diff --git a/CHANGELOG b/CHANGELOG
index 67c6449a8c77ba6a9eae9b7aa2af68ec4d2c97c6..0e9ceb554298f192f7dea1e1b082a380fff4a766 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -5,6 +5,19 @@
Changelog
================================================================================
+Release 2.1.0
+--------------------------------------------------------------------------------
+
+* This is expected to be the last release supporting Python 2.
+* This project now requires a C++11 compatible compiler.
+* Introduced VINA scoring function in the sidechain module. A scoring function
+ specific RotamerConstructor is provided that comes with extensive heuristics
+ to parametrize arbitrary compounds.
+* Motif finding algorithm to identify objects in 3D space, e.g. binding sites.
+ The algorithm is based on principles of geometric hashing.
+* Several minor bug fixes, improvements, and speed-ups
+
+
Release 2.0.0
--------------------------------------------------------------------------------
diff --git a/CMakeLists.txt b/CMakeLists.txt
index b6e88667a2849484a2905d9272388f8e7ff77555..aa019d52d0b506257b02462a669b53b84274f2ae 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -16,7 +16,7 @@ include(PROMOD3)
# versioning info
set(PROMOD3_VERSION_MAJOR 2)
-set(PROMOD3_VERSION_MINOR 0)
+set(PROMOD3_VERSION_MINOR 1)
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})
@@ -93,7 +93,7 @@ if(NOT DISABLE_DOCUMENTATION)
# this URL should always point to the latest version of OST
set(OST_DOC_URL "https://www.openstructure.org/docs")
endif()
-find_package(OPENSTRUCTURE 1.10.0 REQUIRED
+find_package(OPENSTRUCTURE 1.11.0 REQUIRED
COMPONENTS io mol seq seq_alg mol_alg conop img mol_mm)
if(CMAKE_COMPILER_IS_GNUCXX)
diff --git a/cmake_support/PROMOD3.cmake b/cmake_support/PROMOD3.cmake
index bebe5e9f46ac0bef97083bb9ed390419e439e780..7da10d674d174a7a899a0d17f6fcdd227535cc06 100644
--- a/cmake_support/PROMOD3.cmake
+++ b/cmake_support/PROMOD3.cmake
@@ -1000,6 +1000,11 @@ macro(setup_compiler_flags)
# -fno-strict-aliasing
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-strict-aliasing" )
endif()
+ #message(STATUS "GCC VERSION " ${_GCC_VERSION})
+ if (_GCC_VERSION LESS "60")
+ # for older compilers we need to enable C++11
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+ endif()
endif()
if(_ENABLE_SSE)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse4" )
diff --git a/container/Dockerfile b/container/Dockerfile
index d10d4d86de9e23d28dd3e9c30da17885db75cce5..95bba9ad920a7c645ae1f1000d3e6d0b38c9f7b5 100644
--- a/container/Dockerfile
+++ b/container/Dockerfile
@@ -2,8 +2,8 @@ FROM ubuntu:18.04
# ARGUMENTS
###########
-ARG OPENSTRUCTURE_VERSION="1.10.0"
-ARG PROMOD_VERSION="2.0.0"
+ARG OPENSTRUCTURE_VERSION="1.11.0"
+ARG PROMOD_VERSION="2.1.0"
ARG SRC_FOLDER="/usr/local/src"
ARG CPUS_FOR_MAKE=4
ARG COMPLIB_DIR="/usr/local/share/ost_complib"
diff --git a/core/src/eigen_types.hh b/core/src/eigen_types.hh
index 773998c0c393179e37f0c9c89ce1804905217f53..89c90f06a002ddccf925389b887ecca0804b9879 100644
--- a/core/src/eigen_types.hh
+++ b/core/src/eigen_types.hh
@@ -18,35 +18,56 @@
#define PROMOD3_EIGEN_TYPES_HH
#include <ost/base.hh>
+#include <ost/geom/vecmat3_op.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;
+// 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,3,1> EVec3;
+typedef Eigen::Matrix<Real,4,1> EVec4;
+typedef Eigen::Matrix<Real,Eigen::Dynamic,1> EVecX;
- typedef Eigen::Matrix<Real,1,3> ERVec3;
- typedef Eigen::Matrix<Real,1,4> ERVec4;
+typedef Eigen::Matrix<Real,1,3> ERVec3;
+typedef Eigen::Matrix<Real,1,4> ERVec4;
+typedef Eigen::Matrix<Real,1,Eigen::Dynamic> ERVecX;
+// some special matrices used at various locations
+typedef Eigen::Matrix<Real,Eigen::Dynamic,3> EMatX3;
+typedef Eigen::Matrix<Real,3,Eigen::Dynamic> EMat3X;
+typedef Eigen::Matrix<Real, Eigen::Dynamic, Eigen::Dynamic> EMatXX;
+typedef Eigen::Matrix<double,16,3> EMat16_3;
- // 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;
+typedef std::vector<EMatX3,Eigen::aligned_allocator<EMat3X> > EMat3XList;
- // 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;
+// Fill row of given Eigen Matrix with 3 entries of Vec3
+// NOTE: this is 60% faster than "tst.row(row) = core::ERVec3(&v[0]);"
+template <typename EMat>
+inline void EMatFillRow(EMat& mat, uint row, const geom::Vec3& v) {
+ mat(row, 0) = v[0];
+ mat(row, 1) = v[1];
+ mat(row, 2) = v[2];
+}
+
+// Same for col
+template <typename EMat>
+inline void EMatFillCol(EMat& mat, uint col, const geom::Vec3& v) {
+ mat(0, col) = v[0];
+ mat(1, col) = v[1];
+ mat(2, col) = v[2];
+}
}} // ns
diff --git a/core/src/superpose.cc b/core/src/superpose.cc
index 0e06a6e6994588fd83c925f26cabe64b05d5dc4f..9729d23fe60e98a07bab309381c84ac0dc3b9051 100644
--- a/core/src/superpose.cc
+++ b/core/src/superpose.cc
@@ -48,11 +48,12 @@ void TheobaldRMSD(const promod3::core::EMatX3& pos_one,
"superpose!");
}
- promod3::core::EMat3 M = pos_one.transpose() * pos_two;
+ // using floats when calculating M might lead to numerical instabilities
+ // later on, so let's cast to double precision
+ Eigen::Matrix<double,3,3> M =
+ pos_one.cast<double>().transpose() * pos_two.cast<double>();
- // for the calculations itself we enforce double precision
- // for example the newton optimization doesn't converge nicely if
- // Real is a float
+ // using floats for the squared norm is fine
