadPortable")
.def("SavePortable", &TorsionScorer::SavePortable,(arg("filename")))
.def("SetEnergy", &TorsionScorer::SetEnergy,(arg("group_idx"),arg("phi_bin"),arg("psi_bin"),arg("energy")))
- .def("CalculateScore", &TorsionScorer::CalculateScore,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
- .def("CalculateScoreProfile", &WrapScoreProfile,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
+ .def("DoNormalize", &TorsionScorer::DoNormalize)
.def("AttachEnvironment", &TorsionScorer::AttachEnvironment,(arg("env")))
;
class_<PairwiseScorer, PairwiseScorerPtr, bases<BackboneScorer> >
("PairwiseScorer", init<>())
- .def("CalculateScore", &PairwiseScorer::CalculateScore,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
- .def("CalculateScoreProfile", &WrapScoreProfile,(arg("bb_list"), arg("start_resnum"), arg("chain_idx") = 0))
.def("AttachEnvironment", &PairwiseScorer::AttachEnvironment,(arg("env")))
+ .def("DoInternalScores", &PairwiseScorer::DoInternalScores)
+ .def("DoExternalScores", &PairwiseScorer::DoExternalScores)
+ .def("DoNormalize", &PairwiseScorer::DoNormalize)
;
}
diff --git a/scoring/pymod/export_density_scorer.cc b/scoring/pymod/export_density_scorer.cc
new file mode 100644
index 0000000000000000000000000000000000000000..f022f963aee63b41120ca950a1db90d89b14ffec
--- /dev/null
+++ b/scoring/pymod/export_density_scorer.cc
@@ -0,0 +1,11 @@
+#include <boost/python.hpp>
+#include <promod3/scoring/density_score.hh>
+
+using namespace boost::python;
+
+void export_DensityScoring() {
+ def("DensityScore", &promod3::scoring::DensityScore, (arg("bb_list"),
+ arg("map"),
+ arg("resolution"),
+ arg("all_atom")));
+}
diff --git a/scoring/pymod/export_scwrl3_energy_functions.cc b/scoring/pymod/export_scwrl3_energy_functions.cc
new file mode 100644
index 0000000000000000000000000000000000000000..54c5a8e1e8155b575dc8d0971eeaee102c683a89
--- /dev/null
+++ b/scoring/pymod/export_scwrl3_energy_functions.cc
@@ -0,0 +1,18 @@
+#include <boost/python.hpp>
+#include <promod3/scoring/scwrl3_energy_functions.hh>
+#include <promod3/core/export_helper.hh>
+
+using namespace promod3;
+using namespace promod3::scoring;
+using namespace boost::python;
+
+
+void export_SCWRL3EnergyFunctions() {
+
+ def("SCWRL3PairwiseScore", &SCWRL3PairwiseScore, (arg("distance"), arg("summed_vdw_radii")));
+
+ def("SCWRL3DisulfidScore", &SCWRL3DisulfidScore, (arg("ca_pos_one"), arg("cb_pos_one"),
+ arg("sg_pos_one"), arg("ca_pos_two"),
+ arg("cb_pos_two"), arg("sg_pos_two")));
+
+}
diff --git a/scoring/pymod/wrap_scoring.cc b/scoring/pymod/wrap_scoring.cc
index c4384b81842dd601cbba1dc9898707a067198044..4b717f9cbc40743c1e84fcef141dc8e95bdb874f 100644
--- a/scoring/pymod/wrap_scoring.cc
+++ b/scoring/pymod/wrap_scoring.cc
@@ -5,6 +5,8 @@ void export_ObjectLoader();
void export_PairwiseFunction();
void export_constraint_constructor();
void export_AllAtomScore();
+void export_SCWRL3EnergyFunctions();
+void export_DensityScoring();
using namespace boost::python;
@@ -15,4 +17,6 @@ BOOST_PYTHON_MODULE(_scoring)
export_ObjectLoader();
export_PairwiseFunction();
export_constraint_constructor();
+ export_SCWRL3EnergyFunctions();
+ export_DensityScoring();
}
diff --git a/scoring/src/CMakeLists.txt b/scoring/src/CMakeLists.txt
index 37549f126a3e914713972017c4b1bbee2da74ba0..b094b380024947c20e5282ad135f429006b4d8c9 100644
--- a/scoring/src/CMakeLists.txt
+++ b/scoring/src/CMakeLists.txt
@@ -24,6 +24,7 @@ all_atom_interaction_env_listener.hh
all_atom_interaction_score.hh
all_atom_packing_score.hh
all_atom_clash_score.hh
+scwrl3_energy_functions.hh
)
set(SCORING_SOURCES
diff --git a/scoring/src/all_atom_clash_score.cc b/scoring/src/all_atom_clash_score.cc
index 571ca5954569a9e1e22744549ef4fd587ab5ec01..eb011421297ff1de8c10f6fbd5a14533c2c2706e 100644
--- a/scoring/src/all_atom_clash_score.cc
+++ b/scoring/src/all_atom_clash_score.cc
@@ -1,10 +1,14 @@
#include <promod3/scoring/all_atom_clash_score.hh>
#include <promod3/core/runtime_profiling.hh>
#include <promod3/core/check_io.hh>
+#include <promod3/scoring/scwrl3_energy_functions.hh>
namespace promod3 { namespace scoring {
-AllAtomClashScorer::AllAtomClashScorer(): attached_environment_(false) {
+AllAtomClashScorer::AllAtomClashScorer(): do_internal_scores_(true),
+ do_external_scores_(true),
+ normalize_(true),
+ attached_environment_(false) {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"AllAtomClashScorer::AllAtomClashScorer", 2);
@@ -67,14 +71,8 @@ AllAtomClashScorer::AllAtomClashScorer(): attached_environment_(false) {
Rij = 2.5;
}
for (uint bin = 0; bin < bins_; ++bin) {
- Real energy = 0;
- const Real r = bin / bins_per_a_;
- if (r < Real(0.8254) * Rij) {
- energy = 10;
- } else if (r <= Rij) {
- energy = 57.273 * (1 - r/Rij);
- }
- energies_[this->EIdx(a, b, bin)] = energy;
+ const Real d = static_cast<Real>(bin) / bins_per_a_;
+ energies_[this->EIdx(a, b, bin)] = SCWRL3PairwiseScore(d, Rij);
}
}
}
@@ -90,22 +88,35 @@ Real AllAtomClashScorer::CalculateScore(uint start_resnum, uint num_residues,
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"AllAtomClashScorer::CalculateScore", 2);
+ if (!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ // get scores
+ std::vector<uint> idx_vec;
+ std::vector<bool> occupied;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vec, occupied);
+
// get scores
std::vector<Real> ex_scores, in_scores;
- std::vector<uint> counts;
- Score(start_resnum, num_residues, chain_idx, ex_scores, in_scores, counts);
- // sum / normalize them
- // -> we count internal scores half as the same pair appears twice
- uint count = 0;
+ this->Score(idx_vec, ex_scores, in_scores, occupied);
Real ex_score = 0.0;
Real in_score = 0.0;
for (uint i = 0; i < num_residues; ++i) {
ex_score += ex_scores[i];
in_score += in_scores[i];
- count += counts[i];
}
- if (count > 0) return (ex_score + Real(0.5)*in_score) / count;
- else return (ex_score + Real(0.5)*in_score);
+
+ // we count internal scores half as the same pair appears twice
+ Real score = ex_score + Real(0.5)*in_score;
+
+ if(normalize_ && !ex_scores.empty()) {
+ score /= ex_scores.size();
+ }
+
+ return score;
}
void AllAtomClashScorer::CalculateScoreProfile(
@@ -115,14 +126,101 @@ void AllAtomClashScorer::CalculateScoreProfile(
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"AllAtomClashScorer::CalculateScoreProfile", 2);
+ if (!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
// get scores
+ std::vector<uint> idx_vec;
+ std::vector<bool> occupied;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vec, occupied);
+
std::vector<Real> in_scores;
- std::vector<uint> counts;
- Score(start_resnum, num_residues, chain_idx, profile, in_scores, counts);
- // combine and normalize them
+ this->Score(idx_vec, profile, in_scores, occupied);
+ // combine them
for (uint i = 0; i < num_residues; ++i) {
- if (counts[i] > 0) profile[i] = (profile[i] + in_scores[i]) / counts[i];
- else profile[i] += in_scores[i];
+ profile[i] = profile[i] + in_scores[i];
+ }
+}
+
+Real AllAtomClashScorer::CalculateScore(
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "AllAtomClashScorer::CalculateScore", 2);
+
+ if (!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ // setup
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores and sum them up
+ Real external_score = 0.0;
+ Real internal_score = 0.0;
+ uint n_scored_residues = 0;
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ this->Score(indices_vec[i], external_scores, internal_scores, occupied);
+ for (uint j = 0; j < external_scores.size(); ++j) {
+ external_score += external_scores[j];
+ internal_score += internal_scores[j];
+ }
+ n_scored_residues += external_scores.size();
+ }
+
+ // all interactions in internal_score have been observed twice!
+ external_score += Real(0.5)*internal_score;
+
+ if(normalize_ && n_scored_residues > 0) {
+ external_score /= n_scored_residues;
+ }
+
+ return external_score;
+}
+
+void AllAtomClashScorer::CalculateScoreProfile(
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "AllAtomClashScorer::CalculateScore", 2);
+
+ if (!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ // setup
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores
+ profile.resize(start_resnum.size());
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ std::vector<Real>& current_profile = profile[i];
+ this->Score(indices_vec[i], current_profile, internal_scores, occupied);
+ for (uint j = 0; j < current_profile.size(); ++j) {
+ current_profile[j] += internal_scores[j];
+ }
}
}
@@ -134,33 +232,28 @@ void AllAtomClashScorer::AttachEnvironment(loop::AllAtomEnv& env) {
attached_environment_ = true;
}
-void AllAtomClashScorer::Score(
- uint start_resnum, uint num_residues, uint chain_idx,
- std::vector<Real>& ex_scores, std::vector<Real>& in_scores,
- std::vector<uint>& counts) const {
+void AllAtomClashScorer::Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
+ std::vector<Real>& internal_scores,
+ std::vector<bool>& occupied) const {
// setup
- if (!attached_environment_) {
- String err = "Can only calculate score when environment is attached!";
- throw promod3::Error(err);
+ uint n_indices = indices.size();
+ external_scores.resize(n_indices);
+ internal_scores.resize(n_indices);
+
+ if(n_indices == 0) {
+ return;
}
- uint start_idx, end_idx;
- idx_handler_->SetupScoreCalculation(start_resnum, num_residues, chain_idx,
- start_idx, end_idx);
- // get scores
- ex_scores.resize(num_residues);
- in_scores.resize(num_residues);
- counts.resize(num_residues);
// let's go over every atom
AllAtomInteractionSpatialOrganizer::WithinResult within_result;
std::pair<AllAtomInteractionSpatialOrganizerItem*,Real>* a;
// helpers
int min_idx_chain, max_idx_chain, start_neglect, end_neglect;
- for (uint i = 0; i < num_residues; ++i) {
+ for (uint i = 0; i < indices.size(); ++i) {
// init
- const uint res_idx = start_idx + i;
- uint num_set_atoms = 0;
+ const uint res_idx = indices[i];
Real ex_score = 0.0;
Real in_score = 0.0;
// check neglect range for residue
@@ -175,34 +268,35 @@ void AllAtomClashScorer::Score(
for (uint idx = first_idx; idx <= last_idx; ++idx) {
// only if set
if (all_pos_->IsSet(idx)) {
- ++num_set_atoms;
// get clash scores
const AllAtomClashType my_ct = clash_type_[all_pos_->GetAAA(idx)];
within_result = env_->FindWithin(all_pos_->GetPos(idx), cutoff_[my_ct]);
a = within_result.first;
for (uint j = 0; j < within_result.second; ++j) {
// skip if too close
- const int other_idx = int(a[j].first->res_idx);
- if (other_idx < start_neglect || other_idx > end_neglect) {
+ const int other_res_idx = int(a[j].first->res_idx);
+ if (other_res_idx < start_neglect || other_res_idx > end_neglect) {
// score it
const AllAtomClashType other_ct = clash_type_[a[j].first->aaa];
const uint bin = a[j].second * bins_per_a_;
- if (uint(other_idx) < start_idx || uint(other_idx) > end_idx) {
- // external interaction
- ex_score += energies_[this->EIdx(my_ct, other_ct, bin)];
- } else {
+ if (occupied[other_res_idx]) {
// internal interaction
- in_score += energies_[this->EIdx(my_ct, other_ct, bin)];
+ if(do_internal_scores_) {
+ in_score += energies_[this->EIdx(my_ct, other_ct, bin)];
+ }
+ } else {
+ // external interaction
+ if(do_external_scores_) {
+ ex_score += energies_[this->EIdx(my_ct, other_ct, bin)];
+ }
}
-
}
}
}
}
// set values
- ex_scores[i] = ex_score;
- in_scores[i] = in_score;
- counts[i] = num_set_atoms;
+ external_scores[i] = ex_score;
+ internal_scores[i] = in_score;
}
}
diff --git a/scoring/src/all_atom_clash_score.hh b/scoring/src/all_atom_clash_score.hh
index 24c05b1fa9bd29952dda0c9f5f2149a10070330b..df69a60646241c8a1c563c8234b7bc30283ee193 100644
--- a/scoring/src/all_atom_clash_score.hh
+++ b/scoring/src/all_atom_clash_score.hh
@@ -30,12 +30,28 @@ public:
virtual ~AllAtomClashScorer();
- virtual Real CalculateScore(uint start_resnum, uint num_residues,
- uint chain_idx) const;
+ void DoInternalScores(bool do_it) { do_internal_scores_ = do_it; }
+
+ void DoExternalScores(bool do_it) { do_external_scores_ = do_it; }
+
+ void DoNormalize(bool do_it) { normalize_ = do_it; }
+
+ virtual Real
+ CalculateScore(uint start_resnum, uint num_residues, uint chain_idx) const;
+
virtual void
CalculateScoreProfile(uint start_resnum, uint num_residues, uint chain_idx,
std::vector<Real>& profile) const;
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const;
+
virtual void AttachEnvironment(loop::AllAtomEnv& env);
private:
@@ -44,16 +60,20 @@ private:
return (a * ALL_ATOM_CLASH_NUM + b) * bins_ + bin;
}
- void Score(uint start_resnum, uint num_residues, uint chain_idx,
- std::vector<Real>& ex_scores, std::vector<Real>& in_scores,
- std::vector<uint>& counts) const;
+ void Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
+ std::vector<Real>& internal_scores,
+ std::vector<bool>& occupied) const;
// hard coded bounds (safe for dist. < 3.41 (should be enough...))
static const uint bins_ = 341;
- static const Real bins_per_a_ = 100;
+ static const uint bins_per_a_ = 100;
AllAtomClashType clash_type_[loop::XXX_NUM_ATOMS];
Real cutoff_[ALL_ATOM_CLASH_NUM];
- Real* energies_;
+ Real* energies_;
+ bool do_internal_scores_;
+ bool do_external_scores_;
+ bool normalize_;
// environment specific information, set upon calling AttachEnvironment
bool attached_environment_;
diff --git a/scoring/src/all_atom_interaction_score.cc b/scoring/src/all_atom_interaction_score.cc
index 08c61660944238820d9190f193ade731d4818f58..35c9f4955e2a13070a4b6ff4fa3b93731a90ac4f 100644
--- a/scoring/src/all_atom_interaction_score.cc
+++ b/scoring/src/all_atom_interaction_score.cc
@@ -6,8 +6,9 @@ namespace promod3 { namespace scoring {
AllAtomInteractionScorer::AllAtomInteractionScorer(
Real cutoff, uint bins, uint seq_sep)
- : cutoff_(cutoff), bins_(bins), seq_sep_(seq_sep)
- , attached_environment_(false) {
+ : cutoff_(cutoff), bins_(bins), seq_sep_(seq_sep),
+ do_internal_scores_(true), do_external_scores_(true),
+ normalize_(true), attached_environment_(false) {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"AllAtomInteractionScorer::AllAtomInteractionScorer", 2);
@@ -181,6 +182,7 @@ void AllAtomInteractionScorer::SetEnergy(loop::AminoAcidAtom a,
}
energies_[this->EIdx(a, b, bin)] = e;
+ energies_[this->EIdx(b, a, bin)] = e;
}
Real AllAtomInteractionScorer::CalculateScore(uint start_resnum,
@@ -190,27 +192,36 @@ Real AllAtomInteractionScorer::CalculateScore(uint start_resnum,
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"AllAtomInteractionScorer::CalculateScore", 2);
+ if (!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ // setup
+ std::vector<uint> idx_vec;
+ std::vector<bool> occupied;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vec, occupied);
+
// get scores
std::vector<Real> ex_scores, in_scores;
- std::vector<uint> ex_counts, in_counts;
- Score(start_resnum, num_residues, chain_idx, ex_scores, in_scores,
- ex_counts, in_counts);
+ this->Score(idx_vec, ex_scores, in_scores, occupied);
// sum them
- uint ex_count = 0;
- uint in_count = 0;
Real ex_score = 0.0;
Real in_score = 0.0;
for (uint i = 0; i < num_residues; ++i) {
ex_score += ex_scores[i];
in_score += in_scores[i];
- ex_count += ex_counts[i];
- in_count += in_counts[i];
}
- // normalize: we count internal scores half as the same pair appears twice
- const Real score = ex_score + Real(0.5) * in_score;
- const Real count = ex_count + Real(0.5) * in_count;
- if (count > 0) return score / count;
- else return score;
+
+ // we count internal scores half as the same pair appears twice
+ Real score = ex_score + Real(0.5)*in_score;
+
+ if(normalize_ && !in_scores.empty()) {
+ score /= in_scores.size();
+ }
+
+ return score;
}
void AllAtomInteractionScorer::CalculateScoreProfile(
@@ -220,16 +231,101 @@ void AllAtomInteractionScorer::CalculateScoreProfile(
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"AllAtomInteractionScorer::CalculateScoreProfile", 2);
+ if (!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
// get scores
+ std::vector<uint> idx_vec;
+ std::vector<bool> occupied;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vec, occupied);
+
std::vector<Real> in_scores;
- std::vector<uint> ex_counts, in_counts;
- Score(start_resnum, num_residues, chain_idx, profile, in_scores,
- ex_counts, in_counts);
- // combine and normalize them
+ this->Score(idx_vec, profile, in_scores, occupied);
+ // combine them
for (uint i = 0; i < num_residues; ++i) {
- const uint count = ex_counts[i] + in_counts[i];
- if (count > 0) profile[i] = (profile[i] + in_scores[i]) / count;
- else profile[i] += in_scores[i];
+ profile[i] = profile[i] + in_scores[i];
+ }
+}
+
+Real AllAtomInteractionScorer::CalculateScore(
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "AllAtomInteractionScorer::CalculateScore", 2);
+
+ if (!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ // setup
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores and sum them up
+ Real external_score = 0.0;
+ Real internal_score = 0.0;
+ uint n_scored_residues = 0;
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ this->Score(indices_vec[i], external_scores, internal_scores, occupied);
+ for (uint j = 0; j < external_scores.size(); ++j) {
+ external_score += external_scores[j];
+ internal_score += internal_scores[j];
+ }
+ n_scored_residues += external_scores.size();
+ }
+
+ // all interactions in internal_score have been observed twice!
+ external_score += Real(0.5)*internal_score;
+
+ if(normalize_ && n_scored_residues > 0) {
+ external_score /= n_scored_residues;
+ }
+
+ return external_score;
+}
+
+void AllAtomInteractionScorer::CalculateScoreProfile(
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "AllAtomInteractionScorer::CalculateScore", 2);
+
+ if (!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ // setup
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores
+ profile.resize(start_resnum.size());
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ std::vector<Real>& current_profile = profile[i];
+ this->Score(indices_vec[i], current_profile, internal_scores, occupied);
+ for (uint j = 0; j < current_profile.size(); ++j) {
+ current_profile[j] += internal_scores[j];
+ }
}
}
@@ -241,40 +337,35 @@ void AllAtomInteractionScorer::AttachEnvironment(loop::AllAtomEnv& env) {
attached_environment_ = true;
}
-void AllAtomInteractionScorer::Score(
- uint start_resnum, uint num_residues, uint chain_idx,
- std::vector<Real>& ex_scores, std::vector<Real>& in_scores,
- std::vector<uint>& ex_counts, std::vector<uint>& in_counts) const {
+void AllAtomInteractionScorer::Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
+ std::vector<Real>& internal_scores,
+ std::vector<bool>& occupied) const {
// setup
- if (!attached_environment_) {
- String err = "Can only calculate score when environment is attached!";
- throw promod3::Error(err);
+ uint n_indices = indices.size();
+ external_scores.resize(n_indices);
+ internal_scores.resize(n_indices);
+
+ if(n_indices == 0) {
+ return;
}
- uint start_idx, end_idx;
- idx_handler_->SetupScoreCalculation(start_resnum, num_residues, chain_idx,
- start_idx, end_idx);
+
const Real inv_bin_size = bins_ / cutoff_;
// let's reduce the cutoff a bit -> hack to ensure bin always within range
const Real cutoff = cutoff_ - 0.001;
- // get scores
- ex_scores.resize(num_residues);
- ex_counts.resize(num_residues);
- in_scores.resize(num_residues);
- in_counts.resize(num_residues);
// let's go over every residue
AllAtomInteractionSpatialOrganizer::WithinResult within_result;
std::pair<AllAtomInteractionSpatialOrganizerItem*,Real>* a;
// helpers
int neglect_range = int(seq_sep_) - 1;
int min_idx_chain, max_idx_chain, start_neglect, end_neglect;
- for (uint i = 0; i < num_residues; ++i) {
+
+ for (uint i = 0; i < indices.size(); ++i) {
// init
- const uint res_idx = start_idx + i;
- uint ex_count = 0;
+ const uint res_idx = indices[i];
Real ex_score = 0.0;
- uint in_count = 0;
Real in_score = 0.0;
// check neglect range for residue
const uint chain_idx = idx_handler_->GetChainIdx(res_idx);
@@ -292,27 +383,27 @@ void AllAtomInteractionScorer::Score(
within_result = env_->FindWithin(all_pos_->GetPos(idx), cutoff);
a = within_result.first;
for (uint j = 0; j < within_result.second; ++j) {
- const int other_idx = int(a[j].first->res_idx);
- if (other_idx < start_neglect || other_idx > end_neglect) {
+ const int other_res_idx = int(a[j].first->res_idx);
+ if (other_res_idx < start_neglect || other_res_idx > end_neglect) {
const uint bin = a[j].second * inv_bin_size;
- if (uint(other_idx) < start_idx || uint(other_idx) > end_idx) {
- // external interaction
- ex_score += energies_[this->EIdx(myaaa, a[j].first->aaa, bin)];
- ++ex_count;
- } else {
+ if(occupied[other_res_idx]) {
// internal interaction
- in_score += energies_[this->EIdx(myaaa, a[j].first->aaa, bin)];
- ++in_count;
+ if(do_internal_scores_) {
+ in_score += energies_[this->EIdx(myaaa, a[j].first->aaa, bin)];
+ }
+ } else {
+ // external interaction
+ if(do_external_scores_) {
+ ex_score += energies_[this->EIdx(myaaa, a[j].first->aaa, bin)];
+ }
}
}
}
}
}
// set values
- ex_scores[i] = ex_score;
- ex_counts[i] = ex_count;
- in_scores[i] = in_score;
- in_counts[i] = in_count;
+ external_scores[i] = ex_score;
+ internal_scores[i] = in_score;
}
}
diff --git a/scoring/src/all_atom_interaction_score.hh b/scoring/src/all_atom_interaction_score.hh
index e4f21cb1ae827cf6b0982cf95488ce425ac4248b..5aadd05c56ca9b67ac8f86259ef6e06d9350c1fa 100644
--- a/scoring/src/all_atom_interaction_score.hh
+++ b/scoring/src/all_atom_interaction_score.hh
@@ -31,17 +31,36 @@ public:
void SetEnergy(loop::AminoAcidAtom a, loop::AminoAcidAtom b, uint bin,
Real e);
- virtual Real CalculateScore(uint start_resnum, uint num_residues,
- uint chain_idx) const;
+ void DoInternalScores(bool do_it) { do_internal_scores_ = do_it; }
+
+ void DoExternalScores(bool do_it) { do_external_scores_ = do_it; }
+
+ void DoNormalize(bool do_it) { normalize_ = do_it; }
+
+ virtual Real
+ CalculateScore(uint start_resnum, uint num_residues, uint chain_idx) const;
+
virtual void
CalculateScoreProfile(uint start_resnum, uint num_residues, uint chain_idx,
std::vector<Real>& profile) const;
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const;
+
virtual void AttachEnvironment(loop::AllAtomEnv& env);
private:
- AllAtomInteractionScorer(): attached_environment_(false) { }
+ AllAtomInteractionScorer(): do_internal_scores_(true),
+ do_external_scores_(true),
+ normalize_(true),
+ attached_environment_(false) { }
uint EIdx(loop::AminoAcidAtom a, loop::AminoAcidAtom b,
uint bin) const {
@@ -51,9 +70,10 @@ private:
return loop::XXX_NUM_ATOMS * loop::XXX_NUM_ATOMS * bins_;
}
- void Score(uint start_resnum, uint num_residues, uint chain_idx,
- std::vector<Real>& ex_scores, std::vector<Real>& in_scores,
- std::vector<uint>& ex_counts, std::vector<uint>& in_counts) const;
+ void Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
+ std::vector<Real>& internal_scores,
+ std::vector<bool>& occupied) const;
// portable serialization (only stores data relevant for Load/Save!)
// (cleanly element by element with fixed-width base-types)
@@ -73,6 +93,9 @@ private:
uint bins_;
uint seq_sep_;
Real* energies_;
+ bool do_internal_scores_;
+ bool do_external_scores_;
+ bool normalize_;
// environment specific information, set upon calling AttachEnvironment
bool attached_environment_;
diff --git a/scoring/src/all_atom_overall_scorer.cc b/scoring/src/all_atom_overall_scorer.cc
index 9f2ff97d5ee389b8b119f6843ab7c40f82eddb91..314f22d7c5e5336bc30fe62b09af20e414561489 100644
--- a/scoring/src/all_atom_overall_scorer.cc
+++ b/scoring/src/all_atom_overall_scorer.cc
@@ -49,4 +49,25 @@ Real AllAtomOverallScorer::CalculateLinearCombination(
return score;
}
+Real AllAtomOverallScorer::CalculateLinearCombination(
+ const std::map<String, Real>& linear_weights,
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
+ // loop and sum up
+ Real score = 0;
+ for (std::map<String, Real>::const_iterator i = linear_weights.begin();
+ i != linear_weights.end(); ++i) {
+ if (i->first == "intercept") {
+ score += i->second;
+ } else {
+ // error checking done by Get
+ AllAtomScorerPtr scorer = this->Get(i->first);
+ score += i->second * scorer->CalculateScore(start_resnum, num_residues,
+ chain_idx);
+ }
+ }
+ return score;
+}
+
}} // ns
diff --git a/scoring/src/all_atom_overall_scorer.hh b/scoring/src/all_atom_overall_scorer.hh
index a201ef86ff4534f973bbfa75a69f9faa9d2cd05c..ac090a46f7f55b58aba5dd27a09f4a9c0c6c04a1 100644
--- a/scoring/src/all_atom_overall_scorer.hh
+++ b/scoring/src/all_atom_overall_scorer.hh
@@ -22,6 +22,21 @@ public:
std::vector<Real>& profile) const {
profile.assign(num_residues, 1.0);
}
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
+ return 1.0;
+ }
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const {
+ profile.resize(num_residues.size());
+ for(uint i = 0; i < num_residues.size(); ++i) {
+ profile[i].assign(num_residues[i], 1.0);
+ }
+ }
};
// simple map of key-scorer pairs
@@ -60,6 +75,10 @@ public:
uint start_resnum, uint num_residues,
uint chain_idx = 0) const;
+ Real CalculateLinearCombination(const std::map<String, Real>& linear_weights,
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
private:
std::map<String, AllAtomScorerPtr> map_;
};
diff --git a/scoring/src/all_atom_packing_score.cc b/scoring/src/all_atom_packing_score.cc
index b07514b2b963d162918e56cbe7a145fc67f3dd64..aef0d0a0ee488290b48cf5546d863f761c640cdb 100644
--- a/scoring/src/all_atom_packing_score.cc
+++ b/scoring/src/all_atom_packing_score.cc
@@ -7,6 +7,7 @@ namespace promod3 { namespace scoring {
AllAtomPackingScorer::AllAtomPackingScorer(Real cutoff, uint max_count):
cutoff_(cutoff),
max_count_(max_count),
+ normalize_(true),
attached_environment_(false) {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
@@ -183,18 +184,26 @@ Real AllAtomPackingScorer::CalculateScore(uint start_resnum, uint num_residues,
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"AllAtomPackingScorer::CalculateScore", 2);
- // get scores
- std::vector<Real> scores;
- std::vector<uint> counts;
- Score(start_resnum, num_residues, chain_idx, scores, counts);
+ if (!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ std::vector<Real> scores;
+ std::vector<uint> idx_vector =
+ idx_handler_->ToIdxVector(start_resnum, num_residues, chain_idx);
+
+ this->Score(idx_vector, scores);
// sum / normalize them
- uint num_set_atoms = 0;
Real score = 0.0;
for (uint i = 0; i < num_residues; ++i) {
score += scores[i];
- num_set_atoms += counts[i];
}
- if (num_set_atoms > 0) score /= num_set_atoms;
+
+ if(normalize_ && !scores.empty()) {
+ score /= scores.size();
+ }
+
return score;
}
@@ -205,12 +214,96 @@ void AllAtomPackingScorer::CalculateScoreProfile(
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"AllAtomPackingScorer::CalculateScoreProfile", 2);
+ if (!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
// get scores
- std::vector<uint> counts;
- Score(start_resnum, num_residues, chain_idx, profile, counts);
- // normalize them
- for (uint i = 0; i < num_residues; ++i) {
- if (counts[i] > 0) profile[i] /= counts[i];
+ std::vector<uint> idx_vector =
+ idx_handler_->ToIdxVector(start_resnum, num_residues, chain_idx);
+ Score(idx_vector, profile);
+}
+
+Real AllAtomPackingScorer::CalculateScore(
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "AllAtomPackingScorer::CalculateScore", 2);
+
+
+ // setup
+ if (!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ if(start_resnum.size() != num_residues.size()) {
+ throw promod3::Error("Inconsistent input data in CBetaScore!");
+ }
+
+ if(start_resnum.size() != chain_idx.size()) {
+ throw promod3::Error("Inconsistent input data in CBetaScore!");
+ }
+
+ std::vector<std::vector<uint> > indices_vec;
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ indices_vec.push_back(idx_handler_->ToIdxVector(start_resnum[i],
+ num_residues[i],
+ chain_idx[i]));
+ }
+
+ // get scores and sum them up
+ Real score = 0.0;
+ uint n_scored_residues = 0;
+ for(uint i = 0; i < indices_vec.size(); ++i) {
+ std::vector<Real> scores;
+ this->Score(indices_vec[i], scores);
+ for(uint j = 0; j < scores.size(); ++j) {
+ score += scores[j];
+ }
+ n_scored_residues += scores.size();
+ }
+
+ if(normalize_ && n_scored_residues > 0) {
+ score /= n_scored_residues;
+ }
+
+ return score;
+}
+
+void AllAtomPackingScorer::CalculateScoreProfile(
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "CBPackingScorer::CalculateScoreProfile", 2);
+
+ // setup
+ if (!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ if(start_resnum.size() != num_residues.size()) {
+ throw promod3::Error("Inconsistent input data in CBetaScore!");
+ }
+
+ if(start_resnum.size() != chain_idx.size()) {
+ throw promod3::Error("Inconsistent input data in CBetaScore!");
+ }
+
+ // get scores
+ profile.resize(start_resnum.size());
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<uint> idx_vector =
+ idx_handler_->ToIdxVector(start_resnum[i], num_residues[i],
+ chain_idx[i]);
+ this->Score(idx_vector, profile[i]);
}
}
@@ -222,28 +315,22 @@ void AllAtomPackingScorer::AttachEnvironment(loop::AllAtomEnv& env) {
attached_environment_ = true;
}
-void AllAtomPackingScorer::Score(uint start_resnum, uint num_residues,
- uint chain_idx, std::vector<Real>& scores,
- std::vector<uint>& counts) const {
+void AllAtomPackingScorer::Score(const std::vector<uint>& indices,
+ std::vector<Real>& scores) const {
// setup
- if (!attached_environment_) {
- String err = "Can only calculate score when environment is attached!";
- throw promod3::Error(err);
+ uint n_indices = indices.size();
+ scores.resize(n_indices);
+
+ if(n_indices == 0) {
+ return;
}
- uint start_idx, end_idx;
- idx_handler_->SetupScoreCalculation(start_resnum, num_residues, chain_idx,
- start_idx, end_idx);
- // get scores
- scores.resize(num_residues);
- counts.resize(num_residues);
// let's go over every residue
AllAtomInteractionSpatialOrganizer::WithinResult within_result;
std::pair<AllAtomInteractionSpatialOrganizerItem*,Real>* a;
- for (uint i = 0; i < num_residues; ++i) {
- const uint res_idx = start_idx + i;
+ for (uint i = 0; i < n_indices; ++i) {
+ const uint res_idx = indices[i];
// loop over all heavy atoms
- uint num_set_atoms = 0;
Real score = 0.0;
const uint first_idx = all_pos_->GetFirstIndex(res_idx);
const uint last_idx = all_pos_->GetLastIndex(res_idx);
@@ -261,12 +348,10 @@ void AllAtomPackingScorer::Score(uint start_resnum, uint num_residues,
// score it
counter = std::min(counter, max_count_);
score += energies_[this->EIdx(all_pos_->GetAAA(idx), counter)];
- ++num_set_atoms;
}
}
// set values
scores[i] = score;
- counts[i] = num_set_atoms;
}
}
diff --git a/scoring/src/all_atom_packing_score.hh b/scoring/src/all_atom_packing_score.hh
index 59616aaddd057084929447449d77c70f4b15c76e..71cf70ea1a9359398923571105c41bd6e7a6b71f 100644
--- a/scoring/src/all_atom_packing_score.hh
+++ b/scoring/src/all_atom_packing_score.hh
@@ -30,17 +30,28 @@ public:
void SetEnergy(loop::AminoAcidAtom aaa, uint count, Real e);
+ void DoNormalize(bool do_it) { normalize_ = do_it; }
+
virtual Real CalculateScore(uint start_resnum, uint num_residues,
uint chain_idx) const;
virtual void
CalculateScoreProfile(uint start_resnum, uint num_residues, uint chain_idx,
std::vector<Real>& profile) const;
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const;
+
virtual void AttachEnvironment(loop::AllAtomEnv& env);
private:
- AllAtomPackingScorer(): attached_environment_(false) { }
+ AllAtomPackingScorer(): normalize_(true), attached_environment_(false) { }
uint EIdx(loop::AminoAcidAtom aaa, uint count) const {
return aaa * (max_count_ + 1) + count;
@@ -49,9 +60,8 @@ private:
return loop::XXX_NUM_ATOMS * (max_count_ + 1);
}
- void Score(uint start_resnum, uint num_residues, uint chain_idx,
- std::vector<Real>& scores,
- std::vector<uint>& counts) const;
+ void Score(const std::vector<uint>& indices,
+ std::vector<Real>& scores) const;
// portable serialization (only stores data relevant for Load/Save!)
// (cleanly element by element with fixed-width base-types)
@@ -69,6 +79,7 @@ private:
Real cutoff_;
uint max_count_;
Real* energies_;
+ bool normalize_;
// environment specific information, set upon calling AttachEnvironment
bool attached_environment_;
diff --git a/scoring/src/all_atom_score_base.hh b/scoring/src/all_atom_score_base.hh
index ab2c16c63bc2671be4c5595a958107e8445df187..ba17cb0843b8523633bdcb24d530d3a53f89cfcb 100644
--- a/scoring/src/all_atom_score_base.hh
+++ b/scoring/src/all_atom_score_base.hh
@@ -25,6 +25,15 @@ public:
CalculateScoreProfile(uint start_resnum, uint num_residues, uint chain_idx,
std::vector<Real>& profile) const = 0;
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const = 0;
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const = 0;
+
virtual void AttachEnvironment(loop::AllAtomEnv& env) { }
};
diff --git a/scoring/src/backbone_overall_scorer.cc b/scoring/src/backbone_overall_scorer.cc
index 1933a0d73f0d12bc9865d7e9d5c80d96bee71f67..bfa296653be248bcbdca2e27ebe81328abe01840 100644
--- a/scoring/src/backbone_overall_scorer.cc
+++ b/scoring/src/backbone_overall_scorer.cc
@@ -30,30 +30,15 @@ BackboneOverallScorer::GetWeightedScorers(
}
Real BackboneOverallScorer::Calculate(const String& key,
- const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const {
- return this->Get(key)->CalculateScore(bb_list, start_resnum, chain_idx);
-}
-
-std::vector<Real> BackboneOverallScorer::Calculate(
- const String& key,
- const std::vector<loop::BackboneList>& bb_lists,
- uint start_resnum, uint chain_idx) const {
- // get scorer once (avoid check / lookup)
- BackboneScorerPtr scorer = this->Get(key);
- // score all
- const uint N = bb_lists.size();
- std::vector<Real> scores(N);
- for (uint i = 0; i < N; ++i) {
- scores[i] = scorer->CalculateScore(bb_lists[i], start_resnum, chain_idx);
- }
- return scores;
+ uint start_resnum, uint num_residues,
+ uint chain_idx) const {
+ return this->Get(key)->CalculateScore(start_resnum, num_residues, chain_idx);
}
Real BackboneOverallScorer::CalculateLinearCombination(
const std::map<String, Real>& linear_weights,
- const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const {
+ uint start_resnum, uint num_residues,
+ uint chain_idx) const {
// loop and sum up
Real score = 0;
for (std::map<String, Real>::const_iterator i = linear_weights.begin();
@@ -62,35 +47,38 @@ Real BackboneOverallScorer::CalculateLinearCombination(
score += i->second;
} else {
// note: error checking done by Calculate
- score += i->second * this->Calculate(i->first, bb_list, start_resnum,
+ score += i->second * this->Calculate(i->first, start_resnum, num_residues,
chain_idx);
}
}
return score;
}
-std::vector<Real> BackboneOverallScorer::CalculateLinearCombination(
+Real BackboneOverallScorer::Calculate(const String& key,
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
+ return this->Get(key)->CalculateScore(start_resnum, num_residues, chain_idx);
+}
+
+Real BackboneOverallScorer::CalculateLinearCombination(
const std::map<String, Real>& linear_weights,
- const std::vector<loop::BackboneList>& bb_lists,
- uint start_resnum, uint chain_idx) const {
- // get scorers once (avoid check / lookup)
- std::vector<std::pair<Real, BackboneScorerPtr> > scorers;
- scorers = this->GetWeightedScorers(linear_weights);
- const uint Nscores = scorers.size();
- // score all
- const uint N = bb_lists.size();
- std::vector<Real> scores(N);
- for (uint i = 0; i < N; ++i) {
- Real score = 0;
- for (uint j = 0; j < Nscores; ++j) {
- const Real weight = scorers[j].first;
- BackboneScorerPtr scorer = scorers[j].second;
- score += weight * scorer->CalculateScore(bb_lists[i], start_resnum,
- chain_idx);
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
+ // loop and sum up
+ Real score = 0;
+ for (std::map<String, Real>::const_iterator i = linear_weights.begin();
+ i != linear_weights.end(); ++i) {
+ if (i->first == "intercept") {
+ score += i->second;
+ } else {
+ // note: error checking done by Calculate
+ score += i->second * this->Calculate(i->first, start_resnum, num_residues,
+ chain_idx);
}
- scores[i] = score;
}
- return scores;
+ return score;
}
}} // ns
\ No newline at end of file
diff --git a/scoring/src/backbone_overall_scorer.hh b/scoring/src/backbone_overall_scorer.hh
index 17016a75de74d4eaef1703e3598c0e5f3011a90f..94af847f50e8e9bcd99414526e420cdc33da6902 100644
--- a/scoring/src/backbone_overall_scorer.hh
+++ b/scoring/src/backbone_overall_scorer.hh
@@ -13,15 +13,31 @@ typedef boost::shared_ptr<BackboneOverallScorer> BackboneOverallScorerPtr;
// dummy score for intercept -> always returns 1
class InterceptScorer : public BackboneScorer {
public:
- virtual Real CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum,
+
+ virtual Real CalculateScore(uint start_resnum, uint num_residues,
uint chain_idx) const { return 1.0; }
- virtual void CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum,
+ virtual void CalculateScoreProfile(uint start_resnum,
+ uint num_residues,
uint chain_idx,
std::vector<Real>& profile) const{
- profile.assign(bb_list.size(), 1.0);
+ profile.assign(num_residues, 1.0);
+ }
+
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
+ return 1.0;
+ }
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const {
+ profile.resize(num_residues.size());
+ for(uint i = 0; i < num_residues.size(); ++i) {
+ profile[i].assign(num_residues[i], 1.0);
+ }
}
};
@@ -56,21 +72,28 @@ public:
GetWeightedScorers(const std::map<String, Real>& linear_weights) const;
// calculate one single score
- Real Calculate(const String& key, const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx = 0) const;
- std::vector<Real>
- Calculate(const String& key, const std::vector<loop::BackboneList>& bb_lists,
- uint start_resnum, uint chain_idx = 0) const;
+ Real Calculate(const String& key, uint start_resnum, uint num_residues,
+ uint chain_idx = 0) const;
// linear combination of weighted scores
// -> use special key "intercept" to add a constant value to the score
Real CalculateLinearCombination(const std::map<String, Real>& linear_weights,
- const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx = 0) const;
- std::vector<Real>
- CalculateLinearCombination(const std::map<String, Real>& linear_weights,
- const std::vector<loop::BackboneList>& bb_lists,
- uint start_resnum, uint chain_idx = 0) const;
+ uint start_resnum, uint num_residues,
+ uint chain_idx = 0) const;
+
+ // calculate one single score
+ Real Calculate(const String& key,
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
+
+
+ // calculate one single score
+ Real CalculateLinearCombination(const std::map<String, Real>& linear_weights,
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
+
private:
std::map<String, BackboneScorerPtr> map_;
@@ -78,4 +101,4 @@ private:
}} // ns
-#endif
\ No newline at end of file
+#endif
diff --git a/scoring/src/backbone_score_base.cc b/scoring/src/backbone_score_base.cc
index c1bcaa59398baf2d51bcf6bb5c559d3f19618a91..30888ec88eac26787f32d63406ea5f686404ae07 100644
--- a/scoring/src/backbone_score_base.cc
+++ b/scoring/src/backbone_score_base.cc
@@ -63,9 +63,6 @@ BackboneScoreEnvPtr BackboneScoreEnv::Copy() const{
return_ptr->psipred_pred_ = psipred_pred_;
return_ptr->psipred_cfi_ = psipred_cfi_;
return_ptr->env_set_ = env_set_;
- if(density_map_data_.map.IsValid()) {
- return_ptr->density_map_data_ = density_map_data_;
- }
return_ptr->n_pos_ = n_pos_;
return_ptr->ca_pos_ = ca_pos_;
return_ptr->cb_pos_ = cb_pos_;
@@ -146,7 +143,7 @@ void BackboneScoreEnv::SetInitialEnvironment(const ost::mol::EntityHandle& env)
}
for (std::vector<BackboneScoreEnvListener*>::iterator i = listener_.begin();
i != listener_.end(); ++i) {
- (*i)->ClearEnvironment(*this, indices_to_delete);
+ (*i)->ClearEnvironment(indices_to_delete);
}
@@ -198,7 +195,7 @@ void BackboneScoreEnv::SetInitialEnvironment(const ost::mol::EntityHandle& env)
}
for (std::vector<BackboneScoreEnvListener*>::iterator i = listener_.begin();
i != listener_.end(); ++i){
- (*i)->SetEnvironment(*this, indices_to_set);
+ (*i)->SetEnvironment(indices_to_set);
}
}
}
@@ -243,8 +240,8 @@ void BackboneScoreEnv::SetEnvironment(const loop::BackboneList& bb_list,
//and call all listeners
for(std::vector<BackboneScoreEnvListener*>::iterator i = listener_.begin();
i != listener_.end(); ++i){
- (*i)->SetEnvironment(*this, indices_to_set);
- (*i)->ResetEnvironment(*this, indices_to_reset);
+ (*i)->SetEnvironment(indices_to_set);
+ (*i)->ResetEnvironment(indices_to_reset);
}
}
@@ -274,7 +271,7 @@ void BackboneScoreEnv::ClearEnvironment(uint start_resnum, uint num_residues,
// and call all listeners
for (std::vector<BackboneScoreEnvListener*>::iterator i = listener_.begin();
i != listener_.end(); ++i) {
- (*i)->ClearEnvironment(*this, indices_to_clear);
+ (*i)->ClearEnvironment(indices_to_clear);
}
}
@@ -324,13 +321,6 @@ void BackboneScoreEnv::SetPsipredPrediction(std::vector<loop::PsipredPredictionP
}
}
-void BackboneScoreEnv::SetMap(const ost::img::MapHandle& map, Real resolution,
- bool all_atom) {
- density_map_data_.map = map;
- density_map_data_.resolution = resolution;
- density_map_data_.all_atom = all_atom;
-}
-
uint BackboneScoreEnv::AddPairwiseFunction(PairwiseFunctionPtr f,
PairwiseFunctionType ft) {
pairwise_functions_.push_back(f);
@@ -371,6 +361,127 @@ void BackboneScoreEnv::ApplyPairwiseFunction(uint chain_idx_one, uint resnum_one
applied_pairwise_functions_[idx_two].push_back(data_two);
}
+void BackboneScoreEnv::Stash(uint start_resnum, uint num_residues,
+ uint chain_idx) {
+ std::vector<uint> indices = idx_handler_.ToIdxVector(start_resnum,
+ num_residues,
+ chain_idx);
+ this->Stash(indices);
+}
+
+void BackboneScoreEnv::Stash(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) {
+
+ std::vector<uint> start_indices;
+ std::vector<uint> lengths;
+
+ std::vector<uint> indices = idx_handler_.ToIdxVector(start_resnum,
+ num_residues,
+ chain_idx,
+ start_indices,
+ lengths);
+ this->Stash(indices);
+}
+
+void BackboneScoreEnv::Stash(const std::vector<uint>& indices) {
+
+ if(stashed_indices_.size() > 100) {
+ throw promod3::Error("You already performed a 100 stash events... "
+ "Cant do more....");
+ }
+
+ std::vector<uint> stash_indices;
+ std::vector<int> stash_env_set;
+ std::vector<geom::Vec3> stash_n_pos;
+ std::vector<geom::Vec3> stash_ca_pos;
+ std::vector<geom::Vec3> stash_cb_pos;
+ std::vector<geom::Vec3> stash_c_pos;
+ std::vector<geom::Vec3> stash_o_pos;
+
+ uint n_indices = indices.size();
+ stash_indices.reserve(n_indices);
+ stash_env_set.reserve(n_indices);
+ stash_n_pos.reserve(n_indices);
+ stash_ca_pos.reserve(n_indices);
+ stash_cb_pos.reserve(n_indices);
+ stash_c_pos.reserve(n_indices);
+ stash_o_pos.reserve(n_indices);
+
+ for(std::vector<uint>::const_iterator i = indices.begin();
+ i != indices.end(); ++i) {
+ stash_indices.push_back(*i);
+ stash_env_set.push_back(env_set_[*i]);
+ stash_n_pos.push_back(n_pos_[*i]);
+ stash_ca_pos.push_back(ca_pos_[*i]);
+ stash_cb_pos.push_back(cb_pos_[*i]);
+ stash_c_pos.push_back(c_pos_[*i]);
+ stash_o_pos.push_back(o_pos_[*i]);
+ }
+
+ stashed_indices_.push(stash_indices);
+ stashed_env_set_.push(stash_env_set);
+ stashed_n_pos_.push(stash_n_pos);
+ stashed_ca_pos_.push(stash_ca_pos);
+ stashed_cb_pos_.push(stash_cb_pos);
+ stashed_c_pos_.push(stash_c_pos);
+ stashed_o_pos_.push(stash_o_pos);
+}
+
+void BackboneScoreEnv::Pop() {
+
+ if(stashed_indices_.empty()) {
+ throw promod3::Error("Nothing stashed! Cannot pop!");
+ }
+
+ std::vector<uint> indices_to_set;
+ std::vector<uint> indices_to_reset;
+ std::vector<uint> indices_to_clear;
+
+ const std::vector<uint>& stash_indices = stashed_indices_.top();
+ const std::vector<int>& stash_env_set = stashed_env_set_.top();
+ const std::vector<geom::Vec3>& stash_n_pos = stashed_n_pos_.top();
+ const std::vector<geom::Vec3>& stash_ca_pos = stashed_ca_pos_.top();
+ const std::vector<geom::Vec3>& stash_cb_pos = stashed_cb_pos_.top();
+ const std::vector<geom::Vec3>& stash_c_pos = stashed_c_pos_.top();
+ const std::vector<geom::Vec3>& stash_o_pos = stashed_o_pos_.top();
+
+ for(uint i = 0; i < stash_indices.size(); ++i) {
+ uint env_idx = stash_indices[i];
+ n_pos_[env_idx] = stash_n_pos[i];
+ ca_pos_[env_idx] = stash_ca_pos[i];
+ cb_pos_[env_idx] = stash_cb_pos[i];
+ c_pos_[env_idx] = stash_c_pos[i];
+ o_pos_[env_idx] = stash_o_pos[i];
+
+ if(env_set_[env_idx] == 1 && stash_env_set[i] == 1) {
+ indices_to_reset.push_back(env_idx);
+ } else if(env_set_[env_idx] == 1 && stash_env_set[i] == 0) {
+ indices_to_clear.push_back(env_idx);
+ } else if(env_set_[env_idx] == 0 && stash_env_set[i] == 1) {
+ indices_to_set.push_back(env_idx);
+ }
+
+ env_set_[env_idx] = stash_env_set[i];
+ }
+
+ //and call all listeners
+ for(std::vector<BackboneScoreEnvListener*>::iterator i = listener_.begin();
+ i != listener_.end(); ++i){
+ (*i)->SetEnvironment(indices_to_set);
+ (*i)->ResetEnvironment(indices_to_reset);
+ (*i)->ClearEnvironment(indices_to_clear);
+ }
+
+ stashed_indices_.pop();
+ stashed_env_set_.pop();
+ stashed_n_pos_.pop();
+ stashed_ca_pos_.pop();
+ stashed_cb_pos_.pop();
+ stashed_c_pos_.pop();
+ stashed_o_pos_.pop();
+}
+
BackboneScoreEnvListener* BackboneScoreEnv::GetListener(const String& id) const {
for (uint i = 0; i < listener_.size(); ++i) {
if (listener_[i]->WhoAmI() == id) return listener_[i];
@@ -390,7 +501,7 @@ void BackboneScoreEnv::AttachListener(BackboneScoreEnvListener* listener) {
for (uint i = 0; i < env_set_.size(); ++i) {
if (env_set_[i]) indices_to_set.push_back(i);
}
- listener->SetEnvironment(*this, indices_to_set);
+ listener->SetEnvironment(indices_to_set);
listener_.push_back(listener);
}
diff --git a/scoring/src/backbone_score_base.hh b/scoring/src/backbone_score_base.hh
index feade33ead9a28e021a79d4f72f852f4bdce878b..8631f8a888f3cea59db7c5c4ba5638723c17d2e1 100644
--- a/scoring/src/backbone_score_base.hh
+++ b/scoring/src/backbone_score_base.hh
@@ -11,6 +11,7 @@
#include <promod3/scoring/pairwise_scoring_function.hh>
#include <algorithm>
+#include <stack>
namespace promod3 { namespace scoring {
@@ -37,13 +38,6 @@ struct PairwiseFunctionData {
};
-struct DensityMapData {
- ost::img::MapHandle map;
- Real resolution;
- bool all_atom;
-};
-
-
class BackboneScoreEnv {
public:
@@ -68,9 +62,6 @@ public:
void SetPsipredPrediction(std::vector<loop::PsipredPredictionPtr>& pp);
- void SetMap(const ost::img::MapHandle& map, Real resolution,
- bool all_atom = false);
-
uint AddPairwiseFunction(PairwiseFunctionPtr f,
PairwiseFunctionType ft);
@@ -78,6 +69,14 @@ public:
uint chain_idx_two, uint resnum_two,
uint f_idx);
+ void Stash(uint start_resnum, uint num_residues, uint chain_idx = 0);
+
+ void Stash(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx);
+
+ void Pop();
+
ost::seq::SequenceList GetSeqres() const { return seqres_; }
// methods to access internal data intended to be used by the scorer objects
@@ -105,9 +104,6 @@ public:
const std::vector<PairwiseFunctionData>*
GetPairwiseFunctionData() const { return &applied_pairwise_functions_[0]; }
- const DensityMapData* GetDensityMapData() const { return &density_map_data_; }
-
-
// listener related methods
// return listener with that ID or NULL if not existing
@@ -133,6 +129,8 @@ public:
private:
+ void Stash(const std::vector<uint>& indices);
+
ost::seq::SequenceList seqres_;
loop::IdxHandler idx_handler_;
std::vector<ost::conop::AminoAcid> aa_seqres_;
@@ -141,12 +139,19 @@ private:
// the reason to use a vector with int here is that the STL has an optimized
// vector<bool> (bitset, min. memory usage) which can't be used as C arrays
std::vector<int> env_set_;
- DensityMapData density_map_data_;
std::vector<geom::Vec3> n_pos_;
std::vector<geom::Vec3> ca_pos_;
std::vector<geom::Vec3> cb_pos_;
std::vector<geom::Vec3> c_pos_;
std::vector<geom::Vec3> o_pos_;
+ // same as above, but to stash things
+ std::stack<std::vector<uint> > stashed_indices_;
+ std::stack<std::vector<int> > stashed_env_set_;
+ std::stack<std::vector<geom::Vec3> > stashed_n_pos_;
+ std::stack<std::vector<geom::Vec3> > stashed_ca_pos_;
+ std::stack<std::vector<geom::Vec3> > stashed_cb_pos_;
+ std::stack<std::vector<geom::Vec3> > stashed_c_pos_;
+ std::stack<std::vector<geom::Vec3> > stashed_o_pos_;
// every residue gets a vector of pairs
// every pair contains:
// - a function ptr as a first element, i.e. the pairwise
@@ -169,14 +174,11 @@ public:
virtual void Init(const BackboneScoreEnv& base_env) = 0;
- virtual void SetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) = 0;
+ virtual void SetEnvironment(const std::vector<uint>& idx) = 0;
- virtual void ResetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) = 0;
+ virtual void ResetEnvironment(const std::vector<uint>& idx) = 0;
- virtual void ClearEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) = 0;
+ virtual void ClearEnvironment(const std::vector<uint>& idx) = 0;
virtual String WhoAmI() const = 0;
};
@@ -188,15 +190,22 @@ public:
virtual ~BackboneScorer() { }
- virtual Real CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum,
+ virtual Real CalculateScore(uint start_resnum, uint num_residues,
uint chain_idx) const = 0;
- virtual void CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx,
+ virtual void CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
std::vector<Real>& profile) const = 0;
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const = 0;
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const = 0;
+
virtual void AttachEnvironment(BackboneScoreEnv& env) { }
};
diff --git a/scoring/src/cb_packing_score.cc b/scoring/src/cb_packing_score.cc
index fdf9e25203040b4505bfebad7d612b89bf3efbb0..0f0b307df7677da899b0d155d7ced9cd72775f56 100644
--- a/scoring/src/cb_packing_score.cc
+++ b/scoring/src/cb_packing_score.cc
@@ -6,8 +6,7 @@ namespace promod3 { namespace scoring {
CBPackingScorer::CBPackingScorer(Real cutoff, uint max_count):
cutoff_(cutoff),
max_count_(max_count),
- attached_environment_(false),
- include_env_mode_(false),
+ normalize_(true),
env_(NULL) {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
@@ -181,213 +180,180 @@ void CBPackingScorer::SetEnergy(ost::conop::AminoAcid aa, uint count, Real e) {
energies_[this->EIdx(aa, count)] = e;
}
-Real CBPackingScorer::CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx) const{
+Real CBPackingScorer::CalculateScore(uint start_resnum, uint num_residues,
+ uint chain_idx) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"CBPackingScorer::CalculateScore", 2);
- if(include_env_mode_) {
- return this->CalculateScoreIncludeEnv(bb_list, start_resnum, chain_idx);
+ if(env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
}
- else {
- std::vector<Real> scores;
- this->Score(bb_list, start_resnum, chain_idx, scores);
- Real score = 0.0;
- for(uint i = 0; i < scores.size(); ++i){
- score += scores[i];
- }
- if(!scores.empty()){
- score /= scores.size();
- }
- return score;
+ std::vector<Real> scores;
+ std::vector<uint> idx_vector =
+ env_->GetIdxHandler()->ToIdxVector(start_resnum, num_residues, chain_idx);
+
+ this->Score(idx_vector, scores);
+ Real score = 0.0;
+ for(uint i = 0; i < scores.size(); ++i) {
+ score += scores[i];
+ }
+
+ if(normalize_ && !scores.empty()) {
+ score /= scores.size();
}
+
+ return score;
}
-void CBPackingScorer::CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
+void CBPackingScorer::CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
std::vector<Real>& profile) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"CBPackingScorer::CalculateScoreProfile", 2);
- if(include_env_mode_){
- throw promod3::Error("CBPackingScorer cannot generate score profile when "
- "include_env_mode is active! Call the UseClassicMode()"
- "function to deactivate and try again...");
+ if(env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
}
- this->Score(bb_list, start_resnum, chain_idx, profile);
+ std::vector<uint> idx_vector =
+ env_->GetIdxHandler()->ToIdxVector(start_resnum, num_residues, chain_idx);
+ this->Score(idx_vector, profile);
}
-void CBPackingScorer::Score(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx,
- std::vector<Real>& scores) const{
+Real CBPackingScorer::CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "CBPackingScorer::Score", 2);
+ "CBPackingScorer::CalculateScore", 2);
// setup
- if(!attached_environment_){
+ if(env_ == NULL) {
String err = "Can only calculate score when environment is attached!";
throw promod3::Error(err);
}
- uint bb_list_size, start_idx, end_idx;
- idx_handler_->SetupScoreCalculation(bb_list, start_resnum, chain_idx,
- bb_list_size, start_idx, end_idx);
-
- scores.assign(bb_list_size, 0.0);
- if(bb_list_size == 0) return;
-
- // get counts
- std::vector<uint> count_buffer(bb_list_size, 0);
-
- // first internal
- const Real squared_cutoff = cutoff_ * cutoff_;
- for (uint i = 0; i < bb_list_size; ++i) {
- for (uint j = i+1; j < bb_list_size; ++j) {
- if (geom::Length2(bb_list.GetCB(i) - bb_list.GetCB(j)) < squared_cutoff) {
- count_buffer[i] += 1;
- count_buffer[j] += 1;
- }
- }
+
+ if(start_resnum.size() != num_residues.size()) {
+ throw promod3::Error("Inconsistent input data in CBetaScore!");
}
- // then external and sum up score as we go
- CBetaSpatialOrganizer::WithinResult within_result;
- std::pair<CBetaSpatialOrganizerItem*,Real>* a;
- for (uint i = 0; i < bb_list_size; ++i) {
- // add neighbors to internal count
- within_result = env_->FindWithin(bb_list.GetCB(i), cutoff_);
- a = within_result.first;
- uint counter = count_buffer[i];
- for (uint j = 0; j < within_result.second; ++j) {
- if (a[j].first->idx < start_idx || a[j].first->idx > end_idx) {
- ++counter;
- }
+
+ if(start_resnum.size() != chain_idx.size()) {
+ throw promod3::Error("Inconsistent input data in CBetaScore!");
+ }
+
+ std::vector<std::vector<uint> > indices_vec;
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ indices_vec.push_back(env_->GetIdxHandler()->ToIdxVector(start_resnum[i],
+ num_residues[i],
+ chain_idx[i]));
+ }
+
+ // get scores and sum them up
+ Real score = 0.0;
+ uint n_scored_residues = 0;
+ for(uint i = 0; i < indices_vec.size(); ++i) {
+ std::vector<Real> scores;
+ this->Score(indices_vec[i], scores);
+ for(uint j = 0; j < scores.size(); ++j) {
+ score += scores[j];
}
- // score it
- counter = std::min(counter, max_count_);
- scores[i] = energies_[this->EIdx(bb_list.GetAA(i), counter)];
+ n_scored_residues += scores.size();
}
+
+ if(normalize_ && n_scored_residues > 0) {
+ score /= n_scored_residues;
+ }
+
+ return score;
}
-Real CBPackingScorer::CalculateScoreIncludeEnv(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx) const{
+void CBPackingScorer::CalculateScoreProfile(
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const {
+
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "CBPackingScorer::CalculateScoreIncludeEnv", 2);
+ "CBPackingScorer::CalculateScoreProfile", 2);
// setup
- if(!attached_environment_){
+ if(env_ == NULL) {
String err = "Can only calculate score when environment is attached!";
throw promod3::Error(err);
}
- uint bb_list_size, start_idx, end_idx;
- std::map<uint,uint> close_env_residues;
- std::map<uint,uint>::iterator close_env_it;
- uint env_idx;
-
- idx_handler_->SetupScoreCalculation(bb_list, start_resnum, chain_idx,
- bb_list_size, start_idx, end_idx);
-
- // get counts
- std::vector<uint> count_buffer(bb_list_size,0);
-
- // first internal
- Real squared_cutoff = cutoff_ * cutoff_;
- for (uint i = 0; i < bb_list_size; ++i) {
- for (uint j = i+1; j < bb_list_size; ++j) {
- if (geom::Length2(bb_list.GetCB(i) - bb_list.GetCB(j)) < squared_cutoff) {
- count_buffer[i] += 1;
- count_buffer[j] += 1;
- }
- }
- }
- // score the bb_list items and keep track of the surroundings
- Real score = 0.0;
- CBetaSpatialOrganizer::WithinResult within_result;
- std::pair<CBetaSpatialOrganizerItem*,Real>* a;
- for (uint i = 0; i < bb_list_size; ++i) {
- // add neighbors to internal count
- within_result = env_->FindWithin(bb_list.GetCB(i), cutoff_);
- a = within_result.first;
- uint counter = count_buffer[i];
- for (uint j = 0; j < within_result.second; ++j) {
- env_idx = a[j].first->idx;
- if (env_idx < start_idx || env_idx > end_idx) {
- ++counter;
- close_env_it = close_env_residues.find(env_idx);
- if(close_env_it == close_env_residues.end()){
- close_env_residues[env_idx] = 1;
- }
- else{
- close_env_it->second += 1;
- }
- }
- }
- // score it
- counter = std::min(counter, max_count_);
- score += energies_[this->EIdx(bb_list.GetAA(i), counter)];
+ if(start_resnum.size() != num_residues.size()) {
+ throw promod3::Error("Inconsistent input data in CBetaScore!");
}
- // We have now all energies of the residues in the BackboneList...
- // The problem is, that the residues closeby also get affected
- // by the positions of bb_list. The effect gets honoured by calculating
- // a delta in energy for those residue between the energy they would
- // have in the environment and the new energy, given the positions of the
- // bb_list
- Real diff_score = 0.0;
- uint old_env_counter, new_env_counter;
+ if(start_resnum.size() != chain_idx.size()) {
+ throw promod3::Error("Inconsistent input data in CBetaScore!");
+ }
- for(close_env_it = close_env_residues.begin();
- close_env_it != close_env_residues.end(); ++close_env_it){
+ // get scores
+ profile.resize(start_resnum.size());
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<uint> idx_vector =
+ env_->GetIdxHandler()->ToIdxVector(start_resnum[i], num_residues[i],
+ chain_idx[i]);
+ this->Score(idx_vector, profile[i]);
+ }
+}
- const CBetaSpatialOrganizerItem& env_data =
- env_->GetEnvData(close_env_it->first);
- within_result = env_->FindWithin(env_data.pos, cutoff_);
- a = within_result.first;
+void CBPackingScorer::Score(const std::vector<uint>& indices,
+ std::vector<Real>& scores) const {
- // the number of neighbours before looking at the input bb_list
- old_env_counter = within_result.second - 1; // -1, because the position
- // itself also gets found...
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "CBPackingScorer::Score", 2);
- // the number of neighbours when bb_list would be added to env
- new_env_counter = close_env_it->second; // the number of close residues
- // it has from the bb_list
+ // setup
+ uint n_indices = indices.size();
- // we still have to add all the residues from the environment not
- // part of the bb_list
- for(uint j = 0; j < within_result.second; ++j){
- env_idx = a[j].first->idx;
- if(env_idx < start_idx || env_idx > end_idx) ++new_env_counter;
- }
- new_env_counter -= 1;// The position itself will also be found
+ scores.assign(n_indices, 0.0);
- new_env_counter = std::min(new_env_counter, max_count_);
- old_env_counter = std::min(old_env_counter, max_count_);
- diff_score += energies_[this->EIdx(env_data.aa,new_env_counter)];
- diff_score -= energies_[this->EIdx(env_data.aa,old_env_counter)];
+ if(n_indices == 0) {
+ return;
}
- score += diff_score;
+ // then external and sum up score as we go
+ CBetaSpatialOrganizer::WithinResult within_result;
+ std::pair<CBetaSpatialOrganizerItem*,Real>* a;
+ const int* env_set = env_->GetEnvSetData();
+ for (uint i = 0; i < indices.size(); ++i) {
+ uint my_idx = indices[i];
+
+ if(!env_set[my_idx]) {
+ throw promod3::Error("Must set environment before scoring!");
+ }
+
+ ost::conop::AminoAcid my_aa = env_->GetEnvData(my_idx).aa;
- // avg. it
- if (bb_list_size > 0) return (score / bb_list_size);
- else return score;
+ // count neighbours
+ uint count = 0;
+ within_result = env_->FindWithin(env_->GetEnvData(my_idx).pos, cutoff_);
+ a = within_result.first;
+ for (uint j = 0; j < within_result.second; ++j) {
+ if (my_idx != a[j].first->idx) {
+ ++count;
+ }
+ }
+ // score it
+ count = std::min(count, max_count_);
+ scores[i] = energies_[this->EIdx(my_aa, count)];
+ }
}
void CBPackingScorer::AttachEnvironment(BackboneScoreEnv& env) {
env_ = env.UniqueListener<CBetaEnvListener>("CBetaEnvListener");
- idx_handler_ = env.GetIdxHandlerData();
- attached_environment_ = true;
}
}}
diff --git a/scoring/src/cb_packing_score.hh b/scoring/src/cb_packing_score.hh
index d0d7a84da6d7426e155ee00ca1f0ff2dda103fac..0f3e5518e8a17eb2c9eaf7b041a3deafe6c337fb 100644
--- a/scoring/src/cb_packing_score.hh
+++ b/scoring/src/cb_packing_score.hh
@@ -30,39 +30,38 @@ public:
void SetEnergy(ost::conop::AminoAcid aa, uint count, Real e);
- virtual Real CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum,
+ virtual Real CalculateScore(uint start_resnum, uint num_residues,
uint chain_idx) const;
- void CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
- std::vector<Real>& profile) const;
+ virtual void CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
+ std::vector<Real>& profile) const;
- void UseClassicMode() { include_env_mode_ = false; }
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
- void UseIncludeEnvMode() { include_env_mode_ = true; }
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const;
+
+ void DoNormalize(bool do_it) {normalize_ = do_it; }
void AttachEnvironment(BackboneScoreEnv& env);
private:
- CBPackingScorer(): attached_environment_(false),
- include_env_mode_(false),
+ CBPackingScorer(): normalize_(true),
env_(NULL) { }
inline uint EIdx(ost::conop::AminoAcid aa, uint count) const{
return aa * (max_count_ + 1) + count;
}
- void Score(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx,
+ void Score(const std::vector<uint>& indices,
std::vector<Real>& scores) const;
- Real CalculateScoreIncludeEnv(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx) const;
-
// portable serialization (only stores data relevant for Load/Save!)
// (cleanly element by element with fixed-width base-types)
template <typename DS>
@@ -83,13 +82,11 @@ private:
Real cutoff_;
uint max_count_;
Real* energies_;
+ bool normalize_;
//environment specific information, that will be set upon calling
//AttachEnvironment
- bool attached_environment_;
- bool include_env_mode_;
CBetaEnvListener* env_;
- const loop::IdxHandler* idx_handler_;
};
diff --git a/scoring/src/cbeta_env_listener.cc b/scoring/src/cbeta_env_listener.cc
index 00557c561cc7eb8f4ec46de58f92ad203f7e6efc..6b8092f5c7ca8d6c93cc9b0cbe1208e48e88b044 100644
--- a/scoring/src/cbeta_env_listener.cc
+++ b/scoring/src/cbeta_env_listener.cc
@@ -23,8 +23,10 @@ void CBetaEnvListener::Init(const BackboneScoreEnv& base_env) {
env_.Clear();
}
- const loop::IdxHandler* idx_handler = base_env.GetIdxHandlerData();
- uint num_residues = idx_handler->GetNumResidues();
+ idx_handler_ = base_env.GetIdxHandlerData();
+ env_set_ = base_env.GetEnvSetData();
+ cb_pos_data_ = base_env.GetCBPosData();
+ uint num_residues = idx_handler_->GetNumResidues();
env_data_ = new CBetaSpatialOrganizerItem[num_residues];
const ost::conop::AminoAcid* aa_data = base_env.GetAAData();
@@ -34,39 +36,33 @@ void CBetaEnvListener::Init(const BackboneScoreEnv& base_env) {
}
}
-void CBetaEnvListener::SetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void CBetaEnvListener::SetEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"CBetaEnvListener::SetEnvironment", 2);
- const geom::Vec3* cb_pos_data = base_env.GetCBPosData();
-
for (std::vector<uint>::const_iterator i = idx.begin();
i != idx.end(); ++i) {
- env_data_[*i].pos = cb_pos_data[*i];
- env_.Add(&env_data_[*i], cb_pos_data[*i]);
+ env_data_[*i].pos = cb_pos_data_[*i];
+ env_.Add(&env_data_[*i], cb_pos_data_[*i]);
}
}
-void CBetaEnvListener::ResetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void CBetaEnvListener::ResetEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"CBetaEnvListener::ResetEnvironment", 2);
- const geom::Vec3* cb_pos_data = base_env.GetCBPosData();
geom::Vec3 old_pos;
for (std::vector<uint>::const_iterator i = idx.begin();
i != idx.end(); ++i) {
old_pos = env_data_[*i].pos;
- env_data_[*i].pos = cb_pos_data[*i];
- env_.Reset(&env_data_[*i], old_pos, cb_pos_data[*i]);
+ env_data_[*i].pos = cb_pos_data_[*i];
+ env_.Reset(&env_data_[*i], old_pos, cb_pos_data_[*i]);
}
}
-void CBetaEnvListener::ClearEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void CBetaEnvListener::ClearEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"CBetaEnvListener::ClearEnvironment", 2);
diff --git a/scoring/src/cbeta_env_listener.hh b/scoring/src/cbeta_env_listener.hh
index e58d173dcfeac5eeee09a184105a5a6864211ac4..af07e116c9f8386fa9db2313f8ea8b31d5e3ed9c 100644
--- a/scoring/src/cbeta_env_listener.hh
+++ b/scoring/src/cbeta_env_listener.hh
@@ -30,21 +30,22 @@ public:
virtual void Init(const BackboneScoreEnv& base_env);
- virtual void SetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void SetEnvironment(const std::vector<uint>& idx);
- virtual void ResetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void ResetEnvironment(const std::vector<uint>& idx);
- virtual void ClearEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void ClearEnvironment(const std::vector<uint>& idx);
virtual String WhoAmI() const { return "CBetaEnvListener"; }
const CBetaSpatialOrganizerItem& GetEnvData(uint idx) const {
return env_data_[idx];
}
-
+
+ const int* GetEnvSetData() { return env_set_; }
+
+ const loop::IdxHandler* GetIdxHandler() { return idx_handler_; }
+
// get all cbetas within cutoff
// - result.first: std::pair<CBetaSpatialOrganizerItem*,Real>*
// - result.second: uint = size of partners found
@@ -57,6 +58,11 @@ private:
CBetaSpatialOrganizer env_;
CBetaSpatialOrganizerItem* env_data_;
+
+ // data ptrs fetched from base env at initialization
+ const int* env_set_;
+ const loop::IdxHandler* idx_handler_;
+ const geom::Vec3* cb_pos_data_;
};
}} //ns
diff --git a/scoring/src/cbeta_score.cc b/scoring/src/cbeta_score.cc
index a5c2a5b3fcc64fa535a4f59e8de5fcbab00f05b7..1932a20038350aa5d03f1f9c898abd8b62070de3 100644
--- a/scoring/src/cbeta_score.cc
+++ b/scoring/src/cbeta_score.cc
@@ -7,7 +7,9 @@ CBetaScorer::CBetaScorer(Real cutoff, uint bins, uint seq_sep):
cutoff_(cutoff),
bins_(bins),
seq_sep_(seq_sep),
- attached_environment_(false),
+ do_internal_scores_(true),
+ do_external_scores_(true),
+ normalize_(true),
env_(NULL) {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
@@ -179,138 +181,213 @@ void CBetaScorer::SetEnergy(ost::conop::AminoAcid a, ost::conop::AminoAcid b,
}
energies_[this->EIdx(a, b, bin)] = e;
+ energies_[this->EIdx(b, a, bin)] = e;
}
-Real CBetaScorer::CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const {
+Real CBetaScorer::CalculateScore(uint start_resnum, uint num_residues,
+ uint chain_idx) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"CBetaScorer::CalculateScore", 2);
+ if (env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ // setup
+ std::vector<uint> idx_vector;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vector,
+ occupied);
+
// get scores
- std::vector<Real> scores;
+ std::vector<Real> external_scores;
std::vector<Real> internal_scores;
- std::vector<uint> counts;
- std::vector<uint> internal_counts;
- this->Score(bb_list, start_resnum, chain_idx, scores, internal_scores,
- counts, internal_counts);
+ this->Score(idx_vector, external_scores, internal_scores, occupied);
+
// sum them
- Real score = 0.0;
+ Real external_score = 0.0;
Real internal_score = 0.0;
- uint counter = 0;
- uint internal_counter = 0;
- for (uint i = 0; i < scores.size(); ++i) {
- score += scores[i];
+ for (uint i = 0; i < external_scores.size(); ++i) {
+ external_score += external_scores[i];
internal_score += internal_scores[i];
- counter += counts[i];
- internal_counter += internal_counts[i];
}
- // normalize: we count internal scores half as the same pair appears twice
- score += Real(0.5) * internal_score;
- const Real count = counter + Real(0.5) * internal_counter;
- if (count > 0) return score / count;
- else return score;
+
+ // all interactions in internal_score have been observed twice!
+ external_score += Real(0.5)*internal_score;
+
+ if(normalize_ && !external_scores.empty()) {
+ external_score /= external_scores.size();
+ }
+
+ return external_score;
}
-void CBetaScorer::CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
+
+void CBetaScorer::CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
std::vector<Real>& profile) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"CBetaScorer::CalculateScoreProfile", 2);
- std::vector<Real> scores;
+ if (env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ // setup
+ std::vector<uint> idx_vector;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vector,
+ occupied);
+
+ // get scores
std::vector<Real> internal_scores;
- std::vector<uint> counts;
- std::vector<uint> internal_counts;
- this->Score(bb_list, start_resnum, chain_idx, scores, internal_scores,
- counts, internal_counts);
-
- profile.clear();
- for(uint i = 0; i < scores.size(); ++i){
- uint count = counts[i] + internal_counts[i];
- if(count > 0) profile.push_back((scores[i] + internal_scores[i]) / count);
- else profile.push_back(scores[i] + internal_scores[i]);
+ this->Score(idx_vector, profile, internal_scores, occupied);
+
+ for(uint i = 0; i < profile.size(); ++i) {
+ profile[i] += internal_scores[i];
}
}
-void CBetaScorer::Score(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx,
- std::vector<Real>& scores,
- std::vector<Real>& internal_scores,
- std::vector<uint>& counts,
- std::vector<uint>& internal_counts) const{
+Real CBetaScorer::CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "CBetaScorer::CalculateScore", 2);
+
+ if (env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ // setup
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores and sum them up
+ Real external_score = 0.0;
+ Real internal_score = 0.0;
+ uint n_scored_residues = 0;
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ this->Score(indices_vec[i], external_scores, internal_scores, occupied);
+ for (uint j = 0; j < external_scores.size(); ++j) {
+ external_score += external_scores[j];
+ internal_score += internal_scores[j];
+ }
+ n_scored_residues += external_scores.size();
+ }
+
+ // all interactions in internal_score have been observed twice!
+ external_score += Real(0.5)*internal_score;
+
+ if(normalize_ && n_scored_residues > 0) {
+ external_score /= n_scored_residues;
+ }
+
+ return external_score;
+}
+void CBetaScorer::CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const {
+
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "CBetaScorer::Score", 2);
+ "CBetaScorer::CalculateScore", 2);
- // setup
- if (!attached_environment_) {
+ if (env_ == NULL) {
String err = "Can only calculate score when environment is attached!";
throw promod3::Error(err);
}
- uint bb_list_size, start_idx, end_idx;
- idx_handler_->SetupScoreCalculation(bb_list, start_resnum, chain_idx,
- bb_list_size, start_idx, end_idx);
- counts.assign(bb_list_size, 0);
- scores.assign(bb_list_size, 0.0);
- if(bb_list_size == 0) return;
+ // setup
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores
+ profile.resize(start_resnum.size());
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ std::vector<Real>& current_profile = profile[i];
+ this->Score(indices_vec[i], current_profile, internal_scores, occupied);
+ for (uint j = 0; j < current_profile.size(); ++j) {
+ current_profile[j] += internal_scores[j];
+ }
+ }
+}
+
+
+void CBetaScorer::Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
+ std::vector<Real>& internal_scores,
+ std::vector<bool>& occupied) const {
+
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "CBetaScorer::Score", 2);
+
+ // setup
+ uint n_indices = indices.size();
+
+ external_scores.assign(n_indices, 0.0);
+ internal_scores.assign(n_indices, 0.0);
+
+ if(n_indices == 0) return;
const Real inv_bin_size = bins_ / cutoff_;
// let's reduce the cutoff a bit -> hack to ensure bin always within range
- const Real squared_cutoff = cutoff_*cutoff_ - 0.0001;
const Real cutoff = cutoff_ - 0.0001;
- // let's precalculate the idx ranges we have to neglect
- int min_idx_chain = idx_handler_->GetChainStartIdx(chain_idx);
- int max_idx_chain = min_idx_chain + idx_handler_->GetChainSize(chain_idx) - 1;
- std::vector<int> start_neglect(bb_list_size, start_idx);
- std::vector<int> end_neglect(bb_list_size, end_idx);
- int neglect_range = int(seq_sep_) - 1;
-
- int max_i = std::min(neglect_range, static_cast<int>(bb_list_size));
- for (int i = 0; i < max_i; ++i) {
- start_neglect[i] =
- std::max(min_idx_chain, start_neglect[i]-(neglect_range-i));
- end_neglect[bb_list_size-1-i] =
- std::min(max_idx_chain, end_neglect[i]+(neglect_range-i));
- }
-
// let's go over every loop residue
CBetaSpatialOrganizer::WithinResult within_result;
+ const loop::IdxHandler* idx_handler = env_->GetIdxHandler();
+ const int* env_set = env_->GetEnvSetData();
std::pair<CBetaSpatialOrganizerItem*,Real>* a;
- for (uint i = 0; i < bb_list_size; ++i) {
- within_result = env_->FindWithin(bb_list.GetCB(i), cutoff);
+ for (uint i = 0; i < n_indices; ++i) {
+ int my_idx = indices[i];
+
+ if(!env_set[my_idx]) {
+ throw promod3::Error("Must set environment before scoring!");
+ }
+
+ int my_chain_idx = idx_handler->GetChainIdx(my_idx);
+ ost::conop::AminoAcid my_aa = env_->GetEnvData(my_idx).aa;
+
+ within_result = env_->FindWithin(env_->GetEnvData(my_idx).pos, cutoff);
a = within_result.first;
- const ost::conop::AminoAcid myaa = bb_list.GetAA(i);
+
for (uint j = 0; j < within_result.second; ++j) {
- const int my_idx = int(a[j].first->idx);
- if (my_idx < start_neglect[i] || my_idx > end_neglect[i]) {
- const uint bin = a[j].second * inv_bin_size;
- scores[i] += energies_[this->EIdx(myaa, a[j].first->aa, bin)];
- counts[i] += 1;
- }
- }
- }
- // now all the loop internal interactions
- internal_counts.assign(bb_list_size, 0);
- internal_scores.assign(bb_list_size, 0.0);
- if (bb_list_size >= seq_sep_) {
- for (uint i = 0; i < bb_list_size-seq_sep_; ++i) {
- const ost::conop::AminoAcid myaa = bb_list.GetAA(i);
- for (uint j = i+seq_sep_; j < bb_list_size; ++j) {
- const Real dist2 = geom::Length2(bb_list.GetCB(i) - bb_list.GetCB(j));
- if (dist2 < squared_cutoff) {
- const uint bin = std::sqrt(dist2) * inv_bin_size;
- // go symmetric
- internal_scores[i] += energies_[this->EIdx(myaa, bb_list.GetAA(j), bin)];
- internal_scores[j] += energies_[this->EIdx(bb_list.GetAA(j), myaa, bin)];
- internal_counts[i] += 1;
- internal_counts[j] += 1;
+ int other_idx = int(a[j].first->idx);
+ int other_chain_idx = idx_handler->GetChainIdx(other_idx);
+
+ if(my_chain_idx != other_chain_idx ||
+ std::abs(my_idx - other_idx) >= seq_sep_) {
+ uint bin = a[j].second * inv_bin_size;
+ Real e = energies_[this->EIdx(my_aa, a[j].first->aa, bin)];
+
+ if(occupied[other_idx] && do_internal_scores_) {
+ internal_scores[i] += e;
+ }
+
+ if(!occupied[other_idx] && do_external_scores_) {
+ external_scores[i] += e;
}
}
}
@@ -320,8 +397,6 @@ void CBetaScorer::Score(const loop::BackboneList& bb_list,
void CBetaScorer::AttachEnvironment(BackboneScoreEnv& env) {
env_ = env.UniqueListener<CBetaEnvListener>("CBetaEnvListener");
- idx_handler_ = env.GetIdxHandlerData();
- attached_environment_ = true;
}
}}
diff --git a/scoring/src/cbeta_score.hh b/scoring/src/cbeta_score.hh
index 78bbf9c34c4f9a219169238161ec51c542e2f63e..c2686975efc7e187710954e1d3d32952c35134b2 100644
--- a/scoring/src/cbeta_score.hh
+++ b/scoring/src/cbeta_score.hh
@@ -31,33 +31,45 @@ public:
void SetEnergy(ost::conop::AminoAcid a, ost::conop::AminoAcid b, uint bin,
Real e);
- virtual Real CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum,
+ void DoInternalScores(bool do_it) { do_internal_scores_ = do_it; }
+
+ void DoExternalScores(bool do_it) { do_external_scores_ = do_it; }
+
+ void DoNormalize(bool do_it) { normalize_ = do_it; }
+
+ virtual Real CalculateScore(uint start_resnum, uint num_residues,
uint chain_idx) const;
- virtual void CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum,
+ virtual void CalculateScoreProfile(uint start_resnum,
+ uint num_residues,
uint chain_idx,
std::vector<Real>& profile) const;
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const;
+
void AttachEnvironment(BackboneScoreEnv& env);
private:
- CBetaScorer(): attached_environment_(false), env_(NULL) { }
+ CBetaScorer(): do_internal_scores_(true), do_external_scores_(true),
+ normalize_(true), env_(NULL) { }
inline uint EIdx(ost::conop::AminoAcid a, ost::conop::AminoAcid b,
uint bin) const {
return (a * ost::conop::XXX + b) * bins_ + bin;
}
- void Score(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx,
- std::vector<Real>& scores,
+ void Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
std::vector<Real>& internal_scores,
- std::vector<uint>& counts,
- std::vector<uint>& internal_counts) const;
+ std::vector<bool>& occupied) const;
// portable serialization (only stores data relevant for Load/Save!)
// (cleanly element by element with fixed-width base-types)
@@ -77,12 +89,13 @@ private:
uint bins_;
uint seq_sep_;
Real* energies_;
+ bool do_internal_scores_;
+ bool do_external_scores_;
+ bool normalize_;
//environment specific information, that will be set upon calling
//AttachEnvironment
- bool attached_environment_;
CBetaEnvListener* env_;
- const loop::IdxHandler* idx_handler_;
};
diff --git a/scoring/src/clash_env_listener.cc b/scoring/src/clash_env_listener.cc
index 287bcecef49150b7050b46c22672cbcc2806a520..3bf1c656436207a3eb23c2d551d83cb9ed7fe838 100644
--- a/scoring/src/clash_env_listener.cc
+++ b/scoring/src/clash_env_listener.cc
@@ -7,7 +7,10 @@ ClashEnvListener::ClashEnvListener(): env_(8.0),
env_data_(NULL) { }
ClashEnvListener::~ClashEnvListener() {
- if (env_data_ != NULL) delete [] env_data_;
+ if (env_data_ != NULL) {
+ delete [] is_glycine_;
+ delete [] env_data_;
+ }
}
void ClashEnvListener::Init(const BackboneScoreEnv& base_env) {
@@ -18,133 +21,131 @@ void ClashEnvListener::Init(const BackboneScoreEnv& base_env) {
if (env_data_ != NULL) {
// the env listener has already been initialized at some point...
// let's clean up first...
+ delete [] is_glycine_;
delete [] env_data_;
env_data_ = NULL;
env_.Clear();
}
- const loop::IdxHandler* idx_handler = base_env.GetIdxHandlerData();
- uint num_residues = idx_handler->GetNumResidues();
+ idx_handler_ = base_env.GetIdxHandlerData();
+ env_set_ = base_env.GetEnvSetData();
+ n_pos_data_ = base_env.GetNPosData();
+ ca_pos_data_ = base_env.GetCAPosData();
+ c_pos_data_ = base_env.GetCPosData();
+ o_pos_data_ = base_env.GetOPosData();
+ cb_pos_data_ = base_env.GetCBPosData();
+ aa_data_ = base_env.GetAAData();
+
+ uint num_residues = idx_handler_->GetNumResidues();
+
env_data_ = new ClashSpatialOrganizerItem[5*num_residues];
+ is_glycine_ = new bool[num_residues];
for (uint i = 0; i < num_residues; ++i) {
// N
- env_data_[5*i ].clash_type = CLASH_N;
+ env_data_[5*i ].clash_type = BB_CLASH_N;
env_data_[5*i ].idx = i;
// CA
- env_data_[5*i+1].clash_type = CLASH_C;
+ env_data_[5*i+1].clash_type = BB_CLASH_C;
env_data_[5*i+1].idx = i;
// C
- env_data_[5*i+2].clash_type = CLASH_C;
+ env_data_[5*i+2].clash_type = BB_CLASH_C;
env_data_[5*i+2].idx = i;
// O
- env_data_[5*i+3].clash_type = CLASH_O;
+ env_data_[5*i+3].clash_type = BB_CLASH_O;
env_data_[5*i+3].idx = i;
// CB
- env_data_[5*i+4].clash_type = CLASH_C;
+ env_data_[5*i+4].clash_type = BB_CLASH_C;
env_data_[5*i+4].idx = i;
+
+ if(aa_data_[i] == ost::conop::GLY) {
+ is_glycine_[i] = true;
+ }
+ else {
+ is_glycine_[i] = false;
+ }
}
}
-void ClashEnvListener::SetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void ClashEnvListener::SetEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"ClashEnvListener::SetEnvironment", 2);
-
- const geom::Vec3* n_pos_data = base_env.GetNPosData();
- const geom::Vec3* ca_pos_data = base_env.GetCAPosData();
- const geom::Vec3* c_pos_data = base_env.GetCPosData();
- const geom::Vec3* o_pos_data = base_env.GetOPosData();
- const geom::Vec3* cb_pos_data = base_env.GetCBPosData();
- const ost::conop::AminoAcid* aa_data = base_env.GetAAData();
-
geom::Vec3 pos;
for (std::vector<uint>::const_iterator i = idx.begin();
i != idx.end(); ++i) {
// N
- pos = n_pos_data[*i];
+ pos = n_pos_data_[*i];
env_data_[5*(*i)].pos = pos;
env_.Add(&env_data_[5*(*i)], pos);
// CA
- pos = ca_pos_data[*i];
+ pos = ca_pos_data_[*i];
env_data_[5*(*i)+1].pos = pos;
env_.Add(&env_data_[5*(*i)+1], pos);
// C
- pos = c_pos_data[*i];
+ pos = c_pos_data_[*i];
env_data_[5*(*i)+2].pos = pos;
env_.Add(&env_data_[5*(*i)+2], pos);
// O
- pos = o_pos_data[*i];
+ pos = o_pos_data_[*i];
env_data_[5*(*i)+3].pos = pos;
env_.Add(&env_data_[5*(*i)+3], pos);
// CB (if necessary)
- if (aa_data[*i] != ost::conop::GLY) {
- pos = cb_pos_data[*i];
+ if (aa_data_[*i] != ost::conop::GLY) {
+ pos = cb_pos_data_[*i];
env_data_[5*(*i)+4].pos = pos;
env_.Add(&env_data_[5*(*i)+4], pos);
}
}
}
-void ClashEnvListener::ResetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void ClashEnvListener::ResetEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"ClashEnvListener::ResetEnvironment", 2);
- const geom::Vec3* n_pos_data = base_env.GetNPosData();
- const geom::Vec3* ca_pos_data = base_env.GetCAPosData();
- const geom::Vec3* c_pos_data = base_env.GetCPosData();
- const geom::Vec3* o_pos_data = base_env.GetOPosData();
- const geom::Vec3* cb_pos_data = base_env.GetCBPosData();
- const ost::conop::AminoAcid* aa_data = base_env.GetAAData();
-
geom::Vec3 pos, old_pos;
for (std::vector<uint>::const_iterator i = idx.begin();
i != idx.end(); ++i) {
// N
old_pos = env_data_[5*(*i)].pos;
- pos = n_pos_data[*i];
+ pos = n_pos_data_[*i];
env_data_[5*(*i)].pos = pos;
env_.Reset(&env_data_[5*(*i)], old_pos, pos);
// CA
old_pos = env_data_[5*(*i)+1].pos;
- pos = ca_pos_data[*i];
+ pos = ca_pos_data_[*i];
env_data_[5*(*i)+1].pos = pos;
env_.Reset(&env_data_[5*(*i)+1], old_pos, pos);
// C
old_pos = env_data_[5*(*i)+2].pos;
- pos = c_pos_data[*i];
+ pos = c_pos_data_[*i];
env_data_[5*(*i)+2].pos = pos;
env_.Reset(&env_data_[5*(*i)+2], old_pos, pos);
// O
old_pos = env_data_[5*(*i)+3].pos;
- pos = o_pos_data[*i];
+ pos = o_pos_data_[*i];
env_data_[5*(*i)+3].pos = pos;
env_.Reset(&env_data_[5*(*i)+3], old_pos, pos);
// CB (if necessary)
- if (aa_data[*i] != ost::conop::GLY) {
+ if (aa_data_[*i] != ost::conop::GLY) {
old_pos = env_data_[5*(*i)+4].pos;
- pos = cb_pos_data[*i];
+ pos = cb_pos_data_[*i];
env_data_[5*(*i)+4].pos = pos;
env_.Reset(&env_data_[5*(*i)+4], old_pos, pos);
}
}
}
-void ClashEnvListener::ClearEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void ClashEnvListener::ClearEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"ClashEnvListener::ClearEnvironment", 2);
- const ost::conop::AminoAcid* aa_data = base_env.GetAAData();
-
for (std::vector<uint>::const_iterator i = idx.begin();
i != idx.end(); ++i) {
- uint num_clash_items = (aa_data[*i] != ost::conop::GLY) ? 5 : 4;
+ uint num_clash_items = (aa_data_[*i] != ost::conop::GLY) ? 5 : 4;
for (uint j = 0; j < num_clash_items; ++j) {
env_.Remove(&env_data_[5*(*i)+j], env_data_[5*(*i)+j].pos);
}
diff --git a/scoring/src/clash_env_listener.hh b/scoring/src/clash_env_listener.hh
index 686001134af9695a757b5515317e023a873e7174..cb4ee362b1d30c99823e6e3517879a7c56103fa7 100644
--- a/scoring/src/clash_env_listener.hh
+++ b/scoring/src/clash_env_listener.hh
@@ -6,18 +6,19 @@
namespace promod3 { namespace scoring {
-enum ClashType {
- CLASH_C,
- CLASH_N,
- CLASH_O
+enum BBClashType {
+ BB_CLASH_C,
+ BB_CLASH_N,
+ BB_CLASH_O,
+ BB_CLASH_NUM
};
struct ClashSpatialOrganizerItem {
ClashSpatialOrganizerItem() { }
- ClashSpatialOrganizerItem(ClashType type, const geom::Vec3& p, uint i)
+ ClashSpatialOrganizerItem(BBClashType type, const geom::Vec3& p, uint i)
: clash_type(type), pos(p), idx(i) { }
- ClashType clash_type;
+ BBClashType clash_type;
geom::Vec3 pos;
uint idx;
};
@@ -35,14 +36,11 @@ public:
virtual void Init(const BackboneScoreEnv& base_env);
- virtual void SetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void SetEnvironment(const std::vector<uint>& idx);
- virtual void ResetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void ResetEnvironment(const std::vector<uint>& idx);
- virtual void ClearEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void ClearEnvironment(const std::vector<uint>& idx);
virtual String WhoAmI() const { return "ClashEnvListener"; }
@@ -51,11 +49,31 @@ public:
return env_.FindWithin(pos, cutoff);
}
+ const int* GetEnvSetData() { return env_set_; }
+
+ const loop::IdxHandler* GetIdxHandler() { return idx_handler_; }
+
+ // for internal use in the actual scorer to access required per residue data
+ // NO RANGE CHECK!
+ ClashSpatialOrganizerItem* GetParticleData(uint idx) { return &env_data_[5*idx]; };
+ bool IsGlycine(uint idx) { return is_glycine_[idx]; }
+
private:
ClashSpatialOrganizer env_;
// here: 5 atoms stored for each index: use env_data_[5*idx + sub_idx]
+ bool* is_glycine_;
ClashSpatialOrganizerItem* env_data_;
+
+ // data ptrs fetched from base env at initialization
+ const int* env_set_;
+ const loop::IdxHandler* idx_handler_;
+ const geom::Vec3* n_pos_data_;
+ const geom::Vec3* ca_pos_data_;
+ const geom::Vec3* c_pos_data_;
+ const geom::Vec3* o_pos_data_;
+ const geom::Vec3* cb_pos_data_;
+ const ost::conop::AminoAcid* aa_data_;
};
}} //ns
diff --git a/scoring/src/clash_score.cc b/scoring/src/clash_score.cc
index dc0ab88e8aeeeb7015c5b088fa2ab4d3228b9d1b..c7c2849124252180da3e5af0f76a4b63dc4f632f 100644
--- a/scoring/src/clash_score.cc
+++ b/scoring/src/clash_score.cc
@@ -1,384 +1,255 @@
#include <promod3/scoring/clash_score.hh>
+#include <promod3/scoring/scwrl3_energy_functions.hh>
namespace promod3 { namespace scoring {
-namespace {
-// LOOK UP TABLES
-const uint MAX_CLASH_BIN = 320;
-const Real CLASH_BIN_SIZE = 1.0 / 100.0;
-const uint CLASH_BINS_PER_A = 100;
-
-const Real CLASH_SCORE_26[321] = {
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,9.91263461538,9.69235384615,9.47207307692,
- 9.25179230769,9.03151153846,8.81123076923,8.59095,8.37066923077,
- 8.15038846154,7.93010769231,7.70982692308,7.48954615385,7.26926538462,
- 7.04898461538,6.82870384615,6.60842307692,6.38814230769,6.16786153846,
- 5.94758076923,5.7273,5.50701923077,5.28673846154,5.06645769231,
- 4.84617692308,4.62589615385,4.40561538462,4.18533461538,3.96505384615,
- 3.74477307692,3.52449230769,3.30421153846,3.08393076923,2.86365,
- 2.64336923077,2.42308846154,2.20280769231,1.98252692308,1.76224615385,
- 1.54196538462,1.32168461538,1.10140384615,0.881123076923,0.660842307693,
- 0.440561538462,0.220280769231,2.54343213157e-13,0.0,0.0,0.0,0.0,0.0,0.0,0.0,
- 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,
- 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,
- 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0};
-
-const Real CLASH_SCORE_29[321] = {
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 9.87465517241,9.67716206897,9.47966896552,9.28217586207,9.08468275862,
- 8.88718965517,8.68969655172,8.49220344828,8.29471034483,8.09721724138,
- 7.89972413793,7.70223103448,7.50473793103,7.30724482759,7.10975172414,
- 6.91225862069,6.71476551724,6.51727241379,6.31977931035,6.1222862069,
- 5.92479310345,5.7273,5.52980689655,5.3323137931,5.13482068966,4.93732758621,
- 4.73983448276,4.54234137931,4.34484827586,4.14735517241,3.94986206897,
- 3.75236896552,3.55487586207,3.35738275862,3.15988965517,2.96239655172,
- 2.76490344828,2.56741034483,2.36991724138,2.17242413793,1.97493103448,
- 1.77743793103,1.57994482759,1.38245172414,1.18495862069,0.987465517242,
- 0.789972413793,0.592479310345,0.394986206897,0.197493103449,3.49721918091e-13,
- 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,
- 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0};
-
-const Real CLASH_SCORE_32[321] = {
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,
- 10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,10.0,9.843796875,9.66481875,
- 9.485840625,9.3068625,9.127884375,8.94890625,8.769928125,8.59095,8.411971875,
- 8.23299375,8.054015625,7.8750375,7.696059375,7.51708125,7.338103125,7.159125,
- 6.980146875,6.80116875,6.622190625,6.4432125,6.264234375,6.08525625,
- 5.906278125,5.7273,5.548321875,5.36934375,5.190365625,5.0113875,4.832409375,
- 4.65343125,4.474453125,4.295475,4.116496875,3.93751875,3.758540625,3.5795625,
- 3.400584375,3.22160625,3.042628125,2.86365,2.684671875,2.50569375,2.326715625,
- 2.1477375,1.968759375,1.78978125,1.610803125,1.431825,1.252846875,1.07386875,
- 0.894890625,0.7159125,0.536934375,0.35795625,0.178978125,0.0};
-
-const Real* CLASH_SCORES[3][3] = {{CLASH_SCORE_32,CLASH_SCORE_29,CLASH_SCORE_29},
- {CLASH_SCORE_29,CLASH_SCORE_26,CLASH_SCORE_26},
- {CLASH_SCORE_29,CLASH_SCORE_26,CLASH_SCORE_26}};
-
-} // anon ns
-
-
-Real ClashScorer::CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const {
-
- promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "ClashScorer::CalculateScore", 2);
+ClashScorer::ClashScorer(): do_internal_scores_(true),
+ do_external_scores_(true),
+ normalize_(true),
+ env_(NULL) {
- std::vector<Real> scores;
- std::vector<Real> internal_scores;
+ for(uint i = 0; i < BB_CLASH_NUM; ++i) {
+ for(uint j = 0; j < BB_CLASH_NUM; ++j) {
+ clash_scores_[i][j] = new Real[bins_];
+ }
+ }
+
+ // setup radii
+ Real radius[BB_CLASH_NUM] = {1.6, 1.3, 1.3};
+
+ // estimate clash scores
+ for(uint i = 0; i < BB_CLASH_NUM; ++i) {
+ for(uint j = i; j < BB_CLASH_NUM; ++j) {
+ const Real Rij = radius[i] + radius[j];
+ for(uint bin = 0; bin < bins_; ++bin) {
+ Real d = static_cast<Real>(bin) / bins_per_a_;
+ clash_scores_[i][j][bin] = SCWRL3PairwiseScore(d, Rij);
+ }
+ if(i != j) {
+ memcpy(clash_scores_[j][i], clash_scores_[i][j], bins_ * sizeof(Real));
+ }
+ }
+ }
+}
- this->Score(bb_list, start_resnum, chain_idx, scores, internal_scores);
- Real score = 0.0;
+ClashScorer::~ClashScorer() {
+ for(uint i = 0; i < BB_CLASH_NUM; ++i) {
+ for(uint j = 0; j < BB_CLASH_NUM; ++j) {
+ delete [] clash_scores_[i][j];
+ }
+ }
+}
+
+
+Real ClashScorer::CalculateScore(uint start_resnum, uint num_residues,
+ uint chain_idx) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "ClashScorer::CalculateScore", 2);
- for(uint i = 0; i < scores.size(); ++i){
- score += scores[i];
+ if (env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
}
+ // setup
+ std::vector<uint> idx_vector;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vector,
+ occupied);
+
+ // get scores
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ this->Score(idx_vector, external_scores, internal_scores, occupied);
+
+ Real external_score = 0.0;
Real internal_score = 0.0;
- for(uint i = 0; i < internal_scores.size(); ++i){
+ for(uint i = 0; i < external_scores.size(); ++i) {
+ external_score += external_scores[i];
internal_score += internal_scores[i];
}
- score += (0.5 * internal_score);
+ // all interactions in internal score have been observed twice!
+ external_score += Real(0.5)*internal_score;
- if(!scores.empty()){
- score /= scores.size();
+ if(normalize_ && ! external_scores.empty()) {
+ external_score /= external_scores.size();
}
-
- return score;
+
+ return external_score;
}
-void ClashScorer::CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
+void ClashScorer::CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
std::vector<Real>& profile) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"ClashScorer::CalculateScoreProfile", 2);
- std::vector<Real> scores;
- std::vector<Real> internal_scores;
+ if (env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
- this->Score(bb_list, start_resnum, chain_idx, scores, internal_scores);
+ // setup
+ std::vector<uint> idx_vector;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vector,
+ occupied);
+
+ // get scores
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ this->Score(idx_vector, external_scores, internal_scores, occupied);
- profile.clear();
- for(uint i = 0; i < scores.size(); ++i){
- profile.push_back(scores[i] + internal_scores[i]);
+ profile.resize(external_scores.size());
+ for(uint i = 0; i < external_scores.size(); ++i) {
+ profile[i] = external_scores[i] + internal_scores[i];
}
}
-void ClashScorer::Score(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
- std::vector<Real>& scores,
- std::vector<Real>& internal_scores) const {
+Real ClashScorer::CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "ClashScorer::Score", 2);
+ "ClashScorer::CalculateScore", 2);
+
+ if (env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
// setup
- if (!attached_environment_) {
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores and sum them up
+ Real external_score = 0.0;
+ Real internal_score = 0.0;
+ uint n_scored_residues = 0;
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ this->Score(indices_vec[i], external_scores, internal_scores, occupied);
+ for (uint j = 0; j < external_scores.size(); ++j) {
+ external_score += external_scores[j];
+ internal_score += internal_scores[j];
+ }
+ n_scored_residues += external_scores.size();
+ }
+
+ // all interactions in internal_score have been observed twice!
+ external_score += Real(0.5)*internal_score;
+
+ if(normalize_ && n_scored_residues > 0) {
+ external_score /= n_scored_residues;
+ }
+
+ return external_score;
+}
+
+
+void ClashScorer::CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "ClashScorer::CalculateScore", 2);
+
+ if (env_ == NULL) {
String err = "Can only calculate score when environment is attached!";
throw promod3::Error(err);
}
- uint bb_list_size, start_idx, end_idx;
- idx_handler_->SetupScoreCalculation(bb_list, start_resnum, chain_idx,
- bb_list_size, start_idx, end_idx);
-
- // setup result
- scores.assign(bb_list_size, 0.0);
- internal_scores.assign(bb_list_size, 0.0);
- if (bb_list_size == 0) return;
-
- // let's precalculate the idx ranges we have to neglect
- int min_idx_chain = idx_handler_->GetChainStartIdx(chain_idx);
- int max_idx_chain = min_idx_chain + idx_handler_->GetChainSize(chain_idx) - 1;
- std::vector<int> start_neglect(bb_list_size, start_idx);
- std::vector<int> end_neglect(bb_list_size, end_idx);
- // we use a fixed seq. separation of 2 residues
- const uint seq_sep = 2;
- int neglect_range = int(seq_sep) - 1;
- int max_i = std::min(neglect_range, static_cast<int>(bb_list_size));
- for (int i = 0; i < max_i; ++i) {
- start_neglect[i] =
- std::max(min_idx_chain, start_neglect[i]-(neglect_range-i));
- end_neglect[bb_list_size-1-i] =
- std::min(max_idx_chain, end_neglect[i]+(neglect_range-i));
+
+ // setup
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores
+ profile.resize(start_resnum.size());
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ std::vector<Real>& current_profile = profile[i];
+ this->Score(indices_vec[i], current_profile, internal_scores, occupied);
+ for (uint j = 0; j < current_profile.size(); ++j) {
+ current_profile[j] += internal_scores[j];
+
+ }
}
+}
+
+
+void ClashScorer::Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
+ std::vector<Real>& internal_scores,
+ std::vector<bool>& occupied) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "ClashScorer::Score", 2);
+
+ // setup
+
+ uint n_indices = indices.size();
- // get scores to environment
+ external_scores.assign(n_indices, 0.0);
+ internal_scores.assign(n_indices, 0.0);
+
+ if(n_indices == 0) return;
+
+ uint seq_sep = 2;
uint bin;
+ Real score;
+ const int* env_set = env_->GetEnvSetData();
+
// let's go over every loop residue
ClashSpatialOrganizer::WithinResult within_result;
std::pair<ClashSpatialOrganizerItem*,Real>* a;
- for (uint i = 0; i < bb_list_size; ++i) {
- // N
- within_result = env_->FindWithin(bb_list.GetN(i), 2.9);
- a = within_result.first;
- for (uint j = 0; j < within_result.second; ++j) {
- const int my_idx = int(a[j].first->idx);
- if (my_idx < start_neglect[i] || my_idx > end_neglect[i]) {
- bin = a[j].second * CLASH_BINS_PER_A;
- bin = (bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN;
- scores[i] += CLASH_SCORES[CLASH_N][a[j].first->clash_type][bin];
- }
- }
- // CA
- within_result = env_->FindWithin(bb_list.GetCA(i), 3.2);
- a = within_result.first;
- for (uint j = 0; j < within_result.second; ++j) {
- const int my_idx = int(a[j].first->idx);
- if (my_idx < start_neglect[i] || my_idx > end_neglect[i]) {
- bin = a[j].second * CLASH_BINS_PER_A;
- bin = (bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN;
- scores[i] += CLASH_SCORES[CLASH_C][a[j].first->clash_type][bin];
- }
- }
- // C
- within_result = env_->FindWithin(bb_list.GetC(i), 3.2);
- a = within_result.first;
- for (uint j = 0; j < within_result.second; ++j) {
- const int my_idx = int(a[j].first->idx);
- if (my_idx < start_neglect[i] || my_idx > end_neglect[i]) {
- bin = a[j].second * CLASH_BINS_PER_A;
- bin = (bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN;
- scores[i] += CLASH_SCORES[CLASH_C][a[j].first->clash_type][bin];
- }
- }
- // O
- within_result = env_->FindWithin(bb_list.GetO(i), 2.9);
- a = within_result.first;
- for (uint j = 0; j < within_result.second; ++j) {
- const int my_idx = int(a[j].first->idx);
- if (my_idx < start_neglect[i] || my_idx > end_neglect[i]) {
- bin = a[j].second * CLASH_BINS_PER_A;
- bin = (bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN;
- scores[i] += CLASH_SCORES[CLASH_O][a[j].first->clash_type][bin];
- }
+
+ for (uint i = 0; i < n_indices; ++i) {
+ int my_idx = indices[i];
+
+ if(!env_set[my_idx]) {
+ throw promod3::Error("Must set environment before scoring!");
}
- // CB (if needed)
- if (bb_list.GetAA(i) != ost::conop::GLY) {
- within_result = env_->FindWithin(bb_list.GetCB(i), 3.2);
+
+ uint n_particles = env_->IsGlycine(my_idx) ? 4 : 5;
+ ClashSpatialOrganizerItem* particle_data = env_->GetParticleData(my_idx);
+
+ for(uint j = 0; j < n_particles; ++j) {
+ int clash_type = particle_data[j].clash_type;
+ within_result = env_->FindWithin(particle_data[j].pos, 3.2);
a = within_result.first;
- for (uint j = 0; j < within_result.second; ++j) {
- const int my_idx = int(a[j].first->idx);
- if (my_idx < start_neglect[i] || my_idx > end_neglect[i]) {
- bin = a[j].second * CLASH_BINS_PER_A;
- bin = (bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN;
- scores[i] += CLASH_SCORES[CLASH_C][a[j].first->clash_type][bin];
- }
- }
- }
- }
- // skip stuff below if BB list too small
- if (bb_list_size <= seq_sep) return;
-
- // get internal scores -> N^2 loop
- Real clash_score;
- Real d;
- for (uint i = 0; i < bb_list_size-seq_sep; ++i) {
- // do not consider neighbours
- for (uint j = i+seq_sep; j < bb_list_size; ++j) {
- // skip this residue-residue interaction if ca-distance is above 7A
- d = geom::Length2(bb_list.GetCA(i) - bb_list.GetCA(j));
- if (d > Real(49)) continue;
-
- bin = std::sqrt(d) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_32[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetCA(i), bb_list.GetN(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_29[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetCA(i), bb_list.GetC(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_32[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetCA(i), bb_list.GetO(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_29[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
-
- bin = geom::Distance(bb_list.GetN(i), bb_list.GetN(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_26[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetN(i), bb_list.GetCA(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_29[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetN(i), bb_list.GetC(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_29[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetN(i), bb_list.GetO(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_26[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
-
- bin = geom::Distance(bb_list.GetC(i), bb_list.GetN(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_29[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetC(i), bb_list.GetCA(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_32[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetC(i), bb_list.GetC(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_32[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetC(i), bb_list.GetO(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_29[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
-
- bin = geom::Distance(bb_list.GetO(i), bb_list.GetN(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_26[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetO(i), bb_list.GetCA(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_29[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetO(i), bb_list.GetC(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_29[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetO(i), bb_list.GetO(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_26[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
-
- if (bb_list.GetAA(i) != ost::conop::GLY) {
- bin = geom::Distance(bb_list.GetCB(i), bb_list.GetN(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_29[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetCB(i), bb_list.GetCA(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_32[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetCB(i), bb_list.GetC(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_32[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetCB(i), bb_list.GetO(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_29[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- }
+ for(uint k = 0; k < within_result.second; ++k) {
+ int other_idx = int(a[k].first->idx);
+
+ if(std::abs(my_idx - other_idx) >= seq_sep) {
+ bin = a[k].second * bins_per_a_;
+ score = clash_scores_[clash_type][a[k].first->clash_type][bin];
+
+ if(occupied[other_idx] && do_internal_scores_) {
+ internal_scores[i] += score;
+ }
- if (bb_list.GetAA(j) != ost::conop::GLY) {
- bin = geom::Distance(bb_list.GetN(i), bb_list.GetCB(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_29[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetCA(i), bb_list.GetCB(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_32[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetC(i), bb_list.GetCB(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_32[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- bin = geom::Distance(bb_list.GetO(i), bb_list.GetCB(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_29[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
- if (bb_list.GetAA(i) != ost::conop::GLY) {
- bin = geom::Distance(bb_list.GetCB(i), bb_list.GetCB(j)) * CLASH_BINS_PER_A;
- clash_score = CLASH_SCORE_32[(bin<MAX_CLASH_BIN) ? bin : MAX_CLASH_BIN];
- internal_scores[i] += clash_score;
- internal_scores[j] += clash_score;
+ if(!occupied[other_idx] && do_external_scores_) {
+ external_scores[i] += score;
+ }
}
}
}
@@ -387,8 +258,6 @@ void ClashScorer::Score(const loop::BackboneList& bb_list,
void ClashScorer::AttachEnvironment(BackboneScoreEnv& env) {
env_ = env.UniqueListener<ClashEnvListener>("ClashEnvListener");
- idx_handler_ = env.GetIdxHandlerData();
- attached_environment_ = true;
}
}}
diff --git a/scoring/src/clash_score.hh b/scoring/src/clash_score.hh
index 07f15a006b7dcfe00aa66e20aae9dde98082ff22..2a06194ca6bb549c887f362bcb18641dc132511c 100644
--- a/scoring/src/clash_score.hh
+++ b/scoring/src/clash_score.hh
@@ -11,38 +11,58 @@ namespace promod3 { namespace scoring {
class ClashScorer;
typedef boost::shared_ptr<ClashScorer> ClashScorerPtr;
-
class ClashScorer : public BackboneScorer {
public:
- ClashScorer(): attached_environment_(false), env_(NULL) { }
+ ClashScorer();
+
+ ~ClashScorer();
+
+ void DoInternalScores(bool do_it) { do_internal_scores_ = do_it; }
+
+ void DoExternalScores(bool do_it) { do_external_scores_ = do_it; }
+ void DoNormalize(bool do_it) { normalize_ = do_it; }
- virtual Real CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum,
+ virtual Real CalculateScore(uint start_resnum,
+ uint num_residues,
uint chain_idx) const;
- virtual void CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum,
+ virtual void CalculateScoreProfile(uint start_resnum,
+ uint num_residues,
uint chain_idx,
std::vector<Real>& profile) const;
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const;
+
void AttachEnvironment(BackboneScoreEnv& env);
private:
- void Score(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx,
- std::vector<Real>& scores,
- std::vector<Real>& internal_scores) const;
-
+ void Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
+ std::vector<Real>& internal_scores,
+ std::vector<bool>& occupied) const;
+
+ // hard coded bounds (safe for dist. < 3.21A)
+ static const uint bins_ = 321;
+ static const uint bins_per_a_ = 100;
+ Real* clash_scores_[BB_CLASH_NUM][BB_CLASH_NUM];
+ bool do_internal_scores_;
+ bool do_external_scores_;
+ bool normalize_;
+
//environment specific information, that will be set upon calling
//AttachEnvironment
- bool attached_environment_;
ClashEnvListener* env_;
- const loop::IdxHandler* idx_handler_;
};
diff --git a/scoring/src/density_score.cc b/scoring/src/density_score.cc
index 8a8c77aa7816db5afcce9aaa785b713f1e0d2bcb..803a843b68e1dd8396d27b3cd67ef916c5232649 100644
--- a/scoring/src/density_score.cc
+++ b/scoring/src/density_score.cc
@@ -2,28 +2,14 @@
namespace promod3{ namespace scoring{
-Real DensityScorer::CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const {
- promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "DensityScorer::CalculateScore", 2);
-
-
- if (!attached_environment_) {
- String err = "Can only calculate score when environment is attached!";
- throw promod3::Error(err);
- }
-
- if(!map_data_->map.IsValid()){
- String err = "Environment attached to density scorer must have a valid ";
- err += "density map for score calculation!";
- throw promod3::Error(err);
- }
+Real DensityScore(const loop::BackboneList& bb_list, ost::img::MapHandle& map,
+ Real resolution, bool all_atom) {
geom::AlignedCuboid bounding_box = bb_list.GetBounds(true);
geom::Vec3 min = bounding_box.GetMin();
geom::Vec3 max = bounding_box.GetMax();
- geom::Vec3 sampling = map_data_->map.GetSpatialSampling();
+ geom::Vec3 sampling = map.GetSpatialSampling();
//thats the extend of the image we're actually interested in
uint x_extent = std::ceil((max[0] - min[0]) / sampling[0]);
@@ -31,9 +17,9 @@ Real DensityScorer::CalculateScore(const loop::BackboneList& bb_list,
uint z_extent = std::ceil((max[2] - min[2]) / sampling[2]);
//let's enlarge a bit...
- Real x_overlap = Real(2 * map_data_->resolution) / sampling[0];
- Real y_overlap = Real(2 * map_data_->resolution) / sampling[1];
- Real z_overlap = Real(2 * map_data_->resolution) / sampling[2];
+ Real x_overlap = Real(2 * resolution) / sampling[0];
+ Real y_overlap = Real(2 * resolution) / sampling[1];
+ Real z_overlap = Real(2 * resolution) / sampling[2];
x_extent += static_cast<uint>(2 * x_overlap);
y_extent += static_cast<uint>(2 * y_overlap);
z_extent += static_cast<uint>(2 * z_overlap);
@@ -46,20 +32,19 @@ Real DensityScorer::CalculateScore(const loop::BackboneList& bb_list,
ost::img::MapHandle bb_list_map = ost::img::CreateImage(s);
bb_list_map.SetSpatialSampling(sampling);
- geom::Vec3 pixel_coord = map_data_->map.CoordToIndex(min -
- geom::Vec3(x_overlap,
- y_overlap,
- z_overlap));
+ geom::Vec3 pixel_coord = map.CoordToIndex(min - geom::Vec3(x_overlap,
+ y_overlap,
+ z_overlap));
ost::img::Point rounded_pixel_coord(round(pixel_coord[0]),
round(pixel_coord[1]),
round(pixel_coord[2]));
- min = map_data_->map.IndexToCoord(rounded_pixel_coord);
+ min = map.IndexToCoord(rounded_pixel_coord);
bb_list_map.SetAbsoluteOrigin(min);
//let's fill the density of the BackboneList
- bb_list.InsertInto(bb_list_map, map_data_->resolution, map_data_->all_atom);
+ bb_list.InsertInto(bb_list_map, resolution, all_atom);
uint num_voxels = (s[0] * s[1] * s[2]);
@@ -74,164 +59,13 @@ Real DensityScorer::CalculateScore(const loop::BackboneList& bb_list,
p = ost::img::Point(i,j,k);
p_orig = p + rounded_pixel_coord;
//will return 0.0 if outside of map
- map_values[vec_position] = map_data_->map.GetReal(p_orig);
+ map_values[vec_position] = map.GetReal(p_orig);
bb_list_values[vec_position] = bb_list_map.GetReal(p);
++vec_position;
}
}
}
- return this->Correlate(map_values, bb_list_values, num_voxels);
-}
-
-
-void DensityScorer::CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
- std::vector<Real>& profile) const{
-
- promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "DensityScorer::CalculateScore", 2);
-
-
- if (!attached_environment_) {
- String err = "Can only calculate score when environment is attached!";
- throw promod3::Error(err);
- }
-
- if(!map_data_->map.IsValid()){
- String err = "Environment attached to density scorer must have a valid ";
- err += "density map for score calculation!";
- throw promod3::Error(err);
- }
-
- geom::Vec3 sampling = map_data_->map.GetSpatialSampling();
- Real x_overlap = Real(2 * map_data_->resolution) / sampling[0];
- Real y_overlap = Real(2 * map_data_->resolution) / sampling[1];
- Real z_overlap = Real(2 * map_data_->resolution) / sampling[2];
-
- profile.clear();
- for(uint res_idx = 0; res_idx < bb_list.size(); ++res_idx){
-
- //we have to calculate the bounding box for a single residue manually
-
- Real min_x = std::numeric_limits<Real>::max();
- Real max_x = -std::numeric_limits<Real>::max();
- Real min_y = std::numeric_limits<Real>::max();
- Real max_y = -std::numeric_limits<Real>::max();
- Real min_z = std::numeric_limits<Real>::max();
- Real max_z = -std::numeric_limits<Real>::max();
-
- geom::Vec3 pos;
- pos = bb_list.GetN(res_idx);
- min_x = std::min(pos[0], min_x);
- max_x = std::max(pos[0], max_x);
- min_y = std::min(pos[1], min_y);
- max_y = std::max(pos[1], max_y);
- min_z = std::min(pos[2], min_z);
- max_z = std::max(pos[2], max_z);
-
- pos = bb_list.GetCA(res_idx);
- min_x = std::min(pos[0], min_x);
- max_x = std::max(pos[0], max_x);
- min_y = std::min(pos[1], min_y);
- max_y = std::max(pos[1], max_y);
- min_z = std::min(pos[2], min_z);
- max_z = std::max(pos[2], max_z);
-
- if (bb_list.GetAA(res_idx) != ost::conop::GLY) {
- pos = bb_list.GetCB(res_idx);
- min_x = std::min(pos[0], min_x);
- max_x = std::max(pos[0], max_x);
- min_y = std::min(pos[1], min_y);
- max_y = std::max(pos[1], max_y);
- min_z = std::min(pos[2], min_z);
- max_z = std::max(pos[2], max_z);
- }
-
- pos = bb_list.GetC(res_idx);
- min_x = std::min(pos[0], min_x);
- max_x = std::max(pos[0], max_x);
- min_y = std::min(pos[1], min_y);
- max_y = std::max(pos[1], max_y);
- min_z = std::min(pos[2], min_z);
- max_z = std::max(pos[2], max_z);
-
- pos = bb_list.GetO(res_idx);
- min_x = std::min(pos[0], min_x);
- max_x = std::max(pos[0], max_x);
- min_y = std::min(pos[1], min_y);
- max_y = std::max(pos[1], max_y);
- min_z = std::min(pos[2], min_z);
- max_z = std::max(pos[2], max_z);
-
- //thats the extend of the image we're actually interested in
- uint x_extent = std::ceil((max_x - min_x) / sampling[0]);
- uint y_extent = std::ceil((max_y - min_y) / sampling[1]);
- uint z_extent = std::ceil((max_z - min_z) / sampling[2]);
-
- //let's enlarge a bit...
- x_extent += static_cast<uint>(2 * x_overlap);
- y_extent += static_cast<uint>(2 * y_overlap);
- z_extent += static_cast<uint>(2 * z_overlap);
-
- //let's create a new image, where we will fill the density of the bb_list
- //we make sure, that the grid cubes exactly match the ones in the
- //set map
- ost::img::Size s(x_extent,y_extent,z_extent);
-
- ost::img::MapHandle bb_list_map = ost::img::CreateImage(s);
- bb_list_map.SetSpatialSampling(sampling);
-
- geom::Vec3 pixel_coord = map_data_->map.CoordToIndex(geom::Vec3(min_x,
- min_y,
- min_z) -
- geom::Vec3(x_overlap,
- y_overlap,
- z_overlap));
-
- ost::img::Point rounded_pixel_coord(round(pixel_coord[0]),
- round(pixel_coord[1]),
- round(pixel_coord[2]));
-
- geom::Vec3 min = map_data_->map.IndexToCoord(rounded_pixel_coord);
- bb_list_map.SetAbsoluteOrigin(min);
-
- //let's fill the density of the BackboneList
- bb_list.InsertInto(bb_list_map, map_data_->resolution, map_data_->all_atom);
-
- uint num_voxels = (s[0] * s[1] * s[2]);
-
- std::vector<Real> map_values(num_voxels);
- std::vector<Real> bb_list_values(num_voxels);
-
- uint vec_position = 0;
- ost::img::Point p, p_orig;
- for(uint i = 0; i < s[0]; ++i){
- for(uint j = 0; j < s[1]; ++j){
- for(uint k = 0; k < s[2]; ++k){
- p = ost::img::Point(i,j,k);
- p_orig = p + rounded_pixel_coord;
- //will return 0.0 if outside of map
- map_values[vec_position] = map_data_->map.GetReal(p_orig);
- bb_list_values[vec_position] = bb_list_map.GetReal(p);
- ++vec_position;
- }
- }
- }
-
- profile.push_back(this->Correlate(map_values, bb_list_values, num_voxels));
- }
-}
-
-void DensityScorer::AttachEnvironment(BackboneScoreEnv& env) {
- map_data_ = env.GetDensityMapData();
- attached_environment_ = true;
-}
-
-Real DensityScorer::Correlate(const std::vector<Real>& map_values,
- const std::vector<Real>& bb_list_values,
- uint num_voxels) const{
-
//we have to get the means, the standart deviations and the correlation itself...
Real m_one = 0.0;
Real m_two = 0.0;
diff --git a/scoring/src/density_score.hh b/scoring/src/density_score.hh
index 5a8d7bcb961e3ec7c3c0ab68e23f9dc8fc60817a..d5e5123c3f733f2976e47c8928d32b6d11dc8f57 100644
--- a/scoring/src/density_score.hh
+++ b/scoring/src/density_score.hh
@@ -3,42 +3,14 @@
#include <ost/img/map.hh>
#include <promod3/loop/density_creator.hh>
-#include <promod3/scoring/backbone_score_base.hh>
+#include <promod3/loop/backbone.hh>
#include <promod3/core/runtime_profiling.hh>
namespace promod3 { namespace scoring {
-class DensityScorer;
-typedef boost::shared_ptr<DensityScorer> DensityScorerPtr;
-
-
-class DensityScorer : public BackboneScorer {
-
-public:
-
- DensityScorer(): attached_environment_(false) { }
-
- virtual ~DensityScorer() { }
-
- virtual Real CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const;
-
- void CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
- std::vector<Real>& profile) const;
-
-void AttachEnvironment(BackboneScoreEnv& env);
-
-private:
-
- Real Correlate(const std::vector<Real>& map_values,
- const std::vector<Real>& bb_list_values,
- uint num_voxels) const;
-
- const DensityMapData* map_data_;
- bool attached_environment_;
-};
-
+Real DensityScore(const promod3::loop::BackboneList& bb_list,
+ ost::img::MapHandle& map,
+ Real resolution, bool all_atom);
}}//ns
diff --git a/scoring/src/hbond_env_listener.cc b/scoring/src/hbond_env_listener.cc
index ca4fbd672d9899f6da2332d119d399bc454391bb..08a64dce7b0f74939f5d6b7e04580e54038891e2 100644
--- a/scoring/src/hbond_env_listener.cc
+++ b/scoring/src/hbond_env_listener.cc
@@ -1,4 +1,5 @@
#include <promod3/scoring/hbond_env_listener.hh>
+#include <set>
namespace promod3{ namespace scoring{
@@ -22,10 +23,15 @@ void HBondEnvListener::Init(const BackboneScoreEnv& base_env) {
env_.Clear();
}
- const loop::IdxHandler* idx_handler = base_env.GetIdxHandlerData();
- uint num_residues = idx_handler->GetNumResidues();
+ idx_handler_ = base_env.GetIdxHandlerData();
+ env_set_ = base_env.GetEnvSetData();
+ uint num_residues = idx_handler_->GetNumResidues();
env_data_ = new HBondSpatialOrganizerItem[num_residues];
const ost::conop::AminoAcid* aa_data = base_env.GetAAData();
+ n_pos_data_ = base_env.GetNPosData();
+ ca_pos_data_ = base_env.GetCAPosData();
+ c_pos_data_ = base_env.GetCPosData();
+ o_pos_data_ = base_env.GetOPosData();
for(uint i = 0; i < num_residues; ++i){
env_data_[i].idx = i;
@@ -33,56 +39,43 @@ void HBondEnvListener::Init(const BackboneScoreEnv& base_env) {
}
}
-void HBondEnvListener::SetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void HBondEnvListener::SetEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"HBondEnvListener::SetEnvironment", 2);
- const geom::Vec3* n_pos_data = base_env.GetNPosData();
- const geom::Vec3* ca_pos_data = base_env.GetCAPosData();
- const geom::Vec3* c_pos_data = base_env.GetCPosData();
- const geom::Vec3* o_pos_data = base_env.GetOPosData();
-
for(std::vector<uint>::const_iterator i = idx.begin();
i != idx.end(); ++i){
- env_data_[*i].pos = ca_pos_data[*i];
- env_data_[*i].n_pos = n_pos_data[*i];
- env_data_[*i].c_pos = c_pos_data[*i];
- env_data_[*i].o_pos = o_pos_data[*i];
- env_.Add(&env_data_[*i], ca_pos_data[*i]);
+ env_data_[*i].pos = ca_pos_data_[*i];
+ env_data_[*i].n_pos = n_pos_data_[*i];
+ env_data_[*i].c_pos = c_pos_data_[*i];
+ env_data_[*i].o_pos = o_pos_data_[*i];
+ env_.Add(&env_data_[*i], ca_pos_data_[*i]);
}
- this->UpdateStatesAndHPos(idx, base_env);
+ this->UpdateStatesAndHPos(idx);
}
-void HBondEnvListener::ResetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void HBondEnvListener::ResetEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"HBondEnvListener::ResetEnvironment", 2);
- const geom::Vec3* n_pos_data = base_env.GetNPosData();
- const geom::Vec3* ca_pos_data = base_env.GetCAPosData();
- const geom::Vec3* c_pos_data = base_env.GetCPosData();
- const geom::Vec3* o_pos_data = base_env.GetOPosData();
-
geom::Vec3 old_pos;
for(std::vector<uint>::const_iterator i = idx.begin();
i != idx.end(); ++i){
old_pos = env_data_[*i].pos;
- env_data_[*i].pos = ca_pos_data[*i];
- env_data_[*i].n_pos = n_pos_data[*i];
- env_data_[*i].c_pos = c_pos_data[*i];
- env_data_[*i].o_pos = o_pos_data[*i];
- env_.Reset(&env_data_[*i], old_pos, ca_pos_data[*i]);
+ env_data_[*i].pos = ca_pos_data_[*i];
+ env_data_[*i].n_pos = n_pos_data_[*i];
+ env_data_[*i].c_pos = c_pos_data_[*i];
+ env_data_[*i].o_pos = o_pos_data_[*i];
+ env_.Reset(&env_data_[*i], old_pos, ca_pos_data_[*i]);
}
- this->UpdateStatesAndHPos(idx, base_env);
+ this->UpdateStatesAndHPos(idx);
}
-void HBondEnvListener::ClearEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void HBondEnvListener::ClearEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"HBondEnvListener::ClearEnvironment", 2);
@@ -92,116 +85,62 @@ void HBondEnvListener::ClearEnvironment(const BackboneScoreEnv& base_env,
env_.Remove(&env_data_[*i], env_data_[*i].pos);
}
- this->UpdateStatesAndHPos(idx, base_env);
+ this->UpdateStatesAndHPos(idx);
}
-void HBondEnvListener::UpdateStatesAndHPos(uint chain_idx,
- const BackboneScoreEnv& env) {
-
- const loop::IdxHandler* idx_handler = env.GetIdxHandlerData();
- const int* env_set = env.GetEnvSetData();
-
- //the h positions and states of the hbond term get calculated as a
- //postprocessing step
- //note, that we reconstruct the stuff for the full chain, since the state of
- //one residue incluences the neighbouring residues...
- //we dont really know how far this influence goes
- Real phi,psi;
- HBondSpatialOrganizerItem* current_item;
- std::vector<int> states(idx_handler->GetChainSize(chain_idx),0);
- int actual_idx = idx_handler->GetChainStartIdx(chain_idx);
-
- for(uint i = 0; i < idx_handler->GetChainSize(chain_idx); ++i){
- if(env_set[actual_idx]){
- current_item = &env_data_[actual_idx];
- phi = -1.0472;
- psi = -0.78540;
- if(i > 0 && i < idx_handler->GetChainSize(chain_idx)-1){
- if(env_set[actual_idx - 1] &&
- env_set[actual_idx + 1]){
-
- phi = geom::DihedralAngle(env_data_[actual_idx-1].c_pos,
- current_item->n_pos,
- current_item->pos,
- current_item->c_pos);
- psi = geom::DihedralAngle(current_item->n_pos,
- current_item->pos,
- current_item->c_pos,
- env_data_[actual_idx+1].n_pos);
-
- states[i] = GetHBondState(phi,psi);
- }
- }
-
- core::ConstructAtomPos(current_item->c_pos, current_item->pos,
- current_item->n_pos, 0.9970, 2.0420,
- phi + Real(M_PI), current_item->h_pos);
- }
- ++actual_idx;
- }
-
- //we still need to check consistency of consecutive residues
- //if state is 1 or 2, at least one neighbouring residues must
- //have the same state, the state is set to zero otherwise
-
- //first do the first and last residue
- if(idx_handler->GetChainSize(chain_idx) > 2){
- if(states[0] == 1){
- if(states[1] != 1) states[0] = 0;
- }
- if(states[0] == 2){
- if(states[1] != 2) states[0] = 0;
+void HBondEnvListener::UpdateStatesAndHPos(const std::vector<uint>& idx) {
+
+ // we have no guarentee that the indices are consecutive...
+ // we have to do the inefficient way and always add a full triplett
+ // to a set to get a unique set for further processing.
+ std::set<uint> stuff_to_check;
+
+ for(std::vector<uint>::const_iterator i = idx.begin();
+ i != idx.end(); ++i){
+
+ uint chain_idx = idx_handler_->GetChainIdx(*i);
+ uint chain_start_idx = idx_handler_->GetChainIdx(chain_idx);
+ uint chain_last_idx = idx_handler_->GetChainLastIdx(chain_idx);
+
+ if(env_set_[*i]) {
+ stuff_to_check.insert(*i);
}
- if(states.back() == 1){
- if(states[states.size()-2] != 1) states.back() = 0;
+
+ if(*i > chain_start_idx && env_set_[*i - 1]) {
+ stuff_to_check.insert(*i - 1);
}
- if(states.back() == 2){
- if(states[states.size()-2] != 2) states.back() = 0;
+
+ if(*i < chain_last_idx && env_set_[*i + 1]) {
+ stuff_to_check.insert(*i + 1);
}
}
- //let's do the remaining residues in between
- for(uint i = 1; i < states.size()-1; ++i){
- if(states[i] == 0) continue;
- if(states[i] == 1){
- if(states[i-1] == 1 || states[i+1] == 1) continue;
- }
- if(states[i] == 2){
- if(states[i-1] == 2 || states[i+1] == 2) continue;
- }
- states[i] = 0;
- }
-
- //let's finally map the states to the hbond_env
- actual_idx = idx_handler->GetChainStartIdx(chain_idx);
- for(uint i = 0; i < idx_handler->GetChainSize(chain_idx); ++i){
- env_data_[actual_idx].state = states[i];
- ++actual_idx;
- }
-}
-void HBondEnvListener::UpdateStatesAndHPos(const std::vector<uint>& idx,
- const BackboneScoreEnv& env) {
-
- const loop::IdxHandler* idx_handler = env.GetIdxHandlerData();
-
- //we have to figure out to which chains the residue belong to
- std::set<uint> affected_chains;
- uint chain_start, chain_end;
- for(std::vector<uint>::const_iterator i = idx.begin(); i != idx.end(); ++i){
- for(uint j = 0; j < idx_handler->GetNumChains(); ++j){
- chain_start = idx_handler->GetChainStartIdx(j);
- chain_end = chain_start + idx_handler->GetChainSize(j);
- if( (*i >= chain_start) && (*i < chain_end) ){
- affected_chains.insert(j);
- break;
- }
+ for(std::set<uint>::iterator i = stuff_to_check.begin();
+ i != stuff_to_check.end(); ++i) {
+
+ Real phi = -1.0472;
+ Real psi = -0.78540;
+
+ uint chain_idx = idx_handler_->GetChainIdx(*i);
+ uint chain_start_idx = idx_handler_->GetChainIdx(chain_idx);
+ uint chain_last_idx = idx_handler_->GetChainLastIdx(chain_idx);
+
+ if(*i > chain_start_idx && *i < chain_last_idx &&
+ env_set_[*i - 1] && env_set_[*i + 1]) {
+
+ phi = geom::DihedralAngle(env_data_[*i-1].c_pos, env_data_[*i].n_pos,
+ env_data_[*i].pos, env_data_[*i].c_pos);
+ psi = geom::DihedralAngle(env_data_[*i].n_pos, env_data_[*i].pos,
+ env_data_[*i].c_pos, env_data_[*i+1].n_pos);
+
+ // we only assign a state if both, phi and psi, are set
+ env_data_[*i].state = GetHBondState(phi,psi);
+
}
- }
- //call according function for every affected chain
- for(std::set<uint>::iterator i = affected_chains.begin();
- i != affected_chains.end(); ++i){
- this->UpdateStatesAndHPos(*i, env);
+ core::ConstructAtomPos(env_data_[*i].c_pos, env_data_[*i].pos,
+ env_data_[*i].n_pos, 0.9970, 2.0420,
+ phi + Real(M_PI), env_data_[*i].h_pos);
}
}
diff --git a/scoring/src/hbond_env_listener.hh b/scoring/src/hbond_env_listener.hh
index efcc9c5ff118332dd2599b18d699504158c00a78..d5e6ea01849d5de7f3d08abfe36652040bccfee5 100644
--- a/scoring/src/hbond_env_listener.hh
+++ b/scoring/src/hbond_env_listener.hh
@@ -6,7 +6,6 @@
#include <promod3/core/dynamic_spatial_organizer.hh>
#include <promod3/core/portable_binary_serializer.hh>
#include <promod3/core/check_io.hh>
-#include <promod3/loop/sec_struct.hh>
#include <set>
namespace promod3 { namespace scoring {
@@ -42,7 +41,7 @@ struct HBondSpatialOrganizerItem {
geom::Vec3 h_pos; //donor H
geom::Vec3 c_pos; //acceptor C
geom::Vec3 o_pos; //acceptor O
- uint state;
+ uint8_t state;
uint idx;
bool is_proline;
};
@@ -60,20 +59,21 @@ public:
virtual void Init(const BackboneScoreEnv& base_env);
- virtual void SetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void SetEnvironment(const std::vector<uint>& idx);
- virtual void ResetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void ResetEnvironment(const std::vector<uint>& idx);
- virtual void ClearEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void ClearEnvironment(const std::vector<uint>& idx);
virtual String WhoAmI() const { return "HBondEnvListener"; }
const HBondSpatialOrganizerItem& GetEnvData(uint idx) const {
return env_data_[idx];
}
+
+ const int* GetEnvSetData() { return env_set_; }
+
+ const loop::IdxHandler* GetIdxHandler() { return idx_handler_; }
HBondSpatialOrganizer::WithinResult FindWithin(const geom::Vec3& pos,
Real cutoff) const {
@@ -82,14 +82,18 @@ public:
private:
- //update the hbond states and h positions of one particular chain
- void UpdateStatesAndHPos(uint chain_idx, const BackboneScoreEnv& env);
-
- //figures out which chains are affected and calls the function above
- void UpdateStatesAndHPos(const std::vector<uint>& idx, const BackboneScoreEnv& env);
+ void UpdateStatesAndHPos(const std::vector<uint>& idx);
HBondSpatialOrganizer env_;
HBondSpatialOrganizerItem* env_data_;
+
+ // data ptrs fetched from base env at initialization
+ const int* env_set_;
+ const loop::IdxHandler* idx_handler_;
+ const geom::Vec3* n_pos_data_;
+ const geom::Vec3* ca_pos_data_;
+ const geom::Vec3* c_pos_data_;
+ const geom::Vec3* o_pos_data_;
};
}} // ns
diff --git a/scoring/src/hbond_score.cc b/scoring/src/hbond_score.cc
index 0b719390cf0ce6a7899b1a88271aebe921d148f6..19940c002455a7087c7966fbbdcbe7e1bfef8dd8 100644
--- a/scoring/src/hbond_score.cc
+++ b/scoring/src/hbond_score.cc
@@ -20,42 +20,44 @@ HBondScorer::HBondScorer(Real min_d, Real max_d,
alpha_bins_(alpha_bins),
beta_bins_(beta_bins),
gamma_bins_(gamma_bins),
- attached_environment_(false),
+ do_internal_scores_(true),
+ do_external_scores_(true),
+ normalize_(true),
env_(NULL) {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"HBondScorer::HBondScorer", 2);
- if(d_bins == 0){
+ if(d_bins == 0) {
throw promod3::Error("Number of distance bins must be nonzero!");
}
- if(alpha_bins == 0){
+ if(alpha_bins == 0) {
throw promod3::Error("Number of alpha bins must be nonzero!");
}
- if(beta_bins == 0){
+ if(beta_bins == 0) {
throw promod3::Error("Number of beta bins must be nonzero!");
}
- if(gamma_bins == 0){
+ if(gamma_bins == 0) {
throw promod3::Error("Number of gamma bins must be nonzero!");
}
- if(max_d_ <= min_d_){
+ if(max_d_ <= min_d_) {
throw promod3::Error("hb_max_d must be larger than hb_min_d");
}
- if(max_alpha_ <= min_alpha_){
+ if(max_alpha_ <= min_alpha_) {
throw promod3::Error("hb_max_alpha must be larger than hb_min_alpha");
}
- if(max_beta_ <= min_beta_){
+ if(max_beta_ <= min_beta_) {
throw promod3::Error("max_beta must be larger than min_beta");
}
- if(max_gamma_ <= min_gamma_){
+ if(max_gamma_ <= min_gamma_) {
throw promod3::Error("max_gamma must be larger than min_gamma");
}
@@ -249,265 +251,289 @@ void HBondScorer::SetEnergy(uint state, uint d_bin, uint alpha_bin,
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"HBondScorer::SetEnergy", 2);
- if(state >= 3){
+ if(state >= 3) {
throw promod3::Error("Invalid state when setting energy for hbond potential!");
}
- if(d_bin >= d_bins_){
+ if(d_bin >= d_bins_) {
throw promod3::Error("Invalid d bin when setting energy for hbond potential!");
}
- if(alpha_bin >= alpha_bins_){
+ if(alpha_bin >= alpha_bins_) {
throw promod3::Error("Invalid alpha bin when setting energy for hbond potential!");
}
- if(beta_bin >= beta_bins_){
+ if(beta_bin >= beta_bins_) {
throw promod3::Error("Invalid beta bin when setting energy for hbond potential!");
}
- if(gamma_bin >= gamma_bins_){
+ if(gamma_bin >= gamma_bins_) {
throw promod3::Error("Invalid gamma bin when setting energy for hbond potential!");
}
energies_[this->EIdx(state, d_bin, alpha_bin, beta_bin, gamma_bin)] = e;
}
-Real HBondScorer::CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const {
+Real HBondScorer::CalculateScore(uint start_resnum, uint num_residues,
+ uint chain_idx) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"HBondScorer::CalculateScore", 2);
- std::vector<Real> scores;
- std::vector<Real> internal_scores;
+ if (env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
- this->Score(bb_list, start_resnum, chain_idx, scores, internal_scores);
+
+ // setup
+ std::vector<uint> idx_vector;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vector,
+ occupied);
- Real score = 0.0;
- for(uint i = 0; i < scores.size(); ++i){
- score += scores[i];
- }
+ // get scores
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ this->Score(idx_vector, external_scores, internal_scores, occupied);
+ // sum them
+ Real external_score = 0.0;
Real internal_score = 0.0;
- for(uint i = 0; i < internal_scores.size(); ++i){
+ for (uint i = 0; i < external_scores.size(); ++i) {
+ external_score += external_scores[i];
internal_score += internal_scores[i];
}
- score += (0.5 * internal_score);
+ // all interactions in internal_score have been observed twice!
+ external_score += Real(0.5)*internal_score;
- if(!scores.empty()){
- score /= scores.size();
+ if(normalize_ && !external_scores.empty()) {
+ external_score /= external_scores.size();
}
- return score;
+ return external_score;
}
-void HBondScorer::CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
+void HBondScorer::CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
std::vector<Real>& profile) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"HBondScorer::CalculateScoreProfile", 2);
- std::vector<Real> scores;
- std::vector<Real> internal_scores;
+ if (env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
- this->Score(bb_list, start_resnum, chain_idx, scores, internal_scores);
+ // setup
+ std::vector<uint> idx_vector;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vector,
+ occupied);
+
+ // get scores
+ std::vector<Real> internal_scores;
+ this->Score(idx_vector, profile, internal_scores, occupied);
- profile.clear();
- for(uint i = 0; i < scores.size(); ++i){
- profile.push_back(scores[i] + internal_scores[i]);
+ for(uint i = 0; i < profile.size(); ++i) {
+ profile[i] += internal_scores[i];
}
}
-void HBondScorer::Score(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
- std::vector<Real>& scores,
- std::vector<Real>& internal_scores) const {
+Real HBondScorer::CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
+
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "HBondScorer::Score", 2);
+ "HBondScorer::CalculateScore", 2);
- if(!attached_environment_){
+ if (env_ == NULL) {
String err = "Can only calculate score when environment is attached!";
throw promod3::Error(err);
}
// setup
- uint bb_list_size, start_idx, end_idx;
- idx_handler_->SetupScoreCalculation(bb_list, start_resnum, chain_idx,
- bb_list_size, start_idx, end_idx);
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores and sum them up
+ Real external_score = 0.0;
+ Real internal_score = 0.0;
+ uint n_scored_residues = 0;
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ this->Score(indices_vec[i], external_scores, internal_scores, occupied);
+ for (uint j = 0; j < external_scores.size(); ++j) {
+ external_score += external_scores[j];
+ internal_score += internal_scores[j];
+ }
+ n_scored_residues += external_scores.size();
+ }
- scores.assign(bb_list_size, 0.0);
- internal_scores.assign(bb_list_size, 0.0);
- if(bb_list_size == 0) return;
+ // all interactions in internal_score have been observed twice!