double GA = pos_one.squaredNorm();
double GB = pos_two.squaredNorm();
diff --git a/core/src/superpose.hh b/core/src/superpose.hh
index 2fd82314a9fbeb3ab2510ba478963793f4490dfd..46f769d5e74a31f0ca668c6ea3f0bd016092ebcc 100644
--- a/core/src/superpose.hh
+++ b/core/src/superpose.hh
@@ -84,16 +84,6 @@ void RigidBlocks(EMatX3& pos_one, EMatX3& pos_two,
std::vector<std::vector<uint> >& indices,
std::vector<geom::Mat4>& transformations);
-
-// Fill row of given Eigen Matrix with 3 entries of Vec3
-// NOTE: this is 60% faster than "tst.row(row) = core::ERVec3(&v[0]);"
-template <typename EMat>
-inline void EMatFillRow(EMat& mat, uint row, const geom::Vec3& v) {
- mat(row, 0) = v[0];
- mat(row, 1) = v[1];
- mat(row, 2) = v[2];
-}
-
}} //ns
#endif
diff --git a/core/src/tetrahedral_polytope.cc b/core/src/tetrahedral_polytope.cc
index 40bf460479765da8c31d5451a3b14f28fea49154..9c09f4ed02ff0089abdb0ea69948edc05116126b 100644
--- a/core/src/tetrahedral_polytope.cc
+++ b/core/src/tetrahedral_polytope.cc
@@ -45,6 +45,9 @@ void Fill(const std::vector<int>& indices,
std::vector<int>& l,
std::vector<int>& r){
+ l.reserve(indices.size());
+ r.reserve(indices.size());
+
for(std::vector<int>::const_iterator i = indices.begin(),
e = indices.end(); i != e; ++i){
if(values[*i] < boundary) l.push_back(*i);
@@ -135,8 +138,22 @@ void TetrahedralPolytopeTree::ResetTree(const std::vector<Real>& x,
}
num_leaf_nodes_ = x.size();
- nodes_.resize(num_leaf_nodes_);
- connectivity_.resize(num_leaf_nodes_);
+
+ if(num_leaf_nodes_ == 0) {
+ // empty tree... assign some default values, even though it doesn't matter
+ // too much as any call for the Overlapp functions is guarded by a check for
+ // num_leaf_nodes_ == 0
+ root_node_ = 0;
+ nodes_.resize(0);
+ connectivity_.resize(0);
+ return;
+ }
+
+ // we construct a full binary tree (each node has either 0 or 2 children)
+ // the number of nodes can therefore be determined from the number of leafs
+ int num_nodes = 2*num_leaf_nodes_-1;
+ nodes_.resize(num_nodes);
+ connectivity_.resize(num_nodes);
std::vector<int> indices(num_leaf_nodes_);
for(int i = 0; i < num_leaf_nodes_; ++i){
@@ -145,10 +162,7 @@ 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
- }
-
+ idx_helper_ = num_leaf_nodes_;
root_node_ = this->Generate(x, y, z, indices);
}
@@ -158,16 +172,32 @@ int TetrahedralPolytopeTree::Generate(const std::vector<Real>& x,
const std::vector<Real>& z,
const std::vector<int>& indices){
+ // it it's a leaf, it's already contructed in the ResetTree
if(indices.size() == 1){
- // the leaf nodes are already added in the ResetTree function
return indices[0];
}
- int return_idx = nodes_.size();
+ // determine index of that node from idx_helper and construct its Polytope
+ int return_idx = idx_helper_++;
+ this->AssignPolytope(x, y, x, indices, return_idx);
+
+ // separate the members and construct the children
+ std::vector<int> l,r;
+ Separate(x, y, z, indices, l, r);
+ connectivity_[return_idx].first = this->Generate(x, y, z, l);
+ connectivity_[return_idx].second = this->Generate(x, y, z, r);
+
+ return return_idx;
+}
+
+void TetrahedralPolytopeTree::AssignPolytope(const std::vector<Real>& x,
+ const std::vector<Real>& y,
+ const std::vector<Real>& z,
+ const std::vector<int>& indices,
+ int node_idx) {
// find extent of tetrahedral polytope containing all polytopes
// defined in indices
-
#if PM3_ENABLE_SSE && OST_DOUBLE_PRECISION == 0
__m128 min_bounds = _mm_set1_ps(std::numeric_limits<Real>::max());
__m128 max_bounds = _mm_set1_ps(-std::numeric_limits<Real>::max());
@@ -209,20 +239,7 @@ int TetrahedralPolytopeTree::Generate(const std::vector<Real>& x,
}
#endif
- nodes_.push_back(TetrahedralPolytope(min_bounds, max_bounds));
-
- connectivity_.push_back(std::make_pair(-1, -1));
-
- std::vector<int> l,r;
- l.reserve(indices.size());
- r.reserve(indices.size());
-
- Separate(x, y, z, indices, l, r);
-
- connectivity_[return_idx].first = this->Generate(x, y, z, l);
- connectivity_[return_idx].second = this->Generate(x, y, z, r);
-
- return return_idx;
+ nodes_[node_idx] = TetrahedralPolytope(min_bounds, max_bounds);
}
}} // ns
diff --git a/core/src/tetrahedral_polytope.hh b/core/src/tetrahedral_polytope.hh
index 31c88a77d99719ddd68e1da69d51dc0201ed9275..744f05ec39eb6383e48c932ce486b00d1a4e5471 100644
--- a/core/src/tetrahedral_polytope.hh
+++ b/core/src/tetrahedral_polytope.hh
@@ -148,6 +148,12 @@ private:
const std::vector<Real>& z,
const std::vector<int>& indices);
+ void AssignPolytope(const std::vector<Real>& x,
+ const std::vector<Real>& y,
+ const std::vector<Real>& z,
+ const std::vector<int>& indices,
+ int node_idx);
+
inline void TraverseTree(const TetrahedralPolytopeTree& other_tree,
int this_idx, int other_idx,
std::vector<std::pair<int,int> >& result) const{
@@ -180,6 +186,9 @@ private:
int num_leaf_nodes_;
std::vector<TetrahedralPolytope> nodes_;
std::vector<std::pair<int, int> > connectivity_;
+
+ // helper variable to keep track of recursive Generate calls
+ int idx_helper_;
};
}} // ns
diff --git a/core/tests/test_check_io.cc b/core/tests/test_check_io.cc
index 87a951d780c0ed7850e659f39ff0f9729bdc93c7..692e29f2e525bc8527764c402a501625f07c2b0e 100644
--- a/core/tests/test_check_io.cc
+++ b/core/tests/test_check_io.cc
@@ -18,7 +18,6 @@
#include <promod3/core/portable_binary_serializer.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
#include <ost/base.hh>