+ external_score += Real(0.5)*internal_score;
+ if(normalize_ && n_scored_residues > 0) {
+ external_score /= n_scored_residues;
+ }
- HBondSpatialOrganizer::WithinResult within_result;
- std::pair<HBondSpatialOrganizerItem*,Real>* a;
+ return external_score;
+}
- //note, that the n-terminal backbone hydrogen will be constructed below
- std::vector<geom::Vec3> h_positions(bb_list_size);
- for(uint i = 1; i < bb_list_size; ++i){
- Real phi = bb_list.GetPhiTorsion(i);
- core::ConstructAtomPos(bb_list.GetC(i), bb_list.GetCA(i),
- bb_list.GetN(i), 0.9970, 2.0420,
- phi + Real(M_PI), h_positions[i]);
- }
+void HBondScorer::CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "HBondScorer::CalculateScore", 2);
- std::vector<uint> bb_list_states(bb_list_size);
- Real n_phi = -1.0472;
- Real c_psi = -0.78540;
- if(start_resnum > 1){
- if(env_set_[start_idx - 1]){
- n_phi = geom::DihedralAngle(env_->GetEnvData(start_idx - 1).c_pos,
- bb_list.GetN(0),
- bb_list.GetCA(0),
- bb_list.GetC(0));
- }
+ if (env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
}
- if((start_resnum + bb_list_size - 1) < idx_handler_->GetChainSize(chain_idx)){
- if(env_set_[end_idx + 1]){
- c_psi = geom::DihedralAngle(bb_list.GetN(bb_list_size-1),
- bb_list.GetCA(bb_list_size-1),
- bb_list.GetC(bb_list_size-1),
- env_->GetEnvData(end_idx + 1).n_pos);
+ // setup
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores
+ profile.resize(start_resnum.size());
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ std::vector<Real>& current_profile = profile[i];
+ this->Score(indices_vec[i], current_profile, internal_scores, occupied);
+ for (uint j = 0; j < current_profile.size(); ++j) {
+ current_profile[j] += internal_scores[j];
+
}
}
+}
- //we still have to calculate the position of the n-terminal hydrogen
- core::ConstructAtomPos(bb_list.GetC(0), bb_list.GetCA(0),
- bb_list.GetN(0), 0.9970, 2.0420,
- n_phi + Real(M_PI), h_positions[0]);
-
- if(bb_list_size == 1){
- bb_list_states[0] = GetHBondState(n_phi, c_psi);
- }
- else{
- bb_list_states[0] = GetHBondState(n_phi,bb_list.GetPsiTorsion(0));
- bb_list_states[bb_list_size-1] =
- GetHBondState(bb_list.GetPhiTorsion(bb_list_size-1),c_psi);
- }
-
- for(uint i = 1; i < bb_list_size-1; ++i){
- bb_list_states[i] = GetHBondState(bb_list.GetPhiTorsion(i),
- bb_list.GetPsiTorsion(i));
- }
- //handle the terminal states
- int prev_state = 0;
- int next_state = 0;
- if(start_resnum > 1){
- if(env_set_[start_idx - 1]){
- prev_state = env_->GetEnvData(start_idx - 1).state;
- }
- }
- if((start_resnum + bb_list_size - 1) < idx_handler_->GetChainSize(chain_idx)){
- if(env_set_[end_idx + 1]){
- next_state = env_->GetEnvData(end_idx + 1).state;
- }
- }
+void HBondScorer::Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
+ std::vector<Real>& internal_scores,
+ std::vector<bool>& occupied) const {
- if(bb_list_states[0] == 1){
- if(prev_state != 1 && bb_list_states[1] != 1){
- bb_list_states[0] = 0;
- }
- }
- if(bb_list_states[0] == 2){
- if(prev_state != 2 && bb_list_states[1] != 2){
- bb_list_states[0] = 0;
- }
- }
- if(bb_list_states[bb_list_size-1] == 1){
- if(next_state != 1 && bb_list_states[bb_list_size-2] != 1){
- bb_list_states[bb_list_size-1] = 0;
- }
- }
- if(bb_list_states[bb_list_size-1] == 2){
- if(next_state != 2 && bb_list_states[bb_list_size-2] != 2){
- bb_list_states[bb_list_size-1] = 0;
- }
- }
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "HBondScorer::Score", 2);
+
+ // setup
+ uint n_indices = indices.size();
+
+ external_scores.assign(n_indices, 0.0);
+ internal_scores.assign(n_indices, 0.0);
+
+ if(n_indices == 0) return;
+
+ HBondSpatialOrganizer::WithinResult within_result;
+ std::pair<HBondSpatialOrganizerItem*,Real>* a;
+ const int* env_set = env_->GetEnvSetData();
+ const loop::IdxHandler* idx_handler = env_->GetIdxHandler();
+
+ for(uint i = 0; i < n_indices; ++i) {
+ int my_idx = indices[i];
- for(uint i = 1; i < bb_list_size-1; ++i){
- if(bb_list_states[i] == 1){
- if(bb_list_states[i-1] == 1 || bb_list_states[i+1] == 1) continue;
+ if(!env_set[my_idx]) {
+ throw promod3::Error("Must set environment before scoring!");
}
- if(bb_list_states[i] == 2){
- if(bb_list_states[i-1] == 2 || bb_list_states[i+1] == 2) continue;
+
+ int my_chain_idx = idx_handler->GetChainIdx(my_idx);
+ const HBondSpatialOrganizerItem& my_env_data = env_->GetEnvData(my_idx);
+ int my_state = my_env_data.state;
+
+ if(my_state != 0) {
+
+ int my_chain_start_idx = idx_handler->GetChainIdx(my_chain_idx);
+ int my_chain_last_idx = idx_handler->GetChainLastIdx(my_chain_idx);
+ bool consistent_state = false;
+
+ if(my_idx > my_chain_start_idx && env_set[my_idx - 1] &&
+ env_->GetEnvData(my_idx - 1).state == my_state) {
+ consistent_state = true;
+ } else if(my_idx < my_chain_last_idx && env_set[my_idx + 1] &&
+ env_->GetEnvData(my_idx + 1).state == my_state) {
+ consistent_state = true;
+ }
+
+ if(!consistent_state) {
+ my_state = 0;
+ }
}
- bb_list_states[i] = 0;
- }
- //let's go over every bb_list residue
- int state;
- for(uint i = 0; i < bb_list_size; ++i){
- within_result = env_->FindWithin(bb_list.GetCA(i), 9.0);
+ within_result = env_->FindWithin(my_env_data.pos, 9.0);
a = within_result.first;
- for(uint j = 0; j < within_result.second; ++j){
- if(a[j].first->idx < start_idx || a[j].first->idx > end_idx){
+ for(uint j = 0; j < within_result.second; ++j) {
+
+ int state = 0;
+ int other_idx = a[j].first->idx;
+ int other_state = a[j].first->state;
- if(bb_list_states[i] == a[j].first->state) state = bb_list_states[i];
- else state = 0;
+ if(other_state != 0 && other_state == my_state) {
- //case of being donor for current bb item
- if(bb_list.GetOLC(i) != 'P'){
- scores[i] += this->EvalHBondPotential(state,bb_list.GetN(i),
- h_positions[i],
- a[j].first->pos,
- a[j].first->c_pos,
- a[j].first->o_pos);
+ int other_chain_idx = idx_handler->GetChainIdx(other_idx);
+ int other_chain_start_idx = idx_handler->GetChainIdx(other_chain_idx);
+ int other_chain_last_idx = idx_handler->GetChainLastIdx(other_chain_idx);
+
+ bool consistent_state = false;
+
+ if(other_idx > other_chain_start_idx && env_set[other_idx - 1] &&
+ env_->GetEnvData(other_idx - 1).state == other_state) {
+ consistent_state = true;
+ } else if(other_idx < other_chain_last_idx && env_set[other_idx + 1] &&
+ env_->GetEnvData(other_idx + 1).state == other_state) {
+ consistent_state = true;
}
- //case of being acceptor for current bb item
- if(!a[j].first->is_proline){
- scores[i] += this->EvalHBondPotential(state, a[j].first->n_pos,
- a[j].first->h_pos,
- bb_list.GetCA(i),
- bb_list.GetC(i),
- bb_list.GetO(i));
+ if(consistent_state) {
+ state = my_state;
}
}
- }
- }
- // we do not have the loop internal interactions yet...
- for (uint i = 0; i < bb_list_size; ++i) {
- for (uint j = i+3; j < bb_list_size; ++j) {
- // hbonds closer than 3 residues do not really make sense...
- if (geom::Length2(bb_list.GetCA(i) - bb_list.GetCA(j)) > 81) continue;
-
- if (bb_list_states[i] == bb_list_states[j]) state = bb_list_states[i];
- else state = 0;
-
- // case of i being donor
- if(bb_list.GetOLC(i) != 'P'){
- Real score = this->EvalHBondPotential(state,
- bb_list.GetN(i),
- h_positions[i],
- bb_list.GetCA(j),
- bb_list.GetC(j),
- bb_list.GetO(j));
- internal_scores[i] += score;
- internal_scores[j] += score;
+ Real e = 0.0;
+
+ //case of being donor for current bb item
+ if(!my_env_data.is_proline) {
+ e += this->EvalHBondPotential(state, my_env_data.n_pos,
+ my_env_data.h_pos,
+ a[j].first->pos,
+ a[j].first->c_pos,
+ a[j].first->o_pos);
+ }
+
+ //case of being acceptor for current bb item
+ if(!a[j].first->is_proline) {
+ e += this->EvalHBondPotential(state, a[j].first->n_pos,
+ a[j].first->h_pos,
+ my_env_data.pos,
+ my_env_data.c_pos,
+ my_env_data.o_pos);
+ }
+
+ if(occupied[other_idx] && do_internal_scores_) {
+ internal_scores[i] += e;
}
- // case of i being acceptor
- if(bb_list.GetOLC(j) != 'P'){
- Real score = this->EvalHBondPotential(state,
- bb_list.GetN(j),
- h_positions[j],
- bb_list.GetCA(i),
- bb_list.GetC(i),
- bb_list.GetO(i));
-
- internal_scores[i] += score;
- internal_scores[j] += score;
+ if(!occupied[other_idx] && do_external_scores_) {
+ external_scores[i] += e;
}
}
}
@@ -515,9 +541,6 @@ void HBondScorer::Score(const loop::BackboneList& bb_list,
void HBondScorer::AttachEnvironment(BackboneScoreEnv& env) {
env_ = env.UniqueListener<HBondEnvListener>("HBondEnvListener");
- idx_handler_ = env.GetIdxHandlerData();
- env_set_ = env.GetEnvSetData();
- attached_environment_ = true;
}
}} // ns
diff --git a/scoring/src/hbond_score.hh b/scoring/src/hbond_score.hh
index fcf52f216d1dfd87266cb0280bca1ff90319cdb8..e8211fd43cc83e65585c049b9485c704ed17aa9b 100644
--- a/scoring/src/hbond_score.hh
+++ b/scoring/src/hbond_score.hh
@@ -39,21 +39,37 @@ public:
void SetEnergy(uint state, uint d_bin, uint alpha_bin,
uint beta_bin, uint gamma_bin, Real e);
- virtual Real CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const;
+ void DoInternalScores(bool do_it) { do_internal_scores_ = do_it; }
- virtual void CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
+ void DoExternalScores(bool do_it) { do_external_scores_ = do_it; }
+
+ void DoNormalize(bool do_it) { normalize_ = do_it; }
+
+ virtual Real CalculateScore(uint start_resnum, uint num_residues,
+ uint chain_idx) const;
+
+ virtual void CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
std::vector<Real>& profile) const;
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const;
+
void AttachEnvironment(BackboneScoreEnv& env);
private:
- HBondScorer(): attached_environment_(false), env_(NULL) { }
+ HBondScorer(): do_internal_scores_(true), do_external_scores_(true),
+ normalize_(true), env_(NULL) { }
inline uint EIdx(uint state, uint d_bin, uint alpha_bin, uint beta_bin,
- uint gamma_bin) const{
+ uint gamma_bin) const {
return ((((state)*d_bins_+d_bin)*alpha_bins_+alpha_bin)*
beta_bins_+beta_bin)*gamma_bins_+gamma_bin;
@@ -80,12 +96,10 @@ private:
return energies_[this->EIdx(state, d_bin, alpha_bin, beta_bin, gamma_bin)];
}
-
- void Score(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx,
- std::vector<Real>& scores,
- std::vector<Real>& internal_scores) const;
+ void Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
+ std::vector<Real>& internal_scores,
+ std::vector<bool>& occupied) const;
// portable serialization (only stores data relevant for Load/Save!)
// (cleanly element by element with fixed-width base-types)
@@ -108,11 +122,11 @@ private:
core::ConvertBaseType<float>(ds, beta_bin_size_);
core::ConvertBaseType<float>(ds, gamma_bin_size_);
uint num_values = 3 * d_bins_ * alpha_bins_ * beta_bins_ * gamma_bins_;
- if(ds.IsSource()){
+ if(ds.IsSource()) {
energies_ = new Real[num_values];
memset(energies_, 0, num_values * sizeof(Real));
}
- for(uint i = 0; i < num_values; ++i){
+ for(uint i = 0; i < num_values; ++i) {
core::ConvertBaseType<float>(ds, energies_[i]);
}
}
@@ -133,14 +147,14 @@ private:
Real alpha_bin_size_;
Real beta_bin_size_;
Real gamma_bin_size_;
- Real* energies_;
+ Real* energies_;
+ bool do_internal_scores_;
+ bool do_external_scores_;
+ bool normalize_;
//environment specific information, that will be set upon calling
//AttachEnvironment
- bool attached_environment_;
HBondEnvListener* env_;
- const loop::IdxHandler* idx_handler_;
- const int* env_set_;
};
diff --git a/scoring/src/pairwise_score.cc b/scoring/src/pairwise_score.cc
index a650ee28e8fdb1a2439a658026c1d2e66ca7c624..1a0ef644e17b316b17ab735e0d34576efa8b2962 100644
--- a/scoring/src/pairwise_score.cc
+++ b/scoring/src/pairwise_score.cc
@@ -2,64 +2,147 @@
namespace promod3{ namespace scoring{
-PairwiseScorer::PairwiseScorer(): attached_environment_(false) { }
+PairwiseScorer::PairwiseScorer(): do_internal_scores_(true),
+ do_external_scores_(true),
+ normalize_(true),
+ attached_environment_(false) { }
PairwiseScorer::~PairwiseScorer() { }
-Real PairwiseScorer::CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const {
+Real PairwiseScorer::CalculateScore(uint start_resnum, uint num_residues,
+ uint chain_idx) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"PairwiseScorer::CalculateScore", 2);
- std::vector<Real> scores;
+ // setup
+ std::vector<uint> idx_vector;
+ std::vector<bool> occupied;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vector,
+ occupied);
+
+ // get scores
+ std::vector<Real> external_scores;
std::vector<Real> internal_scores;
+ this->Score(idx_vector, external_scores, internal_scores, occupied);
- this->Score(bb_list, start_resnum, chain_idx, scores, internal_scores);
-
- Real score = 0.0;
-
- for(uint i = 0; i < scores.size(); ++i){
- score += scores[i];
- }
-
+ // sum them
+ Real external_score = 0.0;
Real internal_score = 0.0;
- for(uint i = 0; i < internal_scores.size(); ++i){
+ for (uint i = 0; i < external_scores.size(); ++i) {
+ external_score += external_scores[i];
internal_score += internal_scores[i];
}
- score += (0.5 * internal_score);
+ // all interactions in internal_score have been observed twice!
+ external_score += Real(0.5)*internal_score;
- if(!scores.empty()){
- score /= scores.size();
+ if(normalize_ && !external_scores.empty()) {
+ external_score /= external_scores.size();
}
- return score;
+ return external_score;
}
-void PairwiseScorer::CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
+void PairwiseScorer::CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
std::vector<Real>& profile) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"PairwiseScorer::CalculateScoreProfile", 2);
- std::vector<Real> scores;
+ // setup
+ std::vector<uint> idx_vector;
+ std::vector<bool> occupied;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vector,
+ occupied);
+
+ // get scores
std::vector<Real> internal_scores;
+ this->Score(idx_vector, profile, internal_scores, occupied);
+
+ for(uint i = 0; i < profile.size(); ++i) {
+ profile[i] += internal_scores[i];
+ }
+}
+
+
+Real PairwiseScorer::CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "PairwiseScorer::CalculateScore", 2);
+
+ // setup
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores and sum them up
+ Real external_score = 0.0;
+ Real internal_score = 0.0;
+ uint n_scored_residues = 0;
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ this->Score(indices_vec[i], external_scores, internal_scores, occupied);
+ for (uint j = 0; j < external_scores.size(); ++j) {
+ external_score += external_scores[j];
+ internal_score += internal_scores[j];
+ }
+ n_scored_residues += external_scores.size();
+ }
+
+ // all interactions in internal_score have been observed twice!
+ external_score += Real(0.5)*internal_score;
+
+ if(normalize_ && n_scored_residues > 0) {
+ external_score /= n_scored_residues;
+ }
- this->Score(bb_list, start_resnum, chain_idx, scores, internal_scores);
+ return external_score;
+}
+
+
+void PairwiseScorer::CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "PairwiseScorer::CalculateScore", 2);
- profile.clear();
- for(uint i = 0; i < scores.size(); ++i){
- profile.push_back(scores[i] + internal_scores[i]);
+ // setup
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores
+ profile.resize(start_resnum.size());
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ std::vector<Real>& current_profile = profile[i];
+ this->Score(indices_vec[i], current_profile, internal_scores, occupied);
+ for (uint j = 0; j < current_profile.size(); ++j) {
+ current_profile[j] += internal_scores[j];
+ }
}
}
-void PairwiseScorer::Score(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
- std::vector<Real>& scores,
- std::vector<Real>& internal_scores) const {
+
+void PairwiseScorer::Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
+ std::vector<Real>& internal_scores,
+ std::vector<bool>& occupied) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"PairwiseScorer::Score", 2);
@@ -70,51 +153,45 @@ void PairwiseScorer::Score(const loop::BackboneList& bb_list,
throw promod3::Error(err);
}
- uint bb_list_size, start_idx, end_idx;
- idx_handler_->SetupScoreCalculation(bb_list, start_resnum, chain_idx,
- bb_list_size, start_idx, end_idx);
+ uint n_indices = indices.size();
- scores.assign(bb_list_size, 0.0);
- internal_scores.assign(bb_list_size, 0.0);
- if(bb_list_size == 0) return;
+ external_scores.assign(n_indices, 0.0);
+ internal_scores.assign(n_indices, 0.0);
+
+ if(n_indices == 0) return;
+
+ for(uint i = 0; i < n_indices; ++i) {
+ uint my_idx = indices[i];
+
+ if(!env_set_[my_idx]) {
+ throw promod3::Error("Must set environment before scoring!");
+ }
- Real d;
- uint other_idx;
-
- for(uint i = 0; i < bb_list_size; ++i){
const std::vector<PairwiseFunctionData>& functions =
- pairwise_functions_[start_idx + i];
- if(!functions.empty()){
- for(uint j = 0; j < functions.size(); ++j){
- other_idx = functions[j].other_idx;
- if(other_idx < start_idx || other_idx > end_idx){
- //it's a constraint to the environment!
- //let's see wether the env residue is set...
- if(env_set_[other_idx]){
- if(functions[j].ft == CB_PAIRWISE_FUNCTION){
- d = geom::Distance(bb_list.GetCB(i), cb_pos_[other_idx]);
- }
- else{
- d = geom::Distance(bb_list.GetCA(i), ca_pos_[other_idx]);
- }
- scores[i] += functions[j].f->Score(d);
+ pairwise_functions_[my_idx];
+ if(!functions.empty()) {
+ for(uint j = 0; j < functions.size(); ++j) {
+
+ uint other_idx = functions[j].other_idx;
+
+ if(env_set_[other_idx]) {
+ Real val;
+
+ if(functions[j].ft == CB_PAIRWISE_FUNCTION) {
+ val = geom::Distance(cb_pos_[my_idx], cb_pos_[other_idx]);
}
- }
- else{
- //it's an internal contact!
- if(other_idx < start_idx + i){
- //make sure, every constraint gets only evaluated once...
- if(functions[j].ft == CB_PAIRWISE_FUNCTION){
- d = geom::Distance(bb_list.GetCB(i),
- bb_list.GetCB(other_idx - start_idx));
- }
- else{
- d = geom::Distance(bb_list.GetCA(i),
- bb_list.GetCA(other_idx - start_idx));
- }
- Real score = functions[j].f->Score(d);
- internal_scores[i] += score;
- internal_scores[other_idx - start_idx] += score;
+ else{
+ val = geom::Distance(ca_pos_[my_idx], ca_pos_[other_idx]);
+ }
+
+ val = functions[j].f->Score(val);
+
+ if(occupied[other_idx] && do_internal_scores_) {
+ internal_scores[i] += val;
+ }
+
+ if(!occupied[other_idx] && do_external_scores_) {
+ external_scores[i] += val;
}
}
}
diff --git a/scoring/src/pairwise_score.hh b/scoring/src/pairwise_score.hh
index c93e0bda9f71af17b1aec0340c3f56e3f563a834..dcd712e8d3e8ef3564d04252e7a73d2d73435826 100644
--- a/scoring/src/pairwise_score.hh
+++ b/scoring/src/pairwise_score.hh
@@ -19,22 +19,40 @@ public:
virtual ~PairwiseScorer();
- virtual Real CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const;
+ void DoInternalScores(bool do_it) { do_internal_scores_ = do_it; }
- virtual void CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
+ void DoExternalScores(bool do_it) { do_external_scores_ = do_it; }
+
+ void DoNormalize(bool do_it) { normalize_ = do_it; }
+
+ virtual Real CalculateScore(uint start_resnum, uint num_residues,
+ uint chain_idx) const;
+
+ virtual void CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
std::vector<Real>& profile) const;
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const;
+
void AttachEnvironment(BackboneScoreEnv& env);
private:
- void Score(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx,
- std::vector<Real>& scores,
- std::vector<Real>& internal_scores) const;
+ void Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
+ std::vector<Real>& internal_scores,
+ std::vector<bool>& occupied) const;
+
+ bool do_internal_scores_;
+ bool do_external_scores_;
+ bool normalize_;
//environment specific information, that will be set upon calling
//AttachEnvironment
@@ -46,7 +64,6 @@ private:
const geom::Vec3* cb_pos_;
};
-
}}//ns
#endif
diff --git a/scoring/src/reduced_env_listener.cc b/scoring/src/reduced_env_listener.cc
index 1f85e50989b3b15c1ad505c1272dc688a24a2979..14025821515000582ab9144edf70db3abe4e6f31 100644
--- a/scoring/src/reduced_env_listener.cc
+++ b/scoring/src/reduced_env_listener.cc
@@ -23,33 +23,32 @@ void ReducedEnvListener::Init(const BackboneScoreEnv& base_env) {
env_.Clear();
}
- const loop::IdxHandler* idx_handler = base_env.GetIdxHandlerData();
- uint num_residues = idx_handler->GetNumResidues();
+ idx_handler_ = base_env.GetIdxHandlerData();
+ uint num_residues = idx_handler_->GetNumResidues();
env_data_ = new ReducedSpatialOrganizerItem[num_residues];
const ost::conop::AminoAcid* aa_data = base_env.GetAAData();
-
+ env_set_ = base_env.GetEnvSetData();
+ ca_pos_data_ = base_env.GetCAPosData();
+ c_pos_data_ = base_env.GetCPosData();
+ n_pos_data_ = base_env.GetNPosData();
+
for (uint i = 0; i < num_residues; ++i) {
env_data_[i].idx = i;
env_data_[i].aa = aa_data[i];
}
}
-void ReducedEnvListener::SetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void ReducedEnvListener::SetEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"ReducedEnvListener::SetEnvironment", 2);
- const geom::Vec3* ca_pos_data = base_env.GetCAPosData();
- const geom::Vec3* c_pos_data = base_env.GetCPosData();
- const geom::Vec3* n_pos_data = base_env.GetNPosData();
-
geom::Vec3 ca_pos, c_pos, n_pos;
for (std::vector<uint>::const_iterator i = idx.begin();
i != idx.end(); ++i) {
- ca_pos = ca_pos_data[*i];
- c_pos = c_pos_data[*i];
- n_pos = n_pos_data[*i];
+ ca_pos = ca_pos_data_[*i];
+ c_pos = c_pos_data_[*i];
+ n_pos = n_pos_data_[*i];
env_data_[*i].pos = ca_pos;
env_data_[*i].axis = geom::Normalize(geom::Normalize(ca_pos-n_pos) +
geom::Normalize(ca_pos-c_pos));
@@ -57,23 +56,18 @@ void ReducedEnvListener::SetEnvironment(const BackboneScoreEnv& base_env,
}
}
-void ReducedEnvListener::ResetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void ReducedEnvListener::ResetEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"ReducedEnvListener::ResetEnvironment", 2);
- const geom::Vec3* ca_pos_data = base_env.GetCAPosData();
- const geom::Vec3* c_pos_data = base_env.GetCPosData();
- const geom::Vec3* n_pos_data = base_env.GetNPosData();
-
geom::Vec3 ca_pos, c_pos, n_pos, old_pos;
for (std::vector<uint>::const_iterator i = idx.begin();
i != idx.end(); ++i) {
old_pos = env_data_[*i].pos;
- ca_pos = ca_pos_data[*i];
- c_pos = c_pos_data[*i];
- n_pos = n_pos_data[*i];
+ ca_pos = ca_pos_data_[*i];
+ c_pos = c_pos_data_[*i];
+ n_pos = n_pos_data_[*i];
env_data_[*i].pos = ca_pos;
env_data_[*i].axis = geom::Normalize(geom::Normalize(ca_pos-n_pos) +
geom::Normalize(ca_pos-c_pos));
@@ -81,8 +75,7 @@ void ReducedEnvListener::ResetEnvironment(const BackboneScoreEnv& base_env,
}
}
-void ReducedEnvListener::ClearEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void ReducedEnvListener::ClearEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"ReducedEnvListener::ClearEnvironment", 2);
diff --git a/scoring/src/reduced_env_listener.hh b/scoring/src/reduced_env_listener.hh
index d693fd9dc19fa2ea2fe90fa465dd805b21f935b4..52d405e2ac27c5e427f85e1a5e0b9ea5308bd872 100644
--- a/scoring/src/reduced_env_listener.hh
+++ b/scoring/src/reduced_env_listener.hh
@@ -32,20 +32,22 @@ public:
virtual void Init(const BackboneScoreEnv& base_env);
- virtual void SetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void SetEnvironment(const std::vector<uint>& idx);
- virtual void ResetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void ResetEnvironment(const std::vector<uint>& idx);
- virtual void ClearEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void ClearEnvironment(const std::vector<uint>& idx);
virtual String WhoAmI() const { return "ReducedEnvListener"; }
const ReducedSpatialOrganizerItem& GetEnvData(uint idx) const {
return env_data_[idx];
}
+
+ const int* GetEnvSetData() { return env_set_; }
+
+ const loop::IdxHandler* GetIdxHandler() { return idx_handler_; }
+
ReducedSpatialOrganizer::WithinResult FindWithin(const geom::Vec3& pos,
Real cutoff) const {
return env_.FindWithin(pos, cutoff);
@@ -54,6 +56,14 @@ public:
private:
ReducedSpatialOrganizer env_;
ReducedSpatialOrganizerItem* env_data_;
+
+ // data ptrs fetched from base env at initialization
+ const int* env_set_;
+ const loop::IdxHandler* idx_handler_;
+ const geom::Vec3* ca_pos_data_;
+ const geom::Vec3* c_pos_data_;
+ const geom::Vec3* n_pos_data_;
+
};
}} //ns
diff --git a/scoring/src/reduced_score.cc b/scoring/src/reduced_score.cc
index 6098c3a1b38411f6dc2b6cff047200170463db80..a8e992ae8a68642a34d5fdf864ca5e6376945d91 100644
--- a/scoring/src/reduced_score.cc
+++ b/scoring/src/reduced_score.cc
@@ -8,7 +8,7 @@ namespace {
inline void GetReducedAngles(const geom::Vec3& v1, const geom::Vec3& v2,
const geom::Vec3& v3, Real& alpha, Real& beta,
- Real& gamma){
+ Real& gamma) {
// this function expects three vectors.
// v1: normalized direction vector
@@ -50,7 +50,9 @@ ReducedScorer::ReducedScorer(Real cutoff, uint dist_bins, uint angle_bins,
angle_bins_(angle_bins),
dihedral_bins_(dihedral_bins),
seq_sep_(seq_sep),
- attached_environment_(false),
+ do_internal_scores_(true),
+ do_external_scores_(true),
+ normalize_(true),
env_(NULL) {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
@@ -241,125 +243,187 @@ void ReducedScorer::SetEnergy(ost::conop::AminoAcid a, ost::conop::AminoAcid b,
}
energies_[this->EIdx(a, b, dist_bin, alpha_bin, beta_bin, gamma_bin)] = e;
+ energies_[this->EIdx(b, a, dist_bin, beta_bin, alpha_bin, gamma_bin)] = e;
}
-Real ReducedScorer::CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const {
+Real ReducedScorer::CalculateScore(uint start_resnum, uint num_residues,
+ uint chain_idx) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"ReducedScorer::CalculateScore", 2);
+ if (env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ // setup
+ std::vector<uint> idx_vector;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vector,
+ occupied);
+
// get scores
- std::vector<Real> scores;
+ std::vector<Real> external_scores;
std::vector<Real> internal_scores;
- std::vector<uint> counts;
- std::vector<uint> internal_counts;
- this->Score(bb_list, start_resnum, chain_idx, scores, internal_scores,
- counts, internal_counts);
+ this->Score(idx_vector, external_scores, internal_scores, occupied);
+
// sum them
- Real score = 0.0;
+ Real external_score = 0.0;
Real internal_score = 0.0;
- uint counter = 0;
- uint internal_counter = 0;
- for (uint i = 0; i < scores.size(); ++i) {
- score += scores[i];
+ for (uint i = 0; i < external_scores.size(); ++i) {
+ external_score += external_scores[i];
internal_score += internal_scores[i];
- counter += counts[i];
- internal_counter += internal_counts[i];
}
- // normalize: we count internal scores half as the same pair appears twice
- score += Real(0.5) * internal_score;
- const Real count = counter + Real(0.5) * internal_counter;
- if (count > 0) return score / count;
- else return score;
+
+ // all interactions in internal_score have been observed twice!
+ external_score += Real(0.5)*internal_score;
+
+ if(normalize_ && !external_scores.empty()) {
+ external_score /= external_scores.size();
+ }
+
+ return external_score;
}
-void ReducedScorer::CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
+void ReducedScorer::CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
std::vector<Real>& profile) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"ReducedScorer::CalculateScoreProfile", 2);
- std::vector<Real> scores;
+ if (env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ // setup
+ std::vector<uint> idx_vector;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, idx_vector,
+ occupied);
+ // get scores
+ std::vector<Real> external_scores;
std::vector<Real> internal_scores;
- std::vector<uint> counts;
- std::vector<uint> internal_counts;
+ this->Score(idx_vector, external_scores, internal_scores, occupied);
- this->Score(bb_list, start_resnum, chain_idx, scores, internal_scores,
- counts, internal_counts);
+ profile.resize(external_scores.size());
+ for(uint i = 0; i < external_scores.size(); ++i) {
+ profile[i] = external_scores[i] + internal_scores[i];
+ }
+}
- profile.clear();
- for(uint i = 0; i < scores.size(); ++i){
- uint count = counts[i] + internal_counts[i];
- if(count > 0) profile.push_back((scores[i] + internal_scores[i]) / count);
- else profile.push_back(scores[i] + internal_scores[i]);
+Real ReducedScorer::CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "ReducedScorer::CalculateScore", 2);
+
+ if (env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+
+ // setup
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores and sum them up
+ Real external_score = 0.0;
+ Real internal_score = 0.0;
+ uint n_scored_residues = 0;
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ this->Score(indices_vec[i], external_scores, internal_scores, occupied);
+ for (uint j = 0; j < external_scores.size(); ++j) {
+ external_score += external_scores[j];
+ internal_score += internal_scores[j];
+ }
+ n_scored_residues += external_scores.size();
+ }
+
+ // all interactions in internal_score have been observed twice!
+ external_score += Real(0.5)*internal_score;
+
+ if(normalize_ && n_scored_residues > 0) {
+ external_score /= n_scored_residues;
}
+
+ return external_score;
}
-void ReducedScorer::Score(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
- std::vector<Real>& scores,
- std::vector<Real>& internal_scores,
- std::vector<uint>& counts,
- std::vector<uint>& internal_counts) const {
+void ReducedScorer::CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "ReducedScorer::Score", 2);
+ "ReducedScorer::CalculateScore", 2);
- // setup
- if (!attached_environment_) {
+ if (env_ == NULL) {
String err = "Can only calculate score when environment is attached!";
throw promod3::Error(err);
}
- uint bb_list_size, start_idx, end_idx;
- idx_handler_->SetupScoreCalculation(bb_list, start_resnum, chain_idx,
- bb_list_size, start_idx, end_idx);
- counts.assign(bb_list_size, 0);
- scores.assign(bb_list_size, 0.0);
- if(bb_list_size == 0) return;
+ // setup
+ std::vector<std::vector<uint> > indices_vec;
+ std::vector<bool> occupied;
+ env_->GetIdxHandler()->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec,
+ occupied);
+
+ // get scores
+ profile.resize(start_resnum.size());
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> external_scores;
+ std::vector<Real> internal_scores;
+ std::vector<Real>& current_profile = profile[i];
+ this->Score(indices_vec[i], current_profile, internal_scores, occupied);
+ for (uint j = 0; j < current_profile.size(); ++j) {
+ current_profile[j] += internal_scores[j];
+
+ }
+ }
+}
+
+
+void ReducedScorer::Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
+ std::vector<Real>& internal_scores,
+ std::vector<bool>& occupied) const {
+
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "ReducedScorer::Score", 2);
+
+ // setup
+ uint n_indices = indices.size();
+
+ external_scores.assign(n_indices, 0.0);
+ internal_scores.assign(n_indices, 0.0);
+
+ if(n_indices == 0) return;
// let's reduce the cutoff a bit -> hack to ensure bin always within range
- const Real squared_cutoff = cutoff_*cutoff_ - 0.001;
const Real cutoff = cutoff_ - 0.001;
// get inv sizes for binning
const Real inv_dist_bin_size = dist_bins_ / cutoff_;
const Real inv_angle_bin_size = angle_bins_ / Real(M_PI);
const Real inv_dihedral_bin_size = dihedral_bins_ / (2 * Real(M_PI));
- // let's precalculate the idx ranges we have to neglect
- int min_idx_chain = idx_handler_->GetChainStartIdx(chain_idx);
- int max_idx_chain = min_idx_chain + idx_handler_->GetChainSize(chain_idx) - 1;
- std::vector<int> start_neglect(bb_list_size, start_idx);
- std::vector<int> end_neglect(bb_list_size, end_idx);
- int neglect_range = int(seq_sep_) - 1;
-
- int max_i = std::min(neglect_range, static_cast<int>(bb_list_size));
- for (int i = 0; i < max_i; ++i) {
- start_neglect[i] =
- std::max(min_idx_chain, start_neglect[i]-(neglect_range-i));
- end_neglect[bb_list_size-1-i] =
- std::min(max_idx_chain, end_neglect[i]+(neglect_range-i));
- }
-
- // extract bb_list data
- std::vector<geom::Vec3> bb_list_axis(bb_list_size);
- std::vector<geom::Vec3> bb_list_ca_pos(bb_list_size);
- for (uint i = 0; i < bb_list_size; ++i) {
- bb_list_ca_pos[i] = bb_list.GetCA(i);
- bb_list_axis[i] = geom::Normalize(geom::Normalize(bb_list_ca_pos[i]
- -bb_list.GetN(i)) +
- geom::Normalize(bb_list_ca_pos[i]
- -bb_list.GetC(i)));
- }
-
- // get score
- Real dist;
+ // some param required in score calculation
Real alpha;
Real beta;
Real gamma;
@@ -367,70 +431,62 @@ void ReducedScorer::Score(const loop::BackboneList& bb_list,
uint alpha_bin;
uint beta_bin;
uint gamma_bin;
+ Real e;
geom::Vec3 ca_vec;
+
// let's go over every loop residue
ReducedSpatialOrganizer::WithinResult within_result;
std::pair<ReducedSpatialOrganizerItem*,Real>* a;
- for (uint i = 0; i < bb_list_size; ++i) {
- within_result = env_->FindWithin(bb_list_ca_pos[i], cutoff);
+ const loop::IdxHandler* idx_handler = env_->GetIdxHandler();
+ const int* env_set = env_->GetEnvSetData();
+ for (uint i = 0; i < n_indices; ++i) {
+ int my_idx = indices[i];
+
+ if(!env_set[my_idx]) {
+ throw promod3::Error("Must set environment before scoring!");
+ }
+
+ int my_chain_idx = idx_handler->GetChainIdx(my_idx);
+ ost::conop::AminoAcid my_aa = env_->GetEnvData(my_idx).aa;
+ geom::Vec3 my_pos = env_->GetEnvData(my_idx).pos;
+ geom::Vec3 my_axis = env_->GetEnvData(my_idx).axis;
+
+ within_result = env_->FindWithin(my_pos, cutoff);
a = within_result.first;
- const ost::conop::AminoAcid myaa = bb_list.GetAA(i);
+
for (uint j = 0; j < within_result.second; ++j) {
- const int my_idx = int(a[j].first->idx);
- if (my_idx < start_neglect[i] || my_idx > end_neglect[i]) {
- ca_vec = a[j].first->pos - bb_list_ca_pos[i];
+ int other_idx = int(a[j].first->idx);
+ int other_chain_idx = idx_handler->GetChainIdx(other_idx);
+
+ if (my_chain_idx != other_chain_idx ||
+ std::abs(my_idx - other_idx) >= seq_sep_) {
+ ca_vec = a[j].first->pos - my_pos;
ca_vec *= (Real(1.0) / a[j].second);
- GetReducedAngles(bb_list_axis[i], ca_vec, a[j].first->axis,
+ GetReducedAngles(my_axis, ca_vec, a[j].first->axis,
alpha, beta, gamma);
dist_bin = a[j].second * inv_dist_bin_size;
alpha_bin = alpha * inv_angle_bin_size;
beta_bin = beta * inv_angle_bin_size;
gamma_bin = gamma * inv_dihedral_bin_size;
- scores[i] += energies_[this->EIdx(myaa, a[j].first->aa, dist_bin,
- alpha_bin, beta_bin, gamma_bin)];
- counts[i] += 1;
- }
- }
- }
- // now all the loop internal interactions
-
- internal_counts.assign(bb_list_size, 0);
- internal_scores.assign(bb_list_size, 0.0);
- if (bb_list_size >= seq_sep_) {
- for (uint i = 0; i < bb_list_size-seq_sep_; ++i) {
- const ost::conop::AminoAcid myaa = bb_list.GetAA(i);
- for (uint j = i+seq_sep_; j < bb_list_size; ++j) {
- ca_vec = bb_list_ca_pos[j] - bb_list_ca_pos[i];
- dist = geom::Length2(ca_vec);
- if (dist < squared_cutoff) {
- dist = std::sqrt(dist);
- ca_vec *= (Real(1.0) / dist);
- GetReducedAngles(bb_list_axis[i], ca_vec, bb_list_axis[j],
- alpha, beta, gamma);
- dist_bin = dist * inv_dist_bin_size;
- alpha_bin = alpha * inv_angle_bin_size;
- beta_bin = beta * inv_angle_bin_size;
- gamma_bin = gamma * inv_dihedral_bin_size;
-
- // go symmetric
- internal_scores[i] += energies_[this->EIdx(myaa, bb_list.GetAA(j),
- dist_bin, alpha_bin,
- beta_bin, gamma_bin)];
- internal_scores[j] += energies_[this->EIdx(bb_list.GetAA(j), myaa,
- dist_bin, beta_bin,
- alpha_bin, gamma_bin)];
- internal_counts[i] += 1;
- internal_counts[j] += 1;
+
+ e = energies_[this->EIdx(my_aa, a[j].first->aa, dist_bin,
+ alpha_bin, beta_bin, gamma_bin)];
+
+ if(occupied[other_idx] && do_internal_scores_) {
+ internal_scores[i] += e;
+ }
+
+ if(!occupied[other_idx] && do_external_scores_) {
+ external_scores[i] += e;
}
}
}
}
+
}
void ReducedScorer::AttachEnvironment(BackboneScoreEnv& env) {
env_ = env.UniqueListener<ReducedEnvListener>("ReducedEnvListener");
- idx_handler_ = env.GetIdxHandlerData();
- attached_environment_ = true;
}
}}
diff --git a/scoring/src/reduced_score.hh b/scoring/src/reduced_score.hh
index 41d40f0be1e86cc129b0578eb0c5218cf740301a..e41f784c28bfba0b9e053e11e594eb4105b9f24f 100644
--- a/scoring/src/reduced_score.hh
+++ b/scoring/src/reduced_score.hh
@@ -33,18 +33,34 @@ public:
uint dist_bin, uint alpha_bin, uint beta_bin, uint gamma_bin,
Real e);
- virtual Real CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const;
+ void DoInternalScores(bool do_it) { do_internal_scores_ = do_it; }
- virtual void CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
+ void DoExternalScores(bool do_it) { do_external_scores_ = do_it; }
+
+ void DoNormalize(bool do_it) { normalize_ = do_it; }
+
+ virtual Real CalculateScore(uint start_resnum, uint num_residues,
+ uint chain_idx) const;
+
+ virtual void CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
std::vector<Real>& profile) const;
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const;
+
void AttachEnvironment(BackboneScoreEnv& env);
private:
- ReducedScorer(): attached_environment_(false), env_(NULL) { }
+ ReducedScorer(): do_internal_scores_(true), do_external_scores_(true),
+ normalize_(true), env_(NULL) { }
inline uint EIdx(ost::conop::AminoAcid a, ost::conop::AminoAcid b,
uint dist_bin, uint alpha_bin, uint beta_bin,
@@ -58,13 +74,10 @@ private:
* angle_bins_ * dihedral_bins_;
}
- void Score(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx,
- std::vector<Real>& scores,
+ void Score(const std::vector<uint>& indices,
+ std::vector<Real>& external_scores,
std::vector<Real>& internal_scores,
- std::vector<uint>& counts,
- std::vector<uint>& internal_counts) const;
+ std::vector<bool>& occupied) const;
// portable serialization (only stores data relevant for Load/Save!)
// (cleanly element by element with fixed-width base-types)
@@ -87,14 +100,14 @@ private:
uint angle_bins_;
uint dihedral_bins_;
uint seq_sep_;
-
Real* energies_;
+ bool do_internal_scores_;
+ bool do_external_scores_;
+ bool normalize_;
//environment specific information, that will be set upon calling
//AttachEnvironment
- bool attached_environment_;
ReducedEnvListener* env_;
- const loop::IdxHandler* idx_handler_;
};
diff --git a/scoring/src/scoring_object_loader.cc b/scoring/src/scoring_object_loader.cc
index 043225ba2c95a271f79f632fd8ce1a24ee403543..fff223a9fb260b0b4eddbad3d6fae500a45a42b5 100644
--- a/scoring/src/scoring_object_loader.cc
+++ b/scoring/src/scoring_object_loader.cc
@@ -3,7 +3,6 @@
#include <promod3/core/runtime_profiling.hh>
#include <promod3/scoring/clash_score.hh>
#include <promod3/scoring/pairwise_score.hh>
-#include <promod3/scoring/density_score.hh>
#include <promod3/scoring/all_atom_clash_score.hh>
namespace promod3{ namespace scoring {
@@ -81,10 +80,8 @@ BackboneOverallScorerPtr LoadDefaultBackboneOverallScorer() {
(*scorer)["reduced"] = LoadReducedScorer();
(*scorer)["clash"] = ClashScorerPtr(new ClashScorer);
(*scorer)["hbond"] = LoadHBondScorer();
- (*scorer)["ss_agreement"] = LoadSSAgreementScorer();
(*scorer)["torsion"] = LoadTorsionScorer();
(*scorer)["pairwise"] = PairwiseScorerPtr(new PairwiseScorer);
- (*scorer)["density"] = DensityScorerPtr(new DensityScorer);
return scorer;
}
diff --git a/scoring/src/scwrl3_energy_functions.hh b/scoring/src/scwrl3_energy_functions.hh
new file mode 100644
index 0000000000000000000000000000000000000000..7db72ebf5611fd7424e940a63f26c1de8b49222d
--- /dev/null
+++ b/scoring/src/scwrl3_energy_functions.hh
@@ -0,0 +1,49 @@
+#ifndef PM3_SCWRL3_ENERGY_FUNCTIONS_HH
+#define PM3_SCWRL3_ENERGY_FUNCTIONS_HH
+
+#include <ost/geom/vec3.hh>
+#include <ost/geom/vecmat3_op.hh>
+
+namespace promod3 { namespace scoring {
+
+inline Real SCWRL3PairwiseScore(Real d, Real Rij) {
+ Real e = 0.0;
+ if(d < Real(0.8254) * Rij) {
+ e = 10.0;
+ } else if(d <= Rij) {
+ e = 57.273 * (1 - d/Rij);
+ }
+ return e;
+}
+
+
+inline Real SCWRL3DisulfidScore(const geom::Vec3& ca_pos_one,
+ const geom::Vec3& cb_pos_one,
+ const geom::Vec3& sg_pos_one,
+ const geom::Vec3& ca_pos_two,
+ const geom::Vec3& cb_pos_two,
+ const geom::Vec3& sg_pos_two) {
+
+ Real d = geom::Distance(sg_pos_one,sg_pos_two);
+ Real a1 = geom::Angle(cb_pos_one-sg_pos_one, sg_pos_two-sg_pos_one);
+ Real a2 = geom::Angle(sg_pos_one-sg_pos_two, cb_pos_two-sg_pos_two);
+ Real x2 = std::abs(geom::DihedralAngle(ca_pos_one, cb_pos_one, sg_pos_one,
+ sg_pos_two));
+ Real x3 = std::abs(geom::DihedralAngle(cb_pos_one, sg_pos_one, sg_pos_two,
+ cb_pos_two));
+ Real x4 = std::abs(geom::DihedralAngle(sg_pos_one, sg_pos_two, cb_pos_two,
+ ca_pos_two));
+
+ return std::abs(d-2) / Real(0.05)
+ + std::abs(a1-Real(1.8151)) / Real(0.087266)
+ + std::abs(a2-Real(1.8151)) / Real(0.087266)
+ + std::min(std::abs(x2-Real(1.3963)), std::abs(x2-Real(M_PI)))
+ / Real(0.17453)
+ + std::min(std::abs(x4-Real(1.3963)), std::abs(x4-Real(M_PI)))
+ / Real(0.17453)
+ + std::abs(x3-Real(M_PI)*Real(0.5)) / Real(0.34907);
+}
+
+}}//ns
+
+#endif
diff --git a/scoring/src/ss_agreement_env_listener.cc b/scoring/src/ss_agreement_env_listener.cc
index 7456098a432ae9de23a7fe66030dd39daef0f12c..e9a090ee09d03511f421b2d052773ae9798cb647 100644
--- a/scoring/src/ss_agreement_env_listener.cc
+++ b/scoring/src/ss_agreement_env_listener.cc
@@ -27,6 +27,13 @@ void SSAgreementEnvListener::Init(const BackboneScoreEnv& base_env) {
env_data_ = new SSAgreementSpatialOrganizerItem[num_residues];
env_set_ = base_env.GetEnvSetData();
+
+ psipred_pred_ = base_env.GetPsipredPredictionData();;
+ psipred_cfi_ = base_env.GetPsipredConfidenceData();
+ n_pos_data_ = base_env.GetNPosData();
+ ca_pos_data_ = base_env.GetCAPosData();
+ c_pos_data_ = base_env.GetCPosData();
+ o_pos_data_ = base_env.GetOPosData();
const ost::conop::AminoAcid* aa_data = base_env.GetAAData();
@@ -42,75 +49,47 @@ void SSAgreementEnvListener::Init(const BackboneScoreEnv& base_env) {
connected_to_next_.assign(num_residues, 0);
}
-void SSAgreementEnvListener::SetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void SSAgreementEnvListener::SetEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SSAgreementEnvListener::SetEnvironment", 2);
- if(!temp_indices_.empty()) {
- throw promod3::Error("Cannot set SSAgreement environment when temporary"
- " data is set!");
- }
-
- const geom::Vec3* n_pos_data = base_env.GetNPosData();
- const geom::Vec3* ca_pos_data = base_env.GetCAPosData();
- const geom::Vec3* c_pos_data = base_env.GetCPosData();
- const geom::Vec3* o_pos_data = base_env.GetOPosData();
-
for(std::vector<uint>::const_iterator i = idx.begin();
i != idx.end(); ++i){
- env_data_[*i].pos = ca_pos_data[*i];
- env_data_[*i].n_pos = n_pos_data[*i];
- env_data_[*i].c_pos = c_pos_data[*i];
- env_data_[*i].o_pos = o_pos_data[*i];
- env_.Add(&env_data_[*i], ca_pos_data[*i]);
+ env_data_[*i].pos = ca_pos_data_[*i];
+ env_data_[*i].n_pos = n_pos_data_[*i];
+ env_data_[*i].c_pos = c_pos_data_[*i];
+ env_data_[*i].o_pos = o_pos_data_[*i];
+ env_.Add(&env_data_[*i], ca_pos_data_[*i]);
}
this->Update(idx);
}
-void SSAgreementEnvListener::ResetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void SSAgreementEnvListener::ResetEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SSAgreementEnvListener::ResetEnvironment", 2);
- if(!temp_indices_.empty()) {
- throw promod3::Error("Cannot reset SSAgreement environment when temporary"
- " data is set!");
- }
-
- const geom::Vec3* n_pos_data = base_env.GetNPosData();
- const geom::Vec3* ca_pos_data = base_env.GetCAPosData();
- const geom::Vec3* c_pos_data = base_env.GetCPosData();
- const geom::Vec3* o_pos_data = base_env.GetOPosData();
-
geom::Vec3 old_pos;
for(std::vector<uint>::const_iterator i = idx.begin();
i != idx.end(); ++i){
old_pos = env_data_[*i].pos;
- env_data_[*i].pos = ca_pos_data[*i];
- env_data_[*i].n_pos = n_pos_data[*i];
- env_data_[*i].c_pos = c_pos_data[*i];
- env_data_[*i].o_pos = o_pos_data[*i];
- env_.Reset(&env_data_[*i], old_pos, ca_pos_data[*i]);
+ env_data_[*i].pos = ca_pos_data_[*i];
+ env_data_[*i].n_pos = n_pos_data_[*i];
+ env_data_[*i].c_pos = c_pos_data_[*i];
+ env_data_[*i].o_pos = o_pos_data_[*i];
+ env_.Reset(&env_data_[*i], old_pos, ca_pos_data_[*i]);
}
this->Update(idx);
}
-void SSAgreementEnvListener::ClearEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx) {
+void SSAgreementEnvListener::ClearEnvironment(const std::vector<uint>& idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SSAgreementEnvListener::ClearEnvironment", 2);
- if(!temp_indices_.empty()) {
- throw promod3::Error("Cannot clear SSAgreement environment when temporary"
- " data is set!");
- }
-
for(std::vector<uint>::const_iterator i = idx.begin();
i != idx.end(); ++i){
env_.Remove(&env_data_[*i], env_data_[*i].pos);
@@ -147,161 +126,6 @@ void SSAgreementEnvListener::ClearEnvironment(const BackboneScoreEnv& base_env,
}
}
-void SSAgreementEnvListener::SetTemporaryInteractions(
- const promod3::loop::BackboneList& bb_list,
- uint start_idx) {
-
- temp_start_idx_ = start_idx;
- temp_size_ = bb_list.size();
-
- // lets first copy over all the data from the bb_list, as well as one before
- // and one after
- int idx = std::max(0, temp_start_idx_ - 1);
- int end = std::min(static_cast<int>(idx_handler_->GetNumResidues()),
- temp_start_idx_ + temp_size_ + 1);
-
- for(; idx < end; ++idx) {
- temp_indices_.push_back(idx);
- original_env_data_.push_back(env_data_[idx]);
- original_ca_pos_.push_back(ca_positions_[idx]);
- original_donor_for_one_.push_back(donor_for_one_[idx]);
- original_donor_for_two_.push_back(donor_for_two_[idx]);
- original_connected_to_next_.push_back(connected_to_next_[idx]);
- }
-
- // update the env_data_ vector and the spatial organizer
- for(int i = 0; i < temp_size_; ++i) {
-
- // if the env is set, we have to reset the spatial organizer
- // we just add it otherwise
- if(env_set_[temp_start_idx_+i]) {
- env_.Reset(&env_data_[temp_start_idx_+i],
- env_data_[temp_start_idx_+i].pos, bb_list.GetCA(i));
- } else {
- env_.Add(&env_data_[temp_start_idx_+i], bb_list.GetCA(i));
- }
-
- SSAgreementSpatialOrganizerItem& organizer_item = env_data_[temp_start_idx_+i];
- organizer_item.pos = bb_list.GetCA(i);
- organizer_item.n_pos = bb_list.GetN(i);
- organizer_item.c_pos = bb_list.GetC(i);
- organizer_item.o_pos = bb_list.GetO(i);
-
- // and directly copy over the ca position
- ca_positions_[temp_start_idx_+i] = bb_list.GetCA(i);
- }
-
- // lets update connectivity
-
- // first the residue before
- if(temp_start_idx_ > 0 && env_set_[temp_start_idx_-1] &&
- geom::Length2(env_data_[temp_start_idx_-1].c_pos -
- env_data_[temp_start_idx_].n_pos) <= 6.25) {
- connected_to_next_[temp_start_idx_-1] = 1;
- } else {
- connected_to_next_[temp_start_idx_-1] = 0;
- }
-
- // connection of bb_list itself
- for(int i = 0; i < temp_size_ - 1; ++i) {
- if(geom::Length2(bb_list.GetC(i) - bb_list.GetN(i+1)) <= 6.25) {
- connected_to_next_[temp_start_idx_+i] = 1;
- } else {
- connected_to_next_[temp_start_idx_+i] = 0;
- }
- }
-
- // lets see whether the last residue is connected
- if(temp_start_idx_ + temp_size_ <
- static_cast<int>(idx_handler_->GetNumResidues()) &&
- env_set_[temp_start_idx_ + temp_size_] &&
- geom::Length2(env_data_[temp_start_idx_+temp_size_-1].c_pos -
- env_data_[temp_start_idx_+temp_size_].n_pos) <= 6.25) {
- connected_to_next_[temp_start_idx_+temp_size_-1] = 1;
- } else {
- connected_to_next_[temp_start_idx_+temp_size_-1] = 0;
- }
-
- // set h positions of all loop residues, as well as the one
- // residue after (if present)
- idx = temp_start_idx_;
- end = temp_start_idx_ + temp_size_;
- if(static_cast<uint>(end) < idx_handler_->GetNumResidues()) ++end;
- for(; idx < end; ++idx) {
- // h_pos of this residue
- if(!env_data_[idx].is_proline) {
- if(idx > 0 && connected_to_next_[idx-1]) {
- geom::Vec3 dir_vec = geom::Normalize(env_data_[idx-1].c_pos -
- env_data_[idx-1].o_pos);
- env_data_[idx].h_pos = env_data_[idx].n_pos + dir_vec;
- env_data_[idx].valid_h_pos = true;
- }
- else {
- env_data_[idx].valid_h_pos = false;
- }
- }
- }
-
- // find the optimal donor for all bb_list residues
- for(int i = 0; i < temp_size_; ++i) {
- this->FindOptimalDonors(temp_start_idx_ + i, false);
- }
-
- // we have now everything for the bb_list itself! but we also need
- // to update the donor information of close residue and store
- // their original values, so they can be restored!
-
- std::set<int> close_residues;
- for(int i = 0; i < temp_size_; ++i) {
- this->AddCloseResidues(temp_start_idx_ + i, close_residues);
- }
-
- for(std::set<int>::iterator i = close_residues.begin();
- i != close_residues.end(); ++i) {
- // the residues of the bb_list have already been handled
- int idx = *i;
- if(idx >= temp_start_idx_ && idx < temp_start_idx_ + temp_size_) continue;
-
- temp_indices_.push_back(idx);
- original_env_data_.push_back(env_data_[idx]);
- original_ca_pos_.push_back(ca_positions_[idx]);
- original_donor_for_one_.push_back(donor_for_one_[idx]);
- original_donor_for_two_.push_back(donor_for_two_[idx]);
- original_connected_to_next_.push_back(connected_to_next_[idx]);
-
- this->FindOptimalDonors(idx);
- }
-}
-
-void SSAgreementEnvListener::Restore() {
-
- for(uint i = 0; i < temp_indices_.size(); ++i) {
- int temp_idx = temp_indices_[i];
- if(temp_idx >= temp_start_idx_ && temp_idx < temp_start_idx_ + temp_size_) {
- // its in the temporarily set bb_list, so we have to handle the
- // spatial organizer
- if(env_set_[temp_idx]) {
- env_.Reset(&env_data_[temp_idx],
- env_data_[temp_idx].pos, original_ca_pos_[i]);
- } else {
- env_.Remove(&env_data_[temp_idx], env_data_[temp_idx].pos);
- }
- }
- env_data_[temp_idx] = original_env_data_[i];
- ca_positions_[temp_idx] = original_ca_pos_[i];
- donor_for_one_[temp_idx] = original_donor_for_one_[i];
- donor_for_two_[temp_idx] = original_donor_for_two_[i];
- connected_to_next_[temp_idx] = original_connected_to_next_[i];
- }
-
- temp_indices_.clear();
- original_env_data_.clear();
- original_ca_pos_.clear();
- original_donor_for_one_.clear();
- original_donor_for_two_.clear();
- original_connected_to_next_.clear();
-}
-
void SSAgreementEnvListener::AddCloseResidues(uint idx,
std::set<int>& close_residues) const {
SSAgreementSpatialOrganizer::WithinResult within_result =
@@ -312,13 +136,12 @@ void SSAgreementEnvListener::AddCloseResidues(uint idx,
}
}
-void SSAgreementEnvListener::FindOptimalDonors(uint idx, bool check_env_set) {
+void SSAgreementEnvListener::FindOptimalDonors(uint idx) {
donor_for_one_[idx] = -1;
donor_for_two_[idx] = -1;
if(!env_data_[idx].valid_h_pos) return;
- if(check_env_set && !env_set_[idx]) return;
std::pair<Real, Real> donor_energies =
std::make_pair(std::numeric_limits<Real>::max(),
@@ -330,7 +153,7 @@ void SSAgreementEnvListener::FindOptimalDonors(uint idx, bool check_env_set) {
std::pair<SSAgreementSpatialOrganizerItem*,Real>* a = within_result.first;
for (uint j = 0; j < within_result.second; ++j) {
const uint other_idx = a[j].first->idx;
- if((other_idx < idx) || (other_idx > idx + 1)) {
+ if((idx > 0 && (other_idx < idx - 1)) || (other_idx > (idx + 1))) {
Real e = ost::mol::alg::DSSPHBondEnergy(env_data_[idx].h_pos,
env_data_[idx].n_pos,
env_data_[other_idx].c_pos,
@@ -363,9 +186,10 @@ void SSAgreementEnvListener::Update(const std::vector<uint>& idx) {
for(std::vector<uint>::const_iterator i = idx.begin(); i != idx.end(); ++i){
ca_positions_[*i] = env_data_[*i].pos;
+ bool last_residue = (*i >= idx_handler_->GetNumResidues() - 1);
// set connectivity of the residue itself
- if(*i < idx_handler_->GetNumResidues() - 1 && env_set_[*i + 1] &&
+ if(!last_residue && env_set_[*i + 1] &&
geom::Length2(env_data_[*i].c_pos - env_data_[*i+1].n_pos) <= 6.25) {
connected_to_next_[*i] = 1;
} else {
@@ -396,8 +220,6 @@ void SSAgreementEnvListener::Update(const std::vector<uint>& idx) {
}
// the h_pos of the next residue might have changed
- // no check for index validity of idx + 1... this informatin is contained
- // in connected_to_next_
if(connected_to_next_[*i]) {
if(!env_data_[*i+1].is_proline) {
geom::Vec3 dir_vec = geom::Normalize(env_data_[*i].c_pos -
@@ -407,6 +229,8 @@ void SSAgreementEnvListener::Update(const std::vector<uint>& idx) {
} else {
env_data_[*i+1].valid_h_pos = false;
}
+ } else if(!last_residue) {
+ env_data_[*i+1].valid_h_pos = false;
}
}
diff --git a/scoring/src/ss_agreement_env_listener.hh b/scoring/src/ss_agreement_env_listener.hh
index 3d924e23419591bf88567186eaa6f1949cee9687..ad87b4e96753def90f56ff538fa63db1dc30361d 100644
--- a/scoring/src/ss_agreement_env_listener.hh
+++ b/scoring/src/ss_agreement_env_listener.hh
@@ -40,21 +40,21 @@ public:
virtual void Init(const BackboneScoreEnv& base_env);
- virtual void SetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void SetEnvironment(const std::vector<uint>& idx);
- virtual void ResetEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void ResetEnvironment(const std::vector<uint>& idx);
- virtual void ClearEnvironment(const BackboneScoreEnv& base_env,
- const std::vector<uint>& idx);
+ virtual void ClearEnvironment(const std::vector<uint>& idx);
virtual String WhoAmI() const { return "SSAgreementEnvListener"; }
- void SetTemporaryInteractions(const promod3::loop::BackboneList& bb_list,
- uint start_idx);
+ const int* GetEnvSetData() { return env_set_; }
- void Restore();
+ const loop::IdxHandler* GetIdxHandler() { return idx_handler_; }
+
+ const char* GetPsipredPredData() { return psipred_pred_; }
+
+ const int* GetPsipredConfidenceData() { return psipred_cfi_; }
const std::vector<geom::Vec3>& GetCAPositions() const { return ca_positions_; }
const std::vector<int>& GetDonorForOne() const { return donor_for_one_; }
@@ -70,31 +70,26 @@ private:
void AddCloseResidues(uint idx, std::set<int>& close_residues) const;
- void FindOptimalDonors(uint idx, bool check_env_set = true);
+ void FindOptimalDonors(uint idx);
SSAgreementSpatialOrganizer env_;
SSAgreementSpatialOrganizerItem* env_data_;
+
+ // data ptrs fetched from base env at initialization
const int* env_set_;
const loop::IdxHandler* idx_handler_;
-
+ const char* psipred_pred_;
+ const int* psipred_cfi_;
+ const geom::Vec3* n_pos_data_;
+ const geom::Vec3* ca_pos_data_;
+ const geom::Vec3* c_pos_data_;
+ const geom::Vec3* o_pos_data_;
+
+ // thats the input for the ost dssp implementation
std::vector<geom::Vec3> ca_positions_;
std::vector<int> donor_for_one_;
std::vector<int> donor_for_two_;
std::vector<int> connected_to_next_;
-
- // when temporary stuff gets set, the original values get
- // stored in the vectors below. When calling Restore(),
- // the stuff goes back into the original vectors
-
- // the derived data
- int temp_start_idx_;
- int temp_size_;
- std::vector<int> temp_indices_;
- std::vector<SSAgreementSpatialOrganizerItem> original_env_data_;
- std::vector<geom::Vec3> original_ca_pos_;
- std::vector<int> original_donor_for_one_;
- std::vector<int> original_donor_for_two_;
- std::vector<int> original_connected_to_next_;
};
}} // ns
diff --git a/scoring/src/ss_agreement_score.cc b/scoring/src/ss_agreement_score.cc
index aae0afb5b176388714a7b952fce857a1ce723faf..be4d6640415ed05e6074a9fcdda8e5af5d2677d2 100644
--- a/scoring/src/ss_agreement_score.cc
+++ b/scoring/src/ss_agreement_score.cc
@@ -2,11 +2,11 @@
namespace promod3 { namespace scoring {
-SSAgreementScorer::SSAgreementScorer(): attached_environment_(false),
+SSAgreementScorer::SSAgreementScorer(): normalize_(true),
env_(NULL) {
uint num_values = 3 * 10 * 8;
scores_ = new Real[num_values];
- memset(scores_,0,num_values*sizeof(Real));
+ memset(scores_, 0, num_values*sizeof(Real));
}
SSAgreementScorer::~SSAgreementScorer() {
@@ -159,83 +159,148 @@ void SSAgreementScorer::SetScore(char psipred_state, int psipred_cfi,
}
-Real SSAgreementScorer::CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const{
+Real SSAgreementScorer::CalculateScore(uint start_resnum, uint num_residues,
+ uint chain_idx) const{
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SSAgreementScorer::CalculateScore", 2);
- std::vector<Real> scores;
+ std::vector<uint> v_start_resnum(1, start_resnum);
+ std::vector<uint> v_num_residues(1, num_residues);
+ std::vector<uint> v_chain_idx(1, chain_idx);
+
+ return this->CalculateScore(v_start_resnum, v_num_residues, v_chain_idx);
+}
- this->Score(bb_list, start_resnum, chain_idx, scores);
+void SSAgreementScorer::CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
+ std::vector<Real>& profile) const{
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "SSAgreementScorer::CalculateScoreProfile", 2);
+
+ std::vector<uint> v_start_resnum(1, start_resnum);
+ std::vector<uint> v_num_residues(1, num_residues);
+ std::vector<uint> v_chain_idx(1, chain_idx);
+ std::vector<std::vector<Real> > scores;
+
+ this->CalculateScoreProfile(v_start_resnum, v_num_residues, v_chain_idx,
+ scores);
+ profile = scores[0];
+}
+
+
+Real SSAgreementScorer::CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "SSAgreementScorer::CalculateScore", 2);
+
+ std::vector<std::vector<Real> > scores;
+ this->CalculateScoreProfile(start_resnum, num_residues, chain_idx, scores);
Real score = 0.0;
+ uint n = 0;
for(uint i = 0; i < scores.size(); ++i){
- score += scores[i];
+ for(uint j = 0; j < scores[i].size(); ++j) {
+ score += scores[i][j];
+ }
+ n += scores[i].size();
}
- if(!scores.empty()){
- score /= scores.size();
+ if(normalize_ && n > 0) {
+ score /= n;
}
return score;
}
-void SSAgreementScorer::CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
- std::vector<Real>& profile) const{
-
+void SSAgreementScorer::CalculateScoreProfile(
+ const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const {
+
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SSAgreementScorer::CalculateScoreProfile", 2);
- this->Score(bb_list, start_resnum, chain_idx, profile);
-}
+ if (env_ == NULL) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
+ if(start_resnum.size() != num_residues.size()) {
+ throw promod3::Error("Inconsistent input data in Score Setup!");
+ }
+ if(start_resnum.size() != chain_idx.size()) {
+ throw promod3::Error("Inconsistent input data in Score Setup!");
+ }
-void SSAgreementScorer::Score(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
- std::vector<Real>& scores) const{
+ std::vector<uint> start_indices(start_resnum.size());
+ const loop::IdxHandler* idx_handler = env_->GetIdxHandler();
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ start_indices[i] = idx_handler->ToIdx(start_resnum[i], chain_idx[i]);
+ if(start_indices[i] + num_residues[i] - 1 >
+ idx_handler->GetChainLastIdx(chain_idx[i])) {
+ throw promod3::Error("Invalid start_resnum and loop length!");
+ }
+ }
+
+ this->Score(start_indices, num_residues, profile);
+}
+
+
+void SSAgreementScorer::Score(const std::vector<uint>& start_indices,
+ const std::vector<uint>& num_residues,
+ std::vector<std::vector<Real> >& scores) const{
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SSAgreementScorer::Score", 2);
- if(!attached_environment_){
- String err = "Can only calculate score when environment is attached!";
- throw promod3::Error(err);
- }
+ uint n_profiles = start_indices.size();
- // setup
- uint bb_list_size, start_idx, end_idx;
- idx_handler_->SetupScoreCalculation(bb_list, start_resnum, chain_idx,
- bb_list_size, start_idx, end_idx);
+ if(n_profiles == 0) return;
- scores.assign(bb_list_size, 0.0);
- if(bb_list_size == 0) return;
+ scores.assign(n_profiles, std::vector<Real>());
- env_->SetTemporaryInteractions(bb_list, start_idx);
+ const int* env_set = env_->GetEnvSetData();
+ const char* psipred_pred = env_->GetPsipredPredData();
+ const int* psipred_cfi = env_->GetPsipredConfidenceData();
- String ss = ost::mol::alg::RawEstimateSS(env_->GetCAPositions(),
- start_idx, bb_list_size,
- env_->GetDonorForOne(),
- env_->GetDonorForTwo(),
- env_->GetConnection());
- env_->Restore();
+ // check whether the full env is set
+ for(uint i = 0; i < start_indices.size(); ++i) {
+ for(uint j = 0; j < num_residues[i]; ++j) {
+ if(!env_set[start_indices[i] + j]) {
+ throw promod3::Error("Must set environment before scoring!");
+ }
+ }
+ scores[i].assign(num_residues[i], 0.0);
+ }
- for(uint i = 0; i < bb_list_size; ++i){
- scores[i] = scores_[this->SIdx(GetPsipredIdx(psipred_pred_[start_idx + i]),
- psipred_cfi_[start_idx + i],
- GetDSSPIdx(ss[i]))];
+
+ for(uint i = 0; i < n_profiles; ++i) {
+
+ if(num_residues[i] == 0) continue;
+
+ String ss = ost::mol::alg::RawEstimateSS(env_->GetCAPositions(),
+ start_indices[i],
+ num_residues[i],
+ env_->GetDonorForOne(),
+ env_->GetDonorForTwo(),
+ env_->GetConnection());
+
+ for(uint j = 0; j < num_residues[i]; ++j){
+ scores[i][j] = scores_[this->SIdx(GetPsipredIdx(psipred_pred[start_indices[i] + j]),
+ psipred_cfi[start_indices[i] + j],
+ GetDSSPIdx(ss[j]))];
+ }
}
}
void SSAgreementScorer::AttachEnvironment(BackboneScoreEnv& env) {
env_ = env.UniqueListener<SSAgreementEnvListener>("SSAgreementEnvListener");
- idx_handler_ = env.GetIdxHandlerData();
- env_set_ = env.GetEnvSetData();
- psipred_pred_ = env.GetPsipredPredictionData();
- psipred_cfi_ = env.GetPsipredConfidenceData();
- attached_environment_ = true;
}
}} // ns
diff --git a/scoring/src/ss_agreement_score.hh b/scoring/src/ss_agreement_score.hh
index 23bece022eb6766a464ee3a372b36d80b0471c8d..7e9960cffd65184225e68480da4755be32444282 100644
--- a/scoring/src/ss_agreement_score.hh
+++ b/scoring/src/ss_agreement_score.hh
@@ -59,15 +59,24 @@ public:
void SetScore(char psipred_state, int psipred_cfi,
char dssp_state, Real score);
- virtual Real CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum,
+ virtual Real CalculateScore(uint start_resnum, uint num_residues,
uint chain_idx) const;
- virtual void CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum,
+ virtual void CalculateScoreProfile(uint start_resnum, uint num_residues,
uint chain_idx,
std::vector<Real>& profile) const;
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const;
+
+ void DoNormalize(bool do_it) { normalize_ = do_it; }
+
void AttachEnvironment(BackboneScoreEnv& env);
private:
@@ -79,10 +88,9 @@ private:
dssp_idx;
}
- void Score(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx,
- std::vector<Real>& scores) const;
+ void Score(const std::vector<uint>& start_indices,
+ const std::vector<uint>& num_residues,
+ std::vector<std::vector<Real> >& scores) const;
// portable serialization (only stores data relevant for Load/Save!)
// (cleanly element by element with fixed-width base-types)
@@ -100,15 +108,11 @@ private:
}
Real* scores_;
+ bool normalize_;
//environment specific information, that will be set upon calling
//AttachEnvironment
- bool attached_environment_;
SSAgreementEnvListener* env_;
- const loop::IdxHandler* idx_handler_;
- const int* env_set_;
- const char* psipred_pred_;
- const int* psipred_cfi_;
};
}}//ns
diff --git a/scoring/src/torsion_score.cc b/scoring/src/torsion_score.cc
index 97ad3699a44c031d75072965291344f0b9e1b6cb..65cca939dda0a6a59d7ce1bf057a8b9e6329f5bb 100644
--- a/scoring/src/torsion_score.cc
+++ b/scoring/src/torsion_score.cc
@@ -8,13 +8,14 @@ TorsionScorer::TorsionScorer(std::vector<String>& group_definitions,
bins_per_dimension_(bins_per_dimension),
bins_squared_(bins_per_dimension *
bins_per_dimension),
+ normalize_(true),
attached_environment_(false)
{
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"TorsionScorer::TorsionScorer", 2);
- if(bins_per_dimension < 1){
+ if(bins_per_dimension < 1) {
throw promod3::Error("Bins per dimension must be at least one!");
}
@@ -25,9 +26,9 @@ TorsionScorer::TorsionScorer(std::vector<String>& group_definitions,
//Let's check, whether all possible combinations of the 20 standard amino
//acids are covered
std::vector<String> single_ids(3);
- for(int i = 0; i < ost::conop::XXX; ++i){
- for(int j = 0; j < ost::conop::XXX; ++j){
- for(int k = 0; k < ost::conop::XXX; ++k){
+ for(int i = 0; i < ost::conop::XXX; ++i) {
+ for(int j = 0; j < ost::conop::XXX; ++j) {
+ for(int k = 0; k < ost::conop::XXX; ++k) {
single_ids[0] = ost::conop::AminoAcidToResidueName(ost::conop::AminoAcid(i));
single_ids[1] = ost::conop::AminoAcidToResidueName(ost::conop::AminoAcid(j));
single_ids[2] = ost::conop::AminoAcidToResidueName(ost::conop::AminoAcid(k));
@@ -35,33 +36,33 @@ TorsionScorer::TorsionScorer(std::vector<String>& group_definitions,
bool match;
bool found_id(false);
- for(uint l = 0; l < group_definitions.size(); ++l){
+ for(uint l = 0; l < group_definitions.size(); ++l) {
match=true;
ost::StringRef gid(group_definitions[l].c_str(), group_definitions[l].length());
std::vector<ost::StringRef> split_definition=gid.split('-'); //split ids
- if(split_definition.size() != 3){
+ if(split_definition.size() != 3) {
throw promod3::Error("Invalid torsion group definition encountered!");
}
//iterate over all three positions
- for(int m=0;m<3;++m){
+ for(int m=0;m<3;++m) {
//"all" matches every residue
- if(split_definition[m].str().find("all")!=std::string::npos){
+ if(split_definition[m].str().find("all")!=std::string::npos) {
continue;
}
//check, whether currrent residue matches current id position
- if(split_definition[m].str().find(single_ids[m])==std::string::npos){
+ if(split_definition[m].str().find(single_ids[m])==std::string::npos) {
match=false;
break;
}
}
- if(match){
+ if(match) {
index_mapper_[i*400 + j*20 + k] = l;
found_id = true;
break;
}
}
- if(!found_id){
+ if(!found_id) {
std::stringstream ss;
ss << "Could not match residues " << single_ids[0] << ", " << single_ids[1];
ss << " and " << single_ids[2] << " to any of the group_identifiers";
@@ -77,11 +78,11 @@ TorsionScorer::TorsionScorer(std::vector<String>& group_definitions,
memset(energies_, 0, num_values * sizeof(Real));
}
-TorsionScorer::~TorsionScorer(){
+TorsionScorer::~TorsionScorer() {
delete [] energies_;
}
-TorsionScorerPtr TorsionScorer::Load(const String& filename){
+TorsionScorerPtr TorsionScorer::Load(const String& filename) {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"TorsionScorer::Load", 2);
@@ -124,7 +125,7 @@ TorsionScorerPtr TorsionScorer::Load(const String& filename){
return p;
}
-void TorsionScorer::Save(const String& filename){
+void TorsionScorer::Save(const String& filename) {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"TorsionScorer::Save", 2);
@@ -156,7 +157,7 @@ void TorsionScorer::Save(const String& filename){
out_stream.write(reinterpret_cast<char*>(energies_), num_values * sizeof(Real));
}
-TorsionScorerPtr TorsionScorer::LoadPortable(const String& filename){
+TorsionScorerPtr TorsionScorer::LoadPortable(const String& filename) {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"TorsionScorer::LoadPortable", 2);
@@ -193,7 +194,7 @@ TorsionScorerPtr TorsionScorer::LoadPortable(const String& filename){
return p;
}
-void TorsionScorer::SavePortable(const String& filename){
+void TorsionScorer::SavePortable(const String& filename) {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"TorsionScorer::SavePortable", 2);
@@ -223,13 +224,13 @@ void TorsionScorer::SavePortable(const String& filename){
out_stream_.close();
}
-void TorsionScorer::SetEnergy(uint group_idx, uint phi_bin, uint psi_bin, Real e){
+void TorsionScorer::SetEnergy(uint group_idx, uint phi_bin, uint psi_bin, Real e) {
- if(group_idx >= num_groups_){
+ if(group_idx >= num_groups_) {
throw promod3::Error("Invalid torsion group idx!");
}
- if(phi_bin >= bins_per_dimension_ || psi_bin >= bins_per_dimension_){
+ if(phi_bin >= bins_per_dimension_ || psi_bin >= bins_per_dimension_) {
throw promod3::Error("Invalid dihedral angle bin!");
}
@@ -237,190 +238,188 @@ void TorsionScorer::SetEnergy(uint group_idx, uint phi_bin, uint psi_bin, Real e
}
-Real TorsionScorer::CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const {
+Real TorsionScorer::CalculateScore(uint start_resnum, uint num_residues,
+ uint chain_idx) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"TorsionScorer::CalculateScore", 2);
- std::vector<Real> scores;
- std::vector<uint> counts;
+ if(!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
- this->Score(bb_list, start_resnum, chain_idx, scores, counts);
+ // setup
+ std::vector<uint> idx_vector;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues, chain_idx,
+ idx_vector);
+ // get scores and sum them up
+ std::vector<Real> scores;
+ this->Score(idx_vector, scores);
Real score = 0.0;
- uint counter = 0;
-
- for(uint i = 0; i < scores.size(); ++i){
+ for(uint i = 0; i < scores.size(); ++i) {
score += scores[i];
- counter += counts[i];
}
- if(counter > 0){
- score /= counter;
+ if(normalize_ && !scores.empty()){
+ score /= scores.size();
}
return score;
}
-void TorsionScorer::CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
+void TorsionScorer::CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
std::vector<Real>& profile) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"TorsionScorer::CalculateScoreProfile", 2);
- std::vector<Real> scores;
- std::vector<uint> counts;
+ if(!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
- this->Score(bb_list, start_resnum, chain_idx, scores, counts);
+ // setup
+ std::vector<uint> idx_vector;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues, chain_idx,
+ idx_vector);
- profile.clear();
- for(uint i = 0; i < scores.size(); ++i){
- if(counts[i] > 0) profile.push_back(scores[i] / counts[i]);
- else profile.push_back(scores[i]);
- }
+ // score
+ this->Score(idx_vector, profile);
}
+Real TorsionScorer::CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const {
-void TorsionScorer::Score(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
- std::vector<Real>& scores,
- std::vector<uint>& counts) const {
promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "TorsionScorer::Score", 2);
+ "TorsionScorer::CalculateScore", 2);
- if(!attached_environment_){
+ if(!attached_environment_) {
String err = "Can only calculate score when environment is attached!";
throw promod3::Error(err);
}
// setup
- uint bb_list_size, start_idx, end_idx;
- idx_handler_->SetupScoreCalculation(bb_list, start_resnum, chain_idx,
- bb_list_size, start_idx, end_idx);
+ std::vector<std::vector<uint> > indices_vec;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues, chain_idx,
+ indices_vec);
- scores.assign(bb_list_size, 0.0);
- counts.assign(bb_list_size, 0);
- if(bb_list_size == 0) return;
-
- Real angle1, angle2;
- uint bin1, bin2;
- uint torsion_group_idx;
-
- for(uint i = 1; i < bb_list_size - 1; ++i){
- torsion_group_idx = torsion_group_indices_[start_idx + i];
- angle1 = bb_list.GetPhiTorsion(i);
- angle2 = bb_list.GetPsiTorsion(i);
- bin1 = std::min(static_cast<uint>((angle1+Real(M_PI))/bin_size_),
- bins_per_dimension_-1);
- bin2 = std::min(static_cast<uint>((angle2+Real(M_PI))/bin_size_),
- bins_per_dimension_-1);
-
- scores[i] =
- energies_[this->EIdx(torsion_group_idx, bin1 * bins_per_dimension_ + bin2)];
- counts[i] = 1;
+ // get scores and sum them up
+ Real score = 0.0;
+ uint n_scored_residues = 0;
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ std::vector<Real> scores;
+ this->Score(indices_vec[i], scores);
+ for (uint j = 0; j < scores.size(); ++j) {
+ score += scores[j];
+ }
+ n_scored_residues += scores.size();
}
+
+ if(normalize_ && n_scored_residues > 0) {
+ score /= n_scored_residues;
+ }
+
+ return score;
+}
- // first handle the special case of bb_list being of size one
- if(bb_list_size == 1){
- if(start_resnum <= 1 || start_resnum >= idx_handler_->GetChainSize(chain_idx)){
- //there's nothing we can do...
- return;
- }
+void TorsionScorer::CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const {
+
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "TorsionScorer::CalculateScore", 2);
- torsion_group_idx = torsion_group_indices_[start_idx];
+ if(!attached_environment_) {
+ String err = "Can only calculate score when environment is attached!";
+ throw promod3::Error(err);
+ }
- angle1 = geom::DihedralAngle(c_pos_[start_idx - 1],
- bb_list.GetN(0),
- bb_list.GetCA(0),
- bb_list.GetC(0));
+ // setup
+ std::vector<std::vector<uint> > indices_vec;
+ idx_handler_->SetupScoreCalculation(start_resnum, num_residues,
+ chain_idx, indices_vec);
+
+ // get scores
+ profile.resize(start_resnum.size());
+ for(uint i = 0; i < start_resnum.size(); ++i) {
+ this->Score(indices_vec[i], profile[i]);
+ }
+}
- angle2 = geom::DihedralAngle(bb_list.GetN(0),
- bb_list.GetCA(0),
- bb_list.GetC(0),
- n_pos_[end_idx + 1]);
- bin1 = std::min(static_cast<uint>((angle1+Real(M_PI))/bin_size_),
- bins_per_dimension_-1);
- bin2 = std::min(static_cast<uint>((angle2+Real(M_PI))/bin_size_),
- bins_per_dimension_-1);
+void TorsionScorer::Score(const std::vector<uint>& indices,
+ std::vector<Real>& scores) const {
- scores[0] =
- energies_[this->EIdx(torsion_group_idx, bin1 * bins_per_dimension_ + bin2)];
- counts[0] = 1;
+ promod3::core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "TorsionScorer::Score", 2);
- // that's it... since we just dealt with the only residue, the stuff below
- // is not necessary anymore
- return;
- }
+ // setup
+ uint n_indices = indices.size();
+ scores.assign(n_indices, 0.0);
- if(start_resnum > 1){
- //check, whether the environment for the residue before the nstem is set
- if(env_set_[start_idx - 1]){
- torsion_group_idx = torsion_group_indices_[start_idx];
-
- //the data for the residues before and after get extracted from the env
- angle1 = geom::DihedralAngle(c_pos_[start_idx - 1],
- bb_list.GetN(0),
- bb_list.GetCA(0),
- bb_list.GetC(0));
-
- angle2 = bb_list.GetPsiTorsion(0);
-
- bin1 = std::min(static_cast<uint>((angle1+Real(M_PI))/bin_size_),
- bins_per_dimension_-1);
- bin2 = std::min(static_cast<uint>((angle2+Real(M_PI))/bin_size_),
- bins_per_dimension_-1);
+ if(n_indices == 0) return;
+
+ Real angle1, angle2;
+ uint bin1, bin2;
- scores[0] =
- energies_[this->EIdx(torsion_group_idx, bin1 * bins_per_dimension_ +
- bin2)];
- counts[0] = 1;
+ for(uint i = 0; i < n_indices; ++i) {
+ int my_idx = indices[i];
+
+ if(!env_set_[my_idx]) {
+ throw promod3::Error("Must set environment before scoring!");
}
- }
- if((start_resnum + bb_list_size - 1) < idx_handler_->GetChainSize(chain_idx)){
- //check, whether the environment for the residue after the cstem is set
- if(env_set_[end_idx + 1]){
- torsion_group_idx = torsion_group_indices_[end_idx];
-
- //the data for the residues before and after get extracted from the env
- angle1 = bb_list.GetPhiTorsion(bb_list_size-1);
- angle2 = geom::DihedralAngle(bb_list.GetN(bb_list_size-1),
- bb_list.GetCA(bb_list_size-1),
- bb_list.GetC(bb_list_size-1),
- n_pos_[end_idx + 1]);
+ int my_chain_idx = idx_handler_->GetChainIdx(my_idx);
+ int my_chain_first_idx = idx_handler_->GetChainStartIdx(my_chain_idx);
+ int my_chain_last_idx = idx_handler_->GetChainLastIdx(my_chain_idx);
+
+ if(my_idx > my_chain_first_idx && env_set_[my_idx - 1] &&
+ my_idx < my_chain_last_idx && env_set_[my_idx + 1]) {
+
+ angle1 = geom::DihedralAngle(c_pos_[my_idx - 1],
+ n_pos_[my_idx],
+ ca_pos_[my_idx],
+ c_pos_[my_idx]);
+
+ angle2 = geom::DihedralAngle(n_pos_[my_idx],
+ ca_pos_[my_idx],
+ c_pos_[my_idx],
+ n_pos_[my_idx + 1]);
+
bin1 = std::min(static_cast<uint>((angle1+Real(M_PI))/bin_size_),
bins_per_dimension_-1);
bin2 = std::min(static_cast<uint>((angle2+Real(M_PI))/bin_size_),
bins_per_dimension_-1);
- scores[bb_list_size - 1] =
- energies_[this->EIdx(torsion_group_idx, bin1 * bins_per_dimension_ +
- bin2)];
- counts[bb_list_size - 1] = 1;
+ scores[i] = energies_[this->EIdx(torsion_group_indices_[my_idx],
+ bin1 * bins_per_dimension_ + bin2)];
}
}
}
-void TorsionScorer::AttachEnvironment(BackboneScoreEnv& env){
+void TorsionScorer::AttachEnvironment(BackboneScoreEnv& env) {
idx_handler_ = env.GetIdxHandlerData();
env_set_ = env.GetEnvSetData();
n_pos_ = env.GetNPosData();
+ ca_pos_ = env.GetCAPosData();
c_pos_ = env.GetCPosData();
torsion_group_indices_.assign(idx_handler_->GetNumResidues(),0);
const ost::conop::AminoAcid* aa_data = env.GetAAData();
ost::conop::AminoAcid aa_one, aa_two, aa_three;
uint actual_idx;
- for(uint i = 0; i < idx_handler_->GetNumChains(); ++i){
- for(uint j = 1; j < idx_handler_->GetChainSize(i)-1; ++j){
+ for(uint i = 0; i < idx_handler_->GetNumChains(); ++i) {
+ for(uint j = 1; j < idx_handler_->GetChainSize(i)-1; ++j) {
actual_idx = idx_handler_->GetChainStartIdx(i) + j;
aa_one = aa_data[actual_idx - 1];
aa_two = aa_data[actual_idx];
diff --git a/scoring/src/torsion_score.hh b/scoring/src/torsion_score.hh
index ac9f92a19a20bfe894e6a3fbccbe3bfdd2c1900a..4cd298c83dab5097d0544b8825e636b540064a3d 100644
--- a/scoring/src/torsion_score.hh
+++ b/scoring/src/torsion_score.hh
@@ -33,28 +33,36 @@ public:
void SetEnergy(uint group_idx, uint phi_bin, uint psi_bin, Real e);
- virtual Real CalculateScore(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx) const;
+ virtual Real CalculateScore(uint start_resnum, uint num_residues,
+ uint chain_idx) const;
- virtual void CalculateScoreProfile(const loop::BackboneList& bb_list,
- uint start_resnum, uint chain_idx,
+ virtual void CalculateScoreProfile(uint start_resnum, uint num_residues,
+ uint chain_idx,
std::vector<Real>& profile) const;
+ virtual Real CalculateScore(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx) const;
+
+ virtual void CalculateScoreProfile(const std::vector<uint>& start_resnum,
+ const std::vector<uint>& num_residues,
+ const std::vector<uint>& chain_idx,
+ std::vector<std::vector<Real> >& profile) const;
+
+ void DoNormalize(bool do_it) { normalize_ = do_it; }
+
void AttachEnvironment(BackboneScoreEnv& env);
private:
- TorsionScorer(): attached_environment_(false) { }
+ TorsionScorer(): normalize_(true), attached_environment_(false) { }
inline uint EIdx(uint group_idx, uint torsion_bin) const{
return group_idx * bins_squared_ + torsion_bin;
}
- void Score(const loop::BackboneList& bb_list,
- uint start_resnum,
- uint chain_idx,
- std::vector<Real>& scores,
- std::vector<uint>& counts) const;
+ void Score(const std::vector<uint>& indices,
+ std::vector<Real>& scores) const;
// portable serialization (only stores data relevant for Load/Save!)
// (cleanly element by element with fixed-width base-types)
@@ -83,13 +91,15 @@ private:
Real bin_size_;
uint index_mapper_[8000];
Real* energies_;
+ bool normalize_;
- //environment specific information, that will be set upon calling
- //AttachEnvironment
+ // environment specific information, that will be set upon calling
+ // AttachEnvironment
bool attached_environment_;
const loop::IdxHandler* idx_handler_;
const int* env_set_;
const geom::Vec3* n_pos_;
+ const geom::Vec3* ca_pos_;
const geom::Vec3* c_pos_;
std::vector<uint> torsion_group_indices_;
};
diff --git a/scoring/tests/test_all_atom_scorer.cc b/scoring/tests/test_all_atom_scorer.cc
index fda63b33197461508df7c1b3f70bf0606075eedf..e1736b216d42e8cd8d70ef564a89e74f45bdcf2c 100644
--- a/scoring/tests/test_all_atom_scorer.cc
+++ b/scoring/tests/test_all_atom_scorer.cc
@@ -82,7 +82,7 @@ void CheckScorer(AllAtomScorerPtr scorer, const Real exp_score) {
BOOST_CHECK_THROW(scorer->CalculateScore(-1, 9, 0), promod3::Error);
BOOST_CHECK_THROW(scorer->CalculateScore(1000, 9, 0), promod3::Error);
// the first resnum, where 9 residues don't fit anymore...
- BOOST_CHECK_THROW(scorer->CalculateScore(255, 9, 0), promod3::Error)
+ BOOST_CHECK_THROW(scorer->CalculateScore(255, 9, 0), promod3::Error);
// test the actual score outcome
BOOST_CHECK_CLOSE(scorer->CalculateScore(214, 9, 0), exp_score, Real(1e-3));
@@ -125,14 +125,14 @@ BOOST_AUTO_TEST_CASE(test_aa_interaction_score) {
AllAtomInteractionScorerPtr scorer = LoadAllAtomInteractionScorer();
scorer->AttachEnvironment(env);
// NOTE: not comparable to QMEAN anymore as we halve internal ones...
- CheckScorer(scorer, -0.00717731751502);
+ CheckScorer(scorer, -3.58627);
}
BOOST_AUTO_TEST_CASE(test_aa_packing_score) {
promod3::loop::AllAtomEnv env = GenerateAllAtomEnv();
AllAtomPackingScorerPtr scorer = LoadAllAtomPackingScorer();
scorer->AttachEnvironment(env);
- CheckScorer(scorer, -0.367893904448);
+ CheckScorer(scorer, -2.90227);
}
BOOST_AUTO_TEST_CASE(test_aa_clash_score) {
@@ -149,7 +149,7 @@ BOOST_AUTO_TEST_CASE(test_aa_clash_score2) {
AllAtomClashScorerPtr scorer(new AllAtomClashScorer);
scorer->AttachEnvironment(env);
Real clash_score = scorer->CalculateScore(35, 5, 0);
- BOOST_CHECK_CLOSE(clash_score, 1.73935568333, Real(1e-3));
+ BOOST_CHECK_CLOSE(clash_score, 14.2627, Real(1e-3));
}
BOOST_AUTO_TEST_CASE(test_aa_clash_score3) {
@@ -162,6 +162,7 @@ BOOST_AUTO_TEST_CASE(test_aa_clash_score3) {
BOOST_CHECK_CLOSE(clash_score, 0.0, Real(1e-3));
}
+
BOOST_AUTO_TEST_CASE(test_aa_overall_scorer) {
// setup env
promod3::loop::AllAtomEnv env = GenerateAllAtomEnv();
@@ -188,10 +189,10 @@ BOOST_AUTO_TEST_CASE(test_aa_overall_scorer) {
"aa_clash");
// check final score// exp. score from single ones above
- Real exp_score = 0.1 * -0.367893904448 + 0.2 * -0.00717731751502
+ Real exp_score = 0.1 * -2.90227 + 0.2 * -3.58627
+ 0.3 * 0.0 + 1.0;
- BOOST_CHECK_CLOSE(scorer.CalculateLinearCombination(weights, 214, 9, 0),
- exp_score, Real(1e-3));
+ Real calculated_score = scorer.CalculateLinearCombination(weights, 214, 9, 0);
+ BOOST_CHECK(std::abs(calculated_score - exp_score) < Real(0.00001));
// check for more errors
BOOST_CHECK(!scorer.Contains("meh"));
@@ -199,7 +200,141 @@ BOOST_AUTO_TEST_CASE(test_aa_overall_scorer) {
weights["meh"] = 5.0;
BOOST_CHECK_THROW(scorer.CalculateLinearCombination(weights, 214, 9, 0),
promod3::Error);
+}
+
+BOOST_AUTO_TEST_CASE(test_aa_normalize) {
+
+ // setup env with something that clashes
+ String pdb_name = "data/clash_test.pdb";
+ promod3::loop::AllAtomEnv env = GenerateAllAtomEnv(pdb_name, "");
+
+ // setup scorer
+ AllAtomOverallScorer scorer;
+ // setup weights
+ std::map<String, Real> weights;
+ weights["aa_packing"] = 1.0;
+ weights["aa_interaction"] = 1.0;
+ weights["aa_clash"] = 1.0;
+
+ AllAtomPackingScorerPtr packing_scorer = LoadAllAtomPackingScorer();
+ AllAtomInteractionScorerPtr interaction_scorer = LoadAllAtomInteractionScorer();
+ AllAtomClashScorerPtr clash_scorer = AllAtomClashScorerPtr(new AllAtomClashScorer);
+
+ scorer["aa_packing"] = packing_scorer;
+ scorer["aa_interaction"] = interaction_scorer;
+ scorer["aa_clash"] = clash_scorer;
+
+ scorer.AttachEnvironment(env);
+
+ Real exp_score = scorer.CalculateLinearCombination(weights, 2, 44, 0);
+
+ packing_scorer->DoNormalize(false);
+ interaction_scorer->DoNormalize(false);
+ clash_scorer->DoNormalize(false);
+
+ BOOST_CHECK_CLOSE(scorer.CalculateLinearCombination(weights, 2, 44, 0),
+ 44 * exp_score, 1e-3);
+}
+
+
+BOOST_AUTO_TEST_CASE(test_aa_internal_external) {
+
+ // setup env with something that clashes
+ String pdb_name = "data/clash_test.pdb";
+ promod3::loop::AllAtomEnv env = GenerateAllAtomEnv(pdb_name, "");
+
+ // load scorere (only the ones that provide the internal / external mechanism)
+ AllAtomInteractionScorerPtr interaction_scorer =
+ LoadAllAtomInteractionScorer();
+ AllAtomClashScorerPtr clash_scorer =
+ AllAtomClashScorerPtr(new AllAtomClashScorer);
+ interaction_scorer->AttachEnvironment(env);
+ clash_scorer->AttachEnvironment(env);
+
+ // lets do the overall score... this should be well tested by now
+ Real interaction_score = interaction_scorer->CalculateScore(2, 44, 0);
+ Real clash_score = clash_scorer->CalculateScore(2, 44, 0);
+
+ // lets do the internal scores
+ interaction_scorer->DoExternalScores(false);
+ clash_scorer->DoExternalScores(false);
+ Real internal_interaction_score =
+ interaction_scorer->CalculateScore(2, 44, 0);
+ Real internal_clash_score =
+ clash_scorer->CalculateScore(2, 44, 0);
+
+ // lets do the external scores
+ interaction_scorer->DoExternalScores(true);
+ clash_scorer->DoExternalScores(true);
+ interaction_scorer->DoInternalScores(false);
+ clash_scorer->DoInternalScores(false);
+ Real external_interaction_score =
+ interaction_scorer->CalculateScore(2, 44, 0);
+ Real external_clash_score =
+ clash_scorer->CalculateScore(2, 44, 0);
+
+ // the sum between the internal and external score must be the total score
+ BOOST_CHECK_CLOSE(internal_interaction_score + external_interaction_score,
+ interaction_score, Real(1e-3));
+ BOOST_CHECK_CLOSE(internal_clash_score + external_clash_score,
+ clash_score, Real(1e-3));
+
+ // Do internal AND external scores and kill the full environment except the
+ // actual loop to score. As a result, we should get the previously calculated
+ // INTERNAL score.
+ interaction_scorer->DoInternalScores(true);
+ clash_scorer->DoExternalScores(true);
+ interaction_scorer->DoInternalScores(true);
+ clash_scorer->DoExternalScores(true);
+ promod3::loop::AllAtomEnvPositionsPtr env_pos_only_loop =
+ env.GetEnvironment(2, 44, 0);
+ env.ClearEnvironment(1, env.GetIdxHandlerData()->GetChainSize(0), 0);
+ env.SetEnvironment(*env_pos_only_loop);
+ BOOST_CHECK_CLOSE(interaction_scorer->CalculateScore(2, 44, 0),
+ internal_interaction_score, Real(1e-3));
+ BOOST_CHECK_CLOSE(clash_scorer->CalculateScore(2, 44, 0),
+ internal_clash_score, Real(1e-3));
+}
+
+BOOST_AUTO_TEST_CASE(test_aa_multiple_stretches) {
+
+ // setup env with something that clashes
+ String pdb_name = "data/clash_test.pdb";
+ promod3::loop::AllAtomEnv env = GenerateAllAtomEnv(pdb_name, "");
+
+ // setup scorer
+ AllAtomOverallScorer scorer;
+ // setup weights
+ std::map<String, Real> weights;
+ weights["aa_packing"] = 1.0;
+ weights["aa_interaction"] = 1.0;
+ weights["aa_clash"] = 1.0;
+
+ AllAtomPackingScorerPtr packing_scorer = LoadAllAtomPackingScorer();
+ AllAtomInteractionScorerPtr interaction_scorer = LoadAllAtomInteractionScorer();
+ AllAtomClashScorerPtr clash_scorer = AllAtomClashScorerPtr(new AllAtomClashScorer);
+
+ scorer["aa_packing"] = packing_scorer;
+ scorer["aa_interaction"] = interaction_scorer;
+ scorer["aa_clash"] = clash_scorer;
+
+ scorer.AttachEnvironment(env);
+
+ Real exp_score = scorer.CalculateLinearCombination(weights, 2, 44, 0);
+
+ std::vector<uint> start_resnums;
+ std::vector<uint> stretch_lengths;
+ std::vector<uint> chain_indices;
+ uint first_stretch_length = 20;
+ start_resnums.push_back(2);
+ start_resnums.push_back(2 + first_stretch_length);
+ stretch_lengths.push_back(first_stretch_length);
+ stretch_lengths.push_back(44 - first_stretch_length);
+ chain_indices.push_back(0);
+ chain_indices.push_back(0);
+ BOOST_CHECK_CLOSE(scorer.CalculateLinearCombination(weights, start_resnums,
+ stretch_lengths, chain_indices), exp_score, 1e-3);
}
BOOST_AUTO_TEST_SUITE_END();
diff --git a/scoring/tests/test_backbone_scorer.cc b/scoring/tests/test_backbone_scorer.cc
index 6886e0e13a806553755137927b6c2334b6f613bc..49922b4b65c3292dcf9b519bb4d96c2b0d80ba4c 100644
--- a/scoring/tests/test_backbone_scorer.cc
+++ b/scoring/tests/test_backbone_scorer.cc
@@ -119,27 +119,61 @@ void SetPsipredPrediction(BackboneScoreEnv& env) {
// check scorer calls for def. bb_list
void CheckScorerThrows(const promod3::loop::BackboneList& bb_list,
BackboneScorerPtr scorer) {
+
// test check of chain_idx
- BOOST_CHECK_THROW(scorer->CalculateScore(bb_list, 214, -1), promod3::Error);
- BOOST_CHECK_THROW(scorer->CalculateScore(bb_list, 214, 1), promod3::Error);
+ BOOST_CHECK_THROW(scorer->CalculateScore(214, bb_list.size(), -1), promod3::Error);
+ BOOST_CHECK_THROW(scorer->CalculateScore(214, bb_list.size(), 1), promod3::Error);
// test check of start resnum
- BOOST_CHECK_THROW(scorer->CalculateScore(bb_list, 0, 0), promod3::Error);
- BOOST_CHECK_THROW(scorer->CalculateScore(bb_list, -1, 0), promod3::Error);
- BOOST_CHECK_THROW(scorer->CalculateScore(bb_list, 1000, 0), promod3::Error);
+ BOOST_CHECK_THROW(scorer->CalculateScore(0, bb_list.size(), 0), promod3::Error);
+ BOOST_CHECK_THROW(scorer->CalculateScore(-1, bb_list.size(), 0), promod3::Error);
+ BOOST_CHECK_THROW(scorer->CalculateScore(1000, bb_list.size(), 0), promod3::Error);
// the first resnum, where the bb_list doesn't fit anymore...
- BOOST_CHECK_THROW(scorer->CalculateScore(bb_list, 255, 0), promod3::Error)
+ BOOST_CHECK_THROW(scorer->CalculateScore(255, bb_list.size(), 0), promod3::Error);
// check that empty BB list gives score of 0 (always)
promod3::loop::BackboneList sub_bb_list;
- BOOST_CHECK_EQUAL(scorer->CalculateScore(sub_bb_list, 214, 0), Real(0));
+ BOOST_CHECK_EQUAL(scorer->CalculateScore(214, sub_bb_list.size(), 0), Real(0));
// check that border cases don't break
if (bb_list.size() > 1) {
sub_bb_list = bb_list.Extract(0, 1);
- BOOST_CHECK_NO_THROW(scorer->CalculateScore(sub_bb_list, 214, 0));
+ BOOST_CHECK_NO_THROW(scorer->CalculateScore(214, sub_bb_list.size(), 0));
sub_bb_list = bb_list.Extract(0, 2);
- BOOST_CHECK_NO_THROW(scorer->CalculateScore(sub_bb_list, 214, 0));
+ BOOST_CHECK_NO_THROW(scorer->CalculateScore(214, sub_bb_list.size(), 0));
}
+
+ std::vector<uint> start_resnum(1);
+ std::vector<uint> chain_idx(1);
+ std::vector<uint> num_residues(1);
+ num_residues[0] = bb_list.size();
+
+ // test check of chain_idx
+ start_resnum[0] = 214;
+ chain_idx[0] = -1;
+ BOOST_CHECK_THROW(scorer->CalculateScore(start_resnum, num_residues, chain_idx),
+ promod3::Error);
+ chain_idx[0] = 1;
+ BOOST_CHECK_THROW(scorer->CalculateScore(start_resnum, num_residues, chain_idx),
+ promod3::Error);
+
+ // test check of start resnum
+ chain_idx[0] = 0;
+ start_resnum[0] = 0;
+ BOOST_CHECK_THROW(scorer->CalculateScore(start_resnum, num_residues, chain_idx),
+ promod3::Error);
+
+ start_resnum[0] = -1;
+ BOOST_CHECK_THROW(scorer->CalculateScore(start_resnum, num_residues, chain_idx),
+ promod3::Error);
+
+ start_resnum[0] = 1000;
+ BOOST_CHECK_THROW(scorer->CalculateScore(start_resnum, num_residues, chain_idx),
+ promod3::Error);
+
+ start_resnum[0] = 255;
+ // the first resnum, where the bb_list doesn't fit anymore...
+ BOOST_CHECK_THROW(scorer->CalculateScore(start_resnum, num_residues, chain_idx),
+ promod3::Error);
}
// check overall scorer on a single score
@@ -148,12 +182,12 @@ void SanityCheckOverallScorer(BackboneOverallScorer& scorer,
const promod3::loop::BackboneList& bb_list,
const String& key) {
// ref = single score
- Real ref_score = single_scorer->CalculateScore(bb_list, 214, 0);
- Real score = scorer.Calculate(key, bb_list, 214, 0);
+ Real ref_score = single_scorer->CalculateScore(214, bb_list.size(), 0);
+ Real score = scorer.Calculate(key, 214, bb_list.size(), 0);
BOOST_CHECK_CLOSE(score, ref_score, Real(1e-3));
std::map<String, Real> weights;
weights[key] = 1.0;
- score = scorer.CalculateLinearCombination(weights, bb_list, 214, 0);
+ score = scorer.CalculateLinearCombination(weights, 214, bb_list.size(), 0);
BOOST_CHECK_CLOSE(score, ref_score, Real(1e-3));
}
@@ -228,36 +262,37 @@ BOOST_AUTO_TEST_CASE(qmean_comparison) {
orig_cb_packing.push_back(-0.6673);
std::vector<Real> orig_cb;
- orig_cb.push_back(-0.0190);
- orig_cb.push_back(0.0398);
- orig_cb.push_back(-0.0456);
- orig_cb.push_back(0.0262);
- orig_cb.push_back(-0.0427);
- orig_cb.push_back(-0.0237);
- orig_cb.push_back(-0.0228);
- orig_cb.push_back(-0.0182);
- orig_cb.push_back(0.0809);
- orig_cb.push_back(0.0577);
- orig_cb.push_back(0.0107);
- orig_cb.push_back(-0.0284);
- orig_cb.push_back(-0.0311);
- orig_cb.push_back(0.0025);
+ orig_cb.push_back(-0.342035);
+ orig_cb.push_back(0.238565);
+ orig_cb.push_back(-0.410386);
+ orig_cb.push_back(0.340058);
+ orig_cb.push_back(-0.341305);
+ orig_cb.push_back(-0.0710439);
+ orig_cb.push_back(-0.0911381);
+ orig_cb.push_back(-0.0181578);
+ orig_cb.push_back(0.808517);
+ orig_cb.push_back(0.461206);
+ orig_cb.push_back(0.139356);
+ orig_cb.push_back(-0.482617);
+ orig_cb.push_back(-0.497085);
+ orig_cb.push_back(0.0492029);
+
std::vector<Real> orig_reduced;
- orig_reduced.push_back(-0.2539);
- orig_reduced.push_back(0.0478);
- orig_reduced.push_back(-0.5097);
- orig_reduced.push_back(-0.4198);
- orig_reduced.push_back(-0.2336);
- orig_reduced.push_back(-0.3308);
- orig_reduced.push_back(0.1811);
- orig_reduced.push_back(-0.9057);
- orig_reduced.push_back(-0.0299);
- orig_reduced.push_back(-0.3473);
- orig_reduced.push_back(-0.2229);
- orig_reduced.push_back(-0.2734);
- orig_reduced.push_back(-0.4254);
- orig_reduced.push_back(-0.5835);
+ orig_reduced.push_back(-3.55399);
+ orig_reduced.push_back(0.52569);
+ orig_reduced.push_back(-5.0972);
+ orig_reduced.push_back(-5.45686);
+ orig_reduced.push_back(-1.86842);
+ orig_reduced.push_back(-0.992303);
+ orig_reduced.push_back(0.543362);
+ orig_reduced.push_back(-3.62267);
+ orig_reduced.push_back(-0.268999);
+ orig_reduced.push_back(-4.16786);
+ orig_reduced.push_back(-2.89717);
+ orig_reduced.push_back(-4.37486);
+ orig_reduced.push_back(-7.23112);
+ orig_reduced.push_back(-10.5035);
std::vector<Real> orig_torsion;
orig_torsion.push_back(0.4922);
@@ -323,37 +358,37 @@ BOOST_AUTO_TEST_CASE(qmean_comparison) {
reset_cb_packing.push_back(-0.4551);
reset_cb_packing.push_back(-0.6673);
- std::vector<Real> reset_cb;
- reset_cb.push_back(-0.0164);
- reset_cb.push_back(0.0530);
- reset_cb.push_back(-0.0599);
- reset_cb.push_back(-0.0247);
- reset_cb.push_back(-0.0476);
- reset_cb.push_back(-0.0220);
- reset_cb.push_back(-0.0719);
- reset_cb.push_back(-0.0463);
- reset_cb.push_back(-0.0082);
- reset_cb.push_back(0.0286);
- reset_cb.push_back(0.0067);
- reset_cb.push_back(-0.0284);
- reset_cb.push_back(-0.0311);
- reset_cb.push_back(0.0025);
-
+ std::vector<Real> reset_cb;
+ reset_cb.push_back(-0.32877);
+ reset_cb.push_back(0.371232);
+ reset_cb.push_back(-0.479475);
+ reset_cb.push_back(-0.369955);
+ reset_cb.push_back(-0.428097);
+ reset_cb.push_back(-0.0879088);
+ reset_cb.push_back(-0.43112);
+ reset_cb.push_back(-0.324168);
+ reset_cb.push_back(-0.0822164);
+ reset_cb.push_back(0.228412);
+ reset_cb.push_back(0.0871677);
+ reset_cb.push_back(-0.510713);
+ reset_cb.push_back(-0.497085);
+ reset_cb.push_back(0.0492029);
+
std::vector<Real> reset_reduced;
- reset_reduced.push_back(-0.2078);
- reset_reduced.push_back(0.1609);
- reset_reduced.push_back(-0.1293);
- reset_reduced.push_back(-0.3096);
- reset_reduced.push_back(-0.1068);
- reset_reduced.push_back(-0.0871);
- reset_reduced.push_back(0.1635);
- reset_reduced.push_back(0.3477);
- reset_reduced.push_back(-0.1095);
- reset_reduced.push_back(-0.2002);
- reset_reduced.push_back(-0.2179);
- reset_reduced.push_back(-0.2680);
- reset_reduced.push_back(-0.4254);
- reset_reduced.push_back(-0.5835);
+ reset_reduced.push_back(-3.32411);
+ reset_reduced.push_back(1.60945);
+ reset_reduced.push_back(-1.03455);
+ reset_reduced.push_back(-4.02522);
+ reset_reduced.push_back(-0.961522);
+ reset_reduced.push_back(-0.435582);
+ reset_reduced.push_back(0.653847);
+ reset_reduced.push_back(1.73842);
+ reset_reduced.push_back(-0.985268);
+ reset_reduced.push_back(-2.20225);
+ reset_reduced.push_back(-2.83298);
+ reset_reduced.push_back(-4.28751);
+ reset_reduced.push_back(-7.23112);
+ reset_reduced.push_back(-10.5035);
std::vector<Real> reset_torsion;
reset_torsion.push_back(1.0555);
@@ -420,36 +455,37 @@ BOOST_AUTO_TEST_CASE(qmean_comparison) {
deleted_cb_packing.push_back(-0.9996);
std::vector<Real> deleted_cb;
- deleted_cb.push_back(-0.0237);
- deleted_cb.push_back(0.0723);
- deleted_cb.push_back(-0.0599);
- deleted_cb.push_back(-0.0199);
- deleted_cb.push_back(-0.0552);
- deleted_cb.push_back(-0.0220);
- deleted_cb.push_back(-0.0719);
- deleted_cb.push_back(-0.0342);
- deleted_cb.push_back(-0.0096);
- deleted_cb.push_back(0.0040);
- deleted_cb.push_back(-0.0154);
- deleted_cb.push_back(-0.0371);
- deleted_cb.push_back(-0.0592);
- deleted_cb.push_back(0.0104);
+ deleted_cb.push_back(-0.379758);
+ deleted_cb.push_back(0.433782);
+ deleted_cb.push_back(-0.479475);
+ deleted_cb.push_back(-0.27818);
+ deleted_cb.push_back(-0.386644);
+ deleted_cb.push_back(-0.0879088);
+ deleted_cb.push_back(-0.43112);
+ deleted_cb.push_back(-0.20509);
+ deleted_cb.push_back(-0.0771105);
+ deleted_cb.push_back(0.0200806);
+ deleted_cb.push_back(-0.122916);
+ deleted_cb.push_back(-0.482669);
+ deleted_cb.push_back(-0.710032);
+ deleted_cb.push_back(0.175955);
+
std::vector<Real> deleted_reduced;
- deleted_reduced.push_back(-0.1452);
- deleted_reduced.push_back(0.1925);
- deleted_reduced.push_back(-0.1293);
- deleted_reduced.push_back(-0.2941);
- deleted_reduced.push_back(-0.1385);
- deleted_reduced.push_back(-0.0871);
- deleted_reduced.push_back(0.1635);
- deleted_reduced.push_back(0.3477);
- deleted_reduced.push_back(-0.0969);
- deleted_reduced.push_back(-0.0898);
- deleted_reduced.push_back(-0.0146);
- deleted_reduced.push_back(-0.2886);
- deleted_reduced.push_back(-0.4334);
- deleted_reduced.push_back(-0.4495);
+ deleted_reduced.push_back(-1.88819);
+ deleted_reduced.push_back(1.73243);
+ deleted_reduced.push_back(-1.03455);
+ deleted_reduced.push_back(-3.52878);
+ deleted_reduced.push_back(-0.96916);
+ deleted_reduced.push_back(-0.435582);
+ deleted_reduced.push_back(0.653847);
+ deleted_reduced.push_back(1.73842);
+ deleted_reduced.push_back(-0.678642);
+ deleted_reduced.push_back(-0.628393);
+ deleted_reduced.push_back(-0.116555);
+ deleted_reduced.push_back(-3.17463);
+ deleted_reduced.push_back(-5.63371);
+ deleted_reduced.push_back(-6.74281);
std::vector<Real> deleted_torsion;
deleted_torsion.push_back(1.0555);
@@ -507,18 +543,19 @@ BOOST_AUTO_TEST_CASE(qmean_comparison) {
std::vector<Real> ss_agreement_profile;
// compare the orig values
- cb_packing_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ cb_packing_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
cb_packing_profile);
- cb_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ cb_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
cb_profile);
- reduced_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ reduced_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
reduced_profile);
- torsion_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ torsion_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
torsion_profile);
- hbond_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ hbond_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
hbond_profile);
- ss_agreement_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ ss_agreement_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
ss_agreement_profile);
+
Real eps = 0.0001;
for(uint i = 0; i < bb_list.size(); ++i) {
BOOST_CHECK_SMALL(std::abs(orig_cb_packing[i] -
@@ -545,18 +582,21 @@ BOOST_AUTO_TEST_CASE(qmean_comparison) {
bb_list.ReplaceFragment(bb_list_helix, 0, false);
// compare the reset values
- cb_packing_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ cb_packing_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
cb_packing_profile);
- cb_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ cb_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
cb_profile);
- reduced_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ reduced_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
reduced_profile);
- torsion_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ torsion_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
torsion_profile);
- hbond_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ hbond_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
hbond_profile);
- ss_agreement_scorer->CalculateScoreProfile(bb_list, 26, 0,
+
+ ss_agreement_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
ss_agreement_profile);
+
+
for(uint i = 0; i < bb_list.size(); ++i) {
BOOST_CHECK_SMALL(std::abs(reset_cb_packing[i] -
cb_packing_profile[i]), eps);
@@ -576,18 +616,20 @@ BOOST_AUTO_TEST_CASE(qmean_comparison) {
env.ClearEnvironment(83, 6);
// compare the delete values
- cb_packing_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ cb_packing_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
cb_packing_profile);
- cb_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ cb_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
cb_profile);
- reduced_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ reduced_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
reduced_profile);
- torsion_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ torsion_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
torsion_profile);
- hbond_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ hbond_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
hbond_profile);
- ss_agreement_scorer->CalculateScoreProfile(bb_list, 26, 0,
+ ss_agreement_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
ss_agreement_profile);
+
+
for(uint i = 0; i < bb_list.size(); ++i) {
BOOST_CHECK_SMALL(std::abs(deleted_cb_packing[i] -
cb_packing_profile[i]), eps);
@@ -604,6 +646,377 @@ BOOST_AUTO_TEST_CASE(qmean_comparison) {
}
}
+BOOST_AUTO_TEST_CASE(test_env_stashing) {
+
+ // Same test as above, but this time we use some stash / pop
+ // magic from the BackboneScoreEnv
+ BackboneScoreEnv env = GenerateBackboneEnv();
+ promod3::loop::BackboneList bb_list = GenerateTestBBList("data/3DEFA.pdb",
+ 26, 40);
+
+ CBPackingScorerPtr cb_packing_scorer = LoadCBPackingScorer();
+ CBetaScorerPtr cb_scorer = LoadCBetaScorer();
+ ReducedScorerPtr reduced_scorer = LoadReducedScorer();
+ HBondScorerPtr hbond_scorer = LoadHBondScorer();
+ SSAgreementScorerPtr ss_agreement_scorer = LoadSSAgreementScorer();
+ SetPsipredPrediction(env);
+ TorsionScorerPtr torsion_scorer = LoadTorsionScorer();
+
+ cb_packing_scorer->AttachEnvironment(env);
+ cb_scorer->AttachEnvironment(env);
+ reduced_scorer->AttachEnvironment(env);
+ hbond_scorer->AttachEnvironment(env);
+ ss_agreement_scorer->AttachEnvironment(env);
+ torsion_scorer->AttachEnvironment(env);
+
+ // orig means: the current environment
+ // reset means: 8 residues starting from resnum 26 are replaced by a helix as
+ // it is constructed in the default constructor of the
+ // BackboneList. Positioning is performed by superposing first
+ // helix residue on current residue 26
+
+ std::vector<Real> orig_cb_packing;
+ orig_cb_packing.push_back(-1.0796);
+ orig_cb_packing.push_back(-0.5889);
+ orig_cb_packing.push_back(-0.8458);
+ orig_cb_packing.push_back(-0.9514);
+ orig_cb_packing.push_back(-0.6117);
+ orig_cb_packing.push_back(-0.7100);
+ orig_cb_packing.push_back(-0.9639);
+ orig_cb_packing.push_back(-0.5944);
+ orig_cb_packing.push_back(-0.5149);
+ orig_cb_packing.push_back(-1.0095);
+ orig_cb_packing.push_back(-0.8998);
+ orig_cb_packing.push_back(-0.9830);
+ orig_cb_packing.push_back(-0.4551);
+ orig_cb_packing.push_back(-0.6673);
+
+ std::vector<Real> orig_cb;
+ orig_cb.push_back(-0.342035);
+ orig_cb.push_back(0.238565);
+ orig_cb.push_back(-0.410386);
+ orig_cb.push_back(0.340058);
+ orig_cb.push_back(-0.341305);
+ orig_cb.push_back(-0.0710439);
+ orig_cb.push_back(-0.0911381);
+ orig_cb.push_back(-0.0181578);
+ orig_cb.push_back(0.808517);
+ orig_cb.push_back(0.461206);
+ orig_cb.push_back(0.139356);
+ orig_cb.push_back(-0.482617);
+ orig_cb.push_back(-0.497085);
+ orig_cb.push_back(0.0492029);
+
+
+ std::vector<Real> orig_reduced;
+ orig_reduced.push_back(-3.55399);
+ orig_reduced.push_back(0.52569);
+ orig_reduced.push_back(-5.0972);
+ orig_reduced.push_back(-5.45686);
+ orig_reduced.push_back(-1.86842);
+ orig_reduced.push_back(-0.992303);
+ orig_reduced.push_back(0.543362);
+ orig_reduced.push_back(-3.62267);
+ orig_reduced.push_back(-0.268999);
+ orig_reduced.push_back(-4.16786);
+ orig_reduced.push_back(-2.89717);
+ orig_reduced.push_back(-4.37486);
+ orig_reduced.push_back(-7.23112);
+ orig_reduced.push_back(-10.5035);
+
+ std::vector<Real> orig_torsion;
+ orig_torsion.push_back(0.4922);
+ orig_torsion.push_back(0.4896);
+ orig_torsion.push_back(0.9574);
+ orig_torsion.push_back(-0.4831);
+ orig_torsion.push_back(-0.5004);
+ orig_torsion.push_back(-0.4875);
+ orig_torsion.push_back(-0.4739);
+ orig_torsion.push_back(-0.7882);
+ orig_torsion.push_back(0.3369);
+ orig_torsion.push_back(-0.8233);
+ orig_torsion.push_back(-0.4457);
+ orig_torsion.push_back(-0.4084);
+ orig_torsion.push_back(-1.1914);
+ orig_torsion.push_back(-1.1170);
+
+ std::vector<Real> orig_hbond;
+ orig_hbond.push_back(-1.5817);
+ orig_hbond.push_back(-1.4568);
+ orig_hbond.push_back(-2.7138);
+ orig_hbond.push_back(-2.9179);
+ orig_hbond.push_back(-1.4514);
+ orig_hbond.push_back(-1.1016);
+ orig_hbond.push_back(-2.6790);
+ orig_hbond.push_back(-0.4062);
+ orig_hbond.push_back(-0.9520);
+ orig_hbond.push_back(-0.9263);
+ orig_hbond.push_back(0.0000);
+ orig_hbond.push_back(-1.6571);
+ orig_hbond.push_back(-1.0162);
+ orig_hbond.push_back(-1.7538);
+
+ std::vector<Real> orig_ss_agreement;
+ orig_ss_agreement.push_back(1.0960);
+ orig_ss_agreement.push_back(1.0960);
+ orig_ss_agreement.push_back(1.0960);
+ orig_ss_agreement.push_back(0.9231);
+ orig_ss_agreement.push_back(0.9231);
+ orig_ss_agreement.push_back(0.6663);
+ orig_ss_agreement.push_back(0.2756);
+ orig_ss_agreement.push_back(0.4928);
+ orig_ss_agreement.push_back(0.7852);
+ orig_ss_agreement.push_back(0.7852);
+ orig_ss_agreement.push_back(-0.9896);
+ orig_ss_agreement.push_back(-0.1106);
+ orig_ss_agreement.push_back(1.3440);
+ orig_ss_agreement.push_back(1.4422);
+
+ std::vector<Real> reset_cb_packing;
+ reset_cb_packing.push_back(-1.0796);
+ reset_cb_packing.push_back(-0.4539);
+ reset_cb_packing.push_back(-1.0485);
+ reset_cb_packing.push_back(-0.9514);
+ reset_cb_packing.push_back(-0.6117);
+ reset_cb_packing.push_back(-0.7100);
+ reset_cb_packing.push_back(-0.9639);
+ reset_cb_packing.push_back(-0.9962);
+ reset_cb_packing.push_back(-0.5149);
+ reset_cb_packing.push_back(-0.7859);
+ reset_cb_packing.push_back(-0.8998);
+ reset_cb_packing.push_back(-0.9830);
+ reset_cb_packing.push_back(-0.4551);
+ reset_cb_packing.push_back(-0.6673);
+
+ std::vector<Real> reset_cb;
+ reset_cb.push_back(-0.32877);
+ reset_cb.push_back(0.371232);
+ reset_cb.push_back(-0.479475);
+ reset_cb.push_back(-0.369955);
+ reset_cb.push_back(-0.428097);
+ reset_cb.push_back(-0.0879088);
+ reset_cb.push_back(-0.43112);
+ reset_cb.push_back(-0.324168);
+ reset_cb.push_back(-0.0822164);
+ reset_cb.push_back(0.228412);
+ reset_cb.push_back(0.0871677);
+ reset_cb.push_back(-0.510713);
+ reset_cb.push_back(-0.497085);
+ reset_cb.push_back(0.0492029);
+
+ std::vector<Real> reset_reduced;
+ reset_reduced.push_back(-3.32411);
+ reset_reduced.push_back(1.60945);
+ reset_reduced.push_back(-1.03455);
+ reset_reduced.push_back(-4.02522);
+ reset_reduced.push_back(-0.961522);
+ reset_reduced.push_back(-0.435582);
+ reset_reduced.push_back(0.653847);
+ reset_reduced.push_back(1.73842);
+ reset_reduced.push_back(-0.985268);
+ reset_reduced.push_back(-2.20225);
+ reset_reduced.push_back(-2.83298);
+ reset_reduced.push_back(-4.28751);
+ reset_reduced.push_back(-7.23112);
+ reset_reduced.push_back(-10.5035);
+
+ std::vector<Real> reset_torsion;
+ reset_torsion.push_back(1.0555);
+ reset_torsion.push_back(0.5257);
+ reset_torsion.push_back(0.6707);
+ reset_torsion.push_back(-0.4831);
+ reset_torsion.push_back(-0.4842);
+ reset_torsion.push_back(-0.4924);
+ reset_torsion.push_back(0.1419);
+ reset_torsion.push_back(4.7277);
+ reset_torsion.push_back(4.5157);
+ reset_torsion.push_back(-0.8233);
+ reset_torsion.push_back(-0.4457);
+ reset_torsion.push_back(-0.4084);
+ reset_torsion.push_back(-1.1914);
+ reset_torsion.push_back(-1.1170);
+
+ std::vector<Real> reset_hbond;
+ reset_hbond.push_back(-1.3101);
+ reset_hbond.push_back(-0.9559);
+ reset_hbond.push_back(-1.2444);
+ reset_hbond.push_back(-1.8388);
+ reset_hbond.push_back(-0.9559);
+ reset_hbond.push_back(-0.9559);
+ reset_hbond.push_back(-0.9559);
+ reset_hbond.push_back(-0.4811);
+ reset_hbond.push_back(0.0000);
+ reset_hbond.push_back(-0.9263);
+ reset_hbond.push_back(0.0000);
+ reset_hbond.push_back(-1.6571);
+ reset_hbond.push_back(-1.0162);
+ reset_hbond.push_back(-1.7538);
+
+ std::vector<Real> reset_ss_agreement;
+ reset_ss_agreement.push_back(1.0960);
+ reset_ss_agreement.push_back(1.0960);
+ reset_ss_agreement.push_back(1.0960);
+ reset_ss_agreement.push_back(0.9231);
+ reset_ss_agreement.push_back(0.9231);
+ reset_ss_agreement.push_back(0.6663);
+ reset_ss_agreement.push_back(-0.7839);
+ reset_ss_agreement.push_back(0.5699);
+ reset_ss_agreement.push_back(0.7852);
+ reset_ss_agreement.push_back(0.7852);
+ reset_ss_agreement.push_back(-0.9896);
+ reset_ss_agreement.push_back(-0.1106);
+ reset_ss_agreement.push_back(1.3440);
+ reset_ss_agreement.push_back(1.4422);
+
+ std::vector<Real> cb_packing_profile;
+ std::vector<Real> cb_profile;
+ std::vector<Real> reduced_profile;
+ std::vector<Real> torsion_profile;
+ std::vector<Real> hbond_profile;
+ std::vector<Real> ss_agreement_profile;
+
+ // compare the orig values
+ cb_packing_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ cb_packing_profile);
+ cb_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ cb_profile);
+ reduced_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ reduced_profile);
+ torsion_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ torsion_profile);
+ hbond_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ hbond_profile);
+ ss_agreement_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ ss_agreement_profile);
+
+ Real eps = 0.0001;
+ for(uint i = 0; i < bb_list.size(); ++i) {
+ BOOST_CHECK_SMALL(std::abs(orig_cb_packing[i] -
+ cb_packing_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_cb[i] -
+ cb_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_reduced[i] -
+ reduced_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_torsion[i] -
+ torsion_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_hbond[i] -
+ hbond_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_ss_agreement[i] -
+ ss_agreement_profile[i]), eps);
+ }
+
+
+ //////////////////////////////////////////////////////////////////////////
+ // PERFORM A STASH OPERATION AND CHECK, WHETHER THE SCORING RESULTS ARE //
+ // STILL THE SAME //
+ //////////////////////////////////////////////////////////////////////////
+
+ env.Stash(26, bb_list.size(), 0);
+
+ cb_packing_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ cb_packing_profile);
+ cb_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ cb_profile);
+ reduced_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ reduced_profile);
+ torsion_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ torsion_profile);
+ hbond_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ hbond_profile);
+ ss_agreement_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ ss_agreement_profile);
+
+ for(uint i = 0; i < bb_list.size(); ++i) {
+ BOOST_CHECK_SMALL(std::abs(orig_cb_packing[i] -
+ cb_packing_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_cb[i] -
+ cb_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_reduced[i] -
+ reduced_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_torsion[i] -
+ torsion_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_hbond[i] -
+ hbond_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_ss_agreement[i] -
+ ss_agreement_profile[i]), eps);
+ }
+
+ // lets perform the described reset action
+ String helix_sequence = "FGKLKQKD";
+ promod3::loop::BackboneList bb_list_helix =
+ promod3::loop::BackboneList(helix_sequence);
+ geom::Mat4 transform = bb_list_helix.GetTransform(0, bb_list, 0);
+ bb_list_helix.ApplyTransform(transform);
+ env.SetEnvironment(bb_list_helix, 26);
+ bb_list.ReplaceFragment(bb_list_helix, 0, false);
+
+ // compare the reset values
+ cb_packing_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ cb_packing_profile);
+ cb_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ cb_profile);
+ reduced_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ reduced_profile);
+ torsion_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ torsion_profile);
+ hbond_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ hbond_profile);
+
+ ss_agreement_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ ss_agreement_profile);
+
+
+ for(uint i = 0; i < bb_list.size(); ++i) {
+ BOOST_CHECK_SMALL(std::abs(reset_cb_packing[i] -
+ cb_packing_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(reset_cb[i] -
+ cb_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(reset_reduced[i] -
+ reduced_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(reset_torsion[i] -
+ torsion_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(reset_hbond[i] -
+ hbond_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(reset_ss_agreement[i] -
+ ss_agreement_profile[i]), eps);
+ }
+
+ ////////////////////////////////////////////////////////////////////////////
+ // WE PERFORM A POP ACTION AND CHECK WHETHER THE SCORES CORRESPOND TO THE //
+ // ORIGINAL SCORES AGAIN //
+ ////////////////////////////////////////////////////////////////////////////
+
+ env.Pop();
+
+ cb_packing_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ cb_packing_profile);
+ cb_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ cb_profile);
+ reduced_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ reduced_profile);
+ torsion_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ torsion_profile);
+ hbond_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ hbond_profile);
+ ss_agreement_scorer->CalculateScoreProfile(26, bb_list.size(), 0,
+ ss_agreement_profile);
+
+ for(uint i = 0; i < bb_list.size(); ++i) {
+ BOOST_CHECK_SMALL(std::abs(orig_cb_packing[i] -
+ cb_packing_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_cb[i] -
+ cb_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_reduced[i] -
+ reduced_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_torsion[i] -
+ torsion_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_hbond[i] -
+ hbond_profile[i]), eps);
+ BOOST_CHECK_SMALL(std::abs(orig_ss_agreement[i] -
+ ss_agreement_profile[i]), eps);
+ }
+}
+
BOOST_AUTO_TEST_CASE(test_clash_score) {
BackboneScoreEnv env = GenerateBackboneEnv();
promod3::loop::BackboneList bb_list = GenerateTestBBList();
@@ -620,8 +1033,13 @@ BOOST_AUTO_TEST_CASE(test_clash_score2) {
promod3::loop::BackboneList bb_list = GenerateTestBBList(pdb_name, 35, 40);
ClashScorerPtr scorer(new ClashScorer);
scorer->AttachEnvironment(env);
- Real clash_score = scorer->CalculateScore(bb_list, 35, 0);
+ Real clash_score = scorer->CalculateScore(35, bb_list.size(), 0);
BOOST_CHECK_CLOSE(clash_score, 0.107386872172, Real(1e-3));
+
+ // test for normalization, additionally to the one in test_normalize
+ scorer->DoNormalize(false);
+ clash_score = scorer->CalculateScore(35, bb_list.size(), 0);
+ BOOST_CHECK_CLOSE(clash_score, bb_list.size() * 0.107386872172, Real(1e-3));
}
BOOST_AUTO_TEST_CASE(test_pairwise_score) {
@@ -633,7 +1051,7 @@ BOOST_AUTO_TEST_CASE(test_pairwise_score) {
//CheckScorer(bb_list, scorer, 0.0);
CheckScorerThrows(bb_list, scorer);
- BOOST_CHECK_CLOSE(scorer->CalculateScore(bb_list, 214, 0), 0.0,
+ BOOST_CHECK_CLOSE(scorer->CalculateScore(214, bb_list.size(), 0), 0.0,
Real(1e-3));
@@ -658,7 +1076,7 @@ BOOST_AUTO_TEST_CASE(test_pairwise_score) {
//scorer should give 0.0
//CheckScorer(bb_list, scorer, 0.0);
- BOOST_CHECK_CLOSE(scorer->CalculateScore(bb_list, 214, 0), 0.0,
+ BOOST_CHECK_CLOSE(scorer->CalculateScore(214, bb_list.size(), 0), 0.0,
Real(1e-3));
@@ -669,7 +1087,7 @@ BOOST_AUTO_TEST_CASE(test_pairwise_score) {
//CheckScorer(bb_list, scorer, 0.36586231);
- BOOST_CHECK_CLOSE(scorer->CalculateScore(bb_list, 214, 0), 0.36586231,
+ BOOST_CHECK_CLOSE(scorer->CalculateScore(214, bb_list.size(), 0), 0.36586231,
Real(1e-3));
@@ -677,7 +1095,7 @@ BOOST_AUTO_TEST_CASE(test_pairwise_score) {
//that should also have an influence
//CheckScorer(bb_list, scorer, 1.12155807);
- BOOST_CHECK_CLOSE(scorer->CalculateScore(bb_list, 214, 0), 1.12155807,
+ BOOST_CHECK_CLOSE(scorer->CalculateScore(214, bb_list.size(), 0), 1.12155807,
Real(1e-3));
//let's finally try to add a contact function
@@ -690,7 +1108,7 @@ BOOST_AUTO_TEST_CASE(test_pairwise_score) {
//compared to previous check
//CheckScorer(bb_list, scorer, 1.12155807);
- BOOST_CHECK_CLOSE(scorer->CalculateScore(bb_list, 214, 0), 1.12155807,
+ BOOST_CHECK_CLOSE(scorer->CalculateScore(214, bb_list.size(), 0), 1.12155807,
Real(1e-3));
@@ -699,7 +1117,7 @@ BOOST_AUTO_TEST_CASE(test_pairwise_score) {
//therefore doesn't influence the score
//CheckScorer(bb_list, scorer, 1.12155807);
- BOOST_CHECK_CLOSE(scorer->CalculateScore(bb_list, 214, 0), 1.12155807,
+ BOOST_CHECK_CLOSE(scorer->CalculateScore(214, bb_list.size(), 0), 1.12155807,
Real(1e-3));
env.ApplyPairwiseFunction(0,216,0,228,3); //the cb positions of residues 216
@@ -707,8 +1125,13 @@ BOOST_AUTO_TEST_CASE(test_pairwise_score) {
//therefore influences the score
//CheckScorer(bb_list, scorer, 6.67711401);
- BOOST_CHECK_CLOSE(scorer->CalculateScore(bb_list, 214, 0), 6.67711401,
- Real(1e-3));
+ BOOST_CHECK_CLOSE(scorer->CalculateScore(214, bb_list.size(), 0), 6.67711401,
+ Real(1e-3));
+
+ // test for normalization, additionally to the one in test_normalize
+ scorer->DoNormalize(false);
+ BOOST_CHECK_CLOSE(scorer->CalculateScore(214, bb_list.size(), 0),
+ bb_list.size() * 6.67711401, Real(1e-3));
}
BOOST_AUTO_TEST_CASE(test_density_score){
@@ -727,21 +1150,8 @@ BOOST_AUTO_TEST_CASE(test_density_score){
ost::img::MapHandle map = full_bb_list.ToDensity(10.0,geom::Vec3(1.0,1.0,1.0),
5.0, true);
- DensityScorerPtr scorer(new DensityScorer);
-
- //check if error gets thrown when no environment is attached
- BOOST_CHECK_THROW(scorer->CalculateScore(bb_list,5,0), promod3::Error);
-
- scorer->AttachEnvironment(env);
- //check if error gets thrown when no density map is set in the environment
- BOOST_CHECK_THROW(scorer->CalculateScore(bb_list,5,0), promod3::Error);
-
- env.SetMap(map, 5.0, true);
-
- //The CheckScorer function cannot be used, since the resnum and chain idx
- //checks are not permormed in the density scorer
- BOOST_CHECK_CLOSE(scorer->CalculateScore(bb_list, 1, 0), 0.352861583,
- Real(1e-3));
+ BOOST_CHECK_CLOSE(promod3::scoring::DensityScore(bb_list, map, 5.0, true),
+ 0.352861583, Real(1e-3));
}
BOOST_AUTO_TEST_CASE(test_overall_scorer) {
@@ -763,8 +1173,8 @@ BOOST_AUTO_TEST_CASE(test_overall_scorer) {
weights["torsion"] = 0.7;
weights["intercept"] = 1.0;
// check for errors
- BOOST_CHECK_THROW(scorer.Calculate("hbond", bb_list, 214, 0), promod3::Error);
- BOOST_CHECK_THROW(scorer.CalculateLinearCombination(weights, bb_list, 214, 0),
+ BOOST_CHECK_THROW(scorer.Calculate("hbond", 214, bb_list.size(), 0), promod3::Error);
+ BOOST_CHECK_THROW(scorer.CalculateLinearCombination(weights, 214, bb_list.size(), 0),
promod3::Error);
// attach and sanity check single scores
@@ -775,15 +1185,232 @@ BOOST_AUTO_TEST_CASE(test_overall_scorer) {
AttachScorer(scorer, LoadHBondScorer(), bb_list, env, "hbond");
AttachScorer(scorer, LoadSSAgreementScorer(), bb_list, env, "ss_agreement");
AttachScorer(scorer, LoadTorsionScorer(), bb_list, env, "torsion");
-
+
// check final score// exp. score from single ones above
- Real exp_score = 0.1 * -0.657944619656 + 0.2 * 0.00201001879759
- + 0.3 * -0.066393442452 + 0.4 * 0.0 + 0.5 * -0.482397
+ Real exp_score = 0.1 * -0.657944619656 + 0.2 * 0.0189835
+ + 0.3 * -0.64918 + 0.4 * 0.0 + 0.5 * -0.482397
+ 0.6 * 0.498321 + 0.7 * -0.143922114538 + 1.0;
- BOOST_CHECK_CLOSE(scorer.CalculateLinearCombination(weights, bb_list, 214, 0),
+ BOOST_CHECK_CLOSE(scorer.CalculateLinearCombination(weights, 214, bb_list.size(), 0),
exp_score, Real(1e-3));
// check for more errors
- BOOST_CHECK_THROW(scorer.Calculate("meh", bb_list, 214, 0), promod3::Error);
+ BOOST_CHECK_THROW(scorer.Calculate("meh", 214, bb_list.size(), 0), promod3::Error);
+}
+
+
+BOOST_AUTO_TEST_CASE(test_normalize) {
+
+ // The normalization of the pairwise scorer is tested in the
+ // pairwise specific function where we've set actual constraints
+ // Also in case of the clash score, a test has been added there
+ // since zero is not necessarily an ideal score to test normalization.
+
+ // setup env
+ BackboneScoreEnv env = GenerateBackboneEnv();
+ promod3::loop::BackboneList bb_list = GenerateTestBBList();
+ SetPsipredPrediction(env);
+
+ // setup scorer
+ BackboneOverallScorer scorer;
+ // setup weights
+ std::map<String, Real> weights;
+ weights["cb_packing"] = 1.0;
+ weights["cbeta"] = 1.0;
+ weights["reduced"] = 1.0;
+ weights["clash"] = 1.0;
+ weights["hbond"] = 1.0;
+ weights["ss_agreement"] = 1.0;
+ weights["torsion"] = 1.0;
+
+ // attach and sanity check single scores
+
+ // load scorers
+ CBPackingScorerPtr cb_packing_scorer = LoadCBPackingScorer();
+ CBetaScorerPtr cbeta_scorer = LoadCBetaScorer();
+ ReducedScorerPtr reduced_scorer = LoadReducedScorer();
+ ClashScorerPtr clash_scorer = ClashScorerPtr(new ClashScorer);
+ HBondScorerPtr hbond_scorer = LoadHBondScorer();
+ SSAgreementScorerPtr ss_agreement_scorer = LoadSSAgreementScorer();
+ TorsionScorerPtr torsion_scorer = LoadTorsionScorer();
+
+ AttachScorer(scorer, cb_packing_scorer, bb_list, env, "cb_packing");
+ AttachScorer(scorer, cbeta_scorer, bb_list, env, "cbeta");
+ AttachScorer(scorer, reduced_scorer, bb_list, env, "reduced");
+ AttachScorer(scorer, clash_scorer, bb_list, env, "clash");
+ AttachScorer(scorer, hbond_scorer, bb_list, env, "hbond");
+ AttachScorer(scorer, ss_agreement_scorer, bb_list, env, "ss_agreement");
+ AttachScorer(scorer, torsion_scorer, bb_list, env, "torsion");
+
+ // check final score// exp. score from single ones above
+ Real exp_score = - 0.657944619656 + 0.0189835
+ - 0.64918 + 0.0 - 0.482397
+ + 0.498321 - 0.143922114538;
+
+ BOOST_CHECK_CLOSE(scorer.CalculateLinearCombination(weights, 214, bb_list.size(), 0),
+ exp_score, Real(1e-3));
+
+ cb_packing_scorer->DoNormalize(false);
+ cbeta_scorer->DoNormalize(false);
+ reduced_scorer->DoNormalize(false);
+ clash_scorer->DoNormalize(false);
+ hbond_scorer->DoNormalize(false);
+ ss_agreement_scorer->DoNormalize(false);
+ torsion_scorer->DoNormalize(false);
+
+ exp_score *= bb_list.size();
+
+ BOOST_CHECK_CLOSE(scorer.CalculateLinearCombination(weights, 214, bb_list.size(), 0),
+ exp_score, Real(1e-3));
+}
+
+
+BOOST_AUTO_TEST_CASE(test_internal_external) {
+
+ // check sthg with actual clashes
+ String pdb_name = "data/clash_test.pdb";
+ BackboneScoreEnv env = GenerateBackboneEnv(pdb_name, "");
+ promod3::loop::BackboneList bb_list = GenerateTestBBList(pdb_name, 32, 40);
+ BackboneScoreEnv empty_env(env.GetSeqres());
+
+ // load scorers (only the ones that provide an internal / external mechanism)
+ CBetaScorerPtr cbeta_scorer = LoadCBetaScorer();
+ ReducedScorerPtr reduced_scorer = LoadReducedScorer();
+ ClashScorerPtr clash_scorer = ClashScorerPtr(new ClashScorer);
+ HBondScorerPtr hbond_scorer = LoadHBondScorer();
+ cbeta_scorer->AttachEnvironment(env);
+ reduced_scorer->AttachEnvironment(env);
+ clash_scorer->AttachEnvironment(env);
+ hbond_scorer->AttachEnvironment(env);
+
+ // lets do the overall score... this should be well tested by now
+ Real cbeta_score = cbeta_scorer->CalculateScore(32, bb_list.size(), 0);
+ Real reduced_score = reduced_scorer->CalculateScore(32, bb_list.size(), 0);
+ Real clash_score = clash_scorer->CalculateScore(32, bb_list.size(), 0);
+ Real hbond_score = hbond_scorer->CalculateScore(32, bb_list.size(), 0);
+
+ // lets do the internal scores... except clash, they should all be non zero
+ cbeta_scorer->DoExternalScores(false);
+ reduced_scorer->DoExternalScores(false);
+ clash_scorer->DoExternalScores(false);
+ hbond_scorer->DoExternalScores(false);
+ Real internal_cbeta_score =
+ cbeta_scorer->CalculateScore(32, bb_list.size(), 0);
+ Real internal_reduced_score =
+ reduced_scorer->CalculateScore(32, bb_list.size(), 0);
+ Real internal_clash_score =
+ clash_scorer->CalculateScore(32, bb_list.size(), 0);
+ Real internal_hbond_score =
+ hbond_scorer->CalculateScore(32, bb_list.size(), 0);
+
+ // lets do the external scores
+ cbeta_scorer->DoExternalScores(true);
+ reduced_scorer->DoExternalScores(true);
+ clash_scorer->DoExternalScores(true);
+ hbond_scorer->DoExternalScores(true);
+ cbeta_scorer->DoInternalScores(false);
+ reduced_scorer->DoInternalScores(false);
+ clash_scorer->DoInternalScores(false);
+ hbond_scorer->DoInternalScores(false);
+ Real external_cbeta_score =
+ cbeta_scorer->CalculateScore(32, bb_list.size(), 0);
+ Real external_reduced_score =
+ reduced_scorer->CalculateScore(32, bb_list.size(), 0);
+ Real external_clash_score =
+ clash_scorer->CalculateScore(32, bb_list.size(), 0);
+ Real external_hbond_score =
+ hbond_scorer->CalculateScore(32, bb_list.size(), 0);
+
+ // the sum between the internal and external score must be the total score
+ BOOST_CHECK_CLOSE(internal_cbeta_score + external_cbeta_score,
+ cbeta_score, Real(1e-3));
+ BOOST_CHECK_CLOSE(internal_reduced_score + external_reduced_score,
+ reduced_score, Real(1e-3));
+ BOOST_CHECK_CLOSE(internal_clash_score + external_clash_score,
+ clash_score, Real(1e-3));
+ BOOST_CHECK_CLOSE(internal_hbond_score + external_hbond_score,
+ hbond_score, Real(1e-3));
+
+ // we load new scorers that we attach to the empty env
+ CBetaScorerPtr empty_cbeta_scorer = LoadCBetaScorer();
+ ReducedScorerPtr empty_reduced_scorer = LoadReducedScorer();
+ ClashScorerPtr empty_clash_scorer = ClashScorerPtr(new ClashScorer);
+ HBondScorerPtr empty_hbond_scorer = LoadHBondScorer();
+ empty_cbeta_scorer->AttachEnvironment(empty_env);
+ empty_reduced_scorer->AttachEnvironment(empty_env);
+ empty_clash_scorer->AttachEnvironment(empty_env);
+ empty_hbond_scorer->AttachEnvironment(empty_env);
+
+ // we do set the actual bb_list in the empty_env
+ empty_env.SetEnvironment(bb_list, 32, 0);
+
+ // if everything went well, the full scores should be equal to the previously
+ // calculated internal scores
+ BOOST_CHECK_CLOSE(empty_cbeta_scorer->CalculateScore(32, bb_list.size(), 0),
+ internal_cbeta_score, Real(1e-3));
+ BOOST_CHECK_CLOSE(empty_reduced_scorer->CalculateScore(32, bb_list.size(), 0),
+ internal_reduced_score, Real(1e-3));
+ BOOST_CHECK_CLOSE(empty_clash_scorer->CalculateScore(32, bb_list.size(), 0),
+ internal_clash_score, Real(1e-3));
+ BOOST_CHECK_CLOSE(empty_hbond_scorer->CalculateScore(32, bb_list.size(), 0),
+ internal_hbond_score, Real(1e-3));
+}
+
+
+BOOST_AUTO_TEST_CASE(test_multiple_stretches) {
+
+ // check sthg with actual clashes
+ String pdb_name = "data/clash_test.pdb";
+ BackboneScoreEnv env = GenerateBackboneEnv(pdb_name, "");
+ promod3::loop::BackboneList bb_list = GenerateTestBBList(pdb_name, 32, 45);
+ BackboneScoreEnv empty_env(env.GetSeqres());
+
+ // load scorers
+ CBPackingScorerPtr cb_packing_scorer = LoadCBPackingScorer();
+ CBetaScorerPtr cbeta_scorer = LoadCBetaScorer();
+ ReducedScorerPtr reduced_scorer = LoadReducedScorer();
+ ClashScorerPtr clash_scorer = ClashScorerPtr(new ClashScorer);
+ HBondScorerPtr hbond_scorer = LoadHBondScorer();
+ SSAgreementScorerPtr ss_agreement_scorer = LoadSSAgreementScorer();
+ TorsionScorerPtr torsion_scorer = LoadTorsionScorer();
+
+ // setup scorer
+ BackboneOverallScorer scorer;
+ // setup weights
+ std::map<String, Real> weights;
+ weights["cb_packing"] = 1.0;
+ weights["cbeta"] = 1.0;
+ weights["reduced"] = 1.0;
+ weights["clash"] = 1.0;
+ weights["hbond"] = 1.0;
+ weights["ss_agreement"] = 1.0;
+ weights["torsion"] = 1.0;
+
+ scorer["cb_packing"] = cb_packing_scorer;
+ scorer["cbeta"] = cbeta_scorer;
+ scorer["reduced"] = reduced_scorer;
+ scorer["clash"] = clash_scorer;
+ scorer["hbond"] = hbond_scorer;
+ scorer["ss_agreement"] = ss_agreement_scorer;
+ scorer["torsion"] = torsion_scorer;
+ scorer.AttachEnvironment(env);
+
+ std::vector<uint> start_resnums;
+ std::vector<uint> stretch_lengths;
+ std::vector<uint> chain_indices;
+ uint first_stretch_length = 6;
+ start_resnums.push_back(32);
+ start_resnums.push_back(32 + first_stretch_length);
+ stretch_lengths.push_back(first_stretch_length);
+ stretch_lengths.push_back(bb_list.size() - first_stretch_length);
+ chain_indices.push_back(0);
+ chain_indices.push_back(0);
+
+ Real full_score = scorer.CalculateLinearCombination(weights, 32,
+ bb_list.size(), 0);
+ Real patchy_score = scorer.CalculateLinearCombination(weights, start_resnums,
+ stretch_lengths,
+ chain_indices);
+
+ BOOST_CHECK_CLOSE(full_score, patchy_score, Real(1e-3));
}
BOOST_AUTO_TEST_SUITE_END();
diff --git a/sidechain/doc/disulfid.rst b/sidechain/doc/disulfid.rst
index 5b330287975708bdf84fa008b20d2e63315f4895..1cee3075640728b8c205c8bf9d9ff0128d6eeb9d 100644
--- a/sidechain/doc/disulfid.rst
+++ b/sidechain/doc/disulfid.rst
@@ -7,8 +7,9 @@ When calculating the pairwise interaction energy between two rotamers building
a disulfid bond, one would get an unfavourable energy due to "clashes" between
the sulfur atoms. It is possible to improve performance in sidechain
reconstruction regarding cysteins when finding and separately handle
-disulfid bonds. PROMOD3 implements a simple geometrical description
-[canutescu2003b]_ . The paper proposes two rotamers to be in a disulfid
+disulfid bonds. The scoring module implements an empirically derived disulfid
+score (:func:`promod3.scoring.SCWRL3DisulfidScore`) as defined in
+[canutescu2003b]_. The paper proposes two rotamers to be in a disulfid
bonded state, if the resulting disulfid score plus the self energies of the
involved rotamers is below 45. If there are several cysteines close together,
this problem gets another layer of complexity. One has to assure, that
@@ -16,38 +17,18 @@ every cysteine only participates in one disulfid bond but the network
of disulfid bonds is geometrically optimal. SCWRL4 proposes an approach,
that has also been implemented here.