#include <cstdio>
diff --git a/core/tests/test_graph_minimizer.cc b/core/tests/test_graph_minimizer.cc
index c5737eb86718c4856f35e8c3d72e870c3952c8fd..29e60b74cf456909c43af37d663a92dfa1f2850b 100644
--- a/core/tests/test_graph_minimizer.cc
+++ b/core/tests/test_graph_minimizer.cc
@@ -18,7 +18,6 @@
#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>
diff --git a/core/tests/test_portable_binary.cc b/core/tests/test_portable_binary.cc
index 0cadce21d330ade13fe2a620915712672030a395..8fc5f49715d9b53fed9ea87be02d495276325311 100644
--- a/core/tests/test_portable_binary.cc
+++ b/core/tests/test_portable_binary.cc
@@ -17,7 +17,6 @@
#include <promod3/core/portable_binary_serializer.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
#include <ost/base.hh>
#include <cstdio>
diff --git a/core/tests/tests.cc b/core/tests/tests.cc
index 723aa61416a8bb5d5eb9935903958c1ffba5f12f..cb1a39d42c8745d604c876adcf025ac7036dd9ea 100644
--- a/core/tests/tests.cc
+++ b/core/tests/tests.cc
@@ -16,6 +16,4 @@
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_core
-#define BOOST_AUTO_TEST_MAIN
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
diff --git a/doc/buildsystem.rst b/doc/buildsystem.rst
index ac23b70c3bd51d49509b710ab096fce7266829df..2ec26dc0ee6fef295ef194dba1d795681478d920 100644
--- a/doc/buildsystem.rst
+++ b/doc/buildsystem.rst
@@ -24,21 +24,21 @@ Dependencies
--------------------------------------------------------------------------------
|project| is build on top of |ost_l|_ (|ost_s|), requiring at least version
-|ost_version|. |ost_s| must be configured and compiled with ``ENABLE_MM=1`` to
-use |openmm|_. To create the build system, |cmake|_ is required. The same
-versions of |python|_ and |boost|_ are needed as used in |ost_s|. For |eigen3|_
-we need at least version 3.3.0. To build the documentation, |sphinx|_ is
-required.
+|ost_version|. A C++11 compatible compiler is required. |ost_s| must be
+configured and compiled with ``ENABLE_MM=1`` to use |openmm|_. To create the
+build system, |cmake|_ is required. The same versions of |python|_ and |boost|_
+are needed as used in |ost_s|. For |eigen3|_ we need at least version 3.3.0. To
+build the documentation, |sphinx|_ is required.
The currently preferred versions are:
* |ost_s|_ |ost_version|
* |openmm|_ 7.1.1
* |cmake|_ 2.8.12
-* |python|_ 2.7.5
+* |python|_ 2.7.11
* |boost|_ 1.53.0
-* |eigen3|_ 3.3.0
-* |sphinx|_ 1.3.1
+* |eigen3|_ 3.3.1
+* |sphinx|_ 1.4.1
--------------------------------------------------------------------------------
Using |cmake|
diff --git a/doc/conf.py.in b/doc/conf.py.in
index 49f9385d8c0584731e1fb6d4a24db3235d3fb3ca..116d11e729b688038b06a349769f8509fb1af301 100644
--- a/doc/conf.py.in
+++ b/doc/conf.py.in
@@ -58,7 +58,7 @@ master_doc = 'index'
# General information about the project.
project = u'ProMod3'
-copyright = u'2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel'# pylint: disable=redefined-builtin
+copyright = u'2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel'# 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
@@ -286,7 +286,7 @@ rst_epilog = """
.. |cmake| replace:: CMake
.. |ost_l| replace:: OpenStructure
.. |ost_s| replace:: OST
-.. |ost_version| replace:: 1.10.0
+.. |ost_version| replace:: 1.11.0
.. |python| replace:: Python
.. |sphinx| replace:: Sphinx
.. _sphinx: http://sphinx-doc.org/
diff --git a/doc/container/singularity.rst b/doc/container/singularity.rst
index 5079e263ad6f6879aad7d1ee47c6fd65b3981aa2..16af7e051382508f764bddb533647d423db67fd7 100644
--- a/doc/container/singularity.rst
+++ b/doc/container/singularity.rst
@@ -36,6 +36,8 @@ Fire the local Registry and push the promod image to it:
sudo docker tag promod localhost:5000/promod
sudo docker push localhost:5000/promod
+If port 5000 is already taken on your machine, use a different ``<PORT>`` by
+using the flag ``-p <PORT>:5000`` and ``localhost:<PORT>`` in these commands.
Make sure, that on top of your Singularity recipe you have something like:
.. code-block:: bash
@@ -71,7 +73,24 @@ To get help on how to run it:
.. code-block:: bash
- singularity run --app Notebook <IMAGE> --help
+ singularity help --app Notebook <IMAGE>
+
+Within the notebook you can test OST, ProMod3 and nglview as follows:
+
+.. code-block:: python
+
+ from ost import io
+ from promod3 import loop
+ import nglview
+
+ # generate backbone with dihedrals of a helix and store it
+ sequence = "HELLYEAH"
+ bb_list = loop.BackboneList(sequence)
+ io.SavePDB(bb_list.ToEntity(), "test.pdb")
+
+ # display stored file
+ view = nglview.show_file("test.pdb")
+ view
The Compound Library
diff --git a/doc/html/_sources/buildsystem.txt b/doc/html/_sources/buildsystem.txt
index ac23b70c3bd51d49509b710ab096fce7266829df..2ec26dc0ee6fef295ef194dba1d795681478d920 100644
--- a/doc/html/_sources/buildsystem.txt
+++ b/doc/html/_sources/buildsystem.txt
@@ -24,21 +24,21 @@ Dependencies
--------------------------------------------------------------------------------
|project| is build on top of |ost_l|_ (|ost_s|), requiring at least version
-|ost_version|. |ost_s| must be configured and compiled with ``ENABLE_MM=1`` to
-use |openmm|_. To create the build system, |cmake|_ is required. The same
-versions of |python|_ and |boost|_ are needed as used in |ost_s|. For |eigen3|_
-we need at least version 3.3.0. To build the documentation, |sphinx|_ is
-required.