-.. method:: DisulfidRawScore(ca_pos_one, cb_pos_one, sg_pos_one, \
- ca_pos_two, cb_pos_two, sg_pos_two)
-
- Evaluates the geometric expression based on the input positions
-
- :param ca_pos_one: The CA position of first rotamer
- :param cb_pos_one: The CB position of first rotamer
- :param sg_pos_one: The gamma sulfur position of first rotamer
- :param ca_pos_two: The CA position of second rotamer
- :param cb_pos_two: The CB position of second rotamer
- :param sg_pos_two: The gamma sulfur position of second rotamer
-
- :type ca_pos_one: :class:`ost.geom.Vec3`
- :type cb_pos_one: :class:`ost.geom.Vec3`
- :type sg_pos_one: :class:`ost.geom.Vec3`
- :type ca_pos_two: :class:`ost.geom.Vec3`
- :type cb_pos_two: :class:`ost.geom.Vec3`
- :type sg_pos_two: :class:`ost.geom.Vec3`
-
- :returns: The result of the raw score
-
-
.. method:: DisulfidScore(rotamer_one, rotamer_two, ca_pos_one, cb_pos_one, \
ca_pos_two, cb_pos_two)
Directly extracts the positions of the gamma sulfurs from the rotamers by
- searching for particles with the name "SG". In case of :class:`RRMRotamer`
- It expects exactly one gamma sulfur per rotamer. In case of
- :class:`FRMRotamer` there can be an arbitrary number of gamma sulfurs per
- rotamer (at least one), it then evaluates the score for all possible
- combinations of gamma sulfurs and takes the minimum score.
+ searching for particles with the name "SG".
+ The found positions are then passed to
+ :func:`promod3.scoring.SCWRL3DisulfidScore`.
+ In case of :class:`RRMRotamer` it expects exactly one gamma sulfur per
+ rotamer. In case of :class:`FRMRotamer` there can be an arbitrary number
+ of gamma sulfurs per rotamer (at least one), it then evaluates the score
+ for all possible combinations of gamma sulfurs and takes the minimum score.
To get a final DisulfidScore, it finally adds the self energies of the
rotamers to the result of the geometric expression.
@@ -108,6 +89,3 @@ that has also been implemented here.
The tuples in the first list describe the indices of cysteins
participating in disulfid bonds. The tuples in the second list
describe the optimal rotamers in the according rotamer groups.
-
-
-.. [canutescu2003b] Canutescu AA, Shelenkov AA, Dunbrack RL Jr. (2003). A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci (2003).
diff --git a/sidechain/doc/graph.rst b/sidechain/doc/graph.rst
index 33f3da97bd5f34cd341d31a25f09b733b3b015df..118c72eabb98ed98acdc13eafcb6f3af4bbbb867 100644
--- a/sidechain/doc/graph.rst
+++ b/sidechain/doc/graph.rst
@@ -6,15 +6,15 @@ Rotamer Graph
Once having a frame representing the rigid parts, the internal energies in
rotamer groups can be calculated. To come to a final solution of the sidechain
modelling problem, the pairwise energies also have to be evaluated and an
-overall solution has to be found. PROMOD3 implements an interaction graph that
-takes a list of rotamer groups, calculates the pairwise energies, does edge
-decomposition and dead end elimination. Solutions can finally be found
-using Tree decomposition, AStar or Monte Carlo approaches.
+overall solution has to be found. PROMOD3 implements a
+:class:`promod3.core.GraphMinimizer` that allows to find solutions using
+tree decomposition, A* and Monte Carlo algorithms.
.. class:: RotamerGraph
- The Graph object has no constructor exported to python. It is meant to be
- constructed using the static create functions.
+ The :class:`RotamerGraph` objects inherits from
+ :class:`promod3.core.GraphMinimizer` and extends the minimizer by static
+ initialization functions.
.. staticmethod:: CreateFromRRMList(rotamer_groups)
@@ -27,276 +27,3 @@ using Tree decomposition, AStar or Monte Carlo approaches.
:type rotamer_groups: :class:`list`
- .. method:: Prune(epsilon, [e_cut=0.0, consider_all_nodes=False])
-
- Performs edge decomposition followed by dead end elimination in an
- iterative manner until no changes can be observed anymore given
- **epsilon**.
-
- :param epsilon: The energy threshold to perform edge decomposition.
-
- :param e_cut: Parameter to control dead end elimination. If set to
- 0.0, the default goldstein criterion is applied =>
- the rotamer gets removed if it's dominated by all other
- rotamers in the same node. If you increase this value,
- a rotamer must be dominated by at least this **e_cut**.
-
-
- :param consider_all_nodes: Flag, wether the dead end elimination should be
- applied to all nodes, or only those who are
- connected with an edge removed by edge
- decomposition. This is useful if already a Prune
- operation has been performed => only those nodes
- connected to a removed edge have the chance for
- successful dead end elimination.
-
- :type epsilon: :class:`float`
- :type e_cut: :class:`float`
- :type consider_all_nodes: :class:`bool`
-
-
- .. method:: ApplyDEE(node_idx, [e_cut=0.0])
-
- Applies dead end elimination on one particular node and potentially
- deactivates certain rotamers.
-
- :param node_idx: Node to apply dead end elimination
- :param e_cut: If set to
- 0.0, the default goldstein criterion is applied =>
- the rotamer gets removed if it's dominated by all other
- rotamers in the same node. If you increase this value,
- a rotamer must be dominated by at least this **e_cut**.
-
- :type node_idx: :class:`int`
- :type e_cut: :class:`float`
-
- :returns: :class:`bool` whether any rotamer has been deactivated.
-
-
-
- .. method:: ApplyEdgeDecomposition(edge_idx, epsilon)
-
- Applies edge decomposition on one particular edge and potentially
- deactivates it.
-
-
- :param edge_idx: Edge to decompose.
- the idx relates to the list you get back
- when calling the :meth:`GetEdges` function.
-
- :param epsilon: The energy threshold to perform edge decomposition.
-
- :type edge_idx: :class:`int`
- :type epsilon: :class:`float`
-
-
- :returns: :class:`bool` whether the edge has been decomposed and
- deactivated
-
-
- .. method:: Reset()
-
- Resets the graph by undoing any pruning operation (DEE and edge decomposition)
-
-
- .. method:: TreeSolve([max_complexity=inf, initial_epsilon=0.02])
-
- The method solves a rotamer graph using a minimal width tree decomposition
- approach in an iterative manner. In every iteration, the algorithm performs
- a pruning step (DEE / Edge Decomposition) and subsequently tries to solve
- each connected component in the graph separately.
- If the number of possible enumerations in the tree constructetd from a
- particular connected component is is larger **max_complexity**,
- this component is solved in a later iteration. The algorithm iterates until
- all connected components are solved and steadily increases the epsilon value
- resulting in a more and more agressive edge decomposition. This function
- assumes all self energies of the rotamers to be calculated and properly set!
-
- :param max_complexity: Max number of possible permutations, that have to
- be enumerated in the resulting tree after tree
- decomposition.
-
- :param initial_epsilon: The initial energy threshold to perform edge
- decomposition.
-
- :type max_complexity: :class:`int`
- :type initial_epsilon: :class:`float`
-
- :returns: A tuple with the first element being a list of indices
- representing the single rotamers minimizing
- the overall energy functions from every rotamer group.
- The second element is the according energy value.
-
-
- .. method:: AStarSolve(e_thresh, [max_n=100, max_visited_nodes=100000000])
-
- The method solves a rotamer graph using the A\* algorithm. Besides creating
- minimal energy solution, the function produces a maximum of **max_n**
- solutions sorted by energy. It aborts as soon as it sees the first solution
- with an energy difference of **e_thresh** to the optimal solution or hits
- **max_n**. If you're only interested in the optimal solution you should use
- the TreeSolve function since it's much faster and uses less memory.
- There is no automatic pruning of the graph using DEE or edge decomposition,
- so you have to do it by yourself, otherwise you'll have a looooooong
- runtime or even hit the **max_visited_nodes** parameter that caps the memory
- usage.
- To have a valid solution you have to take care that you set the **e_cut**
- parameter in the pruning function to **e_tresh**.
- This function assumes all self energies of the rotamers to be calculated
- and properly set!
-
- :param e_thresh: Maximal energy difference of a solution to the
- optimal solution to be considered.
-
- :param max_n: The maximum number of solutions that will be generated.
-
- :param max_visited_nodes: Caps the memory usage of the algorithm. Besides
- The memory used for pairwise energies and self
- energies, the algorithm uses about
- **max_visited_nodes** * 20 bytes.
-
-
- :type e_thresh: :class:`float`
- :type max_n: :class:`int`
- :type max_visited_nodes: :class:`int`
-
- :returns: A tuple with the first element being a list of
- solutions with indices representing the single rotamers
- selected for that solution. The second element is a list
- of energies for the according solutions.
-
-
- .. method:: MCSolve([n=100, mc_steps=100000, start_temperature=1000.0, \\
- change_frequency=1000, cooling_factor=0.9, seed=0])
-
- Does a total of **n** Monte Carlo runs to find low energy solutions
- of the RotamerGraph. Each run starts with a random rotamer
- configuration. At each of the **mc_steps** steps, a random location and
- a random rotamer at that location is selected and an energy difference
- of that random selection relative to the current configuration is
- estimated. If the difference in energy is negative, the step is
- accepted. If not, the step is accepted with a probability given by
- the temperature dependent Metropolis criterion (exp(-ediff/T)).
- The temperature for every run starts with **start_temperature**
- and is multiplied every **change_frequency** steps with **cooling_factor**
- to achieve a simulated annealing effect.
- There is no automatic pruning of the graph using DEE or edge decomposition,
- you have to do that by yourself.
- This function assumes all self energies of the rotamers to be calculated
- and properly set!
-
- :param n: Number of Monte Carlo runs
- :param mc_steps: Number of Monte Carlo steps per run
- :param start_temperature: Start temperature for the temperature dependent
- Metropolis criterion
- :param change_frequency: Number of steps the temperature stays the same
- :param cooling_factor: Factor to multiply temperature each
- **change_frequency** steps
- :param seed: Seed for random number generator
-
- :type n: :class:`int`
- :type mc_steps: :class:`int`
- :type start_temperature: :class:`float`
- :type change_frequency: :class:`int`
- :type cooling_factor: :class:`float`
- :type seed: :class:`float`
-
- :returns: A tuple with the first element being a list of
- solutions with indices representing the single rotamers
- selected for that solution. The second element is a list
- of energies for the according solutions.
-
-
-
- .. method:: GetNumNodes()
-
- :returns: The number of nodes in the graph
- => every RotamerGroup is a node
-
-
- .. method:: GetNumEdges()
-
- :returns: The number of edges in the graph, representing
- connections between nodes with at least one
- nonzero interaction
-
-
- .. method:: GetNumActiveNodes()
-
- :returns: The number of nodes having more than one active rotamer,
- even after performing pruning operations
-
-
- .. method:: GetNumActiveEdges()
-
- :returns: The number of edges representing nonzero interactions,
- even after performing pruning operations
-
-
- .. method:: GetNumRotamers()
-
- :returns: The total number of rotamers in the graph
-
-
- .. method:: GetNumActiveRotamers()
-
- :returns: The total number of active rotamers (Total number of
- rotamers minus those that have been deactivated by DEE)
-
-
- .. method:: GetEdges()
-
- :returns: A list of tuples describing the edges
- connecting nodes with nonzero pairwise interactions
-
-
- .. method:: GetActiveEdges()
-
- :returns: A :class:`list` of :class:`tuples` describing the edges
- connecting nodes with nonzero pairwise interactions
- (All edges minus those that have been deactived by edge
- decomposition)
-
-
- .. method:: GetActiveRotamers(node_idx)
-
- :param node_idx: Specifies node from which the active rotamers should be
- extracted
-
- :type node_idx: :class:`int`
-
- :returns: list of the rotamers that are active
- in specified node (all rotamers minus those that have
- been deactivated using DEE)
-
-
- .. method:: GetSelfEnergies(node_idx)
-
- :param node_idx: Specifies node from which the self energies should be
- extracted
-
- :type node_idx: :class:`int`
-
- :returns: list of self energies for all rotamers in
- specified node as they are fed into the solving
- algorithms. Note, that they might slightly differ
- from the original self energies in the input rotamers
- because of approximations introduced in edge
- decomposition.
-
-
- .. method:: GetPairwiseEnergies(edge_idx)
-
- :param edge_idx: Specifies edge from which the pairwise energies should
- be extracted, the idx relates to the list you get back
- when calling the :meth:`GetEdges` function.
-
- :type edge_idx: :class:`int`
-
- :returns: list of list where you can extract
- the energy of rotamer i in the first node in the
- edge with rotamer j in the second node in the edge
- with: e = pairwise_energies[i][j]
-
-
-
diff --git a/sidechain/doc/rotamer.rst b/sidechain/doc/rotamer.rst
index a62ca72acb66bab21f99740b7d46912eba07b18a..40f882320bb51f59b604a6ea7de7106d8582ca2a 100644
--- a/sidechain/doc/rotamer.rst
+++ b/sidechain/doc/rotamer.rst
@@ -156,7 +156,8 @@ Rotamers
Iterates over every particle and searches for the according atom in
**res**. If it's present, the position gets reset to the particle position.
- If not, a new atom gets added to **res**.
+ If not, a new atom gets added to **res**. No atoms are removed from **res**
+ in this process.
:param res: Residue to be reconstructed
:param consider_hydrogens: Flag, whether polar hydrogens should be added to
@@ -313,6 +314,7 @@ Rotamers
Iterates over every particle of the active subrotamer and searches for the
according atom in **res**. If it's present, the position gets reset to the
particle position. If not, a new atom gets added to **res**.
+ No atoms are removed from **res** in this process.
:param res: Residue to be reconstructed
:param consider_hydrogens: Flag, whether polar hydrogens should be added to
diff --git a/sidechain/doc/rotamer_constructor.rst b/sidechain/doc/rotamer_constructor.rst
index 316c0aba0559e2c0061d8a5ed23641967093a00f..36c76a2c0857dc5bdbd5b3257e24e8b2bde5eaac 100644
--- a/sidechain/doc/rotamer_constructor.rst
+++ b/sidechain/doc/rotamer_constructor.rst
@@ -11,22 +11,33 @@ Constructing Rotamers and Frame Residues
--------------------------------------------------------------------------------
-.. class:: SCWRLRotamerConstructor()
+.. class:: SCWRLRotamerConstructor(cb_in_sidechain)
Constructing rotamers and frame residues that are parametrized according to
the SCWRL4 method. They contain all heavy atoms, but also the
- polar hydrogens. The rotamers start after the CB atom (typically CG).
+ polar hydrogens.
In case of the :class:`FrameResidue` construction, the
constructor distinguishes between backbone and sidechain frame residues.
+ :param cb_in_sidechain: If set to true, all constructed rotamers will contain
+ the cb atom. This flag also affects the construction
+ of frame residues and controls whether the cb atom
+ shows up in the backbone frame residues or sidechain
+ frame residues.
+ This is useful when you want to represent ALA or
+ GLY with actual rotamers, but be aware of increased
+ runtime. This flag can be set to False for most
+ modeling applications and you just don't generate
+ any rotamers for ALA and GLY.
+
+ :type cb_in_sidechain: :class:`bool`
+
+
.. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib,\
[probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(all_atom_pos, aa_res_idx, id,\
residue_index, rot_lib,\
[probability_cutoff = 0.98])
- .. method:: ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos, id,\
- residue_index, rot_lib,\
- [probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib,\
[phi = -1.0472, psi = -0.7854,\
probability_cutoff = 0.98])
@@ -34,29 +45,19 @@ Constructing Rotamers and Frame Residues
residue_index, rot_lib,\
[phi = -1.0472, psi = -0.7854,\
probability_cutoff = 0.98])
- .. method:: ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos, id,\
- residue_index, rot_lib,\
- [phi = -1.0472, psi = -0.7854,\
- probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib_entries,\
[probability_cutoff = 0.98])
.. method:: ConstructRRMRotamerGroup(all_atom_pos, aa_res_idx, id,\
residue_index, rot_lib_entries,\
[probability_cutoff = 0.98])
- .. method:: ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos, id,\
- residue_index, rot_lib_entries,\
- [probability_cutoff = 0.98])
All functions are also avaible for their flexible rotamer model counterpart.
=>ConstructFRMRotamerGroup(...) with exactly the same parameters.
- :param res: To extract the N, CA, CB backbone anchor
- :param all_atom_pos: To extract the N, CA, CB backbone anchor
+ :param res: To extract the required backbone atoms
+ :param all_atom_pos: To extract the required backbone atoms
:param aa_res_idx: Index of residue in **all_atom_pos** from which to
- extract the backbone anchor
- :param n_pos: To directly feed in the backbone anchor positions
- :param ca_pos: To directly feed in the backbone anchor positions
- :param cb_pos: To directly feed in the backbone anchor positions
+ extract the required backbone atoms
:param id: Identifies the sidechain.
:param residue_index: Important for the energy calculations towards the
:class:`Frame` you don't want to calculate a pairwise
@@ -82,9 +83,6 @@ Constructing Rotamers and Frame Residues
:type res: :class:`ost.mol.ResidueHandle`
:type all_atom_pos: :class:`promod3.loop.AllAtomPositions`
:type aa_res_idx: :class:`int`
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
:type id: :class:`RotamerID`
:type residue_index: :class:`int`
:type rot_lib: :class:`RotamerLib` / :class:`BBDepRotamerLib`
@@ -93,9 +91,8 @@ Constructing Rotamers and Frame Residues
:rtype: :class:`RRMRotamerGroup`
:raises: :exc:`~exceptions.RuntimeError` when not all required backbone
- atoms are present in **residue**, not all required atom
- positions are set in **all_atom_pos** or when the rotamer library
- does not contain any entries for **id**
+ atoms are present in **residue** or not all required atom
+ positions are set in **all_atom_pos**
.. method:: ConstructBackboneFrameResidue(res, id, residue_index, Real phi,\
@@ -105,13 +102,8 @@ Constructing Rotamers and Frame Residues
residue_index, Real phi,\
[n_ter = False, c_ter = False])
- .. method:: ConstructBackboneFrameResidue(n_pos, ca_pos, c_pos, o_pos, cb_pos,\
- id, residue_index, Real phi,\
- [n_ter = False, c_ter = False])
-
- Constructs backbone frame residues for amino acid residues. It extracts
- the n, ca, c, o and cb positions and constructs a frame residue based on
- the parametrizations of SCWRL4. In case of **n_ter**, there are additional
+ Constructs backbone frame residues for amino acid residues based on the
+ parametrizations of SCWRL4. In case of **n_ter**, there are additional
hydrogens added at the nitrogen to represent a proper n-terminus. The same
is true for **c_ter**, an additional oxygen is built instead. In any case,
a single hydrogen is added to the nitrogen (except proline), this is
@@ -121,11 +113,6 @@ Constructing Rotamers and Frame Residues
:param all_atom_pos: To extract the backbone positions
:param aa_res_idx: Index of residue in **all_atom_pos** from which to
extract the backbone positions
- :param n_pos: To directly feed in the backbone positions
- :param ca_pos: To directly feed in the backbone positions
- :param c_pos: To directly feed in the backbone positions
- :param o_pos: To directly feed in the backbone positions
- :param cb_pos: To directly feed in the backbone positions
:param id: Identifies the sidechain
:param residue_index: Important for the energy calculations towards the
:class:`Frame` you don't want to calculate a pairwise
@@ -141,11 +128,6 @@ Constructing Rotamers and Frame Residues
:type res: :class:`ost.mol.ResidueHandle`
:type all_atom_pos: :class:`promod3.loop.AllAtomPositions`
:type aa_res_idx: :class:`int`
- :type n_pos: :class:`ost.geom.Vec3`
- :type ca_pos: :class:`ost.geom.Vec3`
- :type c_pos: :class:`ost.geom.Vec3`
- :type o_pos: :class:`ost.geom.Vec3`
- :type cb_pos: :class:`ost.geom.Vec3`
:type id: :class:`RotamerID`
:type residue_index: :class:`int`
:type phi: :class:`float`
@@ -156,7 +138,7 @@ Constructing Rotamers and Frame Residues
:raises: :exc:`~exceptions.RuntimeError` when not all required backbone
- atoms are present in **residue**, not all required atom
+ atoms are present in **residue** or not all required atom
positions are set in **all_atom_pos**.
diff --git a/sidechain/pymod/CMakeLists.txt b/sidechain/pymod/CMakeLists.txt
index df22822d3ac6a7be57ccc00fcdcf588d77ecf03d..06d95aee0b95b8e331a2ed0581e21c067456d815 100644
--- a/sidechain/pymod/CMakeLists.txt
+++ b/sidechain/pymod/CMakeLists.txt
@@ -2,7 +2,7 @@ set(SIDECHAIN_CPP
export_connector.cc
export_disulfid.cc
export_frame.cc
-export_graph.cc
+export_rotamer_graph.cc
export_particle.cc
export_rotamer.cc
export_rotamer_cruncher.cc
diff --git a/sidechain/pymod/export_disulfid.cc b/sidechain/pymod/export_disulfid.cc
index 72ea6c3c91febe9133ecdfde62ecb92951c63875..b346dc8e834f462a09cdd0a0391775fba05df7d8 100644
--- a/sidechain/pymod/export_disulfid.cc
+++ b/sidechain/pymod/export_disulfid.cc
@@ -82,13 +82,6 @@ boost::python::tuple WrapResolveCysteins(const boost::python::list& rot_groups,
void export_Disulfid(){
- def("DisulfidRawScore", &DisulfidRawScore, (arg("ca_pos_one"),
- arg("cb_pos_one"),
- arg("sg_pos_one"),
- arg("ca_pos_two"),
- arg("cb_pos_two"),
- arg("sg_pos_two")));
-
def("DisulfidScore",&WrapDisulfidOne,(arg("rotamer_one"), arg("rotamer_two"),
arg("ca_pos_one"), arg("cb_pos_one"),
arg("ca_pos_two"), arg("cb_pos_two")));
diff --git a/sidechain/pymod/export_graph.cc b/sidechain/pymod/export_graph.cc
deleted file mode 100644
index e48adbb78d2e5de251505a52ded4ea6c8da50de7..0000000000000000000000000000000000000000
--- a/sidechain/pymod/export_graph.cc
+++ /dev/null
@@ -1,170 +0,0 @@
-#include <boost/python.hpp>
-#include <boost/python/register_ptr_to_python.hpp>
-#include <promod3/sidechain/rotamer_graph.hh>
-#include <promod3/core/export_helper.hh>
-
-using namespace boost::python;
-using namespace promod3::sidechain;
-using namespace promod3;
-
-namespace {
-
-RotamerGraphPtr WrapRRMList(boost::python::list& rotamer_groups) {
- std::vector<RRMRotamerGroupPtr> v_rotamer_groups;
- core::ConvertListToVector(rotamer_groups, v_rotamer_groups);
- return RotamerGraph::CreateFromRRMList(v_rotamer_groups);
-}
-
-RotamerGraphPtr WrapFRMList(boost::python::list& rotamer_groups) {
- std::vector<FRMRotamerGroupPtr> v_rotamer_groups;
- core::ConvertListToVector(rotamer_groups, v_rotamer_groups);
- return RotamerGraph::CreateFromFRMList(v_rotamer_groups);
-}
-
-boost::python::tuple WrapTreeSolve(RotamerGraphPtr graph, uint64_t max_complexity,
- Real initial_epsilon) {
- std::pair<std::vector<int>, Real>
- full_solution = graph->TreeSolve(max_complexity,initial_epsilon);
- std::vector<int> solution = full_solution.first;
- Real energy = full_solution.second;
- boost::python::list return_list;
- core::AppendVectorToList(solution, return_list);
- return boost::python::make_tuple(return_list, energy);
-}
-
-boost::python::tuple WrapAStarSolve(RotamerGraphPtr graph,
- Real e_thresh, uint max_n,
- uint max_visited_nodes) {
- std::pair<std::vector<std::vector<int> >, std::vector<Real> >
- full_solution = graph->AStarSolve(e_thresh, max_n, max_visited_nodes);
-
- std::vector<std::vector<int> > solutions = full_solution.first;
- std::vector<Real> energies = full_solution.second;
-
- boost::python::list solution_list;
- boost::python::list energy_list;
-
- for(uint i = 0; i < solutions.size(); ++i){
- boost::python::list actual_solution;
- core::AppendVectorToList(solutions[i], actual_solution);
- solution_list.append(actual_solution);
- }
- core::AppendVectorToList(energies, energy_list);
-
- return boost::python::make_tuple(solution_list, energy_list);
-}
-
-boost::python::tuple WrapMCSolve(RotamerGraphPtr graph, int n,
- int mc_steps, Real start_temperature,
- int change_frequency, Real cooling_factor,
- int seed) {
-
- std::pair<std::vector<std::vector<int> >, std::vector<Real> >
- full_solution = graph->MCSolve(n, mc_steps, start_temperature,
- change_frequency, cooling_factor,
- seed);
-
- std::vector<std::vector<int> > solutions = full_solution.first;
- std::vector<Real> energies = full_solution.second;
-
- boost::python::list solution_list;
- boost::python::list energy_list;
-
- for(uint i = 0; i < solutions.size(); ++i){
- boost::python::list actual_solution;
- core::AppendVectorToList(solutions[i], actual_solution);
- solution_list.append(actual_solution);
- }
- core::AppendVectorToList(energies, energy_list);
-
- return boost::python::make_tuple(solution_list, energy_list);
-}
-
-boost::python::list WrapGetActiveRotamers(RotamerGraphPtr graph,
- int idx) {
- std::vector<int> active_rotamers;
- graph->GetActiveRotamers(idx, active_rotamers);
- boost::python::list return_list;
- core::AppendVectorToList(active_rotamers, return_list);
- return return_list;
-}
-
-boost::python::list WrapGetEdges(RotamerGraphPtr graph,
- int idx) {
- std::vector<std::pair<int,int> > edges;
- graph->GetEdges(edges);
- boost::python::list return_list;
- core::AppendVectorToList(edges, return_list);
- return return_list;
-}
-
-boost::python::list WrapGetActiveEdges(RotamerGraphPtr graph,
- int idx) {
- std::vector<std::pair<int,int> > edges;
- graph->GetActiveEdges(edges);
- boost::python::list return_list;
- core::AppendVectorToList(edges, return_list);
- return return_list;
-}
-
-boost::python::list WrapGetSelfEnergies(RotamerGraphPtr graph,
- int idx) {
- std::vector<Real> self_energies;
- graph->GetSelfEnergies(idx, self_energies);
- boost::python::list return_list;
- core::AppendVectorToList(self_energies, return_list);
- return return_list;
-}
-
-boost::python::list WrapGetPairwiseEnergies(RotamerGraphPtr graph,
- int idx) {
- std::vector<std::vector<Real> > pairwise_energies;
- graph->GetPairwiseEnergies(idx, pairwise_energies);
- boost::python::list return_list;
-
- for(uint i = 0; i < pairwise_energies.size(); ++i) {
- boost::python::list row;
- core::AppendVectorToList(pairwise_energies[i], row);
- return_list.append(row);
- }
-
- return return_list;
-}
-
-
-}
-
-
-void export_Graph()
-{
- class_<RotamerGraph, boost::noncopyable>("RotamerGraph", no_init)
- .def("CreateFromRRMList", &WrapRRMList, (arg("rotamer_groups")))
- .staticmethod("CreateFromRRMList")
- .def("CreateFromFRMList", &WrapFRMList, (arg("rotamer_groups")))
- .staticmethod("CreateFromFRMList")
- .def("Prune", &RotamerGraph::Prune,
- (arg("epsilon"), arg("e_cut")=0.0, arg("consider_all_nodes")=false))
- .def("Reset", &RotamerGraph::Reset)
- .def("GetNumNodes", &RotamerGraph::GetNumNodes)
- .def("GetNumEdges", &RotamerGraph::GetNumEdges)
- .def("GetNumActiveNodes", &RotamerGraph::GetNumActiveNodes)
- .def("GetNumActiveEdges", &RotamerGraph::GetNumActiveEdges)
- .def("GetActiveRotamers", &WrapGetActiveRotamers, (arg("node_idx")))
- .def("GetEdges", &WrapGetEdges)
- .def("GetActiveEdges", &WrapGetActiveEdges)
- .def("GetSelfEnergies", &WrapGetSelfEnergies, (arg("node_idx")))
- .def("GetPairwiseEnergies", &WrapGetPairwiseEnergies,(arg("edge_idx")))
- .def("ApplyDEE", &RotamerGraph::ApplyDEE,(arg("node_idx"), arg("e_thresh")=0.0))
- .def("ApplyEdgeDecomposition", &RotamerGraph::ApplyEdgeDecomposition,(arg("edge_idx"), arg("e_thresh")=0.02))
- .def("TreeSolve", &WrapTreeSolve,
- (arg("max_complexity")=std::numeric_limits<uint64_t>::max(),
- arg("initial_epsilon")=0.02))
- .def("AStarSolve", &WrapAStarSolve,
- (arg("e_thresh"), arg("max_n")=100, arg("max_visited_nodes")=100000000))
- .def("MCSolve", &WrapMCSolve,
- (arg("n")=100, arg("mc_steps")=100000, arg("start_temperature")=1000.0,
- arg("change_frequency")=1000, arg("cooling_factor")=0.9, arg("seed")=0))
- ;
-
- register_ptr_to_python<RotamerGraphPtr>();
-}
diff --git a/sidechain/pymod/export_rotamer_graph.cc b/sidechain/pymod/export_rotamer_graph.cc
new file mode 100644
index 0000000000000000000000000000000000000000..782d0e81d070cf83c1ee3220d5483f80e09e6998
--- /dev/null
+++ b/sidechain/pymod/export_rotamer_graph.cc
@@ -0,0 +1,39 @@
+#include <boost/python.hpp>
+#include <boost/python/register_ptr_to_python.hpp>
+#include <promod3/core/graph_minimizer.hh>
+#include <promod3/sidechain/rotamer_graph.hh>
+#include <promod3/core/export_helper.hh>
+
+using namespace boost::python;
+using namespace promod3::sidechain;
+using namespace promod3;
+
+namespace {
+
+RotamerGraphPtr WrapRRMList(boost::python::list& rotamer_groups) {
+ std::vector<RRMRotamerGroupPtr> v_rotamer_groups;
+ core::ConvertListToVector(rotamer_groups, v_rotamer_groups);
+ return RotamerGraph::CreateFromList(v_rotamer_groups);
+}
+
+RotamerGraphPtr WrapFRMList(boost::python::list& rotamer_groups) {
+ std::vector<FRMRotamerGroupPtr> v_rotamer_groups;
+ core::ConvertListToVector(rotamer_groups, v_rotamer_groups);
+ return RotamerGraph::CreateFromList(v_rotamer_groups);
+}
+
+}
+
+
+void export_RotamerGraph() {
+
+
+ class_<RotamerGraph,
+ bases<promod3::core::GraphMinimizer> >("RotamerGraph", init<>())
+
+ .def("CreateFromRRMList", &WrapRRMList, (arg("rotamer_groups"))).staticmethod("CreateFromRRMList")
+ .def("CreateFromFRMList", &WrapFRMList, (arg("rotamer_groups"))).staticmethod("CreateFromFRMList")
+ ;
+
+ register_ptr_to_python<RotamerGraphPtr>();
+}
diff --git a/sidechain/pymod/export_scwrl_rotamer_constructor.cc b/sidechain/pymod/export_scwrl_rotamer_constructor.cc
index 1d9cda258ed7f3fe39127025f2e2765aa3f8a0ae..539288e3e6363cee544e8815c484c83da32e6971 100644
--- a/sidechain/pymod/export_scwrl_rotamer_constructor.cc
+++ b/sidechain/pymod/export_scwrl_rotamer_constructor.cc
@@ -13,6 +13,10 @@ using namespace promod3;
namespace{
+SCWRLRotamerConstructorPtr WrapSCWRLRotamerConstructorInit(bool cb_in_sidechain) {
+ SCWRLRotamerConstructorPtr p(new SCWRLRotamerConstructor(cb_in_sidechain));
+ return p;
+}
RRMRotamerGroupPtr WrapRRMGroup_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& res,
@@ -36,18 +40,6 @@ RRMRotamerGroupPtr WrapRRMGroup_aa(SCWRLRotamerConstructor& constructor,
rot_lib, probability_cutoff);
}
-RRMRotamerGroupPtr WrapRRMGroup_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID rotamer_id,
- uint residue_idx,
- RotamerLibPtr rot_lib,
- Real probability_cutoff){
- return constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- rotamer_id, residue_idx,
- rot_lib, probability_cutoff);
-}
-
FRMRotamerGroupPtr WrapFRMGroup_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& res,
RotamerID id,
@@ -70,18 +62,6 @@ FRMRotamerGroupPtr WrapFRMGroup_aa(SCWRLRotamerConstructor& constructor,
rot_lib, probability_cutoff);
}
-FRMRotamerGroupPtr WrapFRMGroup_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID rotamer_id,
- uint residue_idx,
- RotamerLibPtr rot_lib,
- Real probability_cutoff){
- return constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- rotamer_id, residue_idx,
- rot_lib, probability_cutoff);
-}
-
RRMRotamerGroupPtr WrapRRMGroup_bbdep_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& res,
RotamerID id,
@@ -108,20 +88,6 @@ RRMRotamerGroupPtr WrapRRMGroup_bbdep_aa(SCWRLRotamerConstructor& constructor,
probability_cutoff);
}
-RRMRotamerGroupPtr WrapRRMGroup_bbdep_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID rotamer_id,
- uint residue_idx,
- BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi,
- Real probability_cutoff){
- return constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- rotamer_id, residue_idx,
- rot_lib, phi, psi,
- probability_cutoff);
-}
-
FRMRotamerGroupPtr WrapFRMGroup_bbdep_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& res,
RotamerID id,
@@ -148,20 +114,6 @@ FRMRotamerGroupPtr WrapFRMGroup_bbdep_aa(SCWRLRotamerConstructor& constructor,
probability_cutoff);
}
-FRMRotamerGroupPtr WrapFRMGroup_bbdep_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID rotamer_id,
- uint residue_idx,
- BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi,
- Real probability_cutoff){
- return constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- rotamer_id, residue_idx,
- rot_lib, phi, psi,
- probability_cutoff);
-}
-
RRMRotamerGroupPtr WrapRRMGroup_entries_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& res,
RotamerID id,
@@ -190,22 +142,6 @@ RRMRotamerGroupPtr WrapRRMGroup_entries_aa(SCWRLRotamerConstructor& constructor,
probability_cutoff);
}
-RRMRotamerGroupPtr WrapRRMGroup_entries_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos,
- const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID rotamer_id,
- uint residue_idx,
- const boost::python::list& entries,
- Real probability_cutoff){
- std::vector<RotamerLibEntry> v_entries;
- core::ConvertListToVector(entries, v_entries);
- return constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- rotamer_id, residue_idx,
- v_entries,
- probability_cutoff);
-}
-
FRMRotamerGroupPtr WrapFRMGroup_entries_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& res,
RotamerID id,
@@ -234,23 +170,6 @@ FRMRotamerGroupPtr WrapFRMGroup_entries_aa(SCWRLRotamerConstructor& constructor,
probability_cutoff);
}
-FRMRotamerGroupPtr WrapFRMGroup_entries_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos,
- const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID rotamer_id,
- uint residue_idx,
- const boost::python::list& entries,
- Real probability_cutoff){
- std::vector<RotamerLibEntry> v_entries;
- core::ConvertListToVector(entries, v_entries);
- return constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- rotamer_id, residue_idx,
- v_entries,
- probability_cutoff);
-}
-
-
FrameResiduePtr WrapBBFrame_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& residue,
RotamerID id, uint residue_index,
@@ -269,19 +188,6 @@ FrameResiduePtr WrapBBFrame_aa(SCWRLRotamerConstructor& constructor,
phi, n_ter, c_ter);
}
-FrameResiduePtr WrapBBFrame_pos(SCWRLRotamerConstructor& constructor,
- const geom::Vec3& n_pos,
- const geom::Vec3& ca_pos,
- const geom::Vec3& c_pos,
- const geom::Vec3& o_pos,
- const geom::Vec3& cb_pos,
- RotamerID id, uint residue_index,
- Real phi, bool n_ter, bool c_ter){
- return constructor.ConstructBackboneFrameResidue(n_pos, ca_pos, c_pos,
- o_pos, cb_pos, id,
- residue_index,
- phi, n_ter, c_ter);
-}
FrameResiduePtr WrapSCFrame_res(SCWRLRotamerConstructor& constructor,
const ost::mol::ResidueHandle& residue,
@@ -313,7 +219,8 @@ void AssignInternalEnergiesFRM(const SCWRLRotamerConstructor& constructor,
void export_SCWRLRotamerConstructor(){
- class_<SCWRLRotamerConstructor>("SCWRLRotamerConstructor", init<>())
+ class_<SCWRLRotamerConstructor, SCWRLRotamerConstructorPtr>("SCWRLRotamerConstructor", no_init)
+ .def("__init__", boost::python::make_constructor(&WrapSCWRLRotamerConstructorInit))
.def("ConstructRRMRotamerGroup", &WrapRRMGroup_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
@@ -325,13 +232,6 @@ void export_SCWRLRotamerConstructor(){
arg("residue_idx"),
arg("rot_lib"),
arg("probability_cutoff") = 0.98))
- .def("ConstructRRMRotamerGroup", &WrapRRMGroup_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_idx"),
- arg("rot_lib"),
- arg("probability_cutoff") = 0.98))
.def("ConstructFRMRotamerGroup", &WrapFRMGroup_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
@@ -343,13 +243,6 @@ void export_SCWRLRotamerConstructor(){
arg("residue_idx"),
arg("rot_lib"),
arg("probability_cutoff") = 0.98))
- .def("ConstructFRMRotamerGroup", &WrapFRMGroup_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_idx"),
- arg("rot_lib"),
- arg("probability_cutoff") = 0.98))
.def("ConstructRRMRotamerGroup", &WrapRRMGroup_bbdep_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
@@ -365,15 +258,6 @@ void export_SCWRLRotamerConstructor(){
arg("phi") = -1.0472,
arg("psi") = -0.7854,
arg("probability_cutoff") = 0.98))
- .def("ConstructRRMRotamerGroup", &WrapRRMGroup_bbdep_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_idx"),
- arg("rot_lib"),
- arg("phi") = -1.0472,
- arg("psi") = -0.7854,
- arg("probability_cutoff") = 0.98))
.def("ConstructFRMRotamerGroup", &WrapFRMGroup_bbdep_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
@@ -389,15 +273,6 @@ void export_SCWRLRotamerConstructor(){
arg("phi") = -1.0472,
arg("psi") = -0.7854,
arg("probability_cutoff") = 0.98))
- .def("ConstructFRMRotamerGroup", &WrapFRMGroup_bbdep_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_idx"),
- arg("rot_lib"),
- arg("phi") = -1.0472,
- arg("psi") = -0.7854,
- arg("probability_cutoff") = 0.98))
.def("ConstructRRMRotamerGroup", &WrapRRMGroup_entries_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
@@ -409,13 +284,6 @@ void export_SCWRLRotamerConstructor(){
arg("residue_idx"),
arg("entries"),
arg("probability_cutoff") = 0.98))
- .def("ConstructRRMRotamerGroup", &WrapRRMGroup_entries_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_idx"),
- arg("entries"),
- arg("probability_cutoff") = 0.98))
.def("ConstructFRMRotamerGroup", &WrapFRMGroup_entries_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_idx"),
@@ -427,13 +295,6 @@ void export_SCWRLRotamerConstructor(){
arg("residue_idx"),
arg("entries"),
arg("probability_cutoff") = 0.98))
- .def("ConstructFRMRotamerGroup", &WrapFRMGroup_entries_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_idx"),
- arg("entries"),
- arg("probability_cutoff") = 0.98))
.def("ConstructBackboneFrameResidue", &WrapBBFrame_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_index"),
@@ -447,16 +308,6 @@ void export_SCWRLRotamerConstructor(){
arg("phi"),
arg("n_ter")=false,
arg("c_ter")=false))
- .def("ConstructBackboneFrameResidue", &WrapBBFrame_pos,(arg("n_pos"),
- arg("ca_pos"),
- arg("c_pos"),
- arg("o_pos"),
- arg("cb_pos"),
- arg("rotamer_id"),
- arg("residue_index"),
- arg("phi"),
- arg("n_ter")=false,
- arg("c_ter")=false))
.def("ConstructSidechainFrameResidue", &WrapSCFrame_res,(arg("residue"),
arg("rotamer_id"),
arg("residue_index")))
diff --git a/sidechain/pymod/wrap_sidechain.cc b/sidechain/pymod/wrap_sidechain.cc
index 14a3fc9b574d295b970f0fdd6eb874bed7328e81..840b5d3b405eab5f532b7f6cd2de1eccf1a34c4b 100644
--- a/sidechain/pymod/wrap_sidechain.cc
+++ b/sidechain/pymod/wrap_sidechain.cc
@@ -3,7 +3,7 @@
void export_Connector();
void export_Disulfid();
void export_Frame();
-void export_Graph();
+void export_RotamerGraph();
void export_Particle();
void export_Rotamer();
void export_RotamerCruncher();
@@ -21,7 +21,7 @@ BOOST_PYTHON_MODULE(_sidechain)
export_Connector();
export_Disulfid();
export_Frame();
- export_Graph();
+ export_RotamerGraph();
export_Particle();
export_Rotamer();
export_RotamerCruncher();
diff --git a/sidechain/src/CMakeLists.txt b/sidechain/src/CMakeLists.txt
index dfa815fc9ea3d7b5580e11caa46f4eac78534a2b..e6fb514dc9675c86125a23cca4680696761f1010 100644
--- a/sidechain/src/CMakeLists.txt
+++ b/sidechain/src/CMakeLists.txt
@@ -22,7 +22,6 @@ set(SIDECHAIN_SOURCES
bb_dep_rotamer_lib.cc
disulfid.cc
frame.cc
- rotamer_graph.cc
particle.cc
rotamer.cc
rotamer_cruncher.cc
diff --git a/sidechain/src/bb_dep_rotamer_lib.cc b/sidechain/src/bb_dep_rotamer_lib.cc
index 8abeaf7b1c4e2f0af58fe96e1d35c85c6f61fbe8..20bbe7ee31b36798e84440f46939eef176d00b86 100644
--- a/sidechain/src/bb_dep_rotamer_lib.cc
+++ b/sidechain/src/bb_dep_rotamer_lib.cc
@@ -394,13 +394,13 @@ std::pair<RotamerLibEntry*,uint> BBDepRotamerLib::QueryLib(RotamerID id, Real ph
}
}
+ result_buffer_.clear();
+
std::map<RotamerID,std::pair<uint64_t,uint> >::const_iterator it = static_data_helper_.find(id);
if(it == static_data_helper_.end()){
- throw promod3::Error("No rotamers for given id...");
+ return std::make_pair(reinterpret_cast<RotamerLibEntry*>(NULL), 0);
}
- result_buffer_.clear();
-
if(interpolate_){
uint bin00,bin10,bin01,bin11;
diff --git a/sidechain/src/disulfid.cc b/sidechain/src/disulfid.cc
index 388894b0ecc25573898b7326d107c10647a08eaf..620658f2e17954b972d0b996dd3664a9db293b53 100644
--- a/sidechain/src/disulfid.cc
+++ b/sidechain/src/disulfid.cc
@@ -3,6 +3,7 @@
#include <promod3/sidechain/particle.hh>
#include <promod3/core/graph.hh>
#include <promod3/core/enumerator.hh>
+#include <promod3/scoring/scwrl3_energy_functions.hh>
#include <vector>
namespace{
@@ -10,18 +11,18 @@ namespace{
template <typename T>
void ExtractCYSSG(T rot_one, T rot_two,
std::vector<geom::Vec3>& pos_one,
- std::vector<geom::Vec3>& pos_two){
+ std::vector<geom::Vec3>& pos_two) {
for(typename T::iterator i = rot_one.begin();
- i != rot_one.end(); ++i){
- if(i->GetName() == "SG"){
+ i != rot_one.end(); ++i) {
+ if(i->GetName() == "SG") {
pos_one.push_back(i->GetPos());
}
}
for(typename T::iterator i = rot_two.begin();
- i != rot_two.end(); ++i){
- if(i->GetName() == "SG"){
+ i != rot_two.end(); ++i) {
+ if(i->GetName() == "SG") {
pos_two.push_back(i->GetPos());
}
}
@@ -42,16 +43,16 @@ void SingleResolve(const std::vector<Real>& scores,
Real current_score = 0.0;
- for(int i = 0; i < size; ++i){
+ for(int i = 0; i < size; ++i) {
current_score += current_combination[i] * scores[i];
- for(int j = 0; j < size; ++j){
+ for(int j = 0; j < size; ++j) {
if(i != j) current_score += graph.IsConnected(i, j) *
current_combination[i] *
current_combination[j] * Real(1000000.0);
}
}
- if(current_score < optimal_score){
+ if(current_score < optimal_score) {
optimal_score = current_score;
active_bonds = current_combination;
}
@@ -62,7 +63,7 @@ void SingleResolve(const std::vector<Real>& scores,
void Resolve(const std::vector<Real>& scores,
const promod3::core::Graph& graph,
uint max_problem_size,
- std::vector<int>& active_bonds){
+ std::vector<int>& active_bonds) {
uint size = scores.size();
@@ -80,7 +81,7 @@ void Resolve(const std::vector<Real>& scores,
std::vector<std::vector<int> > connected_components(1);
// at the beginning everything is in the same component
- for(int i = 0; i < graph.NumNodes(); ++i){
+ for(int i = 0; i < graph.NumNodes(); ++i) {
connected_components.back().push_back(i);
}
@@ -90,9 +91,9 @@ void Resolve(const std::vector<Real>& scores,
uint largest_idx = 0;
// search for the largest component
- for(uint i = 0; i < connected_components.size(); ++i){
+ for(uint i = 0; i < connected_components.size(); ++i) {
uint current_size = connected_components[i].size();
- if(current_size > largest_size){
+ if(current_size > largest_size) {
largest_size = current_size;
largest_idx = i;
}
@@ -101,25 +102,26 @@ void Resolve(const std::vector<Real>& scores,
// is it small enough?
if(largest_size <= max_problem_size) break;
- const std::vector<int>& largest_component = connected_components[largest_idx];
+ const std::vector<int>& largest_component =
+ connected_components[largest_idx];
// let's search for the item with the worst score
Real worst_score = -std::numeric_limits<Real>::max();
Real worst_score_idx = 0;
- for(uint i = 0; i < largest_component.size(); ++i){
+ for(uint i = 0; i < largest_component.size(); ++i) {
Real actual_score = scores[largest_component[i]];
- if(actual_score > worst_score){
+ if(actual_score > worst_score) {
worst_score = actual_score;
worst_score_idx = i;
}
}
std::vector<int> indices_to_keep;
- for(uint i = 0; i < worst_score_idx; ++i){
+ for(uint i = 0; i < worst_score_idx; ++i) {
indices_to_keep.push_back(largest_component[i]);
}
- for(uint i = worst_score_idx + 1; i < largest_size; ++i){
+ for(uint i = worst_score_idx + 1; i < largest_size; ++i) {
indices_to_keep.push_back(largest_component[i]);
}
@@ -128,9 +130,9 @@ void Resolve(const std::vector<Real>& scores,
subgraph.ConnectedComponents(new_components);
// reorganize connected components
- for(uint i = 0; i < new_components.size(); ++i){
+ for(uint i = 0; i < new_components.size(); ++i) {
connected_components.push_back(std::vector<int>());
- for(uint j = 0; j < new_components[i].size(); ++j){
+ for(uint j = 0; j < new_components[i].size(); ++j) {
int idx_to_add = indices_to_keep[new_components[i][j]];
connected_components.back().push_back(idx_to_add);
}
@@ -140,20 +142,21 @@ void Resolve(const std::vector<Real>& scores,
// all components are now solvable... let's do it!
active_bonds.assign(scores.size(), 0);
- for(uint i = 0; i < connected_components.size(); ++i){
+ for(uint i = 0; i < connected_components.size(); ++i) {
uint component_size = connected_components[i].size();
- if(component_size == 1){
+ if(component_size == 1) {
active_bonds[connected_components[i][0]] = 1;
}
else{
std::vector<Real> component_scores(component_size, 0.0);
- for(uint j = 0; j < component_size; ++j){
+ for(uint j = 0; j < component_size; ++j) {
component_scores[j] = scores[connected_components[i][j]];
}
- promod3::core::Graph component_graph = graph.SubGraph(connected_components[i]);
+ promod3::core::Graph component_graph =
+ graph.SubGraph(connected_components[i]);
std::vector<int> component_active_bonds;
SingleResolve(component_scores, component_graph, component_active_bonds);
- for(uint j = 0; j < component_size; ++j){
+ for(uint j = 0; j < component_size; ++j) {
active_bonds[connected_components[i][j]] = component_active_bonds[j];
}
}
@@ -162,24 +165,24 @@ void Resolve(const std::vector<Real>& scores,
template <typename T>
-void CysteineResolve(const std::vector<T>& rot_groups,
+void CysteinResolve(const std::vector<T>& rot_groups,
const std::vector<geom::Vec3>& ca_pos,
const std::vector<geom::Vec3>& cb_pos,
Real disulfid_score_thresh,
std::vector<std::pair<uint, uint> >& disulfid_indices,
- std::vector<std::pair<uint, uint> >& rotamer_indices){
+ std::vector<std::pair<uint, uint> >& rotamer_indices) {
// do the trivial cases...
- if(rot_groups.size() <= 1){
+ if(rot_groups.size() <= 1) {
return;
}
// do some input checks
- if(ca_pos.size() != cb_pos.size()){
+ if(ca_pos.size() != cb_pos.size()) {
throw promod3::Error("Inconsistency in size of input lists observed!");
}
- if(ca_pos.size() != rot_groups.size()){
+ if(ca_pos.size() != rot_groups.size()) {
throw promod3::Error("Inconsistency in size of input lists observed!");
}
@@ -189,21 +192,21 @@ void CysteineResolve(const std::vector<T>& rot_groups,
std::vector<std::pair<uint, uint> > optimal_rotamers;
uint num_rotamer_groups = rot_groups.size();
- for(uint i = 0; i < num_rotamer_groups; ++i){
- for(uint j = i + 1; j < num_rotamer_groups; ++j){
- if(geom::Distance(ca_pos[i], ca_pos[j]) < Real(8.0)){
+ for(uint i = 0; i < num_rotamer_groups; ++i) {
+ for(uint j = i + 1; j < num_rotamer_groups; ++j) {
+ if(geom::Distance(ca_pos[i], ca_pos[j]) < Real(8.0)) {
// they are close and potentially build a disulfid bond...
Real min_score = std::numeric_limits<Real>::max();
uint min_k = 0;
uint min_l = 0;
Real score;
- for(uint k = 0; k < rot_groups[i]->size(); ++k){
- for(uint l = 0; l < rot_groups[j]->size(); ++l){
+ for(uint k = 0; k < rot_groups[i]->size(); ++k) {
+ for(uint l = 0; l < rot_groups[j]->size(); ++l) {
score = promod3::sidechain::DisulfidScore((*rot_groups[i])[k],
(*rot_groups[j])[l],
ca_pos[i], cb_pos[i],
ca_pos[j], cb_pos[j]);
- if(score < min_score){
+ if(score < min_score) {
min_score = score;
min_k = k;
min_l = l;
@@ -211,7 +214,7 @@ void CysteineResolve(const std::vector<T>& rot_groups,
}
}
- if(min_score < disulfid_score_thresh){
+ if(min_score < disulfid_score_thresh) {
// just found a potential disulfid bond!
scores.push_back(min_score - disulfid_score_thresh);
disulfids.push_back(std::make_pair(i, j));
@@ -224,16 +227,16 @@ void CysteineResolve(const std::vector<T>& rot_groups,
// in here we fill all indices of the active disulfid bonds...
std::vector<int> final_disulfids;
- if(disulfids.size() > 1){
+ if(disulfids.size() > 1) {
// resolve disambiguities
promod3::core::Graph graph(disulfids.size());
- for(uint i = 0; i < disulfids.size(); ++i){
- for(uint j = i + 1; j < disulfids.size(); ++j){
+ for(uint i = 0; i < disulfids.size(); ++i) {
+ for(uint j = i + 1; j < disulfids.size(); ++j) {
// check whether same rotamer group is involved in two disulfid bonds
if(disulfids[j].first == disulfids[i].first ||
disulfids[j].first == disulfids[i].second ||
disulfids[j].second == disulfids[i].first ||
- disulfids[j].second == disulfids[i].second){
+ disulfids[j].second == disulfids[i].second) {
graph.Connect(i, j);
}
}
@@ -243,23 +246,23 @@ void CysteineResolve(const std::vector<T>& rot_groups,
graph.ConnectedComponents(connected_components);
for(uint component_idx = 0; component_idx < connected_components.size();
- ++component_idx){
+ ++component_idx) {
const std::vector<int>& connected_component =
connected_components[component_idx];
- if(connected_component.size() > 1){
+ if(connected_component.size() > 1) {
std::vector<Real> component_scores;
- for(uint i = 0; i < connected_component.size(); ++i){
+ for(uint i = 0; i < connected_component.size(); ++i) {
component_scores.push_back(scores[connected_component[i]]);
}
promod3::core::Graph component_graph =
graph.SubGraph(connected_component);
std::vector<int> active_bonds;
Resolve(component_scores, component_graph, 15, active_bonds);
- for(uint i = 0; i < active_bonds.size(); ++i){
- if(active_bonds[i] == 1){
+ for(uint i = 0; i < active_bonds.size(); ++i) {
+ if(active_bonds[i] == 1) {
final_disulfids.push_back(connected_component[i]);
}
}
@@ -269,13 +272,13 @@ void CysteineResolve(const std::vector<T>& rot_groups,
}
}
}
- else if(disulfids.size() == 1){
+ else if(disulfids.size() == 1) {
final_disulfids.push_back(0);
}
// fill output
for(std::vector<int>::iterator i = final_disulfids.begin();
- i != final_disulfids.end(); ++i){
+ i != final_disulfids.end(); ++i) {
uint group_idx_one = disulfids[*i].first;
uint group_idx_two = disulfids[*i].second;
uint rot_idx_one = optimal_rotamers[*i].first;
@@ -285,43 +288,6 @@ void CysteineResolve(const std::vector<T>& rot_groups,
}
}
-}
-
-
-namespace promod3{ namespace sidechain{
-
-
-Real DisulfidRawScore(const geom::Vec3& ca_pos_one,
- const geom::Vec3& cb_pos_one,
- const geom::Vec3& sg_pos_one,
- const geom::Vec3& ca_pos_two,
- const geom::Vec3& cb_pos_two,
- const geom::Vec3& sg_pos_two){
-
- Real d = geom::Distance(sg_pos_one,sg_pos_two);
- Real a1 = geom::Angle(cb_pos_one-sg_pos_one, sg_pos_two-sg_pos_one);
- Real a2 = geom::Angle(sg_pos_one-sg_pos_two, cb_pos_two-sg_pos_two);
- Real x2 = std::abs(geom::DihedralAngle(ca_pos_one, cb_pos_one, sg_pos_one,
- sg_pos_two));
- Real x3 = std::abs(geom::DihedralAngle(cb_pos_one, sg_pos_one, sg_pos_two,
- cb_pos_two));
- Real x4 = std::abs(geom::DihedralAngle(sg_pos_one, sg_pos_two, cb_pos_two,
- ca_pos_two));
-
- return std::abs(d-2) / Real(0.05)
- + std::abs(a1-Real(1.8151)) / Real(0.087266)
- + std::abs(a2-Real(1.8151)) / Real(0.087266)
- + std::min(std::abs(x2-Real(1.3963)), std::abs(x2-Real(M_PI)))
- / Real(0.17453)
- + std::min(std::abs(x4-Real(1.3963)), std::abs(x4-Real(M_PI)))
- / Real(0.17453)
- + std::abs(x3-Real(M_PI)*Real(0.5)) / Real(0.34907);
-}
-
-
-namespace{
-
-// this is only in here because it requires the DisulfidRawScore function..
void SetOptimalSubrotamer(promod3::sidechain::FRMRotamerPtr rot_one,
promod3::sidechain::FRMRotamerPtr rot_two,
const geom::Vec3& ca_pos_one,
@@ -333,7 +299,7 @@ void SetOptimalSubrotamer(promod3::sidechain::FRMRotamerPtr rot_one,
ExtractCYSSG(*rot_one, *rot_two, sg_pos_one, sg_pos_two);
if(sg_pos_one.size() != rot_one->subrotamer_size() ||
- sg_pos_two.size() != rot_two->subrotamer_size() ){
+ sg_pos_two.size() != rot_two->subrotamer_size() ) {
throw promod3::Error("Expect cysteins to have exactly one gamma sulfur "
"per subrotamer!");
}
@@ -342,13 +308,16 @@ void SetOptimalSubrotamer(promod3::sidechain::FRMRotamerPtr rot_one,
uint min_i = 0;
uint min_j = 0;
- for(uint i = 0; i < sg_pos_one.size(); ++i){
- for(uint j = 0; j < sg_pos_two.size(); ++j){
+ for(uint i = 0; i < sg_pos_one.size(); ++i) {
+ for(uint j = 0; j < sg_pos_two.size(); ++j) {
- Real score = DisulfidRawScore(ca_pos_one,cb_pos_one,
- sg_pos_one[i], ca_pos_two,
- cb_pos_two,sg_pos_two[j]);
- if(score < min_score){
+ Real score = promod3::scoring::SCWRL3DisulfidScore(ca_pos_one,
+ cb_pos_one,
+ sg_pos_one[i],
+ ca_pos_two,
+ cb_pos_two,
+ sg_pos_two[j]);
+ if(score < min_score) {
min_score = score;
min_i = i;
min_j = j;
@@ -356,7 +325,7 @@ void SetOptimalSubrotamer(promod3::sidechain::FRMRotamerPtr rot_one,
}
}
- if(min_score < std::numeric_limits<Real>::max()){
+ if(min_score < std::numeric_limits<Real>::max()) {
rot_one->SetActiveSubrotamer(min_i);
rot_two->SetActiveSubrotamer(min_j);
}
@@ -365,20 +334,28 @@ void SetOptimalSubrotamer(promod3::sidechain::FRMRotamerPtr rot_one,
}
+namespace promod3{ namespace sidechain{
+
+
Real DisulfidScore(RRMRotamerPtr rot_one, RRMRotamerPtr rot_two,
const geom::Vec3& ca_pos_one, const geom::Vec3& cb_pos_one,
- const geom::Vec3& ca_pos_two, const geom::Vec3& cb_pos_two){
+ const geom::Vec3& ca_pos_two, const geom::Vec3& cb_pos_two) {
std::vector<geom::Vec3> sg_pos_one, sg_pos_two;
ExtractCYSSG(*rot_one, *rot_two, sg_pos_one, sg_pos_two);
- if(sg_pos_one.size() != 1 || sg_pos_two.size() != 1){
+ if(sg_pos_one.size() != 1 || sg_pos_two.size() != 1) {
throw promod3::Error("Expect rigid rotamers to have exactly one gamma "
"sulfur particle!");
}
- Real raw_score = DisulfidRawScore(ca_pos_one, cb_pos_one, sg_pos_one[0],
- ca_pos_two, cb_pos_two, sg_pos_two[0]);
+ Real raw_score = promod3::scoring::SCWRL3DisulfidScore(ca_pos_one,
+ cb_pos_one,
+ sg_pos_one[0],
+ ca_pos_two,
+ cb_pos_two,
+ sg_pos_two[0]);
+
Real self_energy = rot_one->GetSelfEnergy() + rot_two->GetSelfEnergy();
self_energy *= Real(0.5);
return raw_score + self_energy;
@@ -386,25 +363,28 @@ Real DisulfidScore(RRMRotamerPtr rot_one, RRMRotamerPtr rot_two,
Real DisulfidScore(FRMRotamerPtr rot_one, FRMRotamerPtr rot_two,
const geom::Vec3& ca_pos_one, const geom::Vec3& cb_pos_one,
- const geom::Vec3& ca_pos_two, const geom::Vec3& cb_pos_two){
+ const geom::Vec3& ca_pos_two, const geom::Vec3& cb_pos_two) {
std::vector<geom::Vec3> sg_pos_one, sg_pos_two;
ExtractCYSSG(*rot_one, *rot_two, sg_pos_one, sg_pos_two);
- if(sg_pos_one.empty() || sg_pos_two.empty()){
+ if(sg_pos_one.empty() || sg_pos_two.empty()) {
throw promod3::Error("Expect flexible rotamers to have at least one gamma "
"sulfur particle!");
}
Real min_raw_score = std::numeric_limits<Real>::max();
- for(uint i = 0; i < sg_pos_one.size(); ++i){
- for(uint j = 0; j < sg_pos_two.size(); ++j){
+ for(uint i = 0; i < sg_pos_one.size(); ++i) {
+ for(uint j = 0; j < sg_pos_two.size(); ++j) {
- min_raw_score = std::min(DisulfidRawScore(ca_pos_one,cb_pos_one,
- sg_pos_one[i], ca_pos_two,
- cb_pos_two,sg_pos_two[j])
- ,min_raw_score);
+ min_raw_score = std::min(promod3::scoring::SCWRL3DisulfidScore(ca_pos_one,
+ cb_pos_one,
+ sg_pos_one[i],
+ ca_pos_two,
+ cb_pos_two,
+ sg_pos_two[j])
+ ,min_raw_score);
}
}
@@ -421,9 +401,9 @@ void ResolveCysteins(
const std::vector<geom::Vec3>& cb_pos,
Real disulfid_score_thresh, bool optimize_subrotamers,
std::vector<std::pair<uint, uint> >& disulfid_indices,
- std::vector<std::pair<uint, uint> >& rotamer_indices){
+ std::vector<std::pair<uint, uint> >& rotamer_indices) {
- CysteineResolve<RRMRotamerGroupPtr>(rot_groups, ca_pos, cb_pos,
+ CysteinResolve<RRMRotamerGroupPtr>(rot_groups, ca_pos, cb_pos,
disulfid_score_thresh, disulfid_indices,
rotamer_indices);
@@ -432,17 +412,17 @@ void ResolveCysteins(
void ResolveCysteins(const std::vector<FRMRotamerGroupPtr>& rot_groups,
const std::vector<geom::Vec3>& ca_pos,
const std::vector<geom::Vec3>& cb_pos,
- Real disulfid_score_thresh, bool optimize_rotamers,
+ Real disulfid_score_thresh, bool optimize_subrotamers,
std::vector<std::pair<uint, uint> >& disulfid_indices,
- std::vector<std::pair<uint, uint> >& rotamer_indices){
+ std::vector<std::pair<uint, uint> >& rotamer_indices) {
- CysteineResolve<FRMRotamerGroupPtr>(rot_groups, ca_pos, cb_pos,
+ CysteinResolve<FRMRotamerGroupPtr>(rot_groups, ca_pos, cb_pos,
disulfid_score_thresh, disulfid_indices,
rotamer_indices);
- if(optimize_rotamers){
+ if(optimize_subrotamers) {
- for(uint i = 0; i < disulfid_indices.size(); ++i){
+ for(uint i = 0; i < disulfid_indices.size(); ++i) {
const std::pair<uint, uint>& group_pair = disulfid_indices[i];
const std::pair<uint, uint>& rotamer_pair = rotamer_indices[i];
@@ -458,4 +438,4 @@ void ResolveCysteins(const std::vector<FRMRotamerGroupPtr>& rot_groups,
}
-}} //ns
+}} // ns
diff --git a/sidechain/src/disulfid.hh b/sidechain/src/disulfid.hh
index 84f98aaed96b86342031e10b9f30ad1cafc4016d..ac6aa87e196c4e4f0873c9068e7e932798021aca 100644
--- a/sidechain/src/disulfid.hh
+++ b/sidechain/src/disulfid.hh
@@ -10,13 +10,6 @@
namespace promod3{ namespace sidechain{
-Real DisulfidRawScore(const geom::Vec3& ca_pos_one,
- const geom::Vec3& cb_pos_one,
- const geom::Vec3& sg_pos_one,
- const geom::Vec3& ca_pos_two,
- const geom::Vec3& cb_pos_two,
- const geom::Vec3& sg_pos_two);
-
Real DisulfidScore(RRMRotamerPtr rot_one, RRMRotamerPtr rot_two,
const geom::Vec3& ca_pos_one, const geom::Vec3& cb_pos_one,
const geom::Vec3& ca_pos_two, const geom::Vec3& cb_pos_two);
@@ -39,6 +32,6 @@ Real DisulfidScore(FRMRotamerPtr rot_one, FRMRotamerPtr rot_two,
std::vector<std::pair<uint, uint> >& disulfid_indices,
std::vector<std::pair<uint, uint> >& rotamer_indices);
-}}//ns
+}} // ns
#endif
diff --git a/sidechain/src/rotamer.cc b/sidechain/src/rotamer.cc
index 0167bec90866fd8e070298b29eeaf5a16e2b73c0..71443cb8feb51f25abc7805f41a5973777f51e99 100644
--- a/sidechain/src/rotamer.cc
+++ b/sidechain/src/rotamer.cc
@@ -7,8 +7,10 @@ namespace promod3{ namespace sidechain{
RRMRotamer::RRMRotamer(const std::vector<Particle>& particles,
Real probability, Real internal_e_prefactor):
particles_(particles), n_particles_(particles.size()),
- internal_energy_(0.0), frame_energy_(0.0), probability_(probability),
- internal_e_prefactor_(internal_e_prefactor){ }
+ internal_energy_(0.0), frame_energy_(0.0),
+ probability_(probability),
+ internal_e_prefactor_(internal_e_prefactor) { }
+
void RRMRotamer::ApplyOnResidue(ost::mol::ResidueHandle& res,
bool consider_hydrogens,
@@ -18,7 +20,7 @@ void RRMRotamer::ApplyOnResidue(ost::mol::ResidueHandle& res,
"RRMRotamer::ApplyOnResidue", 2);
ost::mol::XCSEditor ed = res.GetEntity().EditXCS(ost::mol::BUFFERED_EDIT);
- for(uint i = 0; i < n_particles_; ++i){
+ for(uint i = 0; i < n_particles_; ++i) {
const Particle& p=particles_[i];
const String& particle_name =p.GetName();
if(particle_name[0] == 'H' && !consider_hydrogens) continue;
@@ -38,6 +40,7 @@ void RRMRotamer::ApplyOnResidue(ost::mol::ResidueHandle& res,
}
}
+
void RRMRotamer::ApplyOnResidue(loop::AllAtomPositions& all_atom,
uint res_idx) const {
@@ -55,38 +58,43 @@ void RRMRotamer::ApplyOnResidue(loop::AllAtomPositions& all_atom,
}
}
+
FrameResiduePtr RRMRotamer::ToFrameResidue(uint res_idx) const {
FrameResiduePtr frame_res(new FrameResidue(particles_, res_idx));
return frame_res;
}
+
FRMRotamer::FRMRotamer(const std::vector<Particle>& particles, Real T,
Real probability, Real internal_e_prefactor):
particles_(particles), n_particles_(particles.size()),
active_subrotamer_(0), internal_energy_(0.0),
frame_energy_(0.0), T_(T), probability_(probability),
- internal_e_prefactor_(internal_e_prefactor){
+ internal_e_prefactor_(internal_e_prefactor) {
subrotamer_associations_.resize(n_particles_,std::vector<int>());
}
-void FRMRotamer::AddSubrotamerDefinition(const std::vector<int>& definition){
+
+void FRMRotamer::AddSubrotamerDefinition(const std::vector<int>& definition) {
uint subrotamer_index = subrotamer_definitions_.size();
subrotamer_definitions_.push_back(definition);
for(std::vector<int>::const_iterator i = definition.begin();
- i != definition.end();++i){
+ i != definition.end();++i) {
subrotamer_associations_[*i].push_back(subrotamer_index);
}
frame_energies_.push_back(0.0);
}
+
void FRMRotamer::SetActiveSubrotamer(uint idx) {
- if(idx >= subrotamer_definitions_.size()){
+ if(idx >= subrotamer_definitions_.size()) {
throw promod3::Error("Invalid subrotamer idx provided!");
}
active_subrotamer_ = idx;
}
+
void FRMRotamer::ApplyOnResidue(ost::mol::ResidueHandle& res,
bool consider_hydrogens,
const String& new_res_name) const {
@@ -94,11 +102,11 @@ void FRMRotamer::ApplyOnResidue(ost::mol::ResidueHandle& res,
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"FRMRotamer::ApplyOnResidue", 2);
- if(subrotamer_definitions_.empty()){
+ if(subrotamer_definitions_.empty()) {
throw promod3::Error("At least one subrotamer must be set in FRM rotamer!");
}
- if(active_subrotamer_ >= subrotamer_definitions_.size()){
+ if(active_subrotamer_ >= subrotamer_definitions_.size()) {
throw promod3::Error("Need to add subrotamer definitions to "
"apply FRMRotamer to residue!");
}
@@ -112,7 +120,7 @@ void FRMRotamer::ApplyOnResidue(ost::mol::ResidueHandle& res,
const String& particle_name = p.GetName();
if(particle_name[0] == 'H' && !consider_hydrogens) continue;
a = res.FindAtom(particle_name);
- if (a.IsValid()){
+ if (a.IsValid()) {
// weirdly enough, the commented out command is significantly slower
// (at least on el schdaudoputer) There is no obvious reason for that...
ed.DeleteAtom(a);
@@ -124,20 +132,21 @@ void FRMRotamer::ApplyOnResidue(ost::mol::ResidueHandle& res,
}
}
- if(new_res_name != ""){
+ if(new_res_name != "") {
ed.RenameResidue(res,new_res_name);
res.SetOneLetterCode(ost::conop::ResidueNameToOneLetterCode(new_res_name));
}
ed.UpdateICS();
}
+
void FRMRotamer::ApplyOnResidue(loop::AllAtomPositions& all_atom,
uint res_idx) const {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"FRMRotamer::ApplyOnResidueAA", 2);
- if(active_subrotamer_ >= subrotamer_definitions_.size()){
+ if(active_subrotamer_ >= subrotamer_definitions_.size()) {
throw promod3::Error("Need to add subrotamer definitions to "
"apply FRMRotamer to residue!");
}
@@ -145,7 +154,8 @@ void FRMRotamer::ApplyOnResidue(loop::AllAtomPositions& all_atom,
// check res_idx
all_atom.CheckResidueIndex(res_idx);
// reset all heavy atoms
- const std::vector<int>& sub_def_ = subrotamer_definitions_[active_subrotamer_];
+ const std::vector<int>& sub_def_ =
+ subrotamer_definitions_[active_subrotamer_];
for (uint i = 0; i < sub_def_.size(); ++i) {
const Particle& p = particles_[sub_def_[i]];
const String& particle_name = p.GetName();
@@ -158,36 +168,38 @@ void FRMRotamer::ApplyOnResidue(loop::AllAtomPositions& all_atom,
FrameResiduePtr FRMRotamer::ToFrameResidue(uint res_idx) const {
- if(active_subrotamer_ >= subrotamer_definitions_.size()){
+ if(active_subrotamer_ >= subrotamer_definitions_.size()) {
throw promod3::Error("Need to add subrotamer definitions to "
"generate FrameResidue!");
}
const std::vector<int>& sub_def = subrotamer_definitions_[active_subrotamer_];
std::vector<Particle> particles(sub_def.size());
- for(uint i = 0; i < sub_def.size(); ++i){
+ for(uint i = 0; i < sub_def.size(); ++i) {
particles[i] = particles_[sub_def[i]];
}
FrameResiduePtr frame_res(new FrameResidue(particles, res_idx));
return frame_res;
}
+
RRMRotamerPtr FRMRotamer::ToRRMRotamer() const {
- if(active_subrotamer_ >= subrotamer_definitions_.size()){
+ if(active_subrotamer_ >= subrotamer_definitions_.size()) {
throw promod3::Error("Need to add subrotamer definitions to "
"to generate RRMRotamer!");
}
const std::vector<int>& sub_def = subrotamer_definitions_[active_subrotamer_];
std::vector<Particle> particles(sub_def.size());
- for(uint i = 0; i < sub_def.size(); ++i){
+ for(uint i = 0; i < sub_def.size(); ++i) {
particles[i] = particles_[sub_def[i]];
}
- RRMRotamerPtr rot(new RRMRotamer(particles, probability_, internal_e_prefactor_));
+ RRMRotamerPtr rot(new RRMRotamer(particles, probability_,
+ internal_e_prefactor_));
rot->SetFrameEnergy(frame_energies_[active_subrotamer_]);
rot->SetInternalEnergy(internal_energy_);
return rot;
}
-}}//ns
+}} // ns
diff --git a/sidechain/src/rotamer.hh b/sidechain/src/rotamer.hh
index 14a38769a9b5a2e51e67a714dd0eb5c9a6196412..45ce313939a798828f47988b1158678907f7c0d2 100644
--- a/sidechain/src/rotamer.hh
+++ b/sidechain/src/rotamer.hh
@@ -153,10 +153,12 @@ public:
typedef std::vector<Particle>::iterator iterator;
typedef std::vector<Particle>::const_iterator const_iterator;
- typedef std::vector<std::vector<int> >::const_iterator const_subrotamer_iterator;
+ typedef std::vector<std::vector<int> >::const_iterator
+ const_subrotamer_iterator;
typedef std::vector<std::vector<int> >::iterator subrotamer_iterator;
- typedef std::vector<int>::const_iterator const_subrotamer_association_iterator;
+ typedef std::vector<int>::const_iterator
+ const_subrotamer_association_iterator;
typedef std::vector<int>::iterator subrotamer_association_iterator;
iterator begin() { return particles_.begin(); }
@@ -210,6 +212,6 @@ private:
Real internal_e_prefactor_;
};
-}}//ns
+}} // ns
#endif
diff --git a/sidechain/src/rotamer_graph.cc b/sidechain/src/rotamer_graph.cc
index 43df7f611b5b97d6288015a334b3af4338c841e1..dff604b654ce11ec96ba155db7812207cfd3330f 100644
--- a/sidechain/src/rotamer_graph.cc
+++ b/sidechain/src/rotamer_graph.cc
@@ -1,2024 +1,44 @@
-#include <algorithm>
-#include <queue>
-#include <limits>
-
#include <promod3/sidechain/rotamer_graph.hh>
-#include <promod3/core/tree.hh>
-#include <promod3/core/runtime_profiling.hh>
-#include <promod3/core/enumerator.hh>
-#include <promod3/core/message.hh>
-
-#include <boost/random/mersenne_twister.hpp>
-#include <boost/random/uniform_01.hpp>
-
-
-namespace{
-
-bool active_rotamer_sorter(std::pair<uint,Real> a, std::pair<uint,Real> b){
- return a.second < b.second;
-}
-
-
-
-////////////////////////////////////////////////////////////////
-//FUNCTIONS AND DATA STRUCTURES FOR THE TREE SOLVING ALGORITHM//
-////////////////////////////////////////////////////////////////
-
-typedef promod3::core::TreeBag<int> TreeBag;
-
-//calculates a linear idx for a certain combination in the lset
-struct LSetIdxCalculator{
-
- LSetIdxCalculator() { }
-
- LSetIdxCalculator(const std::vector<unsigned short>& num_candidates){
- lset_size = num_candidates.size();
- for(int i = 0; i < lset_size; ++i){
- int temp = 1;
- for(int j = i + 1; j < lset_size; ++j){
- temp *= num_candidates[j];
- }
- idx_helper.push_back(temp);
- }
- idx_helper.push_back(1);
- }
-
- inline int GetLIdx(const std::vector<unsigned short>& indices) const{
- int idx = 0;
- for(int i = 0; i < lset_size; ++i){
- idx += idx_helper[i] * indices[i];
- }
- return idx;
- }
-
- inline int GetIdxHelper(int idx){
- return idx_helper[idx];
- }
-
- std::vector<int> idx_helper;
- int lset_size;
-};
-
-//wrapper around pairwise rotamer energies considering the fact,
-//that the node with lower idx is by construction defining the row,
-//whereas the other defines the column
-struct PairwiseEWrapper{
-
- PairwiseEWrapper(int node_one,
- int node_two,
- int num_rotamers_one,
- int num_rotamers_two,
- Real* e) {
-
- if(node_two > node_one) {
- multiplicator_one = num_rotamers_two;
- multiplicator_two = 1;
- }
- else {
- multiplicator_one = 1;
- multiplicator_two = num_rotamers_one;
- }
-
- energies = e;
- }
-
- inline Real GetEnergy(int rotamer_one, int rotamer_two) const{
- return energies[rotamer_one * multiplicator_one +
- rotamer_two * multiplicator_two];
- }
-
- int multiplicator_one;
- int multiplicator_two;
- Real* energies;
-};
-
-
-
-struct BagData{
-
- //members of the bag that are also present in parent bag
- std::vector<int> lset;
- //members of the bag that are not present in parent bag
- std::vector<int> rset;
-
- //number of rotamers for every entry in lset/rset
- uint num_l_combinations;
- uint num_r_combinations;
- std::vector<unsigned short> num_l_rotamers;
- std::vector<unsigned short> num_r_rotamers;
-
- // optimal solution in r set given a certain combination in l
- // the index for a certain combination in l can be estimated with
- // l_set_idx_calculator
- // assuming an l_idx of x, the according optimal rset data starts
- // at x * rset.size()
- std::vector<unsigned short> optimal_rset_combination;
-
- //the according score
- std::vector<Real> optimal_r_score;
-
- //calculates an index in optimal_r_combination/optimal_r_score
- //given a certain combination in l
- LSetIdxCalculator lset_idx_calculator;
-
- //the bag data indices for the children attached to this bag
- std::vector<int> children_indices;
- int num_children;
-
- //super complicated mapping structure of getting stuff out from the children
- //the idea is, that we can calculate the lset idx in several steps in the
- //enumeration procedure...