+|ost_version|. A C++11 compatible compiler is required. |ost_s| must be
+configured and compiled with ``ENABLE_MM=1`` to use |openmm|_. To create the
+build system, |cmake|_ is required. The same versions of |python|_ and |boost|_
+are needed as used in |ost_s|. For |eigen3|_ we need at least version 3.3.0. To
+build the documentation, |sphinx|_ is required.
The currently preferred versions are:
* |ost_s|_ |ost_version|
* |openmm|_ 7.1.1
* |cmake|_ 2.8.12
-* |python|_ 2.7.5
+* |python|_ 2.7.11
* |boost|_ 1.53.0
-* |eigen3|_ 3.3.0
-* |sphinx|_ 1.3.1
+* |eigen3|_ 3.3.1
+* |sphinx|_ 1.4.1
--------------------------------------------------------------------------------
Using |cmake|
diff --git a/doc/html/_sources/changelog.txt b/doc/html/_sources/changelog.txt
index 67c6449a8c77ba6a9eae9b7aa2af68ec4d2c97c6..0e9ceb554298f192f7dea1e1b082a380fff4a766 100644
--- a/doc/html/_sources/changelog.txt
+++ b/doc/html/_sources/changelog.txt
@@ -5,6 +5,19 @@
Changelog
================================================================================
+Release 2.1.0
+--------------------------------------------------------------------------------
+
+* This is expected to be the last release supporting Python 2.
+* This project now requires a C++11 compatible compiler.
+* Introduced VINA scoring function in the sidechain module. A scoring function
+ specific RotamerConstructor is provided that comes with extensive heuristics
+ to parametrize arbitrary compounds.
+* Motif finding algorithm to identify objects in 3D space, e.g. binding sites.
+ The algorithm is based on principles of geometric hashing.
+* Several minor bug fixes, improvements, and speed-ups
+
+
Release 2.0.0
--------------------------------------------------------------------------------
diff --git a/doc/html/_sources/container/singularity.txt b/doc/html/_sources/container/singularity.txt
index 5079e263ad6f6879aad7d1ee47c6fd65b3981aa2..16af7e051382508f764bddb533647d423db67fd7 100644
--- a/doc/html/_sources/container/singularity.txt
+++ b/doc/html/_sources/container/singularity.txt
@@ -36,6 +36,8 @@ Fire the local Registry and push the promod image to it:
sudo docker tag promod localhost:5000/promod
sudo docker push localhost:5000/promod
+If port 5000 is already taken on your machine, use a different ``<PORT>`` by
+using the flag ``-p <PORT>:5000`` and ``localhost:<PORT>`` in these commands.
Make sure, that on top of your Singularity recipe you have something like:
.. code-block:: bash
@@ -71,7 +73,24 @@ To get help on how to run it:
.. code-block:: bash
- singularity run --app Notebook <IMAGE> --help
+ singularity help --app Notebook <IMAGE>
+
+Within the notebook you can test OST, ProMod3 and nglview as follows:
+
+.. code-block:: python
+
+ from ost import io
+ from promod3 import loop
+ import nglview
+
+ # generate backbone with dihedrals of a helix and store it
+ sequence = "HELLYEAH"
+ bb_list = loop.BackboneList(sequence)
+ io.SavePDB(bb_list.ToEntity(), "test.pdb")
+
+ # display stored file
+ view = nglview.show_file("test.pdb")
+ view
The Compound Library
diff --git a/doc/html/_sources/loop/backbone.txt b/doc/html/_sources/loop/backbone.txt
index 3acc2f8e1a2b74a97e559c050e71eb97c777802e..e5e2d9964cfb6cd7cce133bd1cd5869c3bd19d19 100644
--- a/doc/html/_sources/loop/backbone.txt
+++ b/doc/html/_sources/loop/backbone.txt
@@ -79,6 +79,22 @@ The BackboneList class
code which is not one of the 20 default amino acids or if
*sequence* and *dihedral_angles* are inconsistent in size.
+ .. method:: BackboneList(residues)
+
+ Creates a BackboneList with positions and sequence extracted from
+ *residues*.
+
+ :param residues: List of :class:`ost.mol.ResidueHandle` objects from
+ which the backbone positions and one letter codes
+ are extracted.
+
+ :type residues: :class:`list`
+
+ :raises: :exc:`~exceptions.RuntimeError` if a residue in *residues*
+ contains a one letter code which is not one of the 20 default
+ amino acids or when there is a residue not providing all
+ required positions.
+
.. method:: BackboneList(sequence, residues)
Creates a BackboneList from given *sequence* and positions extracted from
diff --git a/doc/html/_sources/loop/structure_db.txt b/doc/html/_sources/loop/structure_db.txt
index b3089c7248bc40d5f4bd292125795b2edde82204..756afe78cd46954025953926e787eb618c2f5f58 100644
--- a/doc/html/_sources/loop/structure_db.txt
+++ b/doc/html/_sources/loop/structure_db.txt
@@ -141,6 +141,7 @@ database, you might want to consider two things:
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.
+ For the bare minimum (only backbone coordinates and sequence), use Minimal.
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 :class:`StructureDB`). One important note:
@@ -148,8 +149,8 @@ database, you might want to consider two things:
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
+ Minimal, All, Dihedrals, SolventAccessibilities, ResidueDepths, DSSP,
+ AAFrequencies, AAFrequenciesStruct
.. class:: StructureDB(data_to_store)
@@ -249,7 +250,8 @@ database, you might want to consider two things:
:type id: :class:`str`
:type chain_name: :class:`str`
- :type ent: :class:`ost.mol.EntityView`
+ :type ent: :class:`ost.mol.EntityHandle` /
+ :class:`ost.mol.EntityView`
:type seqres: :class:`ost.seq.SequenceHandle`
:type prof: :class:`ost.seq.ProfileHandle`
:type only_longest_strech: :class:`bool`
@@ -314,14 +316,22 @@ database, you might want to consider two things:
.. method:: GetBackboneList(fragment, sequence)
- GetBackboneList(n_stem, c_stem, fragment, sequence)
+ GetBackboneList(n_stem, c_stem, fragment, sequence="")
+ GetBackboneList(coord_idx, sequence="")
+ GetBackboneList(n_stem, c_stem, coord_idx, sequence="")
- :returns: Backbone list with positions extracted from *fragment*.