-
- //for every child we have a vector of with indices describing the
- //elements in the current lset being part of the childrens lset
- std::vector<std::vector<int> > lset_child_l_indices;
- //the number it has to be multiplied to construct the index for
- //that particular child lset
- std::vector<std::vector<int> > lset_child_l_index_helpers;
- //store the size of the stuff above for every child
- std::vector<int> num_lset_child_l;
-
- //equivalent for the current rset
- std::vector<std::vector<int> > rset_child_l_indices;
- std::vector<std::vector<int> > rset_child_l_index_helpers;
- std::vector<int> num_rset_child_l;
-
- //this data structure will be altered during the calculation and is a
- //placeholder to query optimal solutions for certain lsets of the children
- std::vector<std::vector<int> > children_l_combinations;
-
- //self energies of the rset
- std::vector<Real*> r_self_energies;
-
- //stuff for lr and rl pairwise energies
- std::vector<PairwiseEWrapper> lr_energies;
- std::vector<int> lr_index_in_I;
- std::vector<int> lr_index_in_R;
-
- //stuff for rr pairwise energies
- std::vector<PairwiseEWrapper> rr_energies;
- std::vector<int> rr_index_in_R_one;
- std::vector<int> rr_index_in_R_two;
-};
-
-//Fills only the bare minimum of data into the BagData vector and already
-//estimates the complexity of the tree solving procedure. All other data
-//gets filled in the FillBagData function
-uint64_t FillRawBagData(const std::vector<TreeBag*>& traversal,
- const std::vector<int>& num_active_rotamers,
- std::vector<BagData>& bag_data){
-
- uint64_t complexity = 0;
-
- bag_data.clear();
- bag_data.resize(traversal.size());
-
- for(uint bag_idx = 0; bag_idx < traversal.size(); ++bag_idx){
-
- TreeBag* bag = traversal[bag_idx];
- TreeBag* parent = traversal[bag_idx]->GetParent();
-
- //assign rset and lset
- if(parent == NULL){
- //it's the root, lets shuffle all to rset
- bag_data[bag_idx].rset.assign(bag->members_begin(),
- bag->members_end());
- }
- else{
- for(TreeBag::const_member_iterator it = bag->members_begin();
- it != bag->members_end(); ++it){
- if(parent->HasMember(*it)) bag_data[bag_idx].lset.push_back(*it);
- else bag_data[bag_idx].rset.push_back(*it);
- }
- }
-
- //figure out how many rotamers there are
- bag_data[bag_idx].num_l_combinations = 1;
- bag_data[bag_idx].num_r_combinations = 1;
-
- for(std::vector<int>::iterator i = bag_data[bag_idx].lset.begin();
- i != bag_data[bag_idx].lset.end(); ++i){
- bag_data[bag_idx].num_l_rotamers.push_back(num_active_rotamers[*i]);
- bag_data[bag_idx].num_l_combinations *= num_active_rotamers[*i];
- }
-
- for(std::vector<int>::iterator i = bag_data[bag_idx].rset.begin();
- i != bag_data[bag_idx].rset.end(); ++i){
- bag_data[bag_idx].num_r_rotamers.push_back(num_active_rotamers[*i]);
- bag_data[bag_idx].num_r_combinations *= num_active_rotamers[*i];
- }
-
- complexity += (bag_data[bag_idx].num_l_combinations *
- bag_data[bag_idx].num_r_combinations);
- }
-
- return complexity;
-}
-
-
-void FillBagData(const std::vector<TreeBag*>& traversal,
- std::vector<Real*> self_energies,
- std::map<std::pair<int,int>, Real*> pairwise_energies,
- std::vector<BagData>& bag_data){
-
- for(uint bag_idx = 0; bag_idx < traversal.size(); ++bag_idx){
-
- TreeBag* bag = traversal[bag_idx];
- BagData& current_data = bag_data[bag_idx];
-
- //allocate required space for optimal r combinations for every possible lset
- current_data.optimal_rset_combination.resize(current_data.num_l_combinations *
- current_data.rset.size());
- current_data.optimal_r_score.resize(current_data.num_l_combinations);
-
- //generate a new lset idxgenerator...
- current_data.lset_idx_calculator =
- LSetIdxCalculator(current_data.num_l_rotamers);
-
- //get all the children stuff right
- for(TreeBag::const_child_iterator it = bag->children_begin();
- it != bag->children_end(); ++it){
- current_data.children_indices.push_back((*it)->GetIdx());
- }
- current_data.num_children = current_data.children_indices.size();
-
- //handle current lset
- current_data.lset_child_l_indices.resize(current_data.num_children);
- current_data.lset_child_l_index_helpers.resize(current_data.num_children);
- for(uint i = 0; i < current_data.lset.size(); ++i){
- int val = current_data.lset[i];
- //go through all children
- for(int j = 0; j < current_data.num_children; ++j){
- int ch_idx = current_data.children_indices[j];
- //we can be sure of the children lsets being set due to the postorder
- //traversal of the tree
- const std::vector<int>& child_lset = bag_data[ch_idx].lset;
- std::vector<int>::const_iterator it = std::find(child_lset.begin(),
- child_lset.end(),
- val);
- if(it != child_lset.end()){
- //its in the childs lset!
- int idx_in_child_l = it - child_lset.begin();
- current_data.lset_child_l_indices[j].push_back(i);
- int helper = bag_data[ch_idx].lset_idx_calculator.GetIdxHelper(idx_in_child_l);
- current_data.lset_child_l_index_helpers[j].push_back(helper);
- }
- }
- }
- for(int i = 0; i < current_data.num_children; ++i){
- current_data.num_lset_child_l.push_back(current_data.lset_child_l_indices[i].size());
- }
-
- //do the same for the rset
- current_data.rset_child_l_indices.resize(current_data.num_children);
- current_data.rset_child_l_index_helpers.resize(current_data.num_children);
- for(uint i = 0; i < current_data.rset.size(); ++i){
- int val = current_data.rset[i];
- //go through all children
- for(int j = 0; j < current_data.num_children; ++j){
- int ch_idx = current_data.children_indices[j];
- //we can be sure of the children lsets being set due to the postorder
- //traversal of the tree
- const std::vector<int>& child_lset = bag_data[ch_idx].lset;
- std::vector<int>::const_iterator it = std::find(child_lset.begin(),
- child_lset.end(),
- val);
- if(it != child_lset.end()){
- //its in the childs lset!
- int idx_in_child_l = it - child_lset.begin();
- current_data.rset_child_l_indices[j].push_back(i);
- int helper = bag_data[ch_idx].lset_idx_calculator.GetIdxHelper(idx_in_child_l);
- current_data.rset_child_l_index_helpers[j].push_back(helper);
- }
- }
- }
- for(int i = 0; i < current_data.num_children; ++i){
- current_data.num_rset_child_l.push_back(current_data.rset_child_l_indices[i].size());
- }
-
- //prepare the lset combinations
- for(std::vector<int>::iterator i = current_data.children_indices.begin();
- i != current_data.children_indices.end(); ++i){
- int size = bag_data[*i].lset.size();
- current_data.children_l_combinations.push_back(std::vector<int>(size,0));
- }
-
- //fill the rset self energies
- for(std::vector<int>::iterator i = current_data.rset.begin();
- i != current_data.rset.end(); ++i){
- current_data.r_self_energies.push_back(self_energies[*i]);
- }
-
- //fill the lr pairwise energies
- for(uint i = 0; i < current_data.lset.size(); ++i){
- for(uint j = 0; j < current_data.rset.size(); ++j){
- std::pair<int,int> idx_pair = std::make_pair(current_data.lset[i],
- current_data.rset[j]);
- std::map<std::pair<int,int>, Real*>::iterator e_it =
- pairwise_energies.find(idx_pair);
- if(e_it != pairwise_energies.end()){
- current_data.lr_energies.push_back(PairwiseEWrapper(current_data.lset[i],
- current_data.rset[j],
- current_data.num_l_rotamers[i],
- current_data.num_r_rotamers[j],
- e_it->second));
- current_data.lr_index_in_I.push_back(i);
- current_data.lr_index_in_R.push_back(j);
- continue;
- }
- idx_pair = std::make_pair(current_data.rset[j], current_data.lset[i]);
- e_it = pairwise_energies.find(idx_pair);
- if(e_it != pairwise_energies.end()){
- current_data.lr_energies.push_back(PairwiseEWrapper(current_data.lset[i],
- current_data.rset[j],
- current_data.num_l_rotamers[i],
- current_data.num_r_rotamers[j],
- e_it->second));
- current_data.lr_index_in_I.push_back(i);
- current_data.lr_index_in_R.push_back(j);
- }
- }
- }
-
- //fill the rr pairwise energies
- for(uint i = 0; i < current_data.rset.size(); ++i){
- for(uint j = i + 1; j < current_data.rset.size(); ++j){
-
- std::pair<int,int> idx_pair = std::make_pair(current_data.rset[i],
- current_data.rset[j]);
- std::map<std::pair<int,int>, Real*>::iterator e_it =
- pairwise_energies.find(idx_pair);
- if(e_it != pairwise_energies.end()){
- current_data.rr_energies.push_back(PairwiseEWrapper(current_data.rset[i],
- current_data.rset[j],
- current_data.num_r_rotamers[i],
- current_data.num_r_rotamers[j],
- e_it->second));
- current_data.rr_index_in_R_one.push_back(i);
- current_data.rr_index_in_R_two.push_back(j);
- continue;
- }
- idx_pair = std::make_pair(current_data.rset[j], current_data.rset[i]);
- e_it = pairwise_energies.find(idx_pair);
- if(e_it != pairwise_energies.end()){
- current_data.rr_energies.push_back(PairwiseEWrapper(current_data.rset[i],
- current_data.rset[j],
- current_data.num_r_rotamers[i],
- current_data.num_r_rotamers[j],
- e_it->second));
- current_data.rr_index_in_R_one.push_back(i);
- current_data.rr_index_in_R_two.push_back(j);
- }
- }
- }
- }
-}
-
-void EnumerateBagData(std::vector<BagData>& bag_data){
-
- for(uint bag_idx = 0; bag_idx < bag_data.size(); ++bag_idx){
-
- //data of the current bag
- BagData& data = bag_data[bag_idx];
- int rset_size = data.rset.size();
- int num_lr_energies = data.lr_energies.size();
- int num_rr_energies = data.rr_energies.size();
-
- //the lset of this bag we have to enumerate
- promod3::core::Enumerator<unsigned short>
- l_set_enumerator(data.num_l_rotamers);
- std::vector<unsigned short>& current_l_enum =
- l_set_enumerator.CurrentEnum();
-
- int num_children = data.children_indices.size();
- int partial_l_indices[num_children];
-
- do {
-
- memset(partial_l_indices, 0 , num_children * sizeof(int));
- for(int j = 0; j < num_children; ++j){
- for(int k = 0; k < data.num_lset_child_l[j]; ++k){
- partial_l_indices[j] +=
- (current_l_enum[data.lset_child_l_indices[j][k]] *
- data.lset_child_l_index_helpers[j][k]);
- }
- }
-
- promod3::core::Enumerator<unsigned short>
- r_set_enumerator(data.num_r_rotamers);
- std::vector<unsigned short>& current_r_enum =
- r_set_enumerator.CurrentEnum();
-
- Real score;
- Real best_score = std::numeric_limits<Real>::max();
- std::vector<unsigned short> best_rset = current_r_enum;
-
- //let's find the optimal r combination given the current l combination...
- do {
-
- score = 0;
-
- //sum up the r self energies
- for(int i = 0; i < rset_size; ++i){
- score += data.r_self_energies[i][current_r_enum[i]];
- }
-
- //sum up the lr pairwise energies
- for(int i = 0; i < num_lr_energies; ++i){
- score +=
- data.lr_energies[i].GetEnergy(current_l_enum[data.lr_index_in_I[i]],
- current_r_enum[data.lr_index_in_R[i]]);
- }
-
- //sum up the rr pairwise energies
- for(int i = 0; i < num_rr_energies; ++i){
- score +=
- data.rr_energies[i].GetEnergy(current_r_enum[data.rr_index_in_R_one[i]],
- current_r_enum[data.rr_index_in_R_two[i]]);
- }
-
- for(int i = 0; i < num_children; ++i){
- int l_idx = partial_l_indices[i];
- for(int j = 0; j < data.num_rset_child_l[i]; ++j){
- l_idx += (current_r_enum[data.rset_child_l_indices[i][j]] *
- data.rset_child_l_index_helpers[i][j]);
- }
- score += bag_data[data.children_indices[i]].optimal_r_score[l_idx];
- }
-
- if(score < best_score){
- best_score = score;
- best_rset = current_r_enum;
- }
-
- } while(r_set_enumerator.Next());
-
- int l_idx = data.lset_idx_calculator.GetLIdx(current_l_enum);
- memcpy(&data.optimal_rset_combination[l_idx*rset_size],
- &best_rset[0], rset_size * sizeof(unsigned short));
- data.optimal_r_score[l_idx] = best_score;
-
- } while(l_set_enumerator.Next());
- }
-}
-
-void CollectSolutionFromBagData(const std::vector<BagData>& bag_data,
- int bag_idx, std::vector<int>& solution){
-
- const BagData& bag = bag_data[bag_idx];
-
- //collect the lset values from the solution
- std::vector<unsigned short> l_solution(bag.lset.size(), 0);
- for(uint i = 0; i < l_solution.size(); ++i){
- l_solution[i] = solution[bag.lset[i]];
- }
-
- //get the index of the ideal r_combination given that l solution
- int r_idx = bag.lset_idx_calculator.GetLIdx(l_solution);
- //and fill the according values into the solution
- int rset_size = bag.rset.size();
- int data_start_idx = r_idx * rset_size;
- for(int i = 0; i < rset_size; ++i){
- solution[bag.rset[i]] = bag.optimal_rset_combination[data_start_idx+i];
- }
-
- //recursively call this function for all the children
- for(std::vector<int>::const_iterator i = bag.children_indices.begin();
- i != bag.children_indices.end(); ++i){
- CollectSolutionFromBagData(bag_data, *i, solution);
- }
-}
-
-/////////////////////////////////////////////////////////////////
-//FUNCTIONS AND DATA STRUCTURES FOR THE ASTAR SOLVING ALGORITHM//
-/////////////////////////////////////////////////////////////////
-struct AStarNode{
-
- AStarNode(uint idx, uint p_idx, unsigned short r_idx,
- unsigned short t_d, Real gs, Real hs): node_idx(idx),
- parent_idx(p_idx),
- rotamer_idx(r_idx),
- tree_depth(t_d),
- gstar(gs),
- hstar(hs) { }
-
- uint node_idx;
- uint parent_idx;
- unsigned short rotamer_idx;
- unsigned short tree_depth;
- Real gstar;
- Real hstar;
-};
-
-class CompareAStarNodes{
-public:
- bool operator() (AStarNode* a, AStarNode* b){
- return (a->gstar + a->hstar) > (b->gstar + b->hstar);
- }
-};
-void ReconstructSearchTreePath(const std::vector<AStarNode>& node_array,
- uint start_idx,
- std::vector<int>& path){
- path.resize(node_array[start_idx].tree_depth);
- uint current_node_idx = start_idx;
+namespace promod3 { namespace sidechain {
- while(current_node_idx != 0){
- path[node_array[current_node_idx].tree_depth-1] =
- node_array[current_node_idx].rotamer_idx;
- current_node_idx = node_array[current_node_idx].parent_idx;
- }
-}
-
-/////////////////////////////////////////////////////////////////
-//FUNCTIONS AND DATA STRUCTURES FOR THE MC SOLVING ALGORITHM//
-/////////////////////////////////////////////////////////////////
-
-Real GetRotamerEnergy(int node_idx, int rot_idx,
- const std::vector<int>& current_configuration,
- const std::vector<Real*>& self_energies,
- const std::vector<std::vector<std::pair<int, PairwiseEWrapper> > >&
- pairwise_energies) {
-
- Real e = self_energies[node_idx][rot_idx];
-
- for(std::vector<std::pair<int, PairwiseEWrapper> >::const_iterator
- it = pairwise_energies[node_idx].begin();
- it != pairwise_energies[node_idx].end(); ++it) {
- e += it->second.GetEnergy(rot_idx, current_configuration[it->first]);
- }
-
- return e;
-}
-
-Real GetGlobalEnergy(const std::vector<int>& solution,
- const std::vector<Real*> self_energies,
- const std::vector<std::vector<std::pair<int, PairwiseEWrapper> > >&
- pairwise_energies) {
-
- Real e = 0.0;
- int num_nodes = solution.size();
- for(int i = 0; i < num_nodes; ++i) {
- e += self_energies[i][solution[i]];
- }
-
- for(int i = 0; i < num_nodes; ++i) {
- for(std::vector<std::pair<int, PairwiseEWrapper> >::const_iterator
- j = pairwise_energies[i].begin(); j != pairwise_energies[i].end(); ++j) {
- int other_node = j->first;
- if(other_node > i) {
- const PairwiseEWrapper& e_wrapper = j->second;
- e += e_wrapper.GetEnergy(solution[i], solution[other_node]);
- }
- }
- }
-
- return e;
-}
-
-struct RotamerSelector {
-
- RotamerSelector(std::vector<int> num_rotamers, int random_seed):
- n(num_rotamers.size()),
- n_rot(num_rotamers),
- rng(random_seed),
- zeroone(rng) { }
-
- int SelectNode() {
- return static_cast<int>(zeroone() * n);
- }
-
- int SelectRotamer(int node_idx) {
- return static_cast<int>(zeroone() * n_rot[node_idx]);
- }
-
- void InitRotamerSelection(std::vector<int>& current_solution) {
- current_solution.resize(n);
- for(int i = 0; i < n; ++i) {
- current_solution[i] = this->SelectRotamer(i);
- }
- }
-
- Real GetRandomNumber() {
- return zeroone();
- }
-
- int n;
- std::vector<int> n_rot;
- boost::mt19937 rng;
- boost::uniform_01<boost::mt19937&> zeroone;
-};
-
-
-} // anon ns
-
-namespace promod3{ namespace sidechain{
-
-RotamerGraphEdge::RotamerGraphEdge(uint index,
- RotamerGraphNode* node1,
- RotamerGraphNode* node2,
- uint num_i, uint num_j,
- Real* pairwise_energies): index_(index),
- active_(true),
- node1_(node1),
- node2_(node2),
- maxi_(num_i),
- maxj_(num_j),
- pairwise_energies_(pairwise_energies){
-
-}
-
-RotamerGraphEdge::~RotamerGraphEdge(){
- delete [] pairwise_energies_;
- //Nodes don't get deleted here!
- //It is assumed, that this happens in the graph object
-}
-
-void RotamerGraphEdge::Reset(){
- active_ = true;
-}
-
-void RotamerGraphEdge::Deactivate(){
- if(!active_) return;
- active_ = false;
-}
-
-bool RotamerGraphEdge::Decompose(Real thresh){
-
- if(!active_) return false;
-
- Real summed_e = 0.0;
- uint m = node1_->GetNumActiveRotamers();
- uint n = node2_->GetNumActiveRotamers();
- uint n_total = node2_->GetNumRotamers();
- int temp;
-
- for(RotamerGraphNode::iterator i = node1_->active_rotamers_begin();
- i != node1_->active_rotamers_end(); ++i){
- temp = (*i) * n_total;
- for(RotamerGraphNode::iterator j = node2_->active_rotamers_begin();
- j != node2_->active_rotamers_end(); ++j){
- summed_e += pairwise_energies_[temp + (*j)];
- }
- }
-
- Real avg_value = summed_e/(2*n*m);
-
- std::vector<Real> ak(m);
- std::vector<Real> bl(n);
-
- uint m_counter = 0;
- for(RotamerGraphNode::iterator i = node1_->active_rotamers_begin();
- i != node1_->active_rotamers_end(); ++i){
- summed_e = 0.0;
- int temp = (*i) * n_total;
- for(RotamerGraphNode::iterator j = node2_->active_rotamers_begin();
- j != node2_->active_rotamers_end(); ++j){
- summed_e += pairwise_energies_[temp + (*j)];
- }
- ak[m_counter] = summed_e/n - avg_value;
- ++m_counter;
- }
-
- Real e;
- uint n_counter = 0;
- for(RotamerGraphNode::iterator i = node2_->active_rotamers_begin();
- i != node2_->active_rotamers_end(); ++i){
- summed_e = 0.0;
- for(RotamerGraphNode::iterator j = node1_->active_rotamers_begin();
- j != node1_->active_rotamers_end(); ++j){
- summed_e += pairwise_energies_[(*j) * node2_->GetNumRotamers() + (*i)];
- }
- bl[n_counter] = summed_e/m - avg_value;
-
- m_counter = 0;
- for(RotamerGraphNode::iterator j = node1_->active_rotamers_begin();
- j != node1_->active_rotamers_end(); ++j){
- e = std::abs(pairwise_energies_[(*j)*n_total+(*i)]-
- ak[m_counter]-bl[n_counter]);
- if(e > thresh) return false;
- ++m_counter;
- }
- ++n_counter;
- }
-
- for(uint i = 0; i < m; ++i){
- for(RotamerGraphNode::iterator j = node1_->active_rotamers_begin();
- j != node1_->active_rotamers_end(); ++j){
- node1_->AddValue(*j,ak[i]);
- }
- }
-
- for(uint i = 0; i < n; ++i){
- for(RotamerGraphNode::iterator j = node2_->active_rotamers_begin();
- j != node2_->active_rotamers_end(); ++j){
- node2_->AddValue(*j,bl[i]);
- }
- }
- this->Deactivate();
- node1_->RemoveFromActiveEdges(this);
- node2_->RemoveFromActiveEdges(this);
- return true;
-}
-
-Real RotamerGraphEdge::EMinDiff(const RotamerGraphNode* node_ptr,
- uint idx1, uint idx2) const{
-
- Real min = std::numeric_limits<Real>::max();
- if(node_ptr == node1_){
- int temp1 = idx1 * node2_->GetNumRotamers();
- int temp2 = idx2 * node2_->GetNumRotamers();
- for(RotamerGraphNode::const_iterator i = node2_->active_rotamers_begin();
- i != node2_->active_rotamers_end(); ++i){
- min = std::min(min,pairwise_energies_[temp1 + (*i)] -
- pairwise_energies_[temp2 + (*i)]);
- }
- return min;
- }
- else if(node_ptr == node2_){
- int num = node2_->GetNumRotamers();
- for(RotamerGraphNode::const_iterator i = node1_->active_rotamers_begin();
- i != node1_->active_rotamers_end(); ++i){
- min = std::min(min,pairwise_energies_[(*i)*num + idx1] -
- pairwise_energies_[(*i)*num + idx2]);
- }
- return min;
- }
- String err = "Cannot evaluate Node which is unconnected to the edge of ";
- err += "interest!";
- throw promod3::Error(err);
-}
-
-void RotamerGraphEdge::FillActiveEnergies(Real* pairwise_energies) const{
- for(RotamerGraphNode::const_iterator i = node1_->active_rotamers_begin();
- i != node1_->active_rotamers_end(); ++i){
- for(RotamerGraphNode::const_iterator j = node2_->active_rotamers_begin();
- j != node2_->active_rotamers_end(); ++j){
- *pairwise_energies = pairwise_energies_[*i*node2_->GetNumRotamers() + *j];
- ++pairwise_energies;
- }
- }
-}
-
-RotamerGraphNode* RotamerGraphEdge::GetOtherNode(RotamerGraphNode* node){
- if(node == node1_) return node2_;
- if(node == node2_) return node1_;
- throw promod3::Error("Node does not belong to edge!");
-}
-
-RotamerGraphNode::RotamerGraphNode(uint index,
- uint num_rotamers,
- Real* internal_energies,
- Real* frame_energies): active_(true),index_(index),
- num_rotamers_(num_rotamers),
- internal_energies_(internal_energies),
- frame_energies_(frame_energies){
-
- self_energies_ = new Real[num_rotamers_];
-
- for(uint i = 0; i < num_rotamers_; ++i){
- active_rotamers_.push_back(i);
- self_energies_[i] = internal_energies_[i] + frame_energies_[i];
- sorted_active_rotamers_.push_back(std::make_pair(i,self_energies_[i]));
- }
-
- std::sort(sorted_active_rotamers_.begin(), sorted_active_rotamers_.end(),
- active_rotamer_sorter);
-}
-
-RotamerGraphNode::~RotamerGraphNode(){
- delete [] internal_energies_;
- delete [] frame_energies_;
- delete [] self_energies_;
-}
-
-void RotamerGraphNode::Reset(){
-
- //clear everything
- active_rotamers_.clear();
- active_edges_.clear();
- sorted_active_rotamers_.clear();
- active_ = true;
-
- //and refill
- for(uint i = 0; i < num_rotamers_; ++i){
- active_rotamers_.push_back(i);
- self_energies_[i] = internal_energies_[i] + frame_energies_[i];
- sorted_active_rotamers_.push_back(std::make_pair(i,self_energies_[i]));
- }
- std::sort(sorted_active_rotamers_.begin(), sorted_active_rotamers_.end(),
- active_rotamer_sorter);
-
- for(uint i = 0; i < edges_.size(); ++i){
- active_edges_.push_back(i);
- }
-
- for(std::vector<RotamerGraphEdge*>::iterator i = edges_.begin();
- i != edges_.end(); ++i){
- (*i)->Reset();
- }
-}
-
-void RotamerGraphNode::Deactivate(int index){
- if(!active_) return;
- active_ = false;
+RotamerGraph::~RotamerGraph() { }
- //if the given index is -1 (default), we simply search for the
- //the rotamer with the lowest self energy as the last active rotamer,
- //a.k.a. the solution for this node.
- //In all other cases we take the rotamer at given index as solution.
- if(index == -1){
- //lets first figure out which is the lowest energy
- //rotamer and set it to the only active rotamer
- Real e_min = std::numeric_limits<Real>::max();
- index = 0;
- for(uint i = 0; i < active_rotamers_.size(); ++i){
- if(self_energies_[active_rotamers_[i]] < e_min){
- e_min = self_energies_[active_rotamers_[i]];
- index = active_rotamers_[i];
- }
- }
- }
-
- active_rotamers_.resize(1);
- active_rotamers_[0] = index;
-
- //deactivate all edges connected to this node
- for(iterator i = this->active_edges_begin();
- i != this->active_edges_end(); ++i){
- RotamerGraphNode* other = edges_[*i]->GetOtherNode(this);
- other->RemoveFromActiveEdges(edges_[*i]);
- edges_[*i]->Deactivate();
- }
- active_edges_.clear();
-}
-
-void RotamerGraphNode::AddEdge(RotamerGraphEdge* edge){
- edges_.push_back(edge);
- active_edges_.push_back(edges_.size()-1);
-}
+template<typename RotamerGroupPtr>
+RotamerGraphPtr RotamerGraph::CreateFromList(
+ const std::vector<RotamerGroupPtr>& rotamer_groups) {
-void RotamerGraphNode::AddValue(Real value){
- for(std::vector<uint>::iterator i = active_rotamers_.begin();
- i != active_rotamers_.end(); ++i){
- self_energies_[*i] += value;
- }
-}
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "RotamerGraph::CreateFromList", 2);
-void RotamerGraphNode::AddValue(uint node_idx, Real value){
- self_energies_[node_idx] += value;
-}
+ RotamerGraphPtr graph(new RotamerGraph);
-void RotamerGraphNode::RemoveFromActiveEdges(RotamerGraphEdge* edge){
+ // let's create the nodes
uint counter = 0;
- for(; counter < edges_.size(); ++counter){
- if(edge == edges_[counter]){
- iterator i = std::find(active_edges_.begin(), active_edges_.end(),
- counter);
- if(i != active_edges_.end()) active_edges_.erase(i);
- return;
+ std::vector<Real> self_energies;
+ for(uint i = 0; i < rotamer_groups.size(); ++i) {
+ RotamerGroupPtr rot_group = rotamer_groups[i];
+ self_energies.resize(rot_group->size());
+ for(uint j = 0; j < rot_group->size(); ++j){
+ self_energies[j] = (*rot_group)[j]->GetSelfEnergy();
}
+ graph->AddNode(self_energies);
}
-}
-
-bool RotamerGraphNode::DEE(Real e_cut){
- if(active_rotamers_.size() <= 1) return false;
-
- bool something_happened = false;
- Real sum;
- int rotamer_to_eliminate = sorted_active_rotamers_.size()-1;
- while(rotamer_to_eliminate >= 0){
- for(int i = 0; i < static_cast<int>(active_rotamers_.size()); ++i){
- if(i == rotamer_to_eliminate) continue;
- sum = self_energies_[sorted_active_rotamers_[rotamer_to_eliminate].first] -
- self_energies_[sorted_active_rotamers_[i].first];
- for(iterator j = this->active_edges_.begin();
- j != this->active_edges_.end(); ++j){
- sum += edges_[*j]->EMinDiff(this,
- sorted_active_rotamers_[rotamer_to_eliminate].first,
- sorted_active_rotamers_[i].first);
- }
- if(sum >= e_cut){
- something_happened = true;
- std::vector<uint>::iterator it = std::find(active_rotamers_.begin(),
- active_rotamers_.end(),
- sorted_active_rotamers_[rotamer_to_eliminate].first);
- active_rotamers_.erase(it);
- sorted_active_rotamers_.erase(sorted_active_rotamers_.begin() +
- rotamer_to_eliminate);
- break;
+ // let's create the edges
+ for(uint i = 0; i < rotamer_groups.size(); ++i){
+ for(uint j = i+1; j < rotamer_groups.size(); ++j){
+ promod3::core::EMatXX emat;
+ if(rotamer_groups[i]->CalculatePairwiseEnergies(rotamer_groups[j],
+ 0.01, emat)) {
+ graph->AddEdge(i, j, emat);
}
}
- --rotamer_to_eliminate;
- }
-
- return something_happened;
-}
-
-void RotamerGraphNode::FillActiveSelfEnergies(Real* self_energies) const{
- for(const_iterator i = this->active_rotamers_begin();
- i != this->active_rotamers_end(); ++i){
- *self_energies = self_energies_[*i];
- ++self_energies;
- }
-}
-
-RotamerGraph::~RotamerGraph(){
- for(std::vector<RotamerGraphNode*>::iterator i = nodes_.begin();
- i != nodes_.end(); ++i){
- delete *i;
}
- for(std::vector<RotamerGraphEdge*>::iterator i = edges_.begin();
- i != edges_.end(); ++i){
- delete *i;
- }
+ return graph;
}
-RotamerGraphPtr RotamerGraph::CreateFromRRMList(
- const std::vector<RRMRotamerGroupPtr>& rotamer_groups) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "Graph::CreateFromRRMList", 2);
-
- RotamerGraphPtr graph(new RotamerGraph);
-
- //let's create the nodes
- graph->nodes_.resize(rotamer_groups.size());
- uint counter = 0;
- Real* internal_energies;
- Real* frame_energies;
- for(std::vector<RRMRotamerGroupPtr>::const_iterator i = rotamer_groups.begin();
- i != rotamer_groups.end(); ++i, ++counter){
- internal_energies = new Real[(*i)->size()];
- frame_energies = new Real[(*i)->size()];
- for(uint j = 0; j < (*i)->size(); ++j){
- internal_energies[j] = (**i)[j]->GetInternalEnergy();
- frame_energies[j] = (**i)[j]->GetFrameEnergy();
- }
- graph->nodes_[counter] = new RotamerGraphNode(counter,
- (*i)->size(),
- internal_energies,
- frame_energies);
- }
-
- //let's create the edges and directly add them to the corresponding nodes
-
- for(uint i = 0; i < rotamer_groups.size(); ++i){
- for(uint j = i+1; j < rotamer_groups.size(); ++j){
- Real* pairwise_energies =
- rotamer_groups[i]->CalculatePairwiseEnergies(rotamer_groups[j],0.01);
- if(pairwise_energies!=NULL){
- RotamerGraphEdge* edge = new RotamerGraphEdge(graph->edges_.size(),
- graph->nodes_[i],graph->nodes_[j],
- rotamer_groups[i]->size(),
- rotamer_groups[j]->size(),
- pairwise_energies);
- graph->nodes_[i]->AddEdge(edge);
- graph->nodes_[j]->AddEdge(edge);
- graph->edges_.push_back(edge);
- }
- }
- }
-
- return graph;
-}
-
-
-RotamerGraphPtr RotamerGraph::CreateFromFRMList(
- const std::vector<FRMRotamerGroupPtr>& rotamer_groups) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "Graph::CreateFromFRMList", 2);
-
- RotamerGraphPtr graph(new RotamerGraph);
-
- //let's create the nodes
- graph->nodes_.resize(rotamer_groups.size());
- uint counter = 0;
- Real* internal_energies;
- Real* frame_energies;
- for(std::vector<FRMRotamerGroupPtr>::const_iterator i = rotamer_groups.begin();
- i != rotamer_groups.end(); ++i, ++counter){
- internal_energies = new Real[(*i)->size()];
- frame_energies = new Real[(*i)->size()];
- for(uint j = 0; j < (*i)->size(); ++j){
- internal_energies[j] = (**i)[j]->GetInternalEnergy();
- frame_energies[j] = (**i)[j]->GetFrameEnergy();
- }
- graph->nodes_[counter] = new RotamerGraphNode(counter,
- (*i)->size(),
- internal_energies,
- frame_energies);
- }
-
- //let's create the edges and directly add them to the corresponding nodes
- for(uint i = 0; i < rotamer_groups.size(); ++i){
- for(uint j = i+1; j < rotamer_groups.size(); ++j){
- Real* pairwise_energies =
- rotamer_groups[i]->CalculatePairwiseEnergies(rotamer_groups[j],0.01);
- if(pairwise_energies != NULL){
- RotamerGraphEdge* edge = new RotamerGraphEdge(graph->edges_.size(),
- graph->nodes_[i],
- graph->nodes_[j],
- rotamer_groups[i]->size(),
- rotamer_groups[j]->size(),
- pairwise_energies);
- graph->nodes_[i]->AddEdge(edge);
- graph->nodes_[j]->AddEdge(edge);
- graph->edges_.push_back(edge);
- }
- }
- }
-
- return graph;
-}
-
-RotamerGraphPtr RotamerGraph::CreateFromArbitrarySource(
- const std::vector<uint>& node_sizes,
- const std::vector<Real*>& internal_energies,
- const std::vector<Real*>& frame_energies,
- const std::vector<std::pair<uint,uint> >& edges,
- const std::vector<Real*>& pairwise_energies) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "Graph::CreateArbitrarySource", 2);
-
- // That's how it should look like:
- // for every graph node one element in node_sizes, internal_energies
- // and frame_energies is expected. The frame_energies and internal_energies
- // are Real* allocated with new => number of element corresponds to according
- // node size! The RotamerGraphNodes take the ownership of the pointers
- // => stuff gets deleted when the RotamerGraph is deleted...
- //
- // For every edge, one element in edges and pairwise_energies is expected
- // The elements in edges are pairs of integers defining the involved nodes
- // note, that the first idx is expected to be smaller!
- // The pairwise energies are Real* allocated with new.
- // lets assume to have node A and B and the corresponding size_a and size_b
- // if we want to extract the pairwise energies between the elements a and b
- // we write: S(a,b) = real_ptr[a * size_a + b]
- // The RotamerGraphEdge takes ownership over the pointers
- // => stuff gets deleted when the RotamerGraph is deleted...
-
- uint num_nodes = node_sizes.size();
- uint num_edges = edges.size();
-
- // check the input data
- if(node_sizes.size() != internal_energies.size() ||
- node_sizes.size() != frame_energies.size()) {
- throw promod3::Error("node_sizes, internal_energies and frame_energies "
- "must have the same number of elements!");
- }
-
- if(edges.size() != pairwise_energies.size()) {
- throw promod3::Error("Expect to have one pairwise energy value per edge!");
- }
-
- for(uint i = 0; i < num_edges; ++i) {
- // first element of node idx pair must be smaller
- if(edges[i].first >= edges[i].second) {
- throw promod3::Error("The first element of the edge definition must "
- "always be smaller than the second one!");
- }
-
- // check whether they're too large
- if(edges[i].first >= num_nodes || edges[i].second >= num_nodes) {
- throw promod3::Error("Observed invalid idx in edge definition!");
- }
- }
-
- RotamerGraphPtr graph(new RotamerGraph);
-
- //let's create the nodes
- graph->nodes_.resize(num_nodes);
-
- for(uint i = 0; i < num_nodes; ++i){
- graph->nodes_[i] = new RotamerGraphNode(i, node_sizes[i],
- internal_energies[i],
- frame_energies[i]);
- }
-
- //let's create the edges and directly add them to the corresponding nodes
- for(uint i = 0; i < num_edges; ++i) {
- uint idx_one = edges[i].first;
- uint idx_two = edges[i].second;
-
- RotamerGraphEdge* edge = new RotamerGraphEdge(i,graph->nodes_[idx_one],
- graph->nodes_[idx_two],
- node_sizes[idx_one],
- node_sizes[idx_two],
- pairwise_energies[i]);
- graph->nodes_[idx_one]->AddEdge(edge);
- graph->nodes_[idx_two]->AddEdge(edge);
- graph->edges_.push_back(edge);
- }
-
- return graph;
-}
-
-
-size_t RotamerGraph::GetNumActiveRotamers() const{
- size_t num_rotamers = 0;
- for(std::vector<RotamerGraphNode*>::const_iterator i = nodes_.begin();
- i != nodes_.end(); ++i){
- if(!(*i)->IsActive()) continue;
- num_rotamers += (*i)->GetNumActiveRotamers();
- }
- return num_rotamers;
-}
-
-size_t RotamerGraph::GetNumActiveEdges() const{
- size_t num_edges = 0;
- for(std::vector<RotamerGraphEdge*>::const_iterator i = edges_.begin();
- i != edges_.end(); ++i){
- if((*i)->IsActive()) ++num_edges;
- }
- return num_edges;
-}
-
-size_t RotamerGraph::GetNumActiveNodes() const{
- size_t num_nodes = 0;
- for(std::vector<RotamerGraphNode*>::const_iterator i = nodes_.begin();
- i != nodes_.end(); ++i){
- if((*i)->IsActive()) ++num_nodes;
- }
- return num_nodes;
-}
-
-size_t RotamerGraph::GetNumRotamers() const{
- size_t num_rotamers = 0;
- for(std::vector<RotamerGraphNode*>::const_iterator i = nodes_.begin();
- i != nodes_.end(); ++i){
- num_rotamers += (*i)->GetNumRotamers();
- }
- return num_rotamers;
-}
-
-void RotamerGraph::GetNumRotamers(std::vector<int>& num_rotamers) const{
- num_rotamers.resize(nodes_.size());
- for(uint i = 0; i < nodes_.size(); ++i){
- num_rotamers[i] = nodes_[i]->GetNumRotamers();
- }
-}
-
-void RotamerGraph::GetNumActiveRotamers(std::vector<int>& num_rotamers) const{
- num_rotamers.resize(nodes_.size());
- for(uint i = 0; i < nodes_.size(); ++i){
- num_rotamers[i] = nodes_[i]->GetNumActiveRotamers();
- }
-}
-
-void RotamerGraph::GetActiveRotamers(uint idx,
- std::vector<int>& active_rotamers) const {
-
- if(idx >= nodes_.size()) {
- throw promod3::Error("Invalid Index observed when extracting active "
- "rotamers!");
- }
-
- active_rotamers.clear();
- active_rotamers.reserve(nodes_[idx]->GetNumActiveRotamers());
-
- for(RotamerGraphNode::const_iterator i = nodes_[idx]->active_rotamers_begin();
- i != nodes_[idx]->active_rotamers_end(); ++i) {
- active_rotamers.push_back(*i);
- }
-}
-
-void RotamerGraph::GetEdges(std::vector<std::pair<int,int> >& edges) const{
-
- edges.clear();
- edges.reserve(edges_.size());
- for(uint i = 0; i < edges_.size(); ++i) {
- int idx_one = edges_[i]->GetNode1()->GetIndex();
- int idx_two = edges_[i]->GetNode2()->GetIndex();
- edges.push_back(std::make_pair(idx_one,idx_two));
- }
-}
-
-void RotamerGraph::GetActiveEdges(std::vector<std::pair<int,int> >& active_edges) const{
-
- active_edges.clear();
- active_edges.reserve(edges_.size());
- for(uint i = 0; i < edges_.size(); ++i) {
- if(edges_[i]->IsActive()) {
- int idx_one = edges_[i]->GetNode1()->GetIndex();
- int idx_two = edges_[i]->GetNode2()->GetIndex();
- active_edges.push_back(std::make_pair(idx_one,idx_two));
- }
- }
-}
-
-void RotamerGraph::GetSelfEnergies(uint idx,
- std::vector<Real>& energies) const{
- if(idx >= nodes_.size()) {
- throw promod3::Error("Invalid Index observed when extracting self "
- "energies!");
- }
-
- int num_rotamers = nodes_[idx]->GetNumRotamers();
-
- energies.clear();
- energies.reserve(num_rotamers);
-
- for(int i = 0; i < num_rotamers; ++i) {
- energies.push_back(nodes_[idx]->GetSelfEnergy(i));
- }
-}
-
-void RotamerGraph::GetPairwiseEnergies(uint idx,
- std::vector<std::vector<Real> >& energies) const {
-
- if(idx >= edges_.size()) {
- throw promod3::Error("Invalid Index observed when extracting pairwise "
- "energies!");
- }
-
- RotamerGraphEdge* edge = edges_[idx];
- int num_rotamers_one = edge->GetNode1()->GetNumRotamers();
- int num_rotamers_two = edge->GetNode2()->GetNumRotamers();
-
- energies.clear();
- energies.resize(num_rotamers_one);
-
- for(int i = 0; i < num_rotamers_one; ++i) {
- energies[i].resize(num_rotamers_two);
- for(int j = 0; j < num_rotamers_two; ++j) {
- energies[i][j] = edge->GetPairwiseEnergy(i, j);
- }
- }
-}
-
-bool RotamerGraph::ApplyDEE(uint idx, Real e_thresh) {
-
- if(idx >= nodes_.size()) {
- throw promod3::Error("Invalid Index observed when applying DEE!");
- }
-
- return nodes_[idx]->DEE(e_thresh);
-}
-
-bool RotamerGraph::ApplyEdgeDecomposition(uint idx, Real e_thresh) {
-
- if(idx >= edges_.size()) {
- throw promod3::Error("Invalid Index observed when applying Edge "
- "Decomposition!");
- }
-
- return edges_[idx]->Decompose(e_thresh);
-}
-
-void RotamerGraph::Prune(Real epsilon, Real e_cut, bool consider_all_nodes){
-
- //nodes/edges, where something happened
- std::vector<bool> hot_edges(edges_.size(),true);
- std::vector<bool> hot_nodes;
- if(consider_all_nodes)hot_nodes.resize(nodes_.size(),true);
- else hot_nodes.resize(nodes_.size(),false);
-
- bool something_happened = true;
- while(something_happened){
- something_happened = false;
- //let's first do edge decomposition
- for(uint i = 0; i < hot_edges.size(); ++i){
- if(!hot_edges[i]) continue;
- if(this->ApplyEdgeDecomposition(i, epsilon)){
- //let's set the status hot to the nodes connected by the
- //edge
- hot_nodes[edges_[i]->GetNode1()->GetIndex()] = true;
- hot_nodes[edges_[i]->GetNode2()->GetIndex()] = true;
- something_happened = true;
- }
- //either nothing happened, or successfully decomposed...
- //edge is not hot anymore
- hot_edges[i] = false;
- }
- //let's do DEE
- for(uint i = 0; i < hot_nodes.size(); ++i){
- if(!hot_nodes[i]) continue;
- if(this->ApplyDEE(i, e_cut)){
- //let's set the status hot to the edges, as well as other
- //nodes connected to that node
- for(RotamerGraphNode::iterator j = nodes_[i]->active_edges_begin();
- j != nodes_[i]->active_edges_end(); ++j){
- RotamerGraphEdge* current_edge = nodes_[i]->GetEdge(*j);
- hot_edges[current_edge->GetIndex()] = true;
- //one of the following connected node is the checked node
- //itself... will be set to false again...
- hot_nodes[current_edge->GetNode1()->GetIndex()] = true;
- hot_nodes[current_edge->GetNode2()->GetIndex()] = true;
- }
- something_happened = true;
- }
- //either nothing happened, or successful DEE...
- //node is not hot anymore
- hot_nodes[i] = false;
- }
- }
-}
-
-void RotamerGraph::Reset(){
- for(node_iterator i = nodes_begin(); i != nodes_end(); ++i){
- (*i)->Reset();
- }
- for(edge_iterator i = edges_begin(); i != edges_end(); ++i){
- (*i)->Reset();
- }
-}
-
-promod3::core::Graph RotamerGraph::ToRawGraph() const{
- promod3::core::Graph raw_graph(this->GetNumNodes());
- std::map<RotamerGraphNode*, int> ptr_mapper;
- for(uint i = 0; i < nodes_.size(); ++i){
- ptr_mapper[nodes_[i]] = i;
- }
- for(std::vector<RotamerGraphEdge*>::const_iterator i = edges_.begin();
- i != edges_.end(); ++i){
- if((*i)->IsActive()){
- int idx_one = ptr_mapper[(*i)->GetNode1()];
- int idx_two = ptr_mapper[(*i)->GetNode2()];
- raw_graph.Connect(idx_one,idx_two);
- }
- }
- return raw_graph;
-}
-
-std::pair<std::vector<int>, Real>
-RotamerGraph::TreeSolve(uint64_t max_complexity, Real initial_epsilon) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "RotamerGraph::TreeSolve", 2);
-
- // all nodes must be active in the beginning
- for(std::vector<RotamerGraphNode*>::iterator i = nodes_.begin();
- i != nodes_.end(); ++i){
- if(!(*i)->IsActive()){
- String err = "All nodes of graph must be active for TreeSolving.";
- err += " Either construct a new graph or reset the current one!";
- throw promod3::Error(err);
- }
- }
-
- std::vector<int> overall_solution(this->GetNumNodes(), 0);
- Real overall_energy = 0.0;
-
- // handle the case where graph is empty
- if(this->GetNumNodes() == 0){
- return std::make_pair(overall_solution, overall_energy);
- }
-
- // handle the case where graph only contains one item
- if(this->GetNumNodes() == 1){
- nodes_[0]->Deactivate();
- overall_solution[0] = nodes_[0]->GetOverallIndex(0);
- overall_energy += nodes_[0]->GetSelfEnergy(overall_solution[0]);
- return std::make_pair(overall_solution, overall_energy);
- }
-
- bool first_iteration = true;
-
- do{
- this->Prune(initial_epsilon, 0.0, first_iteration);
-
- //build raw graph and extract connected components
- promod3::core::Graph raw_graph = this->ToRawGraph();
-
- //generate the connected components
- std::vector<std::vector<int> > connected_components;
- raw_graph.ConnectedComponents(connected_components);
-
- //solve the connected components seperately if the according
- //complexity is feasible
-
- Real size_one_energy = 0;
-
- for(uint component_idx = 0; component_idx < connected_components.size();
- ++component_idx){
-
- const std::vector<int>& component = connected_components[component_idx];
-
- if(component.size() == 1){
- if(nodes_[component[0]]->IsActive()){
- nodes_[component[0]]->Deactivate();
- int overall_idx = nodes_[component[0]]->GetOverallIndex(0);
- overall_solution[component[0]] = overall_idx;
- overall_energy += nodes_[component[0]]->GetSelfEnergy(overall_idx);
- size_one_energy += nodes_[component[0]]->GetSelfEnergy(overall_idx);
- }
- continue;
- }
-
- //create initial data required to solve the enumeration problem
- std::vector<int> num_active_rotamers(component.size());
- for(uint i = 0; i < component.size(); ++i){
- // Check, whether any of the rotamer groups has too many rotamers
- // (due to memory reasons we use unsigned shorts as rotamer
- // identifier in the tree solving algorithms)
- if(nodes_[component[i]]->GetNumActiveRotamers() >
- std::numeric_limits<unsigned short>::max()){
- std::stringstream ss;
- ss << "Due to technical reasons the maximum number of rotamers per ";
- ss << "position is limited to ";
- ss << std::numeric_limits<unsigned short>::max();
- ss << ". Observed a location with ";
- ss << nodes_[component[i]]->GetNumActiveRotamers();
- ss << " rotamers. Either use less rotamers or perform more pruning ";
- ss << "operations before using the TreeSolve algorithm.";
- throw promod3::Error(ss.str());
- }
- num_active_rotamers[i] = nodes_[component[i]]->GetNumActiveRotamers();
- }
-
- promod3::core::Graph component_graph = raw_graph.SubGraph(component);
-
- TreeBag* component_tree =
- promod3::core::GenerateMinimalWidthTree(component_graph);
-
- //generate post order traversal of previously constructed tree
- std::vector<TreeBag* > traversal =
- promod3::core::PostOrderTraversal(component_tree);
-
- std::vector<BagData> bag_data;
- uint64_t component_complexity = FillRawBagData(traversal,
- num_active_rotamers,
- bag_data);
-
- //check whether complexity of current connected component is solvable...
- //if not, we simply perform another iteration of pruning.
- if(component_complexity > max_complexity){
- if(initial_epsilon <= 0.0){
- std::stringstream ss;
- ss << "One of the connected components in the RotamerGraph ";
- ss << "reaches a complexity of "<< component_complexity;
- ss << ", which is above the max_complexity of "<<max_complexity;
- ss << ". The idea is to prune more and more aggressively by ";
- ss << "multiplying the initial_epsilon value by a factor of 2.";
- ss << "Your initial_epsilon is "<<initial_epsilon;
- ss << ", the complexity of this connected ";
- ss << "component will therefore never fall below max_complexity. ";
- ss << "To successfully solve the RotamerGraph you either have to ";
- ss << "give initial_epsilon a value above 0.0 or increase ";
- ss << "max_complexity";
- throw promod3::Error(ss.str());
- }
- continue;
- }
-
- //The complexity is low enough... let's fill remaining data and
- //solve it!
-
- //first we have to extract the energies
- std::vector<Real*> self_energies;
- std::map<std::pair<int,int>, Real*> pairwise_energies;
-
- for(uint i = 0; i < component.size(); ++i){
- Real* self_e = new Real[num_active_rotamers[i]];
- nodes_[component[i]]->FillActiveSelfEnergies(self_e);
- self_energies.push_back(self_e);
- }
-
- for(uint i = 0; i < edges_.size(); ++i){
- RotamerGraphEdge* edge = edges_[i];
-
- // is the edge active?
- if(!edge->IsActive()) continue;
-
- //does it affect the current component?
- int a = edge->GetNode1()->GetIndex();
- int b = edge->GetNode2()->GetIndex();
-
- std::vector<int>::const_iterator a_it = std::find(component.begin(),
- component.end(), a);
- if(a_it == component.end()) continue; //it's not part of the component
-
- std::vector<int>::const_iterator b_it = std::find(component.begin(),
- component.end(), b);
- if(b_it == component.end()) continue; //it's not part of the component
-
- int a_in_component = a_it - component.begin();
- int b_in_component = b_it - component.begin();
-
- Real* pairwise_e = new Real[num_active_rotamers[a_in_component] *
- num_active_rotamers[b_in_component]];
- edge->FillActiveEnergies(pairwise_e);
-
- std::pair<int,int> edge_pair = std::make_pair(a_in_component,
- b_in_component);
-
- pairwise_energies[edge_pair] = pairwise_e;
- }
-
- //let's fill in remaining data
- FillBagData(traversal, self_energies, pairwise_energies, bag_data);
-
- //let's do the whole enumeration game
- EnumerateBagData(bag_data);
-
- //let's get the solution out
- std::vector<int> component_solution(component.size(), 0);
- CollectSolutionFromBagData(bag_data, bag_data.size() - 1,
- component_solution);
-
- overall_energy += bag_data.back().optimal_r_score[0];
-
- //alter the graph accordingly
- for(uint i = 0; i < component.size(); ++i){
- uint overall_idx =
- nodes_[component[i]]->GetOverallIndex(component_solution[i]);
- nodes_[component[i]]->Deactivate(overall_idx);
- overall_solution[component[i]] = overall_idx;
- }
-
- //the energies are not needed anymore
- for(std::vector<Real*>::iterator i = self_energies.begin();
- i != self_energies.end(); ++i){
- delete [] (*i);
- }
-
- for(std::map<std::pair<int,int>, Real* >::iterator i =
- pairwise_energies.begin(); i != pairwise_energies.end(); ++i){
- delete [] i->second;
- }
- }
-
- first_iteration = false;
- initial_epsilon *= 2;
-
- }while(this->GetNumActiveNodes() > 0);
-
- return std::make_pair(overall_solution, overall_energy);
-}
-
-
-std::pair<std::vector<std::vector<int> >, std::vector<Real> >
-RotamerGraph::AStarSolve(Real e_thresh, uint max_n, uint max_visited_nodes){
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "RotamerGraph::AStarSolve", 2);
-
- //all nodes must be active in the beginning
- for(std::vector<RotamerGraphNode*>::iterator i = nodes_.begin();
- i != nodes_.end(); ++i){
- if(!(*i)->IsActive()){
- String err = "All nodes of graph must be active for TreeSolving.";
- err += " Either construct a new graph or reset the current one!";
- throw promod3::Error(err);
- }
- }
-
- //e_thresh and max_n must be positive
- if(e_thresh < 0.0) throw promod3::Error("e_thresh must be positive!");
- if(max_n <= 0) throw promod3::Error("max_n must be positive!");
-
- std::vector<std::vector<int> > solutions;
- std::vector<Real> solution_energies;
- int num_graph_nodes = this->GetNumNodes();
- int num_graph_edges = this->GetNumEdges();
-
- //handle the case where graph is empty
- if(num_graph_nodes == 0){
- return std::make_pair(solutions, solution_energies);
- }
-
- //handle the case where graph only contains one item
- if(num_graph_nodes == 1){
- uint num_active_rotamers = nodes_[0]->GetNumActiveRotamers();
- if(num_active_rotamers == 0){
- return std::make_pair(solutions, solution_energies);
- }
- std::vector<std::pair<Real,int> > sorted_rotamers;
- sorted_rotamers.reserve(num_active_rotamers);
- Real* active_energies = new Real[num_active_rotamers];
- nodes_[0]->FillActiveSelfEnergies(active_energies);
- for(uint i = 0; i < num_active_rotamers; ++i){
- sorted_rotamers.push_back(std::make_pair(active_energies[i], i));
- }
- delete [] active_energies;
- std::sort(sorted_rotamers.begin(), sorted_rotamers.end());
- Real emin = sorted_rotamers[0].first;
- for(uint i = 0; i < std::min(max_n, num_active_rotamers); ++i){
- if((sorted_rotamers[i].first - emin) > e_thresh) break;
- int overall_idx = nodes_[0]->GetOverallIndex(sorted_rotamers[i].second);
- solutions.push_back(std::vector<int>(1, overall_idx));
- solution_energies.push_back(sorted_rotamers[i].first);
- }
- return std::make_pair(solutions, solution_energies);
- }
-
- //extract the energies of the active rotamers
- std::vector<int> num_active_rotamers;
- int max_num_active_rotamers = 0;
- std::vector<Real*> self_energies;
- std::vector<std::vector<std::pair<int,Real*> > >
- pairwise_energies(num_graph_nodes, std::vector<std::pair<int,Real*> >());
- std::vector<int> num_pairwise_energies(num_graph_nodes, 0);
-
- for(int i = 0; i < num_graph_nodes; ++i){
- num_active_rotamers.push_back(nodes_[i]->GetNumActiveRotamers());
- max_num_active_rotamers = std::max(max_num_active_rotamers,
- num_active_rotamers.back());
- }
-
- for(int i = 0; i < num_graph_nodes; ++i){
- Real* self_e = new Real[num_active_rotamers[i]];
- nodes_[i]->FillActiveSelfEnergies(self_e);
- self_energies.push_back(self_e);
- }
-
- Real* e_buffer = new Real[max_num_active_rotamers *
- max_num_active_rotamers];
-
- for(int i = 0; i < num_graph_edges; ++i){
- if(edges_[i]->IsActive()){
- RotamerGraphEdge* edge = edges_[i];
- int a = edge->GetNode1()->GetIndex();
- int b = edge->GetNode2()->GetIndex();
- if(a < b){
-
- Real* pairwise_e_inverted = new Real[num_active_rotamers[a] *
- num_active_rotamers[b]];
-
- edge->FillActiveEnergies(e_buffer);
- this->Invert(e_buffer, pairwise_e_inverted,
- num_active_rotamers[a], num_active_rotamers[b]);
-
- pairwise_energies[b].push_back(std::make_pair(a,pairwise_e_inverted));
- }
- else{
- throw promod3::Error("Expect always first node in graph to have lower "
- "idx! The graph construction somehow fucked up...");
- }
- }
- }
-
- delete [] e_buffer;
-
- for(int i = 0; i < num_graph_nodes; ++i){
- num_pairwise_energies[i] = pairwise_energies[i].size();
- }
-
- //following data structure is a precalculation to increase the speed
- //of hstar calculation...
-
- //for every every position there is a vector for every rotamer at
- //that position. Every element in that vector contains the minimal
- //energy towards every position that comes before, zero if no
- //interaction is observed
- std::vector<std::vector<std::vector<Real> > >
- min_pairwise_e_before(num_graph_nodes, std::vector<std::vector<Real> >());
-
- for(int i = 0; i < num_graph_nodes; ++i){
- min_pairwise_e_before[i].resize(num_active_rotamers[i]);
- for(int j = 0; j < num_active_rotamers[i]; ++j){
- min_pairwise_e_before[i][j].assign(i,0.0);
- for(int k = 0; k < num_pairwise_energies[i]; ++k){
- int other_node = pairwise_energies[i][k].first;
- Real* e_ptr = pairwise_energies[i][k].second;
- e_ptr = &e_ptr[j * num_active_rotamers[other_node]];
- Real e_min = std::numeric_limits<Real>::max();
- for(int l = 0; l < num_active_rotamers[other_node]; ++l){
- e_min = std::min(e_min, e_ptr[l]);
- }
- min_pairwise_e_before[i][j][other_node] = e_min;
- }
- }
- }
-
- //Data structures to hold the visited nodes and sort them in a priority queue
- std::priority_queue<AStarNode*,std::vector<AStarNode*>,CompareAStarNodes> node_queue;
- std::vector<AStarNode> node_array;
- //we already have to reserve node_array, since we deal with pointers
- //to it and reallocations are a bit bad in these cases...
- node_array.reserve(max_visited_nodes);
-
- //we first add the root node with g* = 0.0 and h* = max_real
- node_array.push_back(AStarNode(0, 0, 0, 0, 0.0,
- std::numeric_limits<Real>::max()));
-
- node_queue.push(&node_array[0]);
- Real min_energy = std::numeric_limits<Real>::max();
-
- while(!node_queue.empty()){
-
- AStarNode* current_node = node_queue.top();
- node_queue.pop();
-
- std::vector<int> path;
- ReconstructSearchTreePath(node_array, current_node->node_idx, path);
-
- if(current_node->tree_depth >= num_graph_nodes){
- //it is a solution!!!!!
- Real fstar = current_node->gstar; //note, that hstar must be zero...
- if(solutions.empty()){
- //it's the first solution and therefore the GMEC
- //(Global Minimum Energy Conformation Fuck Yeah...)
- min_energy = fstar;
- }
- else{
- //there is at least one solution around! let's check whether
- //the current solution is within e_thresh
- if(fstar - min_energy > e_thresh) break;
- }
-
- //let's add it
- solutions.push_back(path);
- solution_energies.push_back(fstar);
-
- //check whether we have enough solutions
- if(solutions.size() >= max_n) break;
-
- continue;
- }
-
- //current node has to be expanded
- //=> new node for every single rotamer in node
-
- //we first check whether we become bigger than max_visited_nodes
- if(node_array.size() + num_active_rotamers[current_node->tree_depth] >
- max_visited_nodes){
- //clean up
- for(std::vector<Real*>::iterator i = self_energies.begin();
- i != self_energies.end(); ++i){
- delete [] (*i);
- }
-
- for(std::vector<std::vector<std::pair<int,Real*> > >::iterator i =
- pairwise_energies.begin(); i != pairwise_energies.end(); ++i){
- for(std::vector<std::pair<int,Real*> >::iterator j = i->begin();
- j != i->end(); ++j)
- delete [] j->second;
- }
- //and throw an error
- throw promod3::Error("Reached max_visited_nodes => increase this"
- "parameter or reduce the problem size!");
- }
-
- //following variables will be the same for all expaned nodes
- int pos_in_graph = current_node->tree_depth;
- uint parent_idx = current_node->node_idx;
- unsigned short tree_depth = current_node->tree_depth + 1;
-
- //We already add an element to the path for the node to be expaned.
- //This saves an if in the hstar calculation
- path.push_back(0);
-
- for(int rotamer_idx = 0; rotamer_idx < num_active_rotamers[pos_in_graph];
- ++rotamer_idx){
-
- //set the hacky last element of the path
- path.back() = rotamer_idx;
-
- //variable specific for expanded node
- uint node_idx = node_array.size();
- Real gstar = current_node->gstar;
- Real hstar = 0.0;
-
- //we still need to adapt the energy values (gstar and hstar)
-
- //in case of gstar we have to add the self energy of the current
- //rotamer and the pairwise energy towards all previous rotamers in
- //the path towards this node
-
- //let's add the self energy
- gstar += self_energies[pos_in_graph][rotamer_idx];
-
- //let's add all pairwise energies towards the already set rotamers
- for(int i = 0; i < num_pairwise_energies[pos_in_graph]; ++i){
- int other_node = pairwise_energies[pos_in_graph][i].first;
- Real* e = pairwise_energies[pos_in_graph][i].second;
- gstar += e[rotamer_idx * num_active_rotamers[other_node] +
- path[other_node]];
- }
-
- //in case of hstar we have to add the minimal pairwise energy towards
- //all nodes still to be determined
- int last_path_idx = path.size()-1;
- for(int non_set_pos_idx = pos_in_graph + 1;
- non_set_pos_idx < num_graph_nodes; ++non_set_pos_idx){
-
- Real min_e = std::numeric_limits<Real>::max();
-
- //iterate over all possible rotamers at position non_set_pos_idx
- for(int i = 0; i < num_active_rotamers[non_set_pos_idx]; ++i){
-
- //start with its self energy
- Real actual_e = self_energies[non_set_pos_idx][i];
-
- //add all pairwise energies towards rotamers that have already been
- //set in this path, the according minimal energy that could be achieved
- //respectively
- for(int j = 0; j < num_pairwise_energies[non_set_pos_idx]; ++j){
- int other_node = pairwise_energies[non_set_pos_idx][j].first;
- if(other_node <= last_path_idx){
- //add the energy to the already determined energy from the path
- Real* e = pairwise_energies[non_set_pos_idx][j].second;
- actual_e += e[i * num_active_rotamers[other_node] +
- path[other_node]];
- }
- else{
- //add the minimal possible energy...
- actual_e += min_pairwise_e_before[non_set_pos_idx][i][other_node];
- }
- }
- min_e = std::min(min_e, actual_e);
- }
- hstar += min_e;
- }
-
- node_array.push_back(AStarNode(node_idx, parent_idx,
- rotamer_idx, tree_depth, gstar,
- hstar));
-
- //it's all done, we finally have to insert it into the priority queue
- node_queue.push(&node_array[node_idx]);
- }
- }
-
- //the solutions are relative to the active rotamers, we still have to
- //translate them into overall indices
- for(uint i = 0; i < solutions.size(); ++i){
- for(uint j = 0; j < solutions[i].size(); ++j){
- solutions[i][j] = nodes_[j]->GetOverallIndex(solutions[i][j]);
- }
- }
-
- //final cleanup
- for(std::vector<Real*>::iterator i = self_energies.begin();
- i != self_energies.end(); ++i){
- delete [] (*i);
- }
-
- for(std::vector<std::vector<std::pair<int,Real*> > >::iterator i =
- pairwise_energies.begin(); i != pairwise_energies.end(); ++i){
- for(std::vector<std::pair<int,Real*> >::iterator j = i->begin();
- j != i->end(); ++j)
- delete [] j->second;
- }
-
- return std::make_pair(solutions, solution_energies);
-}
-
-
-std::pair<std::vector<std::vector<int> >, std::vector<Real> >
-RotamerGraph::MCSolve(int n, int mc_steps, Real start_temperature,
- int change_frequency, Real cooling_factor, int seed) {
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "RotamerGraph::MCSolve", 2);
-
- //all nodes must be active in the beginning
- for(std::vector<RotamerGraphNode*>::iterator i = nodes_.begin();
- i != nodes_.end(); ++i){
- if(!(*i)->IsActive()){
- String err = "All nodes of graph must be active for TreeSolving.";
- err += " Either construct a new graph or reset the current one!";
- throw promod3::Error(err);
- }
- }
-
- std::vector<std::vector<int> > solutions;
- std::vector<Real> solution_energies;
- int num_graph_nodes = this->GetNumNodes();
- int num_graph_edges = this->GetNumEdges();
-
- //handle the case where graph is empty
- if(num_graph_nodes == 0){
- throw promod3::Error("Cannot run MCSolve on an empty RotamerGraph!");
- }
-
- //handle the case where graph only contains one item
- if(num_graph_nodes == 1){
- throw promod3::Error("Cannot run MCSolve on a RotamerGraph with only "
- "one entry!");
- }
-
- //extract the energies of the active rotamers
- std::vector<int> num_active_rotamers;
- std::vector<Real*> self_energies;
- std::vector<std::vector<std::pair<int, PairwiseEWrapper> > > pairwise_energies;
- pairwise_energies.resize(num_graph_nodes);
- std::vector<Real*> pairwise_energies_ptrs;
-
- for(int i = 0; i < num_graph_nodes; ++i){
- num_active_rotamers.push_back(nodes_[i]->GetNumActiveRotamers());
- }
-
- for(int i = 0; i < num_graph_nodes; ++i){
- Real* self_e = new Real[num_active_rotamers[i]];
- nodes_[i]->FillActiveSelfEnergies(self_e);
- self_energies.push_back(self_e);
- }
-
- for(int i = 0; i < num_graph_edges; ++i){
- if(edges_[i]->IsActive()){
- RotamerGraphEdge* edge = edges_[i];
- int a = edge->GetNode1()->GetIndex();
- int b = edge->GetNode2()->GetIndex();
- if(a < b){
-
- Real* pairwise_e = new Real[num_active_rotamers[a] *
- num_active_rotamers[b]];
- edge->FillActiveEnergies(pairwise_e);
- pairwise_energies_ptrs.push_back(pairwise_e);
-
- PairwiseEWrapper wrapper_one(a, b, num_active_rotamers[a],
- num_active_rotamers[b],
- pairwise_energies_ptrs.back());
- PairwiseEWrapper wrapper_two(b, a, num_active_rotamers[b],
- num_active_rotamers[a],
- pairwise_energies_ptrs.back());
- pairwise_energies[a].push_back(std::make_pair(b, wrapper_one));
- pairwise_energies[b].push_back(std::make_pair(a, wrapper_two));
- }
- else{
- throw promod3::Error("Expect always first node in graph to have lower "
- "idx! The graph construction somehow fucked up...");
- }
- }
- }
-
- // let the sampling begin!
- RotamerSelector rotamer_selector(num_active_rotamers, seed);
-
- for(int trajectory_idx = 0; trajectory_idx < n; ++trajectory_idx) {
-
- std::vector<int> current_solution;
- rotamer_selector.InitRotamerSelection(current_solution);
- Real temperature = start_temperature / cooling_factor;
-
- for(int current_step = 0; current_step < mc_steps; ++current_step) {
-
- if (current_step % change_frequency == 0) {
- temperature *= cooling_factor;
- }
-
- Real e_current, e_new, e_diff;
-
- int node_idx = rotamer_selector.SelectNode();
- int rot_idx = current_solution[node_idx];
- e_current = GetRotamerEnergy(node_idx, rot_idx, current_solution,
- self_energies, pairwise_energies);
-
- rot_idx = rotamer_selector.SelectRotamer(node_idx);
- e_new = GetRotamerEnergy(node_idx, rot_idx, current_solution,
- self_energies, pairwise_energies);
-
- e_diff = e_new - e_current;
-
- if (e_diff <= Real(0.0)) {
- current_solution[node_idx] = rot_idx;
- }
-
- else {
- Real acceptance_probability = std::exp(-e_diff/temperature);
- if (rotamer_selector.GetRandomNumber() < acceptance_probability) {
- current_solution[node_idx] = rot_idx;
- }
- }
- }
-
- //the trajectory solution!!!
- Real e = GetGlobalEnergy(current_solution, self_energies, pairwise_energies);
- solution_energies.push_back(e);
- solutions.push_back(current_solution);
- }
-
- //the solutions are relative to the active rotamers, we still have to
- //translate them into overall indices
- for(uint i = 0; i < solutions.size(); ++i){
- for(uint j = 0; j < solutions[i].size(); ++j){
- solutions[i][j] = nodes_[j]->GetOverallIndex(solutions[i][j]);
- }
- }
-
- //final cleanup
- for(std::vector<Real*>::iterator i = self_energies.begin();
- i != self_energies.end(); ++i) {
- delete [] (*i);
- }
-
- for(std::vector<Real*>::iterator i = pairwise_energies_ptrs.begin();
- i != pairwise_energies_ptrs.end(); ++i) {
- delete [] (*i);
- }
-
- return std::make_pair(solutions, solution_energies);
-}
-
-void RotamerGraph::Invert(Real* energies, Real* inverted_energies,
- int i_size, int j_size){
- Real* e_ptr = energies;
- for(int i = 0; i < i_size; ++i){
- for(int j = 0; j < j_size; ++j){
- inverted_energies[j*i_size+i] = *e_ptr;
- ++e_ptr;
- }
- }
-}
-
-
}}//ns
diff --git a/sidechain/src/rotamer_graph.hh b/sidechain/src/rotamer_graph.hh
index 92ea26405a524ad3fb25bfdf22ef57eafa7c40b4..4e447b684191e0b33b7ab4ef4c8aae860ba3aebd 100644
--- a/sidechain/src/rotamer_graph.hh
+++ b/sidechain/src/rotamer_graph.hh
@@ -7,239 +7,61 @@
#include <boost/shared_ptr.hpp>
#include <promod3/sidechain/rotamer_group.hh>
-#include <promod3/core/graph.hh>
+#include <promod3/core/graph_minimizer.hh>
-namespace promod3{ namespace sidechain{
-class RotamerGraphEdge;
-class RotamerGraphNode;
-class RotamerGraph;
+namespace promod3 { namespace sidechain {
+class RotamerGraph;
typedef boost::shared_ptr<RotamerGraph> RotamerGraphPtr;
-class RotamerGraphEdge{
-
-public:
- RotamerGraphEdge(uint index, RotamerGraphNode* node1, RotamerGraphNode* node2,
- uint num_i, uint num_j, Real* pairwise_energies_);
-
- ~RotamerGraphEdge();
-
- void Reset();
-
- void Deactivate();
-
- bool IsActive() const { return active_; }
-
- uint GetIndex() const { return index_; }
-
- bool Decompose(Real thresh);
- Real GetPairwiseEnergy(uint i, uint j) const { return pairwise_energies_[i * maxj_ + j]; }
-
- RotamerGraphNode* GetNode1() const { return node1_; }
-
- RotamerGraphNode* GetNode2() const { return node2_; }
-
- RotamerGraphNode* GetOtherNode(RotamerGraphNode* node);
-
- //resolves the expression min_x(EPair(idx1,x)-EPair(idx2,x))
- //in the DEE formalism, where x only considers the active
- //rotamers from the OTHER node than node_ptr
- Real EMinDiff(const RotamerGraphNode* node_ptr, uint idx1, uint idx2) const;
-
- void FillActiveEnergies(Real* pairwise_energies) const;
-
-private:
- uint index_;
- bool active_;
- RotamerGraphNode* node1_;
- RotamerGraphNode* node2_;
- uint maxi_;
- uint maxj_;
- Real* pairwise_energies_;
-};
-
-class RotamerGraphNode{
+class RotamerGraph : public promod3::core::GraphMinimizer {
public:
- RotamerGraphNode(uint index,
- uint num_rotamers,
- Real* internal_energies,
- Real* frame_energies);
-
- ~RotamerGraphNode();
-
- void Reset();
-
- void Deactivate(int index = -1);
-
- bool IsActive() const { return active_; }
-
- uint GetIndex() const { return index_; }
-
- void AddEdge(RotamerGraphEdge* edge);
-
- RotamerGraphEdge* GetEdge(uint index) const { return edges_.at(index); }
-
- void RemoveFromActiveEdges(RotamerGraphEdge* edge);
-
- void AddValue(Real val);
-
- void AddValue(uint node_idx, Real val);
-
- bool DEE(Real e_cut = 0.0);
-
- uint GetOverallIndex(uint active_index) const { return active_rotamers_.at(active_index); }
-
- size_t GetNumActiveRotamers() const { return active_rotamers_.size(); }
-
- size_t GetNumActiveEdges() const { return active_edges_.size(); }
-
- size_t GetNumRotamers() const { return num_rotamers_; }
-
- size_t GetNumEdges() const { return edges_.size(); }
-
- Real GetSelfEnergy(uint index) const { return self_energies_[index]; }
-
- void FillActiveSelfEnergies(Real* self_energies) const;
-
- typedef std::vector<uint>::const_iterator const_iterator;
- typedef std::vector<uint>::iterator iterator;
-
- iterator active_rotamers_begin() { return active_rotamers_.begin(); }
- iterator active_rotamers_end() { return active_rotamers_.end(); }
- iterator active_edges_begin() { return active_edges_.begin(); }
- iterator active_edges_end() { return active_edges_.end(); }
-
- const_iterator active_rotamers_begin() const { return active_rotamers_.begin(); }
- const_iterator active_rotamers_end() const { return active_rotamers_.end(); }
- const_iterator active_edges_begin() const { return active_edges_.begin(); }
- const_iterator active_edges_end() const { return active_edges_.end(); }
-private:
-
- bool active_;
- uint index_;
- uint num_rotamers_;
- Real* internal_energies_;
- Real* frame_energies_;
- Real* self_energies_;
- std::vector<uint> active_rotamers_;
- std::vector<uint> active_edges_;
- std::vector<std::pair<uint,Real> > sorted_active_rotamers_;
- std::vector<RotamerGraphEdge*> edges_;
-};
-
-class RotamerGraph{
-
-public:
-
- ~RotamerGraph();
-
- static RotamerGraphPtr CreateFromRRMList(
- const std::vector<RRMRotamerGroupPtr>& rotamer_groups);
-
- static RotamerGraphPtr CreateFromFRMList(
- const std::vector<FRMRotamerGroupPtr>& rotamer_groups);
-
- // for convenience
- static RotamerGraphPtr CreateFromList(
- const std::vector<RRMRotamerGroupPtr>& rotamer_groups) {
- return CreateFromRRMList(rotamer_groups);
+ virtual ~RotamerGraph() { }
+
+ template<typename RotamerGroupPtr>
+ static RotamerGraphPtr CreateFromList(const std::vector<RotamerGroupPtr>&
+ rotamer_groups) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "RotamerGraph::CreateFromList", 2);
+
+ RotamerGraphPtr graph(new RotamerGraph);
+
+ // let's create the nodes
+ std::vector<Real> self_energies;
+ for(uint i = 0; i < rotamer_groups.size(); ++i) {
+ RotamerGroupPtr rot_group = rotamer_groups[i];
+ self_energies.resize(rot_group->size());
+ for(uint j = 0; j < rot_group->size(); ++j){
+ self_energies[j] = (*rot_group)[j]->GetInternalEnergy() +
+ (*rot_group)[j]->GetFrameEnergy();
+ }
+
+ graph->AddNode(self_energies);
+ }
+
+ // let's create the edges
+ for(uint i = 0; i < rotamer_groups.size(); ++i){
+ for(uint j = i+1; j < rotamer_groups.size(); ++j){
+ promod3::core::EMatXX emat;
+ if(rotamer_groups[i]->CalculatePairwiseEnergies(rotamer_groups[j],
+ 0.01, emat)) {
+ graph->AddEdge(i, j, emat);
+ }
+ }
+ }
+
+ return graph;
}
- static RotamerGraphPtr CreateFromList(
- const std::vector<FRMRotamerGroupPtr>& rotamer_groups) {
- return CreateFromFRMList(rotamer_groups);
- }
-
- // for hacky access... more info in function definition
- static RotamerGraphPtr CreateFromArbitrarySource(const std::vector<uint>& node_sizes,
- const std::vector<Real*>& internal_energies,
- const std::vector<Real*>& frame_energies,
- const std::vector<std::pair<uint,uint> >& edges,
- const std::vector<Real*>& pairwise_energies);
-
- size_t GetNumActiveRotamers() const;
-
- size_t GetNumActiveEdges() const;
-
- size_t GetNumActiveNodes() const;
-
- size_t GetNumNodes() const { return nodes_.size(); }
-
- size_t GetNumEdges() const { return edges_.size(); }
-
- size_t GetNumRotamers() const;
-
- void GetNumRotamers(std::vector<int>& num_rotamers) const;
-
- void GetNumActiveRotamers(std::vector<int>& num_rotamers) const;
-
- void GetActiveRotamers(uint idx, std::vector<int>& active_rotamers) const;
-
- void GetEdges(std::vector<std::pair<int, int> >& edges) const;
-
- void GetActiveEdges(std::vector<std::pair<int, int> >& edges) const;
-
- void GetSelfEnergies(uint idx, std::vector<Real>& energies) const;
-
- void GetPairwiseEnergies(uint idx,
- std::vector<std::vector<Real> >& energies) const;
-
- bool ApplyDEE(uint idx, Real e_thresh = 0.0);
-
- bool ApplyEdgeDecomposition(uint idx, Real e_tresh);
-
- void Prune(Real epsilon, Real e_cut = 0.0, bool consider_all_nodes = true);
-
- void Reset();
-
- promod3::core::Graph ToRawGraph() const;
-
- std::pair<std::vector<int>, Real>
- TreeSolve(uint64_t max_complexity = std::numeric_limits<uint64_t>::max(),
- Real intial_epsilon = 0.02);
-
- std::pair<std::vector<std::vector<int> >, std::vector<Real> >
- AStarSolve(Real e_thresh, uint max_n = 100,
- uint max_visited_nodes = 100000000);
-
- std::pair<std::vector<std::vector<int> >, std::vector<Real> >
- MCSolve(int n = 10, int mc_steps = 1000, Real start_temperature = 100.0,
- int change_frequency = 100, Real cooling_factor = 0.9,
- int seed = 0);
-
- RotamerGraphNode* GetNode(uint index) { return nodes_.at(index); }
-
- RotamerGraphEdge* GetEdge(uint index) { return edges_.at(index); }
-
- typedef std::vector<RotamerGraphNode*>::const_iterator const_node_iterator;
- typedef std::vector<RotamerGraphNode*>::iterator node_iterator;
-
- typedef std::vector<RotamerGraphEdge*>::const_iterator const_edge_iterator;
- typedef std::vector<RotamerGraphEdge*>::iterator edge_iterator;
-
- node_iterator nodes_begin() { return nodes_.begin(); }
- node_iterator nodes_end() { return nodes_.end(); }
- edge_iterator edges_begin() { return edges_.begin(); }
- edge_iterator edges_end() { return edges_.end(); }
-
- const_node_iterator nodes_begin() const{ return nodes_.begin(); }
- const_node_iterator nodes_end() const{ return nodes_.end(); }
- const_edge_iterator edges_begin() const{ return edges_.begin(); }
- const_edge_iterator edges_end() const{ return edges_.end(); }
private:
- RotamerGraph() { }
- RotamerGraph(const RotamerGraph& other) { }
- static void Invert(Real* energies, Real* inverted_energies,
- int i_size , int j_size);
- std::vector<RotamerGraphNode*> nodes_;
- std::vector<RotamerGraphEdge*> edges_;
};
}}//ns
diff --git a/sidechain/src/rotamer_group.cc b/sidechain/src/rotamer_group.cc
index 33219f103b5ad2018bb371600686477d40fbd7e5..dd20d27cb85307258a8b00c7693430a018bf49ce 100644
--- a/sidechain/src/rotamer_group.cc
+++ b/sidechain/src/rotamer_group.cc
@@ -3,19 +3,19 @@
namespace{
-Real LogSumExp(double* values, int n){
+Real LogSumExp(double* values, int n) {
double min = std::numeric_limits<double>::max();
double max = -std::numeric_limits<double>::max();
- for(int i = 0; i < n; ++i){
+ for(int i = 0; i < n; ++i) {
min = std::min(min, values[i]);
max = std::max(max, values[i]);
}
double range = max - min;
- if(range > double(100.0)){
+ if(range > double(100.0)) {
// The log sum exp function (LSE) is bound by
// max(x1, x2, ..., xn) <= LSE(x1, x2, ..., xn) <=
// max(x1, x2, ..., xn) + log(n)
@@ -36,6 +36,7 @@ Real LogSumExp(double* values, int n){
namespace promod3 { namespace sidechain {
+
RRMRotamerGroup::RRMRotamerGroup(const std::vector<RRMRotamerPtr>& rotamers,
uint residue_index)
: rotamers_(rotamers)
@@ -52,6 +53,7 @@ RRMRotamerGroup::RRMRotamerGroup(const std::vector<RRMRotamerPtr>& rotamers,
this->Init();
}
+
void RRMRotamerGroup::ApplyOnResidue(uint rotamer_index,
ost::mol::ResidueHandle& res,
bool consider_hydrogens,
@@ -63,6 +65,7 @@ void RRMRotamerGroup::ApplyOnResidue(uint rotamer_index,
new_res_name);
}
+
void RRMRotamerGroup::ApplyOnResidue(uint rotamer_index,
loop::AllAtomPositions& all_atom,
uint res_idx) const {
@@ -72,14 +75,16 @@ void RRMRotamerGroup::ApplyOnResidue(uint rotamer_index,
rotamers_[rotamer_index]->ApplyOnResidue(all_atom, res_idx);
}
+
void RRMRotamerGroup::SetFrameEnergy(FramePtr frame) {
- for(iterator i = this->begin(); i != this->end(); ++i){
+ for(iterator i = this->begin(); i != this->end(); ++i) {
(*i)->SetFrameEnergy(0.0);
}
this->AddFrameEnergy(frame);
}
+
void RRMRotamerGroup::AddFrameEnergy(FramePtr frame) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
@@ -92,28 +97,31 @@ void RRMRotamerGroup::AddFrameEnergy(FramePtr frame) {
const std::vector<uint>& frame_residue_indices = frame->GetResidueIndices();
const std::vector<Particle*>& frame_particles = frame->GetParticles();
std::vector<Real> frame_energies(this->size(), 0.0);
- Real energy;
- for(std::vector<std::pair<int,int> >::iterator i = overlapping_particles.begin(),
- e = overlapping_particles.end(); i != e; ++i){
- if(frame_residue_indices[i->second] != residue_index_){
- energy = particles_[i->first]->PairwiseEnergy(frame_particles[i->second]);
+ for(std::vector<std::pair<int,int> >::iterator i =
+ overlapping_particles.begin(),
+ e = overlapping_particles.end(); i != e; ++i) {
+ if(frame_residue_indices[i->second] != residue_index_) {
+ Real energy =
+ particles_[i->first]->PairwiseEnergy(frame_particles[i->second]);
frame_energies[rotamer_indices_[i->first]] += energy;
}
}
- for(uint i = 0; i < this->size(); ++i){
+ for(uint i = 0; i < this->size(); ++i) {
rotamers_[i]->AddFrameEnergy(frame_energies[i]);
}
}
-Real* RRMRotamerGroup::CalculatePairwiseEnergies(RRMRotamerGroupPtr other,
- Real threshold) {
+
+bool RRMRotamerGroup::CalculatePairwiseEnergies(RRMRotamerGroupPtr other,
+ Real threshold,
+ promod3::core::EMatXX& emat) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"RRMRotamerGroup::CalculatePairwiseEnergies", 2);
- if(!collision_tree_.Overlap(other->GetCollisionTree())) return NULL;
+ if(!collision_tree_.Overlap(other->GetCollisionTree())) return false;
std::vector<std::pair<int,int> > overlapping_particles;
overlapping_particles.reserve(4000);
@@ -121,39 +129,34 @@ Real* RRMRotamerGroup::CalculatePairwiseEnergies(RRMRotamerGroupPtr other,
collision_tree_.OverlappingPolytopes(other->GetCollisionTree(),
overlapping_particles);
- if(overlapping_particles.empty()) return NULL;
+ if(overlapping_particles.empty()) return false;
- int this_size = this->size();
- int other_size = other->size();
- Real* data = new Real[this_size * other_size];
- memset(data, 0, this_size*other_size*sizeof(Real));
- Real energy;
+ emat = promod3::core::EMatXX::Zero(this->size(), other->size());
- for(std::vector<std::pair<int,int> >::iterator i = overlapping_particles.begin(),
- e = overlapping_particles.end(); i!= e; ++i){
- energy = particles_[i->first]->PairwiseEnergy(other->particles_[i->second]);
- if(energy != Real(0.0)){
- data[rotamer_indices_[i->first]*other_size +
- other->rotamer_indices_[i->second]] += energy;
- }
- }
+ for(std::vector<std::pair<int,int> >::iterator i =
+ overlapping_particles.begin(),
+ e = overlapping_particles.end(); i!= e; ++i) {
+
+ Real energy =
+ particles_[i->first]->PairwiseEnergy(other->particles_[i->second]);
- Real max_e = 0.0;
- for(int i = 0; i < this_size*other_size; ++i){
- max_e = (max_e < data[i]) ? data[i] : max_e;
+ if(energy != Real(0.0)) {
+ emat(rotamer_indices_[i->first], other->rotamer_indices_[i->second]) +=
+ energy;
+ }
}
- if(max_e < threshold){
- delete [] data;
- return NULL;
+ if(emat.cwiseAbs().maxCoeff() < threshold) {
+ return false;
}
- return data;
+ return true;
}
-Real RRMRotamerGroup::GetMaxP() const{
+
+Real RRMRotamerGroup::GetMaxP() const {
Real max_p = std::numeric_limits<Real>::min();
- for(const_iterator i = this->begin(); i != this->end(); ++i){
+ for(const_iterator i = this->begin(); i != this->end(); ++i) {
max_p = std::max(max_p,(*i)->GetProbability());
}
return max_p;
@@ -167,20 +170,20 @@ void RRMRotamerGroup::ApplySelfEnergyThresh(Real self_energy_thresh) {
if(rotamers_.size() <= 1) return;
- //find the lowest energy
+ // find the lowest energy
Real e_min = std::numeric_limits<Real>::max();
for(std::vector<RRMRotamerPtr>::iterator i = rotamers_.begin();
- i != rotamers_.end(); ++i){
+ i != rotamers_.end(); ++i) {
if( (*i)->GetSelfEnergy() < e_min) e_min = (*i)->GetSelfEnergy();
}
- //define threshold relative to it
+ // define threshold relative to it
Real thresh = e_min + self_energy_thresh;
- //kill all rotamers with self energies worse than thresh
+ // kill all rotamers with self energies worse than thresh
for(std::vector<RRMRotamerPtr>::iterator i = rotamers_.begin();
- i != rotamers_.end(); ++i){
- if((*i)->GetSelfEnergy() > thresh){
+ i != rotamers_.end(); ++i) {
+ if((*i)->GetSelfEnergy() > thresh) {
i = rotamers_.erase(i);
--i;
}
@@ -189,18 +192,21 @@ void RRMRotamerGroup::ApplySelfEnergyThresh(Real self_energy_thresh) {
this->Init();
}
-void RRMRotamerGroup::Merge(const RRMRotamerGroupPtr other){
- for(RRMRotamerGroup::const_iterator i = other->begin(); i != other->end(); ++i){
+
+void RRMRotamerGroup::Merge(const RRMRotamerGroupPtr other) {
+ for(RRMRotamerGroup::const_iterator i = other->begin();
+ i != other->end(); ++i) {
rotamers_.push_back(*i);
}
this->Init();
}
-void RRMRotamerGroup::Init(){
+
+void RRMRotamerGroup::Init() {
int overall_size = 0;
for(std::vector<RRMRotamerPtr>::iterator i = rotamers_.begin();
- i != rotamers_.end(); ++i){
+ i != rotamers_.end(); ++i) {
overall_size += (*i)->size();
}
@@ -217,9 +223,9 @@ void RRMRotamerGroup::Init(){
geom::Vec3 pos;
for(std::vector<RRMRotamerPtr>::iterator i = rotamers_.begin();
- i != rotamers_.end(); ++i){
+ i != rotamers_.end(); ++i) {
- for(uint j = 0; j < (*i)->size(); ++j){
+ for(uint j = 0; j < (*i)->size(); ++j) {
Particle& p = (**i)[j];
particles_[actual_position] = &p;
rotamer_indices_[actual_position] = actual_rotamer;
@@ -239,6 +245,7 @@ void RRMRotamerGroup::Init(){
collision_distances);
}
+
FRMRotamerGroup::FRMRotamerGroup(const std::vector<FRMRotamerPtr>& rotamers,
uint residue_index)
: rotamers_(rotamers)
@@ -255,6 +262,7 @@ FRMRotamerGroup::FRMRotamerGroup(const std::vector<FRMRotamerPtr>& rotamers,
this->Init();
}
+
void FRMRotamerGroup::ApplyOnResidue(uint rotamer_index,
ost::mol::ResidueHandle& res,
bool consider_hydrogens,
@@ -266,6 +274,7 @@ void FRMRotamerGroup::ApplyOnResidue(uint rotamer_index,
new_res_name);
}
+
void FRMRotamerGroup::ApplyOnResidue(uint rotamer_index,
loop::AllAtomPositions& all_atom,
uint res_idx) const {
@@ -275,25 +284,29 @@ void FRMRotamerGroup::ApplyOnResidue(uint rotamer_index,
rotamers_[rotamer_index]->ApplyOnResidue(all_atom, res_idx);
}
-void FRMRotamerGroup::Merge(const FRMRotamerGroupPtr other){
- for(FRMRotamerGroup::const_iterator i = other->begin(); i != other->end(); ++i){
+
+void FRMRotamerGroup::Merge(const FRMRotamerGroupPtr other) {
+ for(FRMRotamerGroup::const_iterator i = other->begin();
+ i != other->end(); ++i) {
rotamers_.push_back(*i);
}
this->Init();
}
-void FRMRotamerGroup::SetFrameEnergy(FramePtr frame){
- for(iterator i = this->begin(); i != this->end(); ++i){
+void FRMRotamerGroup::SetFrameEnergy(FramePtr frame) {
+
+ for(iterator i = this->begin(); i != this->end(); ++i) {
(*i)->SetFrameEnergy(0);
- for(uint j = 0, e = (*i)->subrotamer_size(); j < e; ++j){
+ for(uint j = 0; j < (*i)->subrotamer_size(); ++j) {
(*i)->SetFrameEnergy(0,j);
}
}
this->AddFrameEnergy(frame);
}
-void FRMRotamerGroup::AddFrameEnergy(FramePtr frame){
+
+void FRMRotamerGroup::AddFrameEnergy(FramePtr frame) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"FRMRotamerGroup::AddFrameEnergy", 2);
@@ -305,38 +318,40 @@ void FRMRotamerGroup::AddFrameEnergy(FramePtr frame){
const std::vector<uint>& frame_residue_indices = frame->GetResidueIndices();
const std::vector<Particle*>& frame_particles = frame->GetParticles();
- //reserve the memory
- Real** frame_energies = new Real*[this->size()];
- int counter = 0;
- int subrotamer_size;
+ std::vector<int> subrotamer_sizes(this->size());
int max_subrotamer_size = 0;
- for(iterator i = this->begin(); i != this->end(); ++i){
- subrotamer_size = (*i)->subrotamer_size();
- frame_energies[counter] = new Real[subrotamer_size];
- //set the subrotamer frame energies to the already existing
- //energies
- for(int j = 0; j < subrotamer_size; ++j){
- frame_energies[counter][j] = (*i)->GetFrameEnergy(j);
- }
- max_subrotamer_size = std::max(max_subrotamer_size, subrotamer_size);
- ++counter;
+ for(uint i = 0; i < this->size(); ++i) {
+ subrotamer_sizes[i] = rotamers_[i]->subrotamer_size();
+ max_subrotamer_size = std::max(max_subrotamer_size,
+ subrotamer_sizes[i]);
}
- Real energy;
- Real* e_ptr;
- for(std::vector<std::pair<int,int> >::iterator i = overlapping_particles.begin(),
- e = overlapping_particles.end(); i != e ; ++i){
+ promod3::core::EMatXX frame_energies =
+ promod3::core::EMatXX::Zero(this->size(), max_subrotamer_size);
- if(frame_residue_indices[i->second] != residue_index_){
- energy = particles_[i->first]->PairwiseEnergy(frame_particles[i->second]);
+ int counter = 0;
+ for(iterator i = this->begin(); i != this->end(); ++i, ++counter) {
+ // set the subrotamer frame energies to the already existing
+ // energies
+ for(int j = 0; j < subrotamer_sizes[counter]; ++j) {
+ frame_energies(counter,j) = (*i)->GetFrameEnergy(j);
+ }
+ }
- if(energy != Real(0.0)){
+ for(std::vector<std::pair<int,int> >::iterator i =
+ overlapping_particles.begin(),
+ e = overlapping_particles.end(); i != e ; ++i) {
- e_ptr = frame_energies[rotamer_indices_[i->first]];
+ if(frame_residue_indices[i->second] != residue_index_) {
- for(FRMRotamer::subrotamer_association_iterator j = ass_ind_b_[i->first];
- j != ass_ind_e_[i->first]; ++j){
- e_ptr[*j] += energy;
+ Real energy =
+ particles_[i->first]->PairwiseEnergy(frame_particles[i->second]);
+
+ if(energy != Real(0.0)) {
+ int row_idx = rotamer_indices_[i->first];
+ for(FRMRotamer::subrotamer_association_iterator j =
+ ass_ind_b_[i->first]; j != ass_ind_e_[i->first]; ++j) {
+ frame_energies(row_idx, *j) += energy;
}
}
}
@@ -344,37 +359,29 @@ void FRMRotamerGroup::AddFrameEnergy(FramePtr frame){
std::vector<double> exp_buffer(max_subrotamer_size, 0.0);
counter = 0;
- Real T;
- Real one_over_T;
- int actual_subrotamer_size;
-
- for(iterator i = this->begin(), e = this->end(); i != e; ++i){
- actual_subrotamer_size = (*i)->subrotamer_size();
- e_ptr = frame_energies[counter];
- T = (*i)->GetTemperature();
- one_over_T = 1.0/T;
- for(int j = 0; j < actual_subrotamer_size; ++j){
- (*i)->SetFrameEnergy(e_ptr[j],j);
- exp_buffer[j] = -e_ptr[j]*one_over_T;
- }
- (*i)->SetFrameEnergy(-T*LogSumExp(&exp_buffer[0], actual_subrotamer_size));
- ++counter;
- }
- for(uint i = 0; i < this->size(); ++i){
- delete [] frame_energies[i];
+ for(iterator i = this->begin(), e = this->end(); i != e; ++i, ++counter) {
+ Real T = (*i)->GetTemperature();
+ Real one_over_T = 1.0 / T;
+ for(int j = 0; j < subrotamer_sizes[counter]; ++j) {
+ Real energy = frame_energies(counter, j);
+ (*i)->SetFrameEnergy(energy, j);
+ exp_buffer[j] = -energy * one_over_T;
+ }
+ (*i)->SetFrameEnergy(-T*LogSumExp(&exp_buffer[0],
+ subrotamer_sizes[counter]));
}
- delete [] frame_energies;
-
}
-Real* FRMRotamerGroup::CalculatePairwiseEnergies(FRMRotamerGroupPtr other,
- Real threshold) {
+
+bool FRMRotamerGroup::CalculatePairwiseEnergies(FRMRotamerGroupPtr other,
+ Real threshold,
+ promod3::core::EMatXX& emat) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"FRMRotamerGroup::CalculatePairwiseEnergies", 2);
- if(!collision_tree_.Overlap(other->GetCollisionTree())) return NULL;
+ if(!collision_tree_.Overlap(other->GetCollisionTree())) return false;
std::vector<std::pair<int,int> > overlapping_particles;
overlapping_particles.reserve(100000);
@@ -382,96 +389,91 @@ Real* FRMRotamerGroup::CalculatePairwiseEnergies(FRMRotamerGroupPtr other,
collision_tree_.OverlappingPolytopes(other->GetCollisionTree(),
overlapping_particles);
- if(overlapping_particles.empty()) return NULL;
+ if(overlapping_particles.empty()) return false;
int this_size = this->size();
int other_size = other->size();
int rotamer_combinations = this_size * other_size;
- Real* data = new Real[rotamer_combinations];
+ emat = promod3::core::EMatXX::Zero(this_size, other_size);
- int other_subrotamer_sizes[other_size];
+ std::vector<int> other_subrotamer_sizes(other_size);
int total_other_subrotamers = 0;
- for(int i = 0; i < other_size; ++i){
+ for(int i = 0; i < other_size; ++i) {
other_subrotamer_sizes[i] = other->rotamers_[i]->subrotamer_size();
total_other_subrotamers += other_subrotamer_sizes[i];
}
- int subrotamer_combinations[rotamer_combinations];
- int max_subrotamer_combinations=0;
- int* int_ptr = &subrotamer_combinations[0];
- int temp;
+ // lets figure out what is the maximum number of subrotamer combinations
+ // among all the rotamer combinations
+ int max_subrotamers_i = 0;
+ int max_subrotamers_j = 0;
- for(int i = 0; i < this_size; ++i){
- temp = rotamers_[i]->subrotamer_size();
- for(int j = 0; j < other_size; ++j){
- *int_ptr = temp * other_subrotamer_sizes[j];
- max_subrotamer_combinations = (max_subrotamer_combinations<(*int_ptr))?(*int_ptr):max_subrotamer_combinations;
- ++int_ptr;
- }
+ for(int i = 0; i < this_size; ++i) {
+ max_subrotamers_i = std::max(max_subrotamers_i,
+ static_cast<int>(rotamers_[i]->subrotamer_size()));
}
- Real** subrotamer_energies = new Real*[rotamer_combinations];
- for(int i = 0; i < rotamer_combinations; ++i){
- subrotamer_energies[i] = new Real[subrotamer_combinations[i]];
- memset(subrotamer_energies[i],0,subrotamer_combinations[i]*sizeof(Real));
+ for(int i = 0; i < other_size; ++i) {
+ max_subrotamers_j = std::max(max_subrotamers_j,
+ other_subrotamer_sizes[i]);
}
+ int max_subrotamer_combinations = max_subrotamers_i * max_subrotamers_j;
+
+ // All pairwise subrotamer energies will be stored in the
+ // subrotamer_energies matrix.
+ // In principle this would be a 4 dimensional problem.
+ // This is how we store it:
+ // Rows: one row per combination of rotamers...
+ // row for combination i,j is at (i * other_size + j)
+ // Cols: the actual subrotamer energies for rotamer pair i,j
+ // it follows the same row-major principle as above
+ // energy for subrotamer combination k, l of rotamers i, j
+ // is stored at col: k * other_subrotamer_sizes[j] + l
+ promod3::core::EMatXX subrotamer_energies =
+ promod3::core::EMatXX::Zero(rotamer_combinations,
+ max_subrotamer_combinations);
+
Real energy;
int r_index_j;
+ int e_row_idx, e_col_idx;
int other_subrotamer_size;
- Real* e_ptr;
-
- FRMRotamer::subrotamer_association_iterator j_b,j_e,k_b,k_e,temp_it;
+ FRMRotamer::subrotamer_association_iterator subrot_i_b, subrot_i_e,
+ subrot_j_b, subrot_j_e, temp_it;
- for(std::vector<std::pair<int,int> >::iterator i = overlapping_particles.begin(),
- e = overlapping_particles.end(); i != e; ++i){
+ for(std::vector<std::pair<int,int> >::iterator i =
+ overlapping_particles.begin(),
+ e = overlapping_particles.end(); i != e; ++i) {
energy = particles_[i->first]->PairwiseEnergy(other->particles_[i->second]);
- if(energy != Real(0.0)){
+ if(energy != Real(0.0)) {
+ // we have to add this energy to all combinations of subrotamers where
+ // this pair of particles is involved in...
r_index_j = other->rotamer_indices_[i->second];
-
+ e_row_idx = rotamer_indices_[i->first] * other_size + r_index_j;
other_subrotamer_size = other_subrotamer_sizes[r_index_j];
-
- j_b = ass_ind_b_[i->first];
- j_e = ass_ind_e_[i->first];
+ subrot_i_b = ass_ind_b_[i->first];
+ subrot_i_e = ass_ind_e_[i->first];
temp_it = other->ass_ind_b_[i->second];
- k_e = other->ass_ind_e_[i->second];
+ subrot_j_e = other->ass_ind_e_[i->second];
- e_ptr = subrotamer_energies[rotamer_indices_[i->first]*other_size+r_index_j];
-
- for(;j_b != j_e; ++j_b){
- k_b = temp_it;
- temp = (*j_b)*other_subrotamer_size;
- for(;k_b != k_e; ++k_b){
- e_ptr[temp+(*k_b)] += energy;
+ for(;subrot_i_b != subrot_i_e; ++subrot_i_b) {
+ subrot_j_b = temp_it;
+ int temp = (*subrot_i_b) * other_subrotamer_size;
+ for(;subrot_j_b != subrot_j_e; ++subrot_j_b) {
+ subrotamer_energies(e_row_idx, temp + (*subrot_j_b)) += energy;
}
}
}
}
- Real max_e = 0.0;
- for(int i = 0; i < rotamer_combinations; ++i){
- e_ptr = subrotamer_energies[i];
- for(int j = 0; j < subrotamer_combinations[i]; ++j){
- max_e = (max_e<std::abs(e_ptr[j]))?std::abs(e_ptr[j]):max_e;
- }
- }
- if(max_e < threshold){
- for(int i = 0; i < rotamer_combinations; ++i){
- delete [] subrotamer_energies[i];
- }
- delete [] subrotamer_energies;
- delete [] data;
- return NULL;
+ if(subrotamer_energies.cwiseAbs().maxCoeff() < threshold) {
+ return false;
}
std::vector<double> exp_buffer(max_subrotamer_combinations, 0.0);
- Real* energy_ptr;
- Real* data_ptr = &data[0];
- double* double_ptr;
- Real* Real_ptr;
int a,b;
Real T;
Real one_over_T;
@@ -479,66 +481,65 @@ Real* FRMRotamerGroup::CalculatePairwiseEnergies(FRMRotamerGroupPtr other,
Real i_frame_energy;
Real k_subrotamer_frame_energy;
- Real j_frame_energies[other_size];
- Real j_temperatures[other_size];
- Real other_subrotamer_frame_energies[total_other_subrotamers];
+ std::vector<Real> j_frame_energies(other_size);
+ std::vector<Real> j_temperatures(other_size);
+ std::vector<Real> other_subrotamer_frame_energies(total_other_subrotamers);
+ // do some caching...
a = 0;
- Real_ptr = &other_subrotamer_frame_energies[0];
- for(iterator i = other->begin(); i != other->end(); ++i,++a){
+ b = 0;
+ for(iterator i = other->begin(); i != other->end(); ++i,++a) {
j_frame_energies[a] = (*i)->GetFrameEnergy();
j_temperatures[a] = (*i)->GetTemperature();
- for(uint j = 0; j < (*i)->subrotamer_size(); ++j){
- *Real_ptr = (*i)->GetFrameEnergy(j);
- ++Real_ptr;
+ for(uint j = 0; j < (*i)->subrotamer_size(); ++j, ++b) {
+ other_subrotamer_frame_energies[b] = (*i)->GetFrameEnergy(j);
}
}
- for(int i = 0; i < this_size; ++i){
+ // Everything is in place, the show can start...
+ for(int i = 0; i < this_size; ++i) {
i_frame_energy = rotamers_[i]->GetFrameEnergy();
a = rotamers_[i]->subrotamer_size();
T_i = rotamers_[i]->GetTemperature();
- temp = i*other_size;
- Real_ptr = &other_subrotamer_frame_energies[0];
- for(int j = 0; j < other_size; ++j){
- energy_ptr = subrotamer_energies[temp+j];
+ Real* other_subrotamer_frame_energy_ptr =
+ &other_subrotamer_frame_energies[0];
+ for(int j = 0; j < other_size; ++j) {
+ e_row_idx = i * other_size + j;
+ e_col_idx = 0;
T = 0.5 * (T_i + j_temperatures[j]);
one_over_T = 1.0/T;
- double_ptr = &exp_buffer[0];
b = other_subrotamer_sizes[j];
-
- for(int k = 0; k < a; ++k){
+ for(int k = 0; k < a; ++k) {
k_subrotamer_frame_energy = rotamers_[i]->GetFrameEnergy(k);
- for(int l = 0; l < b; ++l){
- *double_ptr = -(k_subrotamer_frame_energy+Real_ptr[l]+(*energy_ptr))*one_over_T;
- ++double_ptr;
- ++energy_ptr;
+ for(int l = 0; l < b; ++l, ++e_col_idx) {
+ exp_buffer[e_col_idx] = -(k_subrotamer_frame_energy +
+ other_subrotamer_frame_energy_ptr[l] +
+ subrotamer_energies(e_row_idx, e_col_idx)) *
+ one_over_T;
}
}
- *data_ptr = -T*LogSumExp(&exp_buffer[0], a*b) - i_frame_energy - j_frame_energies[j];
- ++data_ptr;
- Real_ptr+=b;
- }
- }
+ emat(i, j) = -T*LogSumExp(&exp_buffer[0], a*b) -
+ i_frame_energy - j_frame_energies[j];
- for(int i = 0; i < rotamer_combinations; ++i){
- delete [] subrotamer_energies[i];
+ other_subrotamer_frame_energy_ptr += b;
+ }
}
- delete [] subrotamer_energies;
- return data;
+ return true;
}
-Real FRMRotamerGroup::GetMaxP() const{
+
+Real FRMRotamerGroup::GetMaxP() const {
Real max_p = std::numeric_limits<Real>::min();
- for(const_iterator i = this->begin(); i != this->end(); ++i){
+ for(const_iterator i = this->begin(); i != this->end(); ++i) {
max_p = std::max(max_p,(*i)->GetProbability());
}
return max_p;
}
+
void FRMRotamerGroup::ApplySelfEnergyThresh(Real self_energy_thresh) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
@@ -547,37 +548,38 @@ void FRMRotamerGroup::ApplySelfEnergyThresh(Real self_energy_thresh) {
if(rotamers_.size() <= 1) return;
bool something_happened = false;
- //find the lowest energy
+ // find the lowest energy
Real e_min = std::numeric_limits<Real>::max();
for(std::vector<FRMRotamerPtr>::iterator i = rotamers_.begin();
- i != rotamers_.end(); ++i){
+ i != rotamers_.end(); ++i) {
e_min = std::min(e_min,(*i)->GetSelfEnergy());
}
- //define threshold relative to it
+ // define threshold relative to it
Real thresh = e_min + self_energy_thresh;
- //kill all rotamers with self energies worse than thresh
+ // kill all rotamers with self energies worse than thresh
for(std::vector<FRMRotamerPtr>::iterator i = rotamers_.begin();
- i != rotamers_.end(); ++i){
- if((*i)->GetSelfEnergy() > thresh){
+ i != rotamers_.end(); ++i) {
+ if((*i)->GetSelfEnergy() > thresh) {
i = rotamers_.erase(i);
--i;
something_happened = true;
}
}
- if(something_happened){
+ if(something_happened) {
this->Init();
}
}
-void FRMRotamerGroup::Init(){
+
+void FRMRotamerGroup::Init() {
int overall_size = 0;
for(std::vector<FRMRotamerPtr>::iterator i = rotamers_.begin();
- i != rotamers_.end(); ++i){
+ i != rotamers_.end(); ++i) {
overall_size += (*i)->size();
}
@@ -598,16 +600,18 @@ void FRMRotamerGroup::Init(){
geom::Vec3 pos;
for(std::vector<FRMRotamerPtr>::iterator i = rotamers_.begin();
- i != rotamers_.end(); ++i){
+ i != rotamers_.end(); ++i) {
actual_internal_index = 0;
- for(uint j = 0; j < (*i)->size(); ++j){
+ for(uint j = 0; j < (*i)->size(); ++j) {
Particle& p = (**i)[j];
particles_[actual_position] = &p;
rotamer_indices_[actual_position] = actual_rotamer;
- ass_ind_b_[actual_position] = (*i)->subrotamer_association_begin(actual_internal_index);
- ass_ind_e_[actual_position] = (*i)->subrotamer_association_end(actual_internal_index);
+ ass_ind_b_[actual_position] =
+ (*i)->subrotamer_association_begin(actual_internal_index);
+ ass_ind_e_[actual_position] =
+ (*i)->subrotamer_association_end(actual_internal_index);
pos = p.GetPos();
x_particle_positions[actual_position] = pos[0];
y_particle_positions[actual_position] = pos[1];
@@ -625,4 +629,4 @@ void FRMRotamerGroup::Init(){
collision_distances);
}
-}}//ns
+}} // ns
diff --git a/sidechain/src/rotamer_group.hh b/sidechain/src/rotamer_group.hh
index 6c203d792aea4f6d93e665c97d7b30fdc56ebee7..0ed5555e040b2a5f87c45dcdad5568b23ae90a08 100644
--- a/sidechain/src/rotamer_group.hh
+++ b/sidechain/src/rotamer_group.hh
@@ -6,10 +6,11 @@
#include <boost/shared_ptr.hpp>
#include <promod3/core/tetrahedral_polytope.hh>
+#include <promod3/core/eigen_types.hh>
#include <promod3/sidechain/rotamer.hh>
#include <promod3/sidechain/frame.hh>
-namespace promod3{ namespace sidechain{
+namespace promod3 { namespace sidechain {
class RRMRotamerGroup;
class FRMRotamerGroup;
@@ -21,7 +22,8 @@ class RRMRotamerGroup{
public:
- RRMRotamerGroup(const std::vector<RRMRotamerPtr>& rotamers, uint residue_index);
+ RRMRotamerGroup(const std::vector<RRMRotamerPtr>& rotamers,
+ uint residue_index);
void Merge(const RRMRotamerGroupPtr other);
@@ -36,15 +38,16 @@ public:
void AddFrameEnergy(FramePtr p);
- Real* CalculatePairwiseEnergies(RRMRotamerGroupPtr other, Real threshold);
+ bool CalculatePairwiseEnergies(RRMRotamerGroupPtr other, Real threshold,
+ promod3::core::EMatXX& emat);
Real GetMaxP() const;
void ApplySelfEnergyThresh(Real self_energy_thresh = 30);
- uint GetResidueIndex(){ return residue_index_; }
+ uint GetResidueIndex() { return residue_index_; }
- const promod3::core::TetrahedralPolytopeTree& GetCollisionTree() const{
+ const promod3::core::TetrahedralPolytopeTree& GetCollisionTree() const {
return collision_tree_;
}
@@ -87,7 +90,8 @@ class FRMRotamerGroup{
public:
- FRMRotamerGroup(const std::vector<FRMRotamerPtr>& rotamers, uint residue_index);
+ FRMRotamerGroup(const std::vector<FRMRotamerPtr>& rotamers,
+ uint residue_index);
virtual ~FRMRotamerGroup() { rotamers_.clear(); }
@@ -104,7 +108,8 @@ public:
void AddFrameEnergy(FramePtr p);
- Real* CalculatePairwiseEnergies(FRMRotamerGroupPtr other, Real threshold);
+ bool CalculatePairwiseEnergies(FRMRotamerGroupPtr other, Real threshold,
+ promod3::core::EMatXX& emat);
Real GetMaxP() const;
@@ -112,7 +117,7 @@ public:
uint GetResidueIndex() const { return residue_index_; }
- const promod3::core::TetrahedralPolytopeTree& GetCollisionTree() const{
+ const promod3::core::TetrahedralPolytopeTree& GetCollisionTree() const {
return collision_tree_;
}
@@ -154,6 +159,6 @@ private:
-}}//ns
+}} // ns
#endif
diff --git a/sidechain/src/rotamer_lib.cc b/sidechain/src/rotamer_lib.cc
index 4f06f77fc1f36747f26844f080a222fbc828ed9a..10ae3e6438f212aaac69a6e9b7b893e604d0ddde 100644
--- a/sidechain/src/rotamer_lib.cc
+++ b/sidechain/src/rotamer_lib.cc
@@ -237,12 +237,13 @@ std::pair<RotamerLibEntry*,uint> RotamerLib::QueryLib(RotamerID id) const{
}
std::map<RotamerID,std::pair<uint64_t,uint> >::const_iterator it = static_data_helper_.find(id);
- if(it == static_data_helper_.end()){
- throw promod3::Error("No rotamers for given id...");
- }
result_buffer_.clear();
+ if(it == static_data_helper_.end()){
+ return std::make_pair(reinterpret_cast<RotamerLibEntry*>(NULL), 0);
+ }
+
uint64_t pos = it->second.first;
for(uint i = 0; i < it->second.second; ++i){
result_buffer_.push_back(static_data_[pos]);
diff --git a/sidechain/src/scwrl_rotamer_constructor.cc b/sidechain/src/scwrl_rotamer_constructor.cc
index 1ef28876c408c19e689c00c0ca252d9c50cfce77..ed8d8da2f04790a7c2d7b72f5eb189de82c1a420 100644
--- a/sidechain/src/scwrl_rotamer_constructor.cc
+++ b/sidechain/src/scwrl_rotamer_constructor.cc
@@ -53,7 +53,7 @@ void EvalLonePairRule(promod3::sidechain::Particle& p,
promod3::sidechain::SCWRLLPRule rule,
const geom::Vec3& a,
const geom::Vec3& b,
- const geom::Vec3& c){
+ const geom::Vec3& c) {
switch(rule){
case promod3::sidechain::LONE_PAIR_CARBONYL: {
_AddLonePairsCarbonyl(a, b, c, p);
@@ -170,7 +170,8 @@ _AtomSpecCPList _GetCarboxylAtoms(const _AtomInfo& atom_info) {
namespace promod3 { namespace sidechain {
-SCWRLRotamerLookup::SCWRLRotamerLookup() {
+SCWRLRotamerLookup::SCWRLRotamerLookup(bool cb_in_sidechain) {
+
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerLookup::SCWRLRotamerLookup", 2);
@@ -178,6 +179,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[ARG].has_hydrogens = true;
sidechain_infos_[ARG].internal_e_prefactor = 2.27;
sidechain_infos_[ARG].frm_t = 1.23;
+
AddInfo(ARG, CH2Particle, 0.0, "CG", promod3::loop::ARG_CG_INDEX, false);
AddInfo(ARG, CH2Particle, 0.1, "CD", promod3::loop::ARG_CD_INDEX, false);
AddInfo(ARG, NParticle, -0.4, "NE", promod3::loop::ARG_NE_INDEX, false);
@@ -189,11 +191,17 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddInfo(ARG, HParticle, 0.35, "HH12", promod3::loop::ARG_HH12_INDEX, true);
AddInfo(ARG, HParticle, 0.35, "HH21", promod3::loop::ARG_HH21_INDEX, true);
AddInfo(ARG, HParticle, 0.35, "HH22", promod3::loop::ARG_HH22_INDEX, true);
+
+ if(cb_in_sidechain) {
+ AddInfo(ARG, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddPDir(ARG, promod3::loop::ARG_HE_INDEX, promod3::loop::ARG_NE_INDEX, 6);
AddPDir(ARG, promod3::loop::ARG_HH11_INDEX, promod3::loop::ARG_NH1_INDEX, 7);
AddPDir(ARG, promod3::loop::ARG_HH12_INDEX, promod3::loop::ARG_NH1_INDEX, 8);
AddPDir(ARG, promod3::loop::ARG_HH21_INDEX, promod3::loop::ARG_NH2_INDEX, 9);
AddPDir(ARG, promod3::loop::ARG_HH22_INDEX, promod3::loop::ARG_NH2_INDEX, 10);
+
AddFRMRule(ARG, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(ARG, 0, -0.87);
AddFRMPrefactor(ARG, 0, 0.87);
@@ -208,6 +216,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(ARG, 0, 8);
AddFRMRotatingParticle(ARG, 0, 9);
AddFRMRotatingParticle(ARG, 0, 10);
+
AddFRMRule(ARG, promod3::loop::BB_CB_INDEX, promod3::loop::ARG_CG_INDEX);
AddFRMPrefactor(ARG, 1, -1.62);
AddFRMPrefactor(ARG, 1, 1.62);
@@ -222,6 +231,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(ARG, 1, 8);
AddFRMRotatingParticle(ARG, 1, 9);
AddFRMRotatingParticle(ARG, 1, 10);
+
AddFRMRule(ARG, promod3::loop::ARG_CG_INDEX, promod3::loop::ARG_CD_INDEX);
AddFRMPrefactor(ARG, 2, -1.67);
AddFRMPrefactor(ARG, 2, 1.67);
@@ -236,6 +246,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(ARG, 2, 8);
AddFRMRotatingParticle(ARG, 2, 9);
AddFRMRotatingParticle(ARG, 2, 10);
+
AddFRMRule(ARG, promod3::loop::ARG_CD_INDEX, promod3::loop::ARG_NE_INDEX);
AddFRMPrefactor(ARG, 3, -0.73);
AddFRMPrefactor(ARG, 3, 0.73);
@@ -250,14 +261,26 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(ARG, 3, 8);
AddFRMRotatingParticle(ARG, 3, 9);
AddFRMRotatingParticle(ARG, 3, 10);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(ARG, 0, 11);
+ AddFRMFixParticle(ARG, 1, 11);
+ AddFRMFixParticle(ARG, 2, 11);
+ AddFRMFixParticle(ARG, 3, 11);
+ }
+
backbone_infos_[ARG].has_hydrogens = true;
AddBBInfo(ARG, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(ARG, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(ARG, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(ARG, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(ARG, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(ARG, HParticle, 0.25, "H", promod3::loop::ARG_H_INDEX,true);
- AddBBPDir(ARG, promod3::loop::ARG_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(ARG, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(ARG, promod3::loop::ARG_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(ARG, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -265,15 +288,22 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[ASN].has_hydrogens = true;
sidechain_infos_[ASN].internal_e_prefactor = 1.80;
sidechain_infos_[ASN].frm_t = 1.41;
+
AddInfo(ASN, CParticle, 0.55, "CG", promod3::loop::ASN_CG_INDEX, false);
AddInfo(ASN, OParticle, -0.55, "OD1", promod3::loop::ASN_OD1_INDEX, false);
AddInfo(ASN, NParticle, -0.6, "ND2", promod3::loop::ASN_ND2_INDEX, false);
AddInfo(ASN, HParticle, 0.3, "HD21", promod3::loop::ASN_HD21_INDEX, true);
AddInfo(ASN, HParticle, 0.3, "HD22", promod3::loop::ASN_HD22_INDEX, true);
+
+ if(cb_in_sidechain) {
+ AddInfo(ASN, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddPDir(ASN, promod3::loop::ASN_HD21_INDEX, promod3::loop::ASN_ND2_INDEX, 3);
AddPDir(ASN, promod3::loop::ASN_HD22_INDEX, promod3::loop::ASN_ND2_INDEX, 4);
AddLP(ASN, promod3::loop::ASN_ND2_INDEX, promod3::loop::ASN_CG_INDEX,
promod3::loop::ASN_OD1_INDEX, false, false, false, 1, LONE_PAIR_CARBONYL);
+
AddFRMRule(ASN, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(ASN, 0, -0.62);
AddFRMPrefactor(ASN, 0, 0.62);
@@ -282,6 +312,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(ASN, 0, 2);
AddFRMRotatingParticle(ASN, 0, 3);
AddFRMRotatingParticle(ASN, 0, 4);
+
AddFRMRule(ASN, promod3::loop::BB_CB_INDEX, promod3::loop::ASN_CG_INDEX);
AddFRMPrefactor(ASN, 1, -1.93);
AddFRMPrefactor(ASN, 1, 1.93);
@@ -290,47 +321,76 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(ASN, 1, 2);
AddFRMRotatingParticle(ASN, 1, 3);
AddFRMRotatingParticle(ASN, 1, 4);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(ASN, 0, 5);
+ AddFRMFixParticle(ASN, 1, 5);
+ }
+
backbone_infos_[ASN].has_hydrogens = true;
AddBBInfo(ASN, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(ASN, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(ASN, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(ASN, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(ASN, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(ASN, HParticle, 0.25, "H", promod3::loop::ASN_H_INDEX,true);
- AddBBPDir(ASN, promod3::loop::ASN_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(ASN, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(ASN, promod3::loop::ASN_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(ASN, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
// ASP
- AddInfo(ASP, CParticle, 0.36, "CG", promod3::loop::ASP_CG_INDEX, false);
sidechain_infos_[ASP].internal_e_prefactor = 2.44;
sidechain_infos_[ASP].frm_t = 1.48;
+ sidechain_infos_[ASP].has_hydrogens = false;
+
+ AddInfo(ASP, CParticle, 0.36, "CG", promod3::loop::ASP_CG_INDEX, false);
AddInfo(ASP, OParticle, -0.60, "OD1", promod3::loop::ASP_OD1_INDEX, false);
AddInfo(ASP, OParticle, -0.60, "OD2", promod3::loop::ASP_OD2_INDEX, false);
+
+ if(cb_in_sidechain) {
+ AddInfo(ASP, CH2Particle, -0.16, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddLP(ASP, promod3::loop::ASP_OD2_INDEX, promod3::loop::ASP_CG_INDEX,
promod3::loop::ASP_OD1_INDEX, false, false, false, 1, LONE_PAIR_CARBONYL);
AddLP(ASP, promod3::loop::ASP_OD1_INDEX, promod3::loop::ASP_CG_INDEX,
promod3::loop::ASP_OD2_INDEX, false, false, false, 2, LONE_PAIR_CARBONYL);
+
AddFRMRule(ASP, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(ASP, 0, -1.59);
AddFRMPrefactor(ASP, 0, 1.59);
AddFRMRotatingParticle(ASP, 0, 0);
AddFRMRotatingParticle(ASP, 0, 1);
AddFRMRotatingParticle(ASP, 0, 2);
+
AddFRMRule(ASP, promod3::loop::BB_CB_INDEX, promod3::loop::ASP_CG_INDEX);
AddFRMPrefactor(ASP, 1, -0.63);
AddFRMPrefactor(ASP, 1, 0.63);
AddFRMFixParticle(ASP, 1, 0);
AddFRMRotatingParticle(ASP, 1, 1);
AddFRMRotatingParticle(ASP, 1, 2);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(ASP, 0, 3);
+ AddFRMFixParticle(ASP, 1, 3);
+ }
+
backbone_infos_[ASP].has_hydrogens = true;
AddBBInfo(ASP, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(ASP, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(ASP, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(ASP, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(ASP, CH2Particle, -0.16, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(ASP, HParticle, 0.25, "H", promod3::loop::ASP_H_INDEX,true);
- AddBBPDir(ASP, promod3::loop::ASP_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(ASP, CH2Particle, -0.16, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(ASP, promod3::loop::ASP_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(ASP, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -338,16 +398,23 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[GLN].has_hydrogens = true;
sidechain_infos_[GLN].internal_e_prefactor = 1.61;
sidechain_infos_[GLN].frm_t = 1.32;
+
AddInfo(GLN, CH2Particle, 0.0, "CG", promod3::loop::GLN_CG_INDEX, false);
AddInfo(GLN, CParticle, 0.55, "CD", promod3::loop::GLN_CD_INDEX, false);
AddInfo(GLN, OParticle, -0.55, "OE1", promod3::loop::GLN_OE1_INDEX, false);
AddInfo(GLN, NParticle, -0.60, "NE2", promod3::loop::GLN_NE2_INDEX, false);
AddInfo(GLN, HParticle, 0.3, "HE21", promod3::loop::GLN_HE21_INDEX, true);
AddInfo(GLN, HParticle, 0.3, "HE22", promod3::loop::GLN_HE22_INDEX, true);
+
+ if(cb_in_sidechain) {
+ AddInfo(GLN, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddPDir(GLN, promod3::loop::GLN_HE21_INDEX, promod3::loop::GLN_NE2_INDEX, 4);
AddPDir(GLN, promod3::loop::GLN_HE22_INDEX, promod3::loop::GLN_NE2_INDEX, 5);
AddLP(GLN, promod3::loop::GLN_NE2_INDEX, promod3::loop::GLN_CD_INDEX,
promod3::loop::GLN_OE1_INDEX, false, false, false, 2, LONE_PAIR_CARBONYL);
+
AddFRMRule(GLN, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(GLN, 0, -1.55);
AddFRMPrefactor(GLN, 0, 1.55);
@@ -357,6 +424,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(GLN, 0, 3);
AddFRMRotatingParticle(GLN, 0, 4);
AddFRMRotatingParticle(GLN, 0, 5);
+
AddFRMRule(GLN, promod3::loop::BB_CB_INDEX, promod3::loop::GLN_CG_INDEX);
AddFRMPrefactor(GLN, 1, -0.53);
AddFRMPrefactor(GLN, 1, 0.53);
@@ -366,6 +434,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(GLN, 1, 3);
AddFRMRotatingParticle(GLN, 1, 4);
AddFRMRotatingParticle(GLN, 1, 5);
+
AddFRMRule(GLN, promod3::loop::GLN_CG_INDEX, promod3::loop::GLN_CD_INDEX);
AddFRMPrefactor(GLN, 2, -1.89);
AddFRMPrefactor(GLN, 2, 1.89);
@@ -375,14 +444,25 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(GLN, 2, 3);
AddFRMRotatingParticle(GLN, 2, 4);
AddFRMRotatingParticle(GLN, 2, 5);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(GLN, 0, 6);
+ AddFRMFixParticle(GLN, 1, 6);
+ AddFRMFixParticle(GLN, 2, 6);
+ }
+
backbone_infos_[GLN].has_hydrogens = true;
AddBBInfo(GLN, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(GLN, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(GLN, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(GLN, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(GLN, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(GLN, HParticle, 0.25, "H", promod3::loop::GLN_H_INDEX,true);
- AddBBPDir(GLN, promod3::loop::GLN_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(GLN, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(GLN, promod3::loop::GLN_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(GLN, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -390,14 +470,21 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[GLU].has_hydrogens = false;
sidechain_infos_[GLU].internal_e_prefactor = 1.85;
sidechain_infos_[GLU].frm_t = 0.94;
+
AddInfo(GLU, CH2Particle, -0.16, "CG", promod3::loop::GLU_CG_INDEX, false);
AddInfo(GLU, CParticle, 0.36, "CD", promod3::loop::GLU_CD_INDEX, false);
AddInfo(GLU, OParticle, -0.60, "OE1", promod3::loop::GLU_OE1_INDEX, false);
AddInfo(GLU, OParticle, -0.60, "OE2", promod3::loop::GLU_OE2_INDEX, false);
+
+ if(cb_in_sidechain) {
+ AddInfo(GLU, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddLP(GLU, promod3::loop::GLU_OE2_INDEX, promod3::loop::GLU_CD_INDEX,
promod3::loop::GLU_OE1_INDEX, false, false, false, 2, LONE_PAIR_CARBONYL);
AddLP(GLU, promod3::loop::GLU_OE1_INDEX, promod3::loop::GLU_CD_INDEX,
promod3::loop::GLU_OE2_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
+
AddFRMRule(GLU, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(GLU, 0, -0.82);
AddFRMPrefactor(GLU, 0, 0.82);
@@ -405,6 +492,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(GLU, 0, 1);
AddFRMRotatingParticle(GLU, 0, 2);
AddFRMRotatingParticle(GLU, 0, 3);
+
AddFRMRule(GLU, promod3::loop::BB_CB_INDEX, promod3::loop::GLU_CG_INDEX);
AddFRMPrefactor(GLU, 1, -1.57);
AddFRMPrefactor(GLU, 1, 1.57);
@@ -412,6 +500,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(GLU, 1, 1);
AddFRMRotatingParticle(GLU, 1, 2);
AddFRMRotatingParticle(GLU, 1, 3);
+
AddFRMRule(GLU, promod3::loop::GLU_CG_INDEX, promod3::loop::GLU_CD_INDEX);
AddFRMPrefactor(GLU, 2, -0.76);
AddFRMPrefactor(GLU, 2, 0.76);
@@ -419,14 +508,25 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMFixParticle(GLU, 2, 1);
AddFRMRotatingParticle(GLU, 2, 2);
AddFRMRotatingParticle(GLU, 2, 3);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(GLU, 0, 4);
+ AddFRMFixParticle(GLU, 1, 4);
+ AddFRMFixParticle(GLU, 2, 4);
+ }
+
backbone_infos_[GLU].has_hydrogens = true;
AddBBInfo(GLU, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(GLU, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(GLU, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(GLU, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(GLU, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(GLU, HParticle, 0.25, "H", promod3::loop::GLU_H_INDEX,true);
- AddBBPDir(GLU, promod3::loop::GLU_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(GLU, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(GLU, promod3::loop::GLU_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(GLU, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -434,6 +534,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[LYS].has_hydrogens = true;
sidechain_infos_[LYS].internal_e_prefactor = 2.13;
sidechain_infos_[LYS].frm_t = 1.27;
+
AddInfo(LYS, CH2Particle, 0.0, "CG", promod3::loop::LYS_CG_INDEX,false);
AddInfo(LYS, CH2Particle, 0.0, "CD", promod3::loop::LYS_CD_INDEX,false);
AddInfo(LYS, CH2Particle, 0.25, "CE", promod3::loop::LYS_CE_INDEX,false);
@@ -441,9 +542,15 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddInfo(LYS, HParticle, 0.35, "HZ1", promod3::loop::LYS_HZ1_INDEX,true);
AddInfo(LYS, HParticle, 0.35, "HZ2", promod3::loop::LYS_HZ2_INDEX,true);
AddInfo(LYS, HParticle, 0.35, "HZ3", promod3::loop::LYS_HZ3_INDEX,true);
+
+ if(cb_in_sidechain) {
+ AddInfo(LYS, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddPDir(LYS, promod3::loop::LYS_HZ1_INDEX, promod3::loop::LYS_NZ_INDEX, 4);
AddPDir(LYS, promod3::loop::LYS_HZ2_INDEX, promod3::loop::LYS_NZ_INDEX, 5);
AddPDir(LYS, promod3::loop::LYS_HZ3_INDEX, promod3::loop::LYS_NZ_INDEX, 6);
+
AddFRMRule(LYS, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(LYS, 0, -1.62);
AddFRMPrefactor(LYS, 0, 1.62);
@@ -454,6 +561,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(LYS, 0, 4);
AddFRMRotatingParticle(LYS, 0, 5);
AddFRMRotatingParticle(LYS, 0, 6);
+
AddFRMRule(LYS, promod3::loop::BB_CB_INDEX, promod3::loop::LYS_CG_INDEX);
AddFRMPrefactor(LYS, 1, -0.99);
AddFRMPrefactor(LYS, 1, 0.99);
@@ -464,6 +572,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(LYS, 1, 4);
AddFRMRotatingParticle(LYS, 1, 5);
AddFRMRotatingParticle(LYS, 1, 6);
+
AddFRMRule(LYS, promod3::loop::LYS_CG_INDEX, promod3::loop::LYS_CD_INDEX);
AddFRMPrefactor(LYS, 2, -0.96);
AddFRMPrefactor(LYS, 2, 0.96);
@@ -474,6 +583,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(LYS, 2, 4);
AddFRMRotatingParticle(LYS, 2, 5);
AddFRMRotatingParticle(LYS, 2, 6);
+
AddFRMRule(LYS, promod3::loop::LYS_CD_INDEX, promod3::loop::LYS_CE_INDEX);
AddFRMPrefactor(LYS, 3, -1.49);
AddFRMPrefactor(LYS, 3, 1.49);
@@ -484,14 +594,26 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(LYS, 3, 4);
AddFRMRotatingParticle(LYS, 3, 5);
AddFRMRotatingParticle(LYS, 3, 6);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(LYS, 0, 7);
+ AddFRMFixParticle(LYS, 1, 7);
+ AddFRMFixParticle(LYS, 2, 7);
+ AddFRMFixParticle(LYS, 3, 7);
+ }
+
sidechain_infos_[LYS].has_hydrogens = true;
AddBBInfo(LYS, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(LYS, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(LYS, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(LYS, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(LYS, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(LYS, HParticle, 0.25, "H", promod3::loop::LYS_H_INDEX,true);
- AddBBPDir(LYS, promod3::loop::LYS_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(LYS, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(LYS, promod3::loop::LYS_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(LYS, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -499,8 +621,14 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[SER].has_hydrogens = true;
sidechain_infos_[SER].internal_e_prefactor = 2.78;
sidechain_infos_[SER].frm_t = 3.53;
+
AddInfo(SER, OParticle, -0.65, "OG", promod3::loop::SER_OG_INDEX, false);
AddInfo(SER, HParticle, 0.40, "HG", promod3::loop::SER_HG_INDEX, true);
+
+ if(cb_in_sidechain) {
+ AddInfo(SER, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddPDir(SER, promod3::loop::SER_HG_INDEX, promod3::loop::SER_OG_INDEX, 1);
AddLP(SER, promod3::loop::BB_CB_INDEX, promod3::loop::SER_OG_INDEX,
promod3::loop::SER_HG_INDEX, false, false, true, 0, LONE_PAIR_COH);
@@ -508,24 +636,36 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
promod3::loop::SER_OG_INDEX,
0.96, 1.85, 1);
+
AddFRMRule(SER, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(SER, 0, -0.65);
AddFRMPrefactor(SER, 0, 0.65);
AddFRMRotatingParticle(SER, 0, 0);
AddFRMRotatingParticle(SER, 0, 1);
+
AddFRMRule(SER, promod3::loop::BB_CB_INDEX, promod3::loop::SER_OG_INDEX);
AddFRMPrefactor(SER, 1, -2.98);
AddFRMPrefactor(SER, 1, 2.98);
AddFRMFixParticle(SER, 1, 0);
AddFRMRotatingParticle(SER, 1, 1);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(SER, 0, 2);
+ AddFRMFixParticle(SER, 1, 2);
+ }
+
backbone_infos_[SER].has_hydrogens = true;
AddBBInfo(SER, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(SER, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(SER, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(SER, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(SER, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(SER, HParticle, 0.25, "H", promod3::loop::SER_H_INDEX,true);
- AddBBPDir(SER, promod3::loop::SER_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(SER, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(SER, promod3::loop::SER_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(SER, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -533,19 +673,34 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[CYS].has_hydrogens = false;
sidechain_infos_[CYS].internal_e_prefactor = 4.07;
sidechain_infos_[CYS].frm_t = 1.69;
+
AddInfo(CYS, SParticle, -0.19, "SG", promod3::loop::CYS_SG_INDEX, false);
+
+ if(cb_in_sidechain) {
+ AddInfo(CYS, CH2Particle, 0.19, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddFRMRule(CYS, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(CYS, 0, -1.69);
AddFRMPrefactor(CYS, 0, 1.69);
AddFRMRotatingParticle(CYS, 0, 0);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(CYS, 0, 1);
+ }
+
backbone_infos_[CYS].has_hydrogens = true;
AddBBInfo(CYS, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(CYS, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(CYS, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(CYS, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(CYS, CH2Particle, 0.19, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(CYS, HParticle, 0.25, "H", promod3::loop::CYS_H_INDEX,true);
- AddBBPDir(CYS, promod3::loop::CYS_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(CYS, CH2Particle, 0.19, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(CYS, promod3::loop::CYS_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(CYS, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -563,35 +718,54 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[MET].has_hydrogens = false;
sidechain_infos_[MET].internal_e_prefactor = 1.95;
sidechain_infos_[MET].frm_t = 1.77;
+
AddInfo(MET, CH2Particle, 0.06, "CG", promod3::loop::MET_CG_INDEX,false);
AddInfo(MET, SParticle, -0.12, "SD", promod3::loop::MET_SD_INDEX,false);
AddInfo(MET, CH3Particle, 0.06, "CE", promod3::loop::MET_CE_INDEX,false);
+
+ if(cb_in_sidechain) {
+ AddInfo(MET, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddFRMRule(MET, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(MET, 0, -0.97);
AddFRMPrefactor(MET, 0, 0.97);
AddFRMRotatingParticle(MET, 0, 0);
AddFRMRotatingParticle(MET, 0, 1);
AddFRMRotatingParticle(MET, 0, 2);
+
AddFRMRule(MET, promod3::loop::BB_CB_INDEX, promod3::loop::MET_CG_INDEX);
AddFRMPrefactor(MET, 1, -1.54);
AddFRMPrefactor(MET, 1, 1.54);
AddFRMFixParticle(MET, 1, 0);
AddFRMRotatingParticle(MET, 1, 1);
AddFRMRotatingParticle(MET, 1, 2);
+
AddFRMRule(MET, promod3::loop::MET_CG_INDEX, promod3::loop::MET_SD_INDEX);
AddFRMPrefactor(MET, 2, -1.21);
AddFRMPrefactor(MET, 2, 1.21);
AddFRMFixParticle(MET, 2, 0);
AddFRMFixParticle(MET, 2, 1);
AddFRMRotatingParticle(MET, 2, 2);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(MET, 0, 3);
+ AddFRMFixParticle(MET, 1, 3);
+ AddFRMFixParticle(MET, 2, 3);
+ }
+
backbone_infos_[MET].has_hydrogens = true;
AddBBInfo(MET, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(MET, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(MET, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(MET, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(MET, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(MET, HParticle, 0.25, "H", promod3::loop::MET_H_INDEX,true);
- AddBBPDir(MET, promod3::loop::MET_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(MET, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(MET, promod3::loop::MET_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(MET, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -599,6 +773,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[TRP].has_hydrogens = true;
sidechain_infos_[TRP].internal_e_prefactor = 3.24;
sidechain_infos_[TRP].frm_t = 0.99;
+
AddInfo(TRP, CParticle,-0.03, "CG", promod3::loop::TRP_CG_INDEX,false);
AddInfo(TRP, CParticle, 0.06, "CD1", promod3::loop::TRP_CD1_INDEX,false);
AddInfo(TRP, CParticle, 0.10, "CD2", promod3::loop::TRP_CD2_INDEX,false);
@@ -609,7 +784,13 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddInfo(TRP, CParticle, 0.00, "CH2", promod3::loop::TRP_CH2_INDEX,false);
AddInfo(TRP, CParticle, 0.00, "CZ2", promod3::loop::TRP_CZ2_INDEX,false);
AddInfo(TRP, HParticle, 0.30, "HE1", promod3::loop::TRP_HE1_INDEX,true);
+
+ if(cb_in_sidechain) {
+ AddInfo(TRP, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddPDir(TRP, promod3::loop::TRP_HE1_INDEX, promod3::loop::TRP_NE1_INDEX, 9);
+
AddFRMRule(TRP, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(TRP, 0, -1.28);
AddFRMPrefactor(TRP, 0, 1.28);
@@ -623,6 +804,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(TRP, 0, 7);
AddFRMRotatingParticle(TRP, 0, 8);
AddFRMRotatingParticle(TRP, 0, 9);
+
AddFRMRule(TRP, promod3::loop::BB_CB_INDEX, promod3::loop::TRP_CG_INDEX);
AddFRMPrefactor(TRP, 1, -1.48);
AddFRMPrefactor(TRP, 1, 1.48);
@@ -636,14 +818,24 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(TRP, 1, 7);
AddFRMRotatingParticle(TRP, 1, 8);
AddFRMRotatingParticle(TRP, 1, 9);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(TRP, 0, 10);
+ AddFRMFixParticle(TRP, 1, 10);
+ }
+
backbone_infos_[TRP].has_hydrogens = true;
AddBBInfo(TRP, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(TRP, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(TRP, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(TRP, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(TRP, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(TRP, HParticle, 0.25, "H", promod3::loop::TRP_H_INDEX,true);
- AddBBPDir(TRP, promod3::loop::TRP_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(TRP, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(TRP, promod3::loop::TRP_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(TRP, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -651,6 +843,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[TYR].has_hydrogens = true;
sidechain_infos_[TYR].internal_e_prefactor = 2.00;
sidechain_infos_[TYR].frm_t = 1.96;
+
AddInfo(TYR, CParticle, 0.0, "CG", promod3::loop::TYR_CG_INDEX,false);
AddInfo(TYR, CParticle, 0.0, "CD1", promod3::loop::TYR_CD1_INDEX,false);
AddInfo(TYR, CParticle, 0.0, "CD2", promod3::loop::TYR_CD2_INDEX,false);
@@ -659,6 +852,11 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddInfo(TYR, CParticle, 0.25, "CZ", promod3::loop::TYR_CZ_INDEX,false);
AddInfo(TYR, OParticle, -0.65, "OH", promod3::loop::TYR_OH_INDEX,false);
AddInfo(TYR, HParticle, 0.40, "HH", promod3::loop::TYR_HH_INDEX,true);
+
+ if(cb_in_sidechain) {
+ AddInfo(TYR, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddPDir(TYR, promod3::loop::TYR_HH_INDEX, promod3::loop::TYR_OH_INDEX, 7);
AddLP(TYR, promod3::loop::TYR_CZ_INDEX, promod3::loop::TYR_OH_INDEX,
promod3::loop::TYR_HH_INDEX, false, false, true, 6, LONE_PAIR_COH);
@@ -667,6 +865,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
promod3::loop::TYR_CZ_INDEX,
promod3::loop::TYR_OH_INDEX,
0.96, 1.885, 2);
+
AddFRMRule(TYR, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(TYR, 0, -1.48);
AddFRMPrefactor(TYR, 0, 1.48);
@@ -678,6 +877,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(TYR, 0, 5);
AddFRMRotatingParticle(TYR, 0, 6);
AddFRMRotatingParticle(TYR, 0, 7);
+
AddFRMRule(TYR, promod3::loop::BB_CB_INDEX, promod3::loop::TYR_CG_INDEX);
AddFRMPrefactor(TYR, 1, -0.73);
AddFRMPrefactor(TYR, 1, 0.73);
@@ -689,6 +889,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(TYR, 1, 5);
AddFRMRotatingParticle(TYR, 1, 6);
AddFRMRotatingParticle(TYR, 1, 7);
+
AddFRMRule(TYR, promod3::loop::TYR_CZ_INDEX, promod3::loop::TYR_OH_INDEX);
AddFRMPrefactor(TYR, 2, -0.96);
AddFRMPrefactor(TYR, 2, 0.96);
@@ -700,14 +901,25 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMFixParticle(TYR, 2, 5);
AddFRMFixParticle(TYR, 2, 6);
AddFRMRotatingParticle(TYR, 2, 7);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(TYR, 0, 8);
+ AddFRMFixParticle(TYR, 1, 8);
+ AddFRMFixParticle(TYR, 2, 8);
+ }
+
backbone_infos_[TYR].has_hydrogens = true;
AddBBInfo(TYR, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(TYR, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(TYR, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(TYR, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(TYR, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(TYR, HParticle, 0.25, "H", promod3::loop::TYR_H_INDEX,true);
- AddBBPDir(TYR, promod3::loop::TYR_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(TYR, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(TYR, promod3::loop::TYR_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(TYR, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -715,36 +927,54 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[THR].has_hydrogens = true;
sidechain_infos_[THR].internal_e_prefactor = 2.96;
sidechain_infos_[THR].frm_t = 1.11;
+
AddInfo(THR, OParticle, -0.65, "OG1", promod3::loop::THR_OG1_INDEX, false);
AddInfo(THR, CH3Particle, 0.0, "CG2", promod3::loop::THR_CG2_INDEX, false);
AddInfo(THR, HParticle, 0.40, "HG1", promod3::loop::THR_HG1_INDEX, true);
- AddPDir(THR, promod3::loop::THR_HG1_INDEX, promod3::loop::THR_OG1_INDEX, 0);
+
+ if(cb_in_sidechain) {
+ AddInfo(THR, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddPDir(THR, promod3::loop::THR_HG1_INDEX, promod3::loop::THR_OG1_INDEX, 2);
AddLP(THR, promod3::loop::BB_CB_INDEX, promod3::loop::THR_OG1_INDEX,
promod3::loop::THR_HG1_INDEX, false, false, true, 0, LONE_PAIR_COH);
AddCustomHydrogenInfo(THR, promod3::loop::THR_HG1_INDEX,
promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
promod3::loop::THR_OG1_INDEX,
0.96, 1.85, 1);
+
AddFRMRule(THR, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(THR, 0, -0.88);
AddFRMPrefactor(THR, 0, 0.88);
AddFRMRotatingParticle(THR, 0, 0);
AddFRMRotatingParticle(THR, 0, 1);
AddFRMRotatingParticle(THR, 0, 2);
+
AddFRMRule(THR, promod3::loop::BB_CB_INDEX, promod3::loop::THR_OG1_INDEX);
AddFRMPrefactor(THR, 1, -0.88);
AddFRMPrefactor(THR, 1, 0.88);
AddFRMFixParticle(THR, 1, 0);
AddFRMFixParticle(THR, 1, 1);
AddFRMRotatingParticle(THR, 1, 2);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(THR, 0, 3);
+ AddFRMFixParticle(THR, 1, 3);
+ }
+
backbone_infos_[THR].has_hydrogens = true;
AddBBInfo(THR, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(THR, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(THR, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(THR, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(THR, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(THR, HParticle, 0.25, "H", promod3::loop::THR_H_INDEX,true);
- AddBBPDir(THR, promod3::loop::THR_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(THR, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(THR, promod3::loop::THR_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(THR, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -752,21 +982,36 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[VAL].has_hydrogens = false;
sidechain_infos_[VAL].internal_e_prefactor = 1.62;
sidechain_infos_[VAL].frm_t = 2.20;
+
AddInfo(VAL, CH3Particle, 0.0, "CG1", promod3::loop::VAL_CG1_INDEX, false);
AddInfo(VAL, CH3Particle, 0.0, "CG2", promod3::loop::VAL_CG2_INDEX, false);
+
+ if(cb_in_sidechain) {
+ AddInfo(VAL, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddFRMRule(VAL, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(VAL, 0, -2.09);
AddFRMPrefactor(VAL, 0, 2.09);
AddFRMRotatingParticle(VAL, 0, 0);
AddFRMRotatingParticle(VAL, 0, 1);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(VAL, 0, 2);
+ }
+
backbone_infos_[VAL].has_hydrogens = true;
AddBBInfo(VAL, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(VAL, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(VAL, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(VAL, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(VAL, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(VAL, HParticle, 0.25, "H", promod3::loop::VAL_H_INDEX,true);
- AddBBPDir(VAL, promod3::loop::VAL_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(VAL, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(VAL, promod3::loop::VAL_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(VAL, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -774,29 +1019,46 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[ILE].has_hydrogens = false;
sidechain_infos_[ILE].internal_e_prefactor = 2.18;
sidechain_infos_[ILE].frm_t = 2.03;
+
AddInfo(ILE, CH2Particle, 0.0, "CG1", promod3::loop::ILE_CG1_INDEX, false);
AddInfo(ILE, CH3Particle, 0.0, "CG2", promod3::loop::ILE_CG2_INDEX, false);
AddInfo(ILE, CH3Particle, 0.0, "CD1", promod3::loop::ILE_CD1_INDEX, false);
+
+ if(cb_in_sidechain) {
+ AddInfo(ILE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddFRMRule(ILE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(ILE, 0, -1.23);
AddFRMPrefactor(ILE, 0, 1.23);
AddFRMRotatingParticle(ILE, 0, 0);
AddFRMRotatingParticle(ILE, 0, 1);
AddFRMRotatingParticle(ILE, 0, 2);
+
AddFRMRule(ILE, promod3::loop::BB_CB_INDEX, promod3::loop::ILE_CG1_INDEX);
AddFRMPrefactor(ILE, 1, -0.98);
AddFRMPrefactor(ILE, 1, 0.98);
AddFRMFixParticle(ILE, 1, 0);
AddFRMFixParticle(ILE, 1, 1);
AddFRMRotatingParticle(ILE, 1, 2);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(ILE, 0, 3);
+ AddFRMFixParticle(ILE, 1, 3);
+ }
+
backbone_infos_[ILE].has_hydrogens = true;
AddBBInfo(ILE, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(ILE, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(ILE, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(ILE, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(ILE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(ILE, HParticle, 0.25, "H", promod3::loop::ILE_H_INDEX,true);
- AddBBPDir(ILE, promod3::loop::ILE_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(ILE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(ILE, promod3::loop::ILE_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(ILE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -804,49 +1066,76 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[LEU].has_hydrogens = false;
sidechain_infos_[LEU].internal_e_prefactor = 2.25;
sidechain_infos_[LEU].frm_t = 2.55;
+
AddInfo(LEU, CH1Particle, 0.0, "CG", promod3::loop::LEU_CG_INDEX, false);
AddInfo(LEU, CH3Particle, 0.0, "CD1", promod3::loop::LEU_CD1_INDEX, false);
AddInfo(LEU, CH3Particle, 0.0, "CD2", promod3::loop::LEU_CD2_INDEX, false);
+
+ if(cb_in_sidechain) {
+ AddInfo(LEU, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddFRMRule(LEU, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(LEU, 0, -1.15);
AddFRMPrefactor(LEU, 0, 1.15);
AddFRMRotatingParticle(LEU, 0, 0);
AddFRMRotatingParticle(LEU, 0, 1);
AddFRMRotatingParticle(LEU, 0, 2);
+
AddFRMRule(LEU, promod3::loop::BB_CB_INDEX, promod3::loop::LEU_CG_INDEX);
AddFRMPrefactor(LEU, 1, -1.48);
AddFRMPrefactor(LEU, 1, 1.48);
- AddFRMFixParticle(LEU, 1, 0);
+ AddFRMFixParticle(LEU, 1, 0);
AddFRMRotatingParticle(LEU, 1, 1);
AddFRMRotatingParticle(LEU, 1, 2);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(LEU, 0, 3);
+ AddFRMFixParticle(LEU, 1, 3);
+ }
+
backbone_infos_[LEU].has_hydrogens = true;
AddBBInfo(LEU, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(LEU, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(LEU, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(LEU, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(LEU, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(LEU, HParticle, 0.25, "H", promod3::loop::LEU_H_INDEX,true);
- AddBBPDir(LEU, promod3::loop::LEU_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(LEU, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(LEU, promod3::loop::LEU_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(LEU, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
// PROLINES DO NOT HAVE FRM DEFINITIONS!