+
+ :returns: Backbone list with positions extracted from *fragment* or
+ full entry at *coord_idx*
:rtype: :class:`BackboneList`
:param fragment: Fragment definition from which to extract positions.
:type fragment: :class:`FragmentInfo`
- :param sequence: Sequence to set for the returned backbone list.
+ :param coord_idx: Idx of entry from which to extract positions.
+ :type coord_idx: :class:`int`
+ :param sequence: Sequence of the returned backbone list. If not
+ set, the original sequence at specified location in the
+ database is used.
:type sequence: :class:`str`
:param n_stem: Positions on which the backbone list's N-terminus should be
superposed onto.
@@ -330,89 +340,116 @@ database, you might want to consider two things:
superposed onto.
: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 connected
- stretches in the database) or if *sequence* contains a one letter
- code which is not one of the 20 default amino acids.
-
+ :raises: :exc:`~exceptions.RuntimeError` if the length of *sequence* does
+ not match with the desired backbone list, if *sequence* contains
+ a character which does not belong to the 20 proteinogenic amino
+ acids or if *fragment* or *coord_idx* is invalid. Fragment can
+ be invalid when it does not fully fit into one of the connected
+ stretches of residues in the database.
.. method:: GetSequence(fragment)
+ GetSequence(coord_idx)
- :returns: The sequence of *fragment*
+ :returns: The sequence of *fragment* or full entry at *coord_idx*
:rtype: :class:`str`
:param fragment: Fragment definition from which to extract the sequence.
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
- the case when the fragment does not fully fit into one of the
- connected stretches of residues in the database.
+ :param coord_idx: Idx of entry from which to extract the sequence
+ :type coord_idx: :class:`int`
+
+ :raises: :exc:`~exceptions.RuntimeError` if fragment or coord_idx is
+ invalid. Fragment can be invalid when it does not fully fit into
+ one of the connected stretches of residues in the database.
.. method:: GetDSSPStates(fragment)
+ GetDSSPStates(coord_idx)
- :returns: The dssp states of *fragment*
+ :returns: The dssp states of *fragment* or full entry at *coord_idx*
:rtype: :class:`str`
:param fragment: Fragment definition from which to extract the states.
:type fragment: :class:`FragmentInfo`
+ :param coord_idx: Idx of entry from which to extract the dssp states
+ :type coord_idx: :class:`int`
+
: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
- connected stretches of residues in the database.
+ data or if fragment/ coord_idx is invalid. Fragment can be invalid
+ when it does not fully fit into one of the connected stretches of
+ residues in the database.
.. method:: GetDihedralAngles(fragment)
+ GetDihedralAngles(coord_idx)
:returns: The phi and psi dihedral angles of every residue of *fragment*
+ or full entry at *coord_idx*
:rtype: :class:`list` of pairs (:class:`tuple`)
:param fragment: Fragment definition from which to extract the dihedrals.
:type fragment: :class:`FragmentInfo`
+ :param coord_idx: Idx of entry from which to extract the dihedral angles
+ :type coord_idx: :class:`int`
+
: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
+ dihedral angle data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
.. method:: GetResidueDepths(fragment)
+ GetResidueDepths(coord_idx)
- :returns: Residue depth for each residue of *fragment*.
+ :returns: Residue depth for each residue of *fragment* or full entry
+ at *coord_idx*
:rtype: :class:`list` of :class:`float`
:param fragment: Fragment definition from which to extract the residue
depths
:type fragment: :class:`FragmentInfo`
+ :param coord_idx: Idx of entry from which to extract the residue depths
+ :type coord_idx: :class:`int`
+
: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
+ residue depth data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
.. method:: GetSolventAccessibilitites(fragment)
+ GetSolventAccessibilitites(coord_idx)
- :returns: Solvent accessibility for each residue of *fragment* in square A
- as calculated by :meth:`~ost.mol.alg.Accessibility` when adding
- the structure to the database.
+ :returns: Solvent accessibility for each residue of *fragment* or full entry
+ at *coord_idx* in square A as calculated by
+ :meth:`~ost.mol.alg.Accessibility` when adding the structure to
+ the database.
:rtype: :class:`list` of :class:`float`
:param fragment: Fragment definition from which to extract the solvent
accessibilities
:type fragment: :class:`FragmentInfo`
+ :param coord_idx: Idx of entry from which to extract the solvent
+ accessibilities
+ :type coord_idx: :class:`int`
+
: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
+ solvent accessibility data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
.. method:: GetSequenceProfile(fragment)
+ GetSequenceProfile(coord_idx)
- :returns: The sequence profile for the residues defined by *fragment* with
- the BLOSUM62 probabilities as NULL model.
+ :returns: The sequence profile for the residues defined by *fragment* or
+ full entry at *coord_idx* with the BLOSUM62 probabilities as NULL
+ model.
:rtype: :class:`ost.seq.ProfileHandle`
:param fragment: Fragment definition from which to extract the sequence
@@ -420,16 +457,21 @@ database, you might want to consider two things:
:type fragment: :class:`FragmentInfo`
- :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
+ :param coord_idx: Idx of entry from which to extract the sequence profile
+ :type coord_idx: :class:`int`
+
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ sequence profile data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
.. method:: GetStructureProfile(fragment)
+ GetStructureProfile(coord_idx)
- :returns: The structure profile for the residues defined by *fragment* with
- the BLOSUM62 probabilities as NULL model.
+ :returns: The structure profile for the residues defined by *fragment* or
+ full entry at *coord_idx* with the BLOSUM62 probabilities as NULL
+ model.
:rtype: :class:`ost.seq.ProfileHandle`
:param fragment: Fragment definition from which to extract the structure
@@ -437,9 +479,12 @@ database, you might want to consider two things:
:type fragment: :class:`FragmentInfo`
- :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
+ :param coord_idx: Idx of entry from which to extract the structure profile
+ :type coord_idx: :class:`int`
+
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ structure profile data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
@@ -461,7 +506,7 @@ database, you might want to consider two things:
:raises: :exc:`~exceptions.RuntimeError` if *bb_list* and
*residue_depths* differ in size, when their size is 0
- or when database does not contain aa frequencies struct data.
+ or when database does not contain residue depth data.
.. method:: SetStructureProfile(coord_idx, prof)
diff --git a/doc/html/_sources/modelling/algorithms.txt b/doc/html/_sources/modelling/algorithms.txt
index 51357bc0615a49e58f2ef12f3efad67eeb3b003d..7c775b0a1ba537244c4f7e22bdff9a38cb5ef582 100644
--- a/doc/html/_sources/modelling/algorithms.txt
+++ b/doc/html/_sources/modelling/algorithms.txt
@@ -164,3 +164,165 @@ example pipeline.
.. autofunction:: GenerateDeNovoTrajectories
+Motif Finder
+--------------------------------------------------------------------------------
+
+Distinct spatial arrangements of atoms or functional groups are key for protein
+function. For their detection, ProMod3 implements the MotifFinder algorithm
+which is based on geometric hashing as described by Nussinov and Wolfson
+[nussinov1991]_. The algorithm consists of a learning stage, a detection stage
+and a refinement stage.
+
+Learning Stage: A motif (query) is represented by a set of coordinates. Triplets
+(p1, p2, p3) of coordinates are selected that define triangles. For each
+triangle one can define an orthogonal vector basis
+(in our case v1 = norm(p2-p1), v3 = norm(cross(v1,p3-p1),
+v2 = norm(cross(v1,v3)))). For each coordinate not in [p1,p2,p3], we add the
+identity of the query/triangle as value to a hash map.
+The corresponding key consists of discretized values describing the edge lengths
+of the triangle, as well as the coordinate transformed into the triangle
+specific orthogonal vector basis. That's 6 numbers in total.
+
+Detection Stage: The goal is to identify one or several subsets of target
+coordinates that resemble an input query.
+We first setup an accumulator containing a counter for each triangle observed
+in the input query. We then iterate over each possible triangle with vertices
+p1, p2 and p3 in the target coordinates. At the beginning of each iteration,
+all counters in the accumulator are set to zero. Again, we build a vector basis
+given that triangle and transform all coordinates not in [p1,p2,p3] into that
+vector space. For each transformed coordinate we obtain a key for the query hash
+map. If there is one or several values at that location in the hash map,
+we increment the corresponding locations in the accumulator.
+Once all coordinates are processed, we search for high counts in the
+accumulator. Given *N* query coordinates, we keep a solution for further
+refinement if count/(*N*-3) >= *hash_tresh*. This is repeated until all
+triangles in the target are processed. One key problem with this approach is
+the discretization of floating point numbers that give raise to the hash map
+keys. Two extremely close values might end up in different bins just because
+they are close to the bin boundaries. For each of the 6 relevant numbers
+we estimate the actual bin as well as the closest neighbouring bin. Processing
+all possible combinations results in 64 hash map lookups instead of only one.
+
+Refinement Stage: Every potential solution identified in the detection stage is
+further refined based on the *distance_thresh* and *refine_thresh* parameters.
+A potential solution found in the detection stage is a pair of triangles, one
+in the query and one in the target, for which we find many matching coordinates
+in their respective vector space. We start with a coordinate mapping based on
+the triangle vertices from the query and the target (3 pairs).
+This coordinate mapping is iteratively updated by estimating the minimum RMSD
+superposition of the mapped query coordinates onto the target, apply that
+superposition on the query, find the closest target coordinate for each
+coordinate in the query and redo the mapping by including all pairs with
+minimum distance < *distance_thresh*. Iteration stops if nothing changes
+anymore. The solution is returned to the user if the final fraction of mapped
+query coordinates is larger or equal *refine_thresh*.
+The larger the mapping, the more accurate the superposition. As we start with
+only the three triangle vertices, *distance_thresh* is doubled for the initial
+iteration.
+
+.. literalinclude:: ../../../tests/doc/scripts/modelling_motif_finder.py
+
+.. class:: MotifQuery(positions, identifier, min_triangle_edge_length, \
+ max_triangle_edge_length, bin_size)
+ MotifQuery(positions, identifier, min_triangle_edge_length, \
+ max_triangle_edge_length, bin_size, flags)
+ MotifQuery(query_list)
+
+ A single query or a container of queries.
+ The constructor performs the learning stage of a single query or combines
+ several queries, so they can be searched at once.
+
+ :param positions: Coordinates of the query
+ :param identifier: Descriptor of the query
+ :param min_triangle_edge_length: To avoid the full O(n^3) hell, triangles
+ with any edge length below *min_triangle_edge_length*
+ are skipped
+ :param max_triangle_edge_length: Same as *min_triangle_edge_length* but
+ upper bound
+ :param bin_size: Bin size in A, relevant to generate hash map keys
+ :param flags: Flag in range [0,63] for every coordinate in *positions*.
+ They're also added to the hash map keys (default: 0).
+ This means that additionally to having a matching
+ relative position, the coordinates must also have a
+ matching flag in the detection/refinement stage.
+ If not provided (in the query and in the search),
+ only coordinates matter.
+ :param query_list: E pluribus unum
+
+ :type positions: :class:`ost.geom.Vec3List`
+ :type identifier: :class:`str`
+ :type min_triangle_edge_length: :class:`float`
+ :type max_triangle_edge_length: :class:`float`
+ :type bin_size: :class:`float`
+ :type flags: :class:`list` of :class:`int`
+ :type query_list: :class:`list` of :class:`MotifQuery`
+
+
+ .. method:: Save(filename)
+
+ Saves the query down to disk
+
+ :param filename: filename
+ :type filename: :class:`str`
+
+ .. staticmethod:: Load(filename)
+
+ Load query from disk
+
+ :param filename: filename
+ :type filename: :class:`str`
+
+ .. method:: GetPositions(query_idx)
+
+ Returns coordinates of specified query
+
+ :param query_idx: Query from which you want the positions
+ :type query_idx: :class:`int`
+
+ .. method:: GetIdentifiers()
+
+ Returns a list of all query identifiers.
+
+ .. method:: GetN()
+
+ Returns the number of queries
+
+
+
+.. class:: MotifMatch
+
+ Object that holds information about a match found in :meth:`FindMotifs`
+
+ .. attribute:: query_idx
+
+ Index of matching query
+
+ .. attribute:: mat
+
+ Transformation matrix to superpose matching query onto target
+
+ .. attribute:: alignment
+
+ List of tuples which define matching pairs of query/target coordinates
+
+
+.. method:: FindMotifs(query, target_positions, hash_tresh=0.4, \
+ distance_thresh=1.0, refine_thresh=0.7, \
+ flags=list())
+
+ Performs the detection and refinement stages of the geometric hashing
+ algorithm.
+
+ :param query: Query to be searched
+ :param target_positions: Coordinates of the target
+ :param hash_thresh: Parameter relevant for detection stage
+ :param distance_thresh: Parameter relevant for refinement stage
+ :param refine_thresh: Parameter relevant for refinement stage
+ :param flags: Equivalent to *flags* in :class:`MotifQuery`
+ constructor. If you didn't provide anything there,
+ this can be ignored. Only the actual coordinates
+ matter in this case.