// large scale benchmarks showed, that varying around chi angles in case
- // of prolines has a negative effect on performance => reduce to onoe single
+ // of prolines has a negative effect on performance => reduce to one single
// subrotamer...
// PRO
sidechain_infos_[PRO].has_hydrogens = false;
sidechain_infos_[PRO].internal_e_prefactor = 0.76;
sidechain_infos_[PRO].frm_t = 2.62;
+
AddInfo(PRO, CH2Particle, 0.0, "CG", promod3::loop::PRO_CG_INDEX, false);
AddInfo(PRO, CH2Particle, 0.0, "CD", promod3::loop::PRO_CD_INDEX, false);
+
+ if(cb_in_sidechain) {
+ AddInfo(PRO, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
backbone_infos_[PRO].has_hydrogens = false;
AddBBInfo(PRO, NParticle, -0.20, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(PRO, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(PRO, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(PRO, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(PRO, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(PRO, CH2Particle, 0.25, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddBBLP(PRO, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -864,15 +1153,23 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[HSD].has_hydrogens = true;
sidechain_infos_[HSD].internal_e_prefactor = 2.01;
sidechain_infos_[HSD].frm_t = 1.35;
+
AddInfo(HSD, CParticle, 0.10, "CG", promod3::loop::HIS_CG_INDEX,false);
AddInfo(HSD, NParticle, -0.40, "ND1", promod3::loop::HIS_ND1_INDEX,false);
AddInfo(HSD, CParticle, 0.10, "CD2", promod3::loop::HIS_CD2_INDEX,false);
AddInfo(HSD, CParticle, 0.30, "CE1", promod3::loop::HIS_CE1_INDEX,false);
AddInfo(HSD, NParticle, -0.40, "NE2", promod3::loop::HIS_NE2_INDEX,false);
AddInfo(HSD, HParticle, 0.30, "HD1", promod3::loop::HIS_HD1_INDEX,true);
+
+ if(cb_in_sidechain) {
+ AddInfo(HSD, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddPDir(HSD, promod3::loop::HIS_HD1_INDEX, promod3::loop::HIS_ND1_INDEX, 5);
AddLP(HSD, promod3::loop::HIS_CD2_INDEX, promod3::loop::HIS_NE2_INDEX,
promod3::loop::HIS_CE1_INDEX, false, false, false, 4, LONE_PAIR_CNC);
+
+
AddFRMRule(HSD, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(HSD, 0, -1.84);
AddFRMPrefactor(HSD, 0, 1.84);
@@ -882,6 +1179,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(HSD, 0, 3);
AddFRMRotatingParticle(HSD, 0, 4);
AddFRMRotatingParticle(HSD, 0, 5);
+
AddFRMRule(HSD, promod3::loop::BB_CB_INDEX, promod3::loop::HIS_CG_INDEX);
AddFRMPrefactor(HSD, 1, -0.85);
AddFRMPrefactor(HSD, 1, 0.85);
@@ -891,14 +1189,24 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(HSD, 1, 3);
AddFRMRotatingParticle(HSD, 1, 4);
AddFRMRotatingParticle(HSD, 1, 5);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(HSD, 0, 6);
+ AddFRMFixParticle(HSD, 1, 6);
+ }
+
backbone_infos_[HSD].has_hydrogens = true;
AddBBInfo(HSD, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(HSD, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(HSD, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(HSD, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(HSD, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(HSD, HParticle, 0.25, "H", promod3::loop::HIS_H_INDEX,true);
- AddBBPDir(HSD, promod3::loop::HIS_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddInfo(HSD, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(HSD, promod3::loop::HIS_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(HSD, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -906,15 +1214,22 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[HSE].has_hydrogens = true;
sidechain_infos_[HSE].internal_e_prefactor = 2.01;
sidechain_infos_[HSE].frm_t = 1.35;
+
AddInfo(HSE, CParticle, 0.10, "CG", promod3::loop::HIS_CG_INDEX,false);
AddInfo(HSE, NParticle, -0.40, "ND1", promod3::loop::HIS_ND1_INDEX,false);
AddInfo(HSE, CParticle, 0.10, "CD2", promod3::loop::HIS_CD2_INDEX,false);
AddInfo(HSE, CParticle, 0.30, "CE1", promod3::loop::HIS_CE1_INDEX,false);
AddInfo(HSE, NParticle, -0.40, "NE2", promod3::loop::HIS_NE2_INDEX,false);
AddInfo(HSE, HParticle, 0.30, "HE2", promod3::loop::HIS_HE2_INDEX,true);
+
+ if(cb_in_sidechain) {
+ AddInfo(HSE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddPDir(HSE, promod3::loop::HIS_HE2_INDEX, promod3::loop::HIS_NE2_INDEX, 5);
AddLP(HSE, promod3::loop::HIS_CG_INDEX, promod3::loop::HIS_ND1_INDEX,
promod3::loop::HIS_CE1_INDEX, false, false, false, 1, LONE_PAIR_CNC);
+
AddFRMRule(HSE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(HSE, 0, -1.84);
AddFRMPrefactor(HSE, 0, 1.84);
@@ -924,6 +1239,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(HSE, 0, 3);
AddFRMRotatingParticle(HSE, 0, 4);
AddFRMRotatingParticle(HSE, 0, 5);
+
AddFRMRule(HSE, promod3::loop::BB_CB_INDEX, promod3::loop::HIS_CG_INDEX);
AddFRMPrefactor(HSE, 1, -0.85);
AddFRMPrefactor(HSE, 1, 0.85);
@@ -933,14 +1249,24 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(HSE, 1, 3);
AddFRMRotatingParticle(HSE, 1, 4);
AddFRMRotatingParticle(HSE, 1, 5);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(HSE, 0, 6);
+ AddFRMFixParticle(HSE, 1, 6);
+ }
+
backbone_infos_[HSE].has_hydrogens = true;
AddBBInfo(HSE, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(HSE, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(HSE, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(HSE, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(HSE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(HSE, HParticle, 0.25, "H", promod3::loop::HIS_H_INDEX,true);
- AddBBPDir(HSE, promod3::loop::HIS_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(HSE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(HSE, promod3::loop::HIS_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(HSE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
@@ -954,12 +1280,18 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
sidechain_infos_[PHE].has_hydrogens = false;
sidechain_infos_[PHE].internal_e_prefactor = 1.71;
sidechain_infos_[PHE].frm_t = 1.07;
+
AddInfo(PHE, CParticle, 0.0, "CG", promod3::loop::PHE_CG_INDEX, false);
AddInfo(PHE, CParticle, 0.0, "CD1", promod3::loop::PHE_CD1_INDEX, false);
AddInfo(PHE, CParticle, 0.0, "CD2", promod3::loop::PHE_CD2_INDEX, false);
AddInfo(PHE, CParticle, 0.0, "CE1", promod3::loop::PHE_CE1_INDEX, false);
AddInfo(PHE, CParticle, 0.0, "CE2", promod3::loop::PHE_CE2_INDEX, false);
AddInfo(PHE, CParticle, 0.0, "CZ", promod3::loop::PHE_CZ_INDEX, false);
+
+ if(cb_in_sidechain) {
+ AddInfo(PHE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
AddFRMRule(PHE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX);
AddFRMPrefactor(PHE, 0, -1.45);
AddFRMPrefactor(PHE, 0, 1.45);
@@ -969,6 +1301,7 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(PHE, 0, 3);
AddFRMRotatingParticle(PHE, 0, 4);
AddFRMRotatingParticle(PHE, 0, 5);
+
AddFRMRule(PHE, promod3::loop::BB_CB_INDEX, promod3::loop::PHE_CG_INDEX);
AddFRMPrefactor(PHE, 1, -1.35);
AddFRMPrefactor(PHE, 1, 1.35);
@@ -978,32 +1311,56 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
AddFRMRotatingParticle(PHE, 1, 3);
AddFRMRotatingParticle(PHE, 1, 4);
AddFRMRotatingParticle(PHE, 1, 5);
+
+ if(cb_in_sidechain) {
+ AddFRMFixParticle(PHE, 0, 6);
+ AddFRMFixParticle(PHE, 1, 6);
+ }
+
backbone_infos_[PHE].has_hydrogens = true;
AddBBInfo(PHE, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(PHE, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(PHE, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(PHE, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(PHE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(PHE, HParticle, 0.25, "H", promod3::loop::PHE_H_INDEX,true);
- AddBBPDir(PHE, promod3::loop::PHE_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(PHE, CH2Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(PHE, promod3::loop::PHE_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(PHE, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
// ALA
sidechain_infos_[ALA].has_hydrogens = false;
+ sidechain_infos_[ALA].internal_e_prefactor = 1.0;
+ sidechain_infos_[ALA].frm_t = 1.0;
+
+ if(cb_in_sidechain) {
+ AddInfo(ALA, CH3Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
backbone_infos_[ALA].has_hydrogens = true;
AddBBInfo(ALA, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(ALA, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(ALA, CParticle, 0.55, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(ALA, OParticle, -0.55, "O", promod3::loop::BB_O_INDEX, false);
- AddBBInfo(ALA, CH3Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
AddBBInfo(ALA, HParticle, 0.25, "H", promod3::loop::ALA_H_INDEX,true);
- AddBBPDir(ALA, promod3::loop::ALA_H_INDEX, promod3::loop::BB_N_INDEX, 5);
+
+ if(!cb_in_sidechain) {
+ AddBBInfo(ALA, CH3Particle, 0.0, "CB", promod3::loop::BB_CB_INDEX, false);
+ }
+
+ AddBBPDir(ALA, promod3::loop::ALA_H_INDEX, promod3::loop::BB_N_INDEX, 4);
AddBBLP(ALA, promod3::loop::BB_CA_INDEX, promod3::loop::BB_C_INDEX,
promod3::loop::BB_O_INDEX, false, false, false, 3, LONE_PAIR_CARBONYL);
// GLY
sidechain_infos_[GLY].has_hydrogens = false;
+ sidechain_infos_[GLY].internal_e_prefactor = 1.0;
+ sidechain_infos_[GLY].frm_t = 1.0;
+
backbone_infos_[GLY].has_hydrogens = true;
AddBBInfo(GLY, NParticle, -0.35, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(GLY, CH1Particle, 0.1, "CA", promod3::loop::BB_CA_INDEX, false);
@@ -1025,7 +1382,8 @@ SCWRLRotamerLookup::SCWRLRotamerLookup() {
}
}
-SCWRLRotamerConstructor::SCWRLRotamerConstructor(){
+SCWRLRotamerConstructor::SCWRLRotamerConstructor(bool cb_in_sidechain):
+ rotamer_lookup_(cb_in_sidechain) {
String s(XXX,'X');
for(uint i = 0; i < XXX; ++i){
s[i] = RotIDToOLC(RotamerID(i));
@@ -1038,7 +1396,13 @@ SCWRLRotamerConstructor::SCWRLRotamerConstructor(){
RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index, RotamerLibPtr rot_lib,
- Real probability_cutoff){
+ Real probability_cutoff) {
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct RRMRotamerGroup for unknown "
+ "rotamer id!");
+ }
+
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id);
this->SetPosBuffer(res, id);
return this->ConstructRRMRotamerGroup(id, residue_index, lib_entries,
@@ -1048,19 +1412,15 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
uint aa_res_idx, RotamerID id, uint residue_index,
- RotamerLibPtr rot_lib, Real probability_cutoff){
- std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id);
- this->SetPosBuffer(all_atom, aa_res_idx, id);
- return this->ConstructRRMRotamerGroup(id, residue_index, lib_entries,
- probability_cutoff);
-}
+ RotamerLibPtr rot_lib, Real probability_cutoff) {
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct RRMRotamerGroup for unknown "
+ "rotamer id!");
+ }
-RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- RotamerLibPtr rot_lib, Real probability_cutoff){
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id);
- this->SetPosBuffer(n_pos, ca_pos, cb_pos, id);
+ this->SetPosBuffer(all_atom, aa_res_idx, id);
return this->ConstructRRMRotamerGroup(id, residue_index, lib_entries,
probability_cutoff);
}
@@ -1068,7 +1428,13 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index, RotamerLibPtr rot_lib,
- Real probability_cutoff){
+ Real probability_cutoff) {
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FRMRotamerGroup for unknown "
+ "rotamer id!");
+ }
+
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id);
this->SetPosBuffer(res, id);
return this->ConstructFRMRotamerGroup(id, residue_index, lib_entries,
@@ -1078,19 +1444,15 @@ FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
uint aa_res_idx, RotamerID id, uint residue_index,
- RotamerLibPtr rot_lib, Real probability_cutoff){
- std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id);
- this->SetPosBuffer(all_atom, aa_res_idx, id);
- return this->ConstructFRMRotamerGroup(id, residue_index, lib_entries,
- probability_cutoff);
-}
+ RotamerLibPtr rot_lib, Real probability_cutoff) {
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FRMRotamerGroup for unknown "
+ "rotamer id!");
+ }
-FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- RotamerLibPtr rot_lib, Real probability_cutoff){
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id);
- this->SetPosBuffer(n_pos, ca_pos, cb_pos, id);
+ this->SetPosBuffer(all_atom, aa_res_idx, id);
return this->ConstructFRMRotamerGroup(id, residue_index, lib_entries,
probability_cutoff);
}
@@ -1098,7 +1460,13 @@ FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index, BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi, Real probability_cutoff){
+ Real phi, Real psi, Real probability_cutoff) {
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct RRMRotamerGroup for unknown "
+ "rotamer id!");
+ }
+
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id, phi, psi);
this->SetPosBuffer(res, id);
return this->ConstructRRMRotamerGroup(id, residue_index, lib_entries,
@@ -1109,20 +1477,15 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
uint aa_res_idx, RotamerID id, uint residue_index,
BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi, Real probability_cutoff){
- std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id, phi, psi);
- this->SetPosBuffer(all_atom, aa_res_idx, id);
- return this->ConstructRRMRotamerGroup(id, residue_index, lib_entries,
- probability_cutoff);
-}
+ Real phi, Real psi, Real probability_cutoff) {
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct RRMRotamerGroup for unknown "
+ "rotamer id!");
+ }
-RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi, Real probability_cutoff){
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id, phi, psi);
- this->SetPosBuffer(n_pos, ca_pos, cb_pos, id);
+ this->SetPosBuffer(all_atom, aa_res_idx, id);
return this->ConstructRRMRotamerGroup(id, residue_index, lib_entries,
probability_cutoff);
}
@@ -1130,7 +1493,13 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index, BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi, Real probability_cutoff){
+ Real phi, Real psi, Real probability_cutoff) {
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FRMRotamerGroup for unknown "
+ "rotamer id!");
+ }
+
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id, phi, psi);
this->SetPosBuffer(res, id);
return this->ConstructFRMRotamerGroup(id, residue_index, lib_entries,
@@ -1141,20 +1510,15 @@ FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
uint aa_res_idx, RotamerID id, uint residue_index,
BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi, Real probability_cutoff){
- std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id, phi, psi);
- this->SetPosBuffer(all_atom, aa_res_idx, id);
- return this->ConstructFRMRotamerGroup(id, residue_index, lib_entries,
- probability_cutoff);
-}
+ Real phi, Real psi, Real probability_cutoff) {
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FRMRotamerGroup for unknown "
+ "rotamer id!");
+ }
-FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- BBDepRotamerLibPtr rot_lib,
- Real phi, Real psi, Real probability_cutoff){
std::pair<RotamerLibEntry*,uint> lib_entries = rot_lib->QueryLib(id, phi, psi);
- this->SetPosBuffer(n_pos, ca_pos, cb_pos, id);
+ this->SetPosBuffer(all_atom, aa_res_idx, id);
return this->ConstructFRMRotamerGroup(id, residue_index, lib_entries,
probability_cutoff);
}
@@ -1163,11 +1527,13 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index,
std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff){
- if(lib_entries.empty()){
- throw promod3::Error("How do you want me to construct rotamers with an "
- "empty input?");
+ Real probability_cutoff) {
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct RRMRotamerGroup for unknown "
+ "rotamer id!");
}
+
std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
std::make_pair(&lib_entries[0], lib_entries.size());
this->SetPosBuffer(res, id);
@@ -1179,30 +1545,16 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
uint aa_res_idx, RotamerID id, uint residue_index,
std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff){
- if(lib_entries.empty()){
- throw promod3::Error("How do you want me to construct rotamers with an "
- "empty input?");
- }
- std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
- std::make_pair(&lib_entries[0], lib_entries.size());
- this->SetPosBuffer(all_atom, aa_res_idx, id);
- return this->ConstructRRMRotamerGroup(id, residue_index, I_LIKE_CHEESE,
- probability_cutoff);
-}
+ Real probability_cutoff) {
-RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff){
- if(lib_entries.empty()){
- throw promod3::Error("How do you want me to construct rotamers with an "
- "empty input?");
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct RRMRotamerGroup for unknown "
+ "rotamer id!");
}
+
std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
std::make_pair(&lib_entries[0], lib_entries.size());
- this->SetPosBuffer(n_pos, ca_pos, cb_pos, id);
+ this->SetPosBuffer(all_atom, aa_res_idx, id);
return this->ConstructRRMRotamerGroup(id, residue_index, I_LIKE_CHEESE,
probability_cutoff);
}
@@ -1210,11 +1562,13 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
uint residue_index, std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff){
- if(lib_entries.empty()){
- throw promod3::Error("How do you want me to construct rotamers with an "
- "empty input?");
+ Real probability_cutoff) {
+
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FRMRotamerGroup for unknown "
+ "rotamer id!");
}
+
std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
std::make_pair(&lib_entries[0], lib_entries.size());
this->SetPosBuffer(res, id);
@@ -1226,30 +1580,16 @@ FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
const promod3::loop::AllAtomPositions& all_atom,
uint aa_res_idx, RotamerID id, uint residue_index,
std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff){
- if(lib_entries.empty()){
- throw promod3::Error("How do you want me to construct rotamers with an "
- "empty input?");
- }
- std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
- std::make_pair(&lib_entries[0], lib_entries.size());
- this->SetPosBuffer(all_atom, aa_res_idx, id);
- return this->ConstructFRMRotamerGroup(id, residue_index, I_LIKE_CHEESE,
- probability_cutoff);
-}
+ Real probability_cutoff) {
-FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff){
- if(lib_entries.empty()){
- throw promod3::Error("How do you want me to construct rotamers with an "
- "empty input?");
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FRMRotamerGroup for unknown "
+ "rotamer id!");
}
+
std::pair<RotamerLibEntry*,uint> I_LIKE_CHEESE =
std::make_pair(&lib_entries[0], lib_entries.size());
- this->SetPosBuffer(n_pos, ca_pos, cb_pos, id);
+ this->SetPosBuffer(all_atom, aa_res_idx, id);
return this->ConstructFRMRotamerGroup(id, residue_index, I_LIKE_CHEESE,
probability_cutoff);
}
@@ -1257,13 +1597,17 @@ FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
FrameResiduePtr SCWRLRotamerConstructor::ConstructBackboneFrameResidue(
const ost::mol::ResidueHandle& res, RotamerID id, uint residue_index,
- Real phi, bool n_ter, bool c_ter){
+ Real phi, bool n_ter, bool c_ter) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructBackboneFrameResidue", 2);
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetBackboneInfo(id);
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FrameResidue for unknown "
+ "rotamer id!");
+ }
+
+ const SCWRLRotamerInfo& info = rotamer_lookup_.GetBackboneInfo(id);
for(uint i = 0; i < info.particles.size(); ++i){
if(!info.particles[i].is_hydrogen){
@@ -1296,13 +1640,17 @@ FrameResiduePtr SCWRLRotamerConstructor::ConstructBackboneFrameResidue(
FrameResiduePtr SCWRLRotamerConstructor::ConstructBackboneFrameResidue(
const promod3::loop::AllAtomPositions& all_atom, uint aa_res_idx,
RotamerID id, uint residue_index,
- Real phi, bool n_ter, bool c_ter){
+ Real phi, bool n_ter, bool c_ter) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructBackboneFrameResidue", 2);
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetBackboneInfo(id);
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FrameResidue for unknown "
+ "rotamer id!");
+ }
+
+ const SCWRLRotamerInfo& info = rotamer_lookup_.GetBackboneInfo(id);
for(uint i = 0; i < info.particles.size(); ++i){
if(!info.particles[i].is_hydrogen){
@@ -1334,49 +1682,18 @@ FrameResiduePtr SCWRLRotamerConstructor::ConstructBackboneFrameResidue(
return p;
}
-FrameResiduePtr SCWRLRotamerConstructor::ConstructBackboneFrameResidue(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& c_pos, const geom::Vec3& o_pos,
- const geom::Vec3& cb_pos,
- RotamerID id, uint residue_index,
- Real phi, bool n_ter, bool c_ter){
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRLRotamerConstructor::ConstructBackboneFrameResidue", 2);
-
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetBackboneInfo(id);
-
- pos_buffer_->SetPos(id, promod3::loop::BB_N_INDEX, n_pos);
- pos_buffer_->SetPos(id, promod3::loop::BB_CA_INDEX, ca_pos);
- pos_buffer_->SetPos(id, promod3::loop::BB_C_INDEX, c_pos);
- pos_buffer_->SetPos(id, promod3::loop::BB_O_INDEX, o_pos);
- if(id != GLY) pos_buffer_->SetPos(id, promod3::loop::BB_CB_INDEX, cb_pos);
-
- //set hydrogens
- if(info.has_hydrogens){
- promod3::loop::ConstructHydrogenN(*pos_buffer_, id, phi, *hydrogen_buffer_);
- }
-
- int num_particles = info.particles.size();
- if(n_ter) num_particles += 2;
- if(c_ter) num_particles += 1;
- std::vector<Particle> particles(num_particles);
- this->ConstructBBFrameParticles(info, id, n_ter, c_ter, particles);
-
- FrameResiduePtr p = boost::make_shared<FrameResidue>(particles, residue_index);
-
- return p;
-}
-
FrameResiduePtr SCWRLRotamerConstructor::ConstructSidechainFrameResidue(
- const ost::mol::ResidueHandle& res, RotamerID id, uint residue_index){
+ const ost::mol::ResidueHandle& res, RotamerID id, uint residue_index) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructSidechainFrameResidue", 2);
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetSidechainInfo(id);
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FrameResidue for unknown "
+ "rotamer id!");
+ }
+
+ const SCWRLRotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id);
for(uint i = 0; i < info.particles.size(); ++i){
if(!info.particles[i].is_hydrogen){
@@ -1408,13 +1725,17 @@ FrameResiduePtr SCWRLRotamerConstructor::ConstructSidechainFrameResidue(
FrameResiduePtr SCWRLRotamerConstructor::ConstructSidechainFrameResidue(
const promod3::loop::AllAtomPositions& all_atom, uint aa_res_idx,
- RotamerID id, uint residue_index){
+ RotamerID id, uint residue_index) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructSidechainFrameResidue", 2);
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetSidechainInfo(id);
+ if(id == XXX) {
+ throw promod3::Error("Cannot construct FrameResidue for unknown "
+ "rotamer id!");
+ }
+
+ const SCWRLRotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id);
for(uint i = 0; i < info.particles.size(); ++i){
if(!info.particles[i].is_hydrogen){
@@ -1447,7 +1768,7 @@ FrameResiduePtr SCWRLRotamerConstructor::ConstructSidechainFrameResidue(
}
FrameResiduePtr SCWRLRotamerConstructor::ConstructFrameResidue(
- const ost::mol::ResidueHandle& res, uint residue_index){
+ const ost::mol::ResidueHandle& res, uint residue_index) {
// get atoms and count non-hydrogens (= num. particles to add)
ost::mol::AtomHandleList atom_list = res.GetAtomList();
@@ -1547,7 +1868,7 @@ FrameResiduePtr SCWRLRotamerConstructor::ConstructFrameResidueHeuristic(
return boost::make_shared<FrameResidue>(particles, residue_index);
}
-void SCWRLRotamerConstructor::AssignInternalEnergies(RRMRotamerGroupPtr group) const{
+void SCWRLRotamerConstructor::AssignInternalEnergies(RRMRotamerGroupPtr group) const {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::AssignInternalEnergies", 2);
@@ -1562,7 +1883,7 @@ void SCWRLRotamerConstructor::AssignInternalEnergies(RRMRotamerGroupPtr group) c
}
}
-void SCWRLRotamerConstructor::AssignInternalEnergies(FRMRotamerGroupPtr group) const{
+void SCWRLRotamerConstructor::AssignInternalEnergies(FRMRotamerGroupPtr group) const {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::AssignInternalEnergies", 2);
@@ -1582,7 +1903,7 @@ void SCWRLRotamerConstructor::AssignInternalEnergies(FRMRotamerGroupPtr group) c
RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
RotamerID id, uint residue_index,
std::pair<RotamerLibEntry*,uint> lib_entries,
- Real probability_cutoff){
+ Real probability_cutoff) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructRRMRotamerGroup", 2);
@@ -1597,6 +1918,20 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
MVBBPosBuffer(HIS, HSE);
}
+ // in case of alanine and glycine, the rotamer libraries won't have any
+ // entries. For consistency we nevertheless construct rotamers.
+ // We simply add a fake RotamerLibEntry in this case that has
+ // no sidechain dihedrals set.
+ std::vector<RotamerLibEntry> fake_rotamers(1);
+ if(lib_entries.second == 0 && (id == ALA || id == GLY)) {
+ // we have to make sure, that the according probability really is one!
+ fake_rotamers[0].probability = 1.0;
+ lib_entries = std::make_pair(&fake_rotamers[0], 1);
+ }
+ else if(lib_entries.second == 0) {
+ throw promod3::Error("Did not find any rotamers in Rotamer Library!");
+ }
+
for(uint i = 0; i < lib_entries.second; ++i){
probability_ = lib_entries.first[i].probability;
@@ -1654,7 +1989,7 @@ RRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructRRMRotamerGroup(
FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
RotamerID id, uint residue_index,
std::pair<RotamerLibEntry*,uint> lib_entries,
- Real probability_cutoff){
+ Real probability_cutoff) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructFRMRotamerGroup", 2);
@@ -1669,6 +2004,20 @@ FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
MVBBPosBuffer(HIS, HSE);
}
+ // in case of alanine and glycine, the rotamer libraries won't have any
+ // entries. For consistency we nevertheless construct rotamers.
+ // We simply add a fake RotamerLibEntry in this case that has
+ // no sidechain dihedrals set.
+ std::vector<RotamerLibEntry> fake_rotamers(1);
+ if(lib_entries.second == 0 && (id == ALA || id == GLY)) {
+ // we have to make sure, that the according probability really is one!
+ fake_rotamers[0].probability = 1.0;
+ lib_entries = std::make_pair(&fake_rotamers[0], 1);
+ }
+ else if(lib_entries.second == 0) {
+ throw promod3::Error("Did not find any rotamers in Rotamer Library!");
+ }
+
for(uint i = 0; i < lib_entries.second; ++i){
probability_ = lib_entries.first[i].probability;
summed_prob += probability_;
@@ -1728,15 +2077,13 @@ FRMRotamerGroupPtr SCWRLRotamerConstructor::ConstructFRMRotamerGroup(
}
RRMRotamerPtr SCWRLRotamerConstructor::ConstructRRMRotamer(RotamerID id,
- uint residue_idx){
+ uint residue_idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructRRMRotamer", 2);
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetSidechainInfo(id);
- int num_particles =
- SCWRLRotamerLookup::GetInstance().GetNumSidechainParticles(id);
+ const SCWRLRotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id);
+ int num_particles = rotamer_lookup_.GetNumSidechainParticles(id);
std::vector<Particle> particles(num_particles);
//set the positions
@@ -1749,7 +2096,7 @@ RRMRotamerPtr SCWRLRotamerConstructor::ConstructRRMRotamer(RotamerID id,
promod3::loop::ConstructHydrogens(*pos_buffer_, id, *hydrogen_buffer_, true,
promod3::loop::PROT_STATE_HISH);
- // If there are any custom rules, we apply them now an overrule the
+ // If there are any custom rules, we apply them now and overrule the
// default hydrogen construction
if(!info.custom_hydrogens.empty()){
for(uint i = 0; i < info.custom_hydrogens.size(); ++i){
@@ -1776,17 +2123,14 @@ RRMRotamerPtr SCWRLRotamerConstructor::ConstructRRMRotamer(RotamerID id,
}
FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
- uint residue_idx){
+ uint residue_idx) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructFRMRotamer", 2);
- const SCWRLRotamerInfo& info =
- SCWRLRotamerLookup::GetInstance().GetSidechainInfo(id);
- int num_rrm_particles =
- SCWRLRotamerLookup::GetInstance().GetNumSidechainParticles(id);
- int num_particles =
- SCWRLRotamerLookup::GetInstance().GetNumFRMSidechainParticles(id);
+ const SCWRLRotamerInfo& info = rotamer_lookup_.GetSidechainInfo(id);
+ int num_rrm_particles = rotamer_lookup_.GetNumSidechainParticles(id);
+ int num_particles = rotamer_lookup_.GetNumFRMSidechainParticles(id);
std::vector<Particle> particles(num_particles);
//set the positions
@@ -1823,8 +2167,7 @@ FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
for(int i = 0; i < num_rrm_particles; ++i) actual_definition[i] = i;
subrotamer_definitions.push_back(actual_definition);
- const std::vector<SCWRLFRMRule>& frm_rules =
- SCWRLRotamerLookup::GetInstance().GetFRMRules(id);
+ const std::vector<SCWRLFRMRule>& frm_rules = rotamer_lookup_.GetFRMRules(id);
geom::Vec3 rotation_axis, rotation_anchor;
geom::Vec3 orig_pos, rot_pos;
geom::Mat4 rot;
@@ -1836,8 +2179,10 @@ FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
int num_rotating_particles = frm_rule.rotating_particles.size();
// Update the subrotamer definition... all particles that are fixed are taken
- // from the first subrotamer, the indices therefore start from 0
- for(int i = 0; i < num_fix_particles; ++i) actual_definition[i] = i;
+ // from the first subrotamer.
+ for(int i = 0; i < num_fix_particles; ++i) {
+ actual_definition[i] = frm_rule.fix_particles[i];
+ }
// The data required for the rotation around the specified axis
rotation_anchor = pos_buffer_->GetPos(id, frm_rule.anchor_idx_two);
@@ -1853,9 +2198,10 @@ FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
rotation_angle);
for(int i = 0; i < num_rotating_particles; ++i){
+ int orig_particle_idx = frm_rule.rotating_particles[i];
int new_particle_idx = base_idx + i;
- int orig_particle_idx = num_fix_particles + i;
+ // replace the old with the new index...
actual_definition[orig_particle_idx] = new_particle_idx;
// get the new position
@@ -1877,10 +2223,10 @@ FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
// instead of building them from scratch, they get extracted from the
// initial particles and transformed
for(int i = 0; i < num_rotating_particles; ++i){
- int orig_particle_idx = num_fix_particles + i;
+ int orig_particle_idx = frm_rule.rotating_particles[i];
+ int new_particle_idx = base_idx + i;
if(particles[orig_particle_idx].IsHBondDonor()){
- int new_particle_idx = base_idx + i;
orig_pos = particles[orig_particle_idx].GetPos() +
particles[orig_particle_idx].GetPolarDirection();
rot_pos[0] = rot(0,0) * orig_pos[0] + rot(0,1) * orig_pos[1] +
@@ -1895,7 +2241,6 @@ FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
}
if(particles[orig_particle_idx].IsHBondAcceptor()){
- int new_particle_idx = base_idx + i;
const std::vector<geom::Vec3>& lp =
particles[orig_particle_idx].GetLonePairs();
for(uint j = 0; j < lp.size(); ++j){
@@ -1923,7 +2268,7 @@ FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
info.frm_t, probability_,
info.internal_e_prefactor);
- for(uint i = 0; i < subrotamer_definitions.size(); ++i){
+ for(uint i = 0; i < subrotamer_definitions.size(); ++i) {
r->AddSubrotamerDefinition(subrotamer_definitions[i]);
}
@@ -1931,7 +2276,7 @@ FRMRotamerPtr SCWRLRotamerConstructor::ConstructFRMRotamer(RotamerID id,
}
void SCWRLRotamerConstructor::SetPosBuffer(const ost::mol::ResidueHandle& res,
- RotamerID id){
+ RotamerID id) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::SetPosBuffer_residue", 2);
@@ -1939,61 +2284,87 @@ void SCWRLRotamerConstructor::SetPosBuffer(const ost::mol::ResidueHandle& res,
ost::mol::AtomHandle n = res.FindAtom("N");
ost::mol::AtomHandle ca = res.FindAtom("CA");
ost::mol::AtomHandle cb = res.FindAtom("CB");
+ ost::mol::AtomHandle c = res.FindAtom("C");
+ ost::mol::AtomHandle o = res.FindAtom("O");
- if(!(n.IsValid() && ca.IsValid() && cb.IsValid())){
- throw promod3::Error("N, CA and CB must be valid to construct rotamer!");
+ if(!(n.IsValid() && ca.IsValid() && c.IsValid() && o.IsValid())) {
+ throw promod3::Error("All backbone atoms must be valid to construct "
+ "rotamer!");
}
pos_buffer_->SetPos(id, promod3::loop::BB_N_INDEX, n.GetPos());
pos_buffer_->SetPos(id, promod3::loop::BB_CA_INDEX, ca.GetPos());
- pos_buffer_->SetPos(id, promod3::loop::BB_CB_INDEX, cb.GetPos());
+ pos_buffer_->SetPos(id, promod3::loop::BB_C_INDEX, c.GetPos());
+ pos_buffer_->SetPos(id, promod3::loop::BB_O_INDEX, o.GetPos());
+
+ if(id != GLY) {
+ if(!cb.IsValid()) {
+ throw promod3::Error("All backbone atoms must be valid to construct "
+ "rotamer!");
+ }
+ pos_buffer_->SetPos(id, promod3::loop::BB_CB_INDEX, cb.GetPos());
+ }
}
void SCWRLRotamerConstructor::SetPosBuffer(const promod3::loop::AllAtomPositions& all_atom_pos,
- uint all_atom_idx, RotamerID id){
+ uint all_atom_idx, RotamerID id) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::SetPosBuffer_all_atom_pos", 2);
+
if(!(all_atom_pos.IsSet(all_atom_idx, promod3::loop::BB_N_INDEX) &&
all_atom_pos.IsSet(all_atom_idx, promod3::loop::BB_CA_INDEX) &&
- all_atom_pos.IsSet(all_atom_idx, promod3::loop::BB_CB_INDEX))){
- throw promod3::Error("N, CA and CB must be set to construct rotamer!");
+ all_atom_pos.IsSet(all_atom_idx, promod3::loop::BB_C_INDEX) &&
+ all_atom_pos.IsSet(all_atom_idx, promod3::loop::BB_O_INDEX))){
+ throw promod3::Error("All backbone atoms must be set to construct "
+ "rotamer!");
}
pos_buffer_->SetPos(id, promod3::loop::BB_N_INDEX,
- all_atom_pos.GetPos(all_atom_idx, promod3::loop::BB_N_INDEX));
+ all_atom_pos.GetPos(all_atom_idx,
+ promod3::loop::BB_N_INDEX));
pos_buffer_->SetPos(id, promod3::loop::BB_CA_INDEX,
- all_atom_pos.GetPos(all_atom_idx, promod3::loop::BB_CA_INDEX));
- pos_buffer_->SetPos(id, promod3::loop::BB_CB_INDEX,
- all_atom_pos.GetPos(all_atom_idx, promod3::loop::BB_CB_INDEX));
-}
-
-void SCWRLRotamerConstructor::SetPosBuffer(const geom::Vec3& n_pos,
- const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos,
- RotamerID id){
-
- core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
- "SCWRLRotamerConstructor::SetPosBuffer_vec3", 2);
+ all_atom_pos.GetPos(all_atom_idx,
+ promod3::loop::BB_CA_INDEX));
+ pos_buffer_->SetPos(id, promod3::loop::BB_C_INDEX,
+ all_atom_pos.GetPos(all_atom_idx,
+ promod3::loop::BB_C_INDEX));
+ pos_buffer_->SetPos(id, promod3::loop::BB_O_INDEX,
+ all_atom_pos.GetPos(all_atom_idx,
+ promod3::loop::BB_O_INDEX));
+
+ if(id != GLY) {
+ if(!all_atom_pos.IsSet(all_atom_idx, promod3::loop::BB_CB_INDEX)) {
+ throw promod3::Error("All backbone atoms must be valid to construct "
+ "rotamer!");
+ }
+ pos_buffer_->SetPos(id, promod3::loop::BB_CB_INDEX,
+ all_atom_pos.GetPos(all_atom_idx,
+ promod3::loop::BB_CB_INDEX));
- pos_buffer_->SetPos(id, promod3::loop::BB_N_INDEX, n_pos);
- pos_buffer_->SetPos(id, promod3::loop::BB_CA_INDEX, ca_pos);
- pos_buffer_->SetPos(id, promod3::loop::BB_CB_INDEX, cb_pos);
+ }
}
-void SCWRLRotamerConstructor::MVBBPosBuffer(RotamerID from, RotamerID to){
+void SCWRLRotamerConstructor::MVBBPosBuffer(RotamerID from, RotamerID to) {
pos_buffer_->SetPos(to, promod3::loop::BB_N_INDEX,
pos_buffer_->GetPos(from, promod3::loop::BB_N_INDEX));
pos_buffer_->SetPos(to, promod3::loop::BB_CA_INDEX,
pos_buffer_->GetPos(from, promod3::loop::BB_CA_INDEX));
+ pos_buffer_->SetPos(to, promod3::loop::BB_C_INDEX,
+ pos_buffer_->GetPos(from, promod3::loop::BB_C_INDEX));
+ pos_buffer_->SetPos(to, promod3::loop::BB_O_INDEX,
+ pos_buffer_->GetPos(from, promod3::loop::BB_O_INDEX));
+ // Even though we officially count CB as a sidechain atom, we still move it
+ // since its completely independent of any sidechain dihedral angle and
+ // cannot be constructed anyway
pos_buffer_->SetPos(to, promod3::loop::BB_CB_INDEX,
pos_buffer_->GetPos(from, promod3::loop::BB_CB_INDEX));
}
void SCWRLRotamerConstructor::ConstructBaseParticles(const SCWRLRotamerInfo& info,
RotamerID id,
- std::vector<Particle>& particles){
+ std::vector<Particle>& particles) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructBaseParticles", 2);
@@ -2037,7 +2408,7 @@ void SCWRLRotamerConstructor::ConstructBaseParticles(const SCWRLRotamerInfo& inf
void SCWRLRotamerConstructor::ConstructBBFrameParticles(
const SCWRLRotamerInfo& info, RotamerID id,
bool n_ter, bool c_ter,
- std::vector<Particle>& particles){
+ std::vector<Particle>& particles) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"SCWRLRotamerConstructor::ConstructBBFrameParticles", 2);
@@ -2062,54 +2433,38 @@ void SCWRLRotamerConstructor::ConstructBBFrameParticles(
}
if(n_ter){
- if(id == PRO || id == TPR || id == CPR){
- // there are two hydrogens
- geom::Vec3 ht1_pos, ht2_pos;
- geom::Vec3 cb_pos, ca_pos, n_pos;
- // Actually we would have to reconstruct the hydrogens using the prolines
- // CD atom... since we only have bb info, we use the CB atom.
- // rather crude, I know...
- cb_pos = pos_buffer_->GetPos(id, promod3::loop::BB_CB_INDEX);
- ca_pos = pos_buffer_->GetPos(id, promod3::loop::BB_CA_INDEX);
- n_pos = pos_buffer_->GetPos(id, promod3::loop::BB_N_INDEX);
- promod3::core::ConstructAtomPos(cb_pos, ca_pos, n_pos, 0.997, 2.042,
- 2.0944, ht1_pos);
- promod3::core::ConstructAtomPos(cb_pos,ca_pos,n_pos,0.997, 2.042,
- -2.0944, ht2_pos);
- particles[p_idx] = Particle(HParticle, ht1_pos, 0.35, "HT1");
- particles[p_idx].SetPolarDirection(ht1_pos - n_pos);
- particles[p_idx + 1] = Particle(HParticle, ht2_pos, 0.35, "HT2");
- particles[p_idx + 1].SetPolarDirection(ht2_pos - n_pos);
+ geom::Vec3 ht1_pos, ht2_pos, ht3_pos;
+ geom::Vec3 n_pos, ca_pos, c_pos;
+ n_pos = pos_buffer_->GetPos(id, promod3::loop::BB_N_INDEX);
+ ca_pos = pos_buffer_->GetPos(id, promod3::loop::BB_CA_INDEX);
+ c_pos = pos_buffer_->GetPos(id, promod3::loop::BB_C_INDEX);
+ promod3::core::ConstructAtomPos(c_pos, ca_pos, n_pos, 0.997, 2.042,
+ 1.0472, ht1_pos);
+ promod3::core::ConstructAtomPos(c_pos,ca_pos,n_pos,0.997, 2.042,
+ -1.0472, ht2_pos);
+ particles[p_idx] = Particle(HParticle, ht1_pos, 0.35, "HT1");
+ particles[p_idx].SetPolarDirection(ht1_pos - n_pos);
+ particles[p_idx + 1] = Particle(HParticle, ht2_pos, 0.35, "HT2");
+ particles[p_idx + 1].SetPolarDirection(ht2_pos - n_pos);
+
+ if(id == PRO || id == TPR || id == CPR) {
+ // there are only two hydrogens... please note, that they are not
+ // optimally placed in case of proline.
+ // we would have to consider CD for that. This costs a good bottle
+ // of wine that I implement that correctly...
+ return;
}
- else{
- // there are three hydrogens
- geom::Vec3 ht1_pos, ht2_pos, ht3_pos;
- geom::Vec3 cb_pos, ca_pos, n_pos;
- if(id == GLY) cb_pos = pos_buffer_->GetPos(id, promod3::loop::BB_C_INDEX);
- else cb_pos = pos_buffer_->GetPos(id, promod3::loop::BB_CB_INDEX);
- ca_pos = pos_buffer_->GetPos(id, promod3::loop::BB_CA_INDEX);
- n_pos = pos_buffer_->GetPos(id, promod3::loop::BB_N_INDEX);
- promod3::core::ConstructAtomPos(cb_pos, ca_pos, n_pos, 0.997, 2.042,
- M_PI, ht1_pos);
- promod3::core::ConstructAtomPos(cb_pos, ca_pos, n_pos, 0.997, 2.042,
- 1.0472, ht2_pos);
- promod3::core::ConstructAtomPos(cb_pos, ca_pos, n_pos, 0.997, 2.042,
- -1.0472, ht3_pos);
-
- // we assume, that there is currently one hydrogen and replace it with ht1
- for(uint i = 0; i < info.particles.size(); ++i){
- if(info.particles[i].is_hydrogen){
- particles[i] = Particle(HParticle, ht1_pos, 0.35, "HT1");
- particles[i].SetPolarDirection(ht1_pos - n_pos);
- break;
- }
- }
- // set ht2 and ht3
- particles[p_idx] = Particle(HParticle, ht2_pos, 0.35, "HT2");
- particles[p_idx].SetPolarDirection(ht2_pos - n_pos);
- particles[p_idx + 1] = Particle(HParticle, ht3_pos, 0.35, "HT3");
- particles[p_idx + 1].SetPolarDirection(ht3_pos - n_pos);
+ promod3::core::ConstructAtomPos(c_pos, ca_pos, n_pos, 0.997, 2.042,
+ M_PI, ht3_pos);
+ // we assume, that there is currently one hydrogen apart from ht1 and ht2
+ // and replace it with ht3
+ for(uint i = 0; i < info.particles.size(); ++i){
+ if(info.particles[i].is_hydrogen){
+ particles[i] = Particle(HParticle, ht3_pos, 0.35, "HT3");
+ particles[i].SetPolarDirection(ht3_pos - n_pos);
+ break;
+ }
}
}
}
diff --git a/sidechain/src/scwrl_rotamer_constructor.hh b/sidechain/src/scwrl_rotamer_constructor.hh
index cc0b38b392d9a5231a9d94a335bd469f15920014..8beea0819bacefa5d12de50ce1500740b23c20ed 100644
--- a/sidechain/src/scwrl_rotamer_constructor.hh
+++ b/sidechain/src/scwrl_rotamer_constructor.hh
@@ -18,6 +18,9 @@
namespace promod3 { namespace sidechain {
+class SCWRLRotamerConstructor;
+typedef boost::shared_ptr<SCWRLRotamerConstructor> SCWRLRotamerConstructorPtr;
+
/// \brief Types of lone pair construction
enum SCWRLLPRule {
LONE_PAIR_CARBONYL, LONE_PAIR_COH, LONE_PAIR_CNC
@@ -135,11 +138,9 @@ struct SCWRLRotamerInfo{
/// \brief Defines lookups to build rotamer stuff.
class SCWRLRotamerLookup {
public:
- // Singleton access to one constant instance (see AminoAcidLookup for details)
- static const SCWRLRotamerLookup& GetInstance() {
- static SCWRLRotamerLookup instance;
- return instance;
- }
+
+ SCWRLRotamerLookup(bool cb_in_sidechain);
+
// Data access
const SCWRLRotamerInfo& GetSidechainInfo(RotamerID id) const {
return sidechain_infos_[id];
@@ -227,8 +228,6 @@ private:
frm_rules_[id][rule_idx].fix_particles.push_back(p_idx);
}
- SCWRLRotamerLookup();
-
// To construct classical rotamers or as lookup for sidechain frame residues
SCWRLRotamerInfo sidechain_infos_[XXX + 1];
@@ -248,7 +247,7 @@ class SCWRLRotamerConstructor{
public:
- SCWRLRotamerConstructor();
+ SCWRLRotamerConstructor(bool cb_in_sidechain = false);
// Construct rotamer groups from non backbone dependent library
RRMRotamerGroupPtr ConstructRRMRotamerGroup(
@@ -261,12 +260,6 @@ public:
uint aa_res_idx, RotamerID id, uint residue_index,
RotamerLibPtr rot_lib,
Real probability_cutoff = 0.98);
-
- RRMRotamerGroupPtr ConstructRRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- RotamerLibPtr rot_lib,
- Real probability_cutoff = 0.98);
FRMRotamerGroupPtr ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
@@ -279,12 +272,6 @@ public:
RotamerLibPtr rot_lib,
Real probability_cutoff = 0.98);
- FRMRotamerGroupPtr ConstructFRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- RotamerLibPtr rot_lib,
- Real probability_cutoff = 0.98);
-
// Construct rotamer groups from backbone dependent library
RRMRotamerGroupPtr ConstructRRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
@@ -300,14 +287,6 @@ public:
Real phi = -1.0472,
Real psi = -0.7854,
Real probability_cutoff = 0.98);
-
- RRMRotamerGroupPtr ConstructRRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- BBDepRotamerLibPtr rot_lib,
- Real phi = -1.0472,
- Real psi = -0.7854,
- Real probability_cutoff = 0.98);
FRMRotamerGroupPtr ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
@@ -324,14 +303,6 @@ public:
Real psi = -0.7854,
Real probability_cutoff = 0.98);
- FRMRotamerGroupPtr ConstructFRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- BBDepRotamerLibPtr rot_lib,
- Real phi = -1.0472,
- Real psi = -0.7854,
- Real probability_cutoff = 0.98);
-
// Construct rotamer groups directly from rotamerlib entries
RRMRotamerGroupPtr ConstructRRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
@@ -344,12 +315,6 @@ public:
uint aa_res_idx, RotamerID id, uint residue_index,
std::vector<RotamerLibEntry>& lib_entries,
Real probability_cutoff = 0.98);
-
- RRMRotamerGroupPtr ConstructRRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff = 0.98);
FRMRotamerGroupPtr ConstructFRMRotamerGroup(
const ost::mol::ResidueHandle& res, RotamerID id,
@@ -363,26 +328,12 @@ public:
std::vector<RotamerLibEntry>& lib_entries,
Real probability_cutoff = 0.98);
- FRMRotamerGroupPtr ConstructFRMRotamerGroup(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id, uint residue_index,
- std::vector<RotamerLibEntry>& lib_entries,
- Real probability_cutoff = 0.98);
-
// Construct frame residues
FrameResiduePtr ConstructBackboneFrameResidue(
const ost::mol::ResidueHandle& res, RotamerID id, uint residue_index,
Real phi, bool n_ter = false,
bool c_ter = false);
- FrameResiduePtr ConstructBackboneFrameResidue(
- const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& c_pos, const geom::Vec3& o_pos,
- const geom::Vec3& cb_pos,
- RotamerID id, uint residue_index,
- Real phi, bool n_ter = false,
- bool c_ter = false);
-
FrameResiduePtr ConstructBackboneFrameResidue(
const promod3::loop::AllAtomPositions& all_atom, uint aa_res_idx,
RotamerID id, uint residue_index,
@@ -434,9 +385,6 @@ private:
void SetPosBuffer(const promod3::loop::AllAtomPositions&,
uint aa_res_index, RotamerID id);
- void SetPosBuffer(const geom::Vec3& n_pos, const geom::Vec3& ca_pos,
- const geom::Vec3& cb_pos, RotamerID id);
-
void MVBBPosBuffer(RotamerID from, RotamerID to);
void ConstructBaseParticles(const SCWRLRotamerInfo& info, RotamerID id,
@@ -449,6 +397,7 @@ private:
Real chi_angles_[4];
Real chi_dev_[4];
Real probability_;
+ SCWRLRotamerLookup rotamer_lookup_;
promod3::loop::AllAtomPositionsPtr pos_buffer_;
promod3::loop::HydrogenStoragePtr hydrogen_buffer_;
};
diff --git a/sidechain/src/subrotamer_optimizer.cc b/sidechain/src/subrotamer_optimizer.cc
index 64067573a88c06f741216c3faf6ef8f7254bd788..3594a5bcbe07e39b76c0e1098ac7eb440c031e15 100644
--- a/sidechain/src/subrotamer_optimizer.cc
+++ b/sidechain/src/subrotamer_optimizer.cc
@@ -38,7 +38,7 @@ void SubrotamerOptimizer(std::vector<FRMRotamerPtr>& rotamers,
}
// generate a graph from the RRMRotamerGroups to find the optimal subrotamers
- RotamerGraphPtr graph = RotamerGraph::CreateFromRRMList(rrm_rotamer_groups);
+ RotamerGraphPtr graph = RotamerGraph::CreateFromList(rrm_rotamer_groups);
std::pair<std::vector<int>, Real> full_solution =
graph->TreeSolve(max_complexity, initial_epsilon);
diff --git a/sidechain/tests/test_frame_construction.cc b/sidechain/tests/test_frame_construction.cc
index edae739c5d13546fd4d3f3f550de1726e6fafc46..5c6801168270bd96ee3ae08bde1c0486fa8ce8b0 100644
--- a/sidechain/tests/test_frame_construction.cc
+++ b/sidechain/tests/test_frame_construction.cc
@@ -59,13 +59,7 @@ void CheckBackboneFrameConstruction(ost::mol::ResidueHandleList& res_list,
// frame residues
fr1 = rc.ConstructBackboneFrameResidue(res_list[i], r_id, i,
phi, n_ter, c_ter);
- const geom::Vec3 n_pos = all_atoms.GetPos(i, loop::BB_N_INDEX);
- const geom::Vec3 ca_pos = all_atoms.GetPos(i, loop::BB_CA_INDEX);
- const geom::Vec3 c_pos = all_atoms.GetPos(i, loop::BB_C_INDEX);
- const geom::Vec3 o_pos = all_atoms.GetPos(i, loop::BB_O_INDEX);
- if (r_id != GLY) cb_pos = all_atoms.GetPos(i, loop::BB_CB_INDEX);
- fr2 = rc.ConstructBackboneFrameResidue(n_pos, ca_pos, c_pos, o_pos, cb_pos,
- r_id, i, phi, n_ter, c_ter);
+ fr2 = rc.ConstructBackboneFrameResidue(all_atoms, i, r_id, i, phi, n_ter, c_ter);
CompareFrameResidues(*fr1, *fr2);
}
}
diff --git a/sidechain/tests/test_rotamers.cc b/sidechain/tests/test_rotamers.cc
index 702bfd1d5c246bc7dca25132ea18b29b5ff8a90c..0b49ec0bd4a76442941fdc4555df4ec18aa99c8d 100644
--- a/sidechain/tests/test_rotamers.cc
+++ b/sidechain/tests/test_rotamers.cc
@@ -96,7 +96,6 @@ void CheckRotamerGroupConstruction(ost::mol::ResidueHandleList& res_list,
RotamerLibPtr rot_lib) {
// check all frames
BOOST_CHECK_EQUAL(res_list.size(), all_atoms.GetNumResidues());
- geom::Vec3 cb_pos;
RRMRotamerGroupPtr rrm1, rrm2;
FRMRotamerGroupPtr frm1, frm2;
SCWRLRotamerConstructor rot_constructor;
@@ -108,81 +107,33 @@ void CheckRotamerGroupConstruction(ost::mol::ResidueHandleList& res_list,
// angles
const Real phi = (n_ter) ? -1.0472 : all_atoms.GetPhiTorsion(i);
const Real psi = (c_ter) ? -0.7854 : all_atoms.GetPsiTorsion(i);
- // pos
- const geom::Vec3 n_pos = all_atoms.GetPos(i, loop::BB_N_INDEX);
- const geom::Vec3 ca_pos = all_atoms.GetPos(i, loop::BB_CA_INDEX);
- if (r_id != GLY) cb_pos = all_atoms.GetPos(i, loop::BB_CB_INDEX);
// do it
- if (r_id == ALA || r_id == GLY) {
- // should all throw exceptions
- BOOST_CHECK_THROW(
- rot_constructor.ConstructRRMRotamerGroup(res_list[i], r_id, i,
- bbd_rot_lib,
- phi, psi),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, bbd_rot_lib,
- phi, psi),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructRRMRotamerGroup(res_list[i], r_id, i,
- rot_lib),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, rot_lib),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructFRMRotamerGroup(res_list[i], r_id, i,
- bbd_rot_lib,
- phi, psi),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i,
- bbd_rot_lib,
- phi, psi),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructFRMRotamerGroup(res_list[i], r_id, i,
- rot_lib),
- promod3::Error);
- BOOST_CHECK_THROW(
- rot_constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, rot_lib),
- promod3::Error);
- } else {
- // RRM ROTAMER (bbdep)
- rrm1 = rot_constructor.ConstructRRMRotamerGroup(res_list[i], r_id, i,
- bbd_rot_lib,
- phi, psi);
-
- rrm2 = rot_constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, bbd_rot_lib,
- phi, psi);
- CompareRotamerGroups(*rrm1, *rrm2);
- // RRM ROTAMER (non-bbdep)
- rrm1 = rot_constructor.ConstructRRMRotamerGroup(res_list[i], r_id, i,
- rot_lib);
- rrm2 = rot_constructor.ConstructRRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, rot_lib);
- CompareRotamerGroups(*rrm1, *rrm2);
- // FRM ROTAMER (bbdep)
- frm1 = rot_constructor.ConstructFRMRotamerGroup(res_list[i], r_id, i,
- bbd_rot_lib,
- phi, psi);
- frm2 = rot_constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, bbd_rot_lib,
- phi, psi);
- CompareRotamerGroups(*frm1, *frm2);
- // RRM ROTAMER (non-bbdep)
- frm1 = rot_constructor.ConstructFRMRotamerGroup(res_list[i], r_id, i,
- rot_lib);
- frm2 = rot_constructor.ConstructFRMRotamerGroup(n_pos, ca_pos, cb_pos,
- r_id, i, rot_lib);
- CompareRotamerGroups(*frm1, *frm2);
- }
+ // RRM ROTAMER (bbdep)
+ rrm1 = rot_constructor.ConstructRRMRotamerGroup(res_list[i], r_id, i,
+ bbd_rot_lib,
+ phi, psi);
+
+ rrm2 = rot_constructor.ConstructRRMRotamerGroup(all_atoms, i, r_id, i,
+ bbd_rot_lib, phi, psi);
+ CompareRotamerGroups(*rrm1, *rrm2);
+ // RRM ROTAMER (non-bbdep)
+ rrm1 = rot_constructor.ConstructRRMRotamerGroup(res_list[i], r_id, i,
+ rot_lib);
+ rrm2 = rot_constructor.ConstructRRMRotamerGroup(all_atoms, i, r_id, i,
+ rot_lib);
+ CompareRotamerGroups(*rrm1, *rrm2);
+ // FRM ROTAMER (bbdep)
+ frm1 = rot_constructor.ConstructFRMRotamerGroup(res_list[i], r_id, i,
+ bbd_rot_lib, phi, psi);
+ frm2 = rot_constructor.ConstructFRMRotamerGroup(all_atoms, i, r_id, i,
+ bbd_rot_lib, phi, psi);
+ CompareRotamerGroups(*frm1, *frm2);
+ // RRM ROTAMER (non-bbdep)
+ frm1 = rot_constructor.ConstructFRMRotamerGroup(res_list[i], r_id, i,
+ rot_lib);
+ frm2 = rot_constructor.ConstructFRMRotamerGroup(all_atoms, i, r_id, i,
+ rot_lib);
+ CompareRotamerGroups(*frm1, *frm2);
}
}