+
+ :returns: All found matches
+
+ :rtype: :class:`list` of :class:`MotifMatch`
diff --git a/doc/html/_sources/references.txt b/doc/html/_sources/references.txt
index 927de6ddbad6c032f0f760c17384e977d1ed31e9..18a5a3b25ba4779ccd336b9bbfdae278f04735ab 100644
--- a/doc/html/_sources/references.txt
+++ b/doc/html/_sources/references.txt
@@ -62,6 +62,10 @@ References
Exploring the conformational space of protein side chains using
dead-end elimination and the A* algorithm. Proteins.
+.. [nussinov1991] Nussinov R and Wolfson HJ (1991).
+ Efficient detection of three-dimensional structural motifs in
+ biological macromolecules by computer vision techniques. PNAS.
+
.. [shapovalov2011] Shapovalov MV and Dunbrack RL Jr. (2011).
A smoothed backbone-dependent rotamer library for proteins
derived from adaptive kernel density estimates and
@@ -75,6 +79,10 @@ References
potentials and threading score functions using information
maximization. Proteins.
+.. [trott2010] Trott O, Olson AJ (2010). AutoDock Vina: improving the speed and
+ accuracy of docking with a new scoring function, efficient
+ optimization and multithreading. J Comput Chem
+
.. [zhou2005] Zhou H, Zhou Y (2005).
Fold Recognition by Combining Sequence Profiles Derived From
Evolution and From Depth-Dependent Structural Alignment of
diff --git a/doc/html/_sources/sidechain/frame.txt b/doc/html/_sources/sidechain/frame.txt
index d8365f4a5316d2efebaaaafb50a87238b1b3ac2d..94a3150d0361fa6fe2b468b35752f0f19d57cebb 100644
--- a/doc/html/_sources/sidechain/frame.txt
+++ b/doc/html/_sources/sidechain/frame.txt
@@ -14,7 +14,7 @@
.. limitations under the License.
-Frame
+Frame - The Rigid Part
================================================================================
.. currentmodule:: promod3.sidechain
diff --git a/doc/html/_sources/sidechain/index.txt b/doc/html/_sources/sidechain/index.txt
index aeac7212ce7a9232b81c95d2178cb32d07ff6595..192257b499d3826c3ed5891cadb39ede1f7a7291 100644
--- a/doc/html/_sources/sidechain/index.txt
+++ b/doc/html/_sources/sidechain/index.txt
@@ -42,11 +42,10 @@ Contents:
.. toctree::
:maxdepth: 2
- rotamer_id
rotamer
frame
- rotamer_lib
rotamer_constructor
+ rotamer_lib
graph
disulfid
loading
diff --git a/doc/html/_sources/sidechain/rotamer.txt b/doc/html/_sources/sidechain/rotamer.txt
index d3ae44ebe66b3f2139cd7a5ba04e29de80efc9ac..56b95301448e5a955ef38ee0105c9d60b9de291f 100644
--- a/doc/html/_sources/sidechain/rotamer.txt
+++ b/doc/html/_sources/sidechain/rotamer.txt
@@ -14,22 +14,96 @@
.. limitations under the License.
-Rotamers
+Representing Sidechains - Rotamers & Co.
================================================================================
.. currentmodule:: promod3.sidechain
-A rotamer represents an amino acid sidechain and is basically a set of
-:class:`Particle` objects. There exist two types. The :class:`RRMRotamer` and
-:class:`FRMRotamer`.
-To gather all possible rotamers for one particular sidechain position,
+A rotamer represents an amino acid sidechain identified by a :class:`RotamerID`
+and is a set of :class:`Particle` objects.
+Two types of rotamers exist. The :class:`RRMRotamer` and :class:`FRMRotamer`.
+To gather all possible rotamers for one location,
ProMod3 offers the :class:`RRMRotamerGroup` and :class:`FRMRotamerGroup`.
-Pairwise interactions between particles give raise to pairwise energies between
-rotamers. Nevertheless, the energy calculation itself happens on the level
-of RotamerGroups and is mostly hidden away in the construction of the
-the :class:`RotamerGraph`. If you're too lazy to build up your rotamers
-by hand, you might be interested in the :class:`RotamerConstructor`.
+All parts of the structure that are kept rigid can be represented by
+a :class:`Frame` object.
+
+RotamerID
+--------------------------------------------------------------------------------
+
+The sidechain module has its own definition of amino acids to satisfy custom
+requirements for the implemented sidechain construction algorithms.
+As an example there are histidine in two possible protonation states,
+that affect the hbond term or different versions of proline/cysteine.
+
+.. class:: RotamerID
+
+ Enumerates the amino acids. Possible values:
+
+ .. hlist::
+ :columns: 2
+
+ * ARG - Arginine
+ * ASN - Asparagine
+ * ASP - Aspartate
+ * GLN - Glutamine
+ * GLU - Glutamate
+ * LYS - Lysine
+ * SER - Serine
+ * CYS - Cystein
+ * CYH - "free" Cystein
+ * CYD - disulfid bonded Cystein
+ * MET - Methionine
+ * TRP - Tryptophane
+ * TYR - Tyrosine
+ * THR - Threonine
+ * VAL - Valine
+ * ILE - Isoleucine
+ * LEU - Leucine
+ * PRO - Proline
+ * CPR - cis-Proline
+ * TPR - trans-Proline
+ * HIS - Histidine
+ * HSD - d-protonated Histidine
+ * HSE - e-protonated Histidine
+ * PHE - Phenylalanine
+ * GLY - Glycine
+ * ALA - Alanine
+ * XXX - Invalid
+
+ The RotamerID enum can be accessed either directly as ``promod3.sidechain.ARG``
+ or as ``promod3.sidechain.RotamerID.ARG``.
+
+
+How can I get an ID?
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The RotamerID enum can directly be accessed from Python. Two convenient
+functions exist to get RotamerIDs from the :class:`ost.conop.AminoAcid` enum
+or from amino acid three letter codes.
+
+.. method:: TLCToRotID(tlc)
+
+ Directly translates the three letter code into a RotamerID. Following
+ exactly the naming convention defined above.
+
+ :param tlc: Three letter code of amino acid
+ :type tlc: :class:`str`
+
+ :returns: :class:`RotamerID`, XXX if **tlc** cannot be recoginzed.
+
+
+.. method:: AAToRotID(aa)
+
+ Directly translates **aa** 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 :class:`ost.conop.AminoAcid`
+
+ :param aa: AA enum of amino acid
+ :type aa: :class:`ost.conop.AminoAcid`
+
+ :returns: :class:`RotamerID`, XXX if **aa** is invalid.
The Smallest Building Block - The Particle
@@ -44,7 +118,9 @@ function.
The available scoring functions between :class:`Particle` objects
- * SCWRL4
+ * SCWRL4 - :ref:`scwrl4-scoring-function`
+ * SCWRL3 - :ref:`scwrl3-scoring-function`
+ * VINA - :ref:`vina-scoring-function`
.. class:: Particle
@@ -93,13 +169,19 @@ function.
+.. _scwrl4-scoring-function:
The SCWRL4 scoring function
---------------------------------------------------------------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The SCWRL4 scoring function combines a Lennard-Jones style term with
+a hydrogen bond term. Details can be found in the relevant publication
+[krivov2009]_.
.. class:: SCWRL4ParticleType
The SCWRL4 energy function differentiates between following particle types
+ that define the behaviour of the Lennard-Jones style term:
* HParticle - represents hydrogen
* CParticle - default representation of a carbon
@@ -123,9 +205,17 @@ The SCWRL4 scoring function
:param charge: The charge of the particle, relevant for the hydrogen
bond term
:param lone_pairs: Direction of all possible lone pairs of the particle,
- relevant for the hydrogen bond term
+ relevant for the hydrogen bond term. If set, the
+ particle is a potential hydrogen bond acceptor.
+ An example would be the Serine OG atom, where you can
+ represent the two lone pairs with vectors pointing
+ from the OG position towards the lone pair centers.
:param polar_direction: The polar direction of the particle,
- relevant for the hdrogen bond term
+ relevant for the hydrogen bond term. If set, the
+ particle is a potential hydrogen bond donor. An
+ example would be the Serine HG hydrogen. The
+ *polar_direction* would be a vector
+ estimated as follows: hg_pos-og_pos.
:type name: :class:`str`
:type particle_type: :class:`SCWRL4ParticleType`
@@ -135,6 +225,82 @@ The SCWRL4 scoring function
:type polar_direction: :class:`ost.geom.Vec3`
+.. _scwrl3-scoring-function:
+
+The SCWRL3 scoring function
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The SCWRL3 scoring function implements a simple repulsion term that depends on
+the hard-sphere radius of the involved particles.
+Details can be found in the relevant publication [canutescu2003]_.
+
+.. method:: CreateSCWRL3Particle(name, radius, pos)
+
+ Creates and returns a :class:`Particle` that can evaluate the SCWRL3 scoring
+ function
+
+ :param name: The name of the particle
+ :param radius: The hard-sphere radius of the particle, relevant for the
+ repulsion term.
+ :param pos: The position of the particle
+
+ :type name: :class:`str`
+ :type radius: :class:`float`
+ :type pos: :class:`ost.geom.Vec3`
+
+
+.. _vina-scoring-function:
+
+The VINA scoring function
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The VINA scoring function is a combination of scores that are named
+gaussian1, gaussian2, repulsion, hydrophobic and hbond in the Autodock Vina
+software [trott2010]_. VINA only evaluates heavy atoms. Gaussian1, gaussian2
+and repulsion are evaluated for all pairs of particles. Hydrophobic is only
+evaluated between C_VINAParticle :class:`VINAParticleType` and hbond is
+evaluated between hydrogen bond donor/acceptor pairs. While SCWRL3 and SCWRL4
+are intended to evaluate sidechain-sidechain interactions in proteins,
+VINA is mainly targeted at interactions between sidechains and ligands.
+
+The VINA scoring function differentiates between the following particle types:
+
+.. class:: VINAParticleType
+
+ * O_D_VINAParticle - Oxygen that can be a hydrogen bond donor
+ * N_D_VINAParticle - Nitrogen that can be a hydrogen bond donor
+ * O_A_VINAParticle - Oxygen that can be a hydrogen bond acceptor
+ * N_A_VINAParticle - Nitrogen that can be a hydrogen bond acceptor
+ * O_AD_VINAParticle - Oxygen that can be a hydrogen bond donor and acceptor
+ * N_AD_VINAParticle - Nitrogen that can be a hydrogen bond donor and acceptor
+ * O_VINAParticle - Oxygen
+ * N_VINAParticle - Nitrogen
+ * S_VINAParticle - Sulfur
+ * P_VINAParticle - Phosphorus
+ * C_P_VINAParticle - Polar carbon that is covalently bound to a charged atom
+ * C_VINAParticle - Hydrophobic carbon that is only bound to other carbons or hydrogens
+ * F_VINAParticle - Fluorine
+ * Cl_VINAParticle - Chlorine
+ * Br_VINAParticle - Bromine
+ * I_VINAParticle - Iodine
+ * M_VINAParticle - Metals
+ * INVALID_VINAParticle - Invalid particle...
+
+
+.. method:: CreateVINAParticle(name, particle_type, pos)
+
+ Creates and returns a :class:`Particle` that can evaluate the VINA scoring
+ function
+
+ :param name: The name of the particle
+ :param radius: The type of the particle
+ :param pos: The position of the particle
+
+ :type name: :class:`str`
+ :type radius: :class:`VINAParticleType`
+ :type pos: :class:`ost.geom.Vec3`
+
+
Rotamers
--------------------------------------------------------------------------------
@@ -692,3 +858,4 @@ Rotamer Groups
Searches rotamer with lowest self energy *l_e* and deletes all
rotamers with *self_energy* > *l_e* + *thresh*
+
diff --git a/doc/html/_sources/sidechain/rotamer_constructor.txt b/doc/html/_sources/sidechain/rotamer_constructor.txt
index 3a297d5d0846dd0808cad22419dad15add0bf11b..c8cca8deb12f3b56c889c32e9c9bcc954d38599f 100644
--- a/doc/html/_sources/sidechain/rotamer_constructor.txt
+++ b/doc/html/_sources/sidechain/rotamer_constructor.txt
@@ -19,18 +19,18 @@ Rotamer Constructor
.. currentmodule:: promod3.sidechain
-Instead of creating rotamers by yourself, you can simply use the convenient
-functionality provided by ProMod3.
+Instead of creating rotamers or frame residues by yourself, you can use the
+convenient functionality provided by ProMod3.
-Constructing Rotamers and Frame Residues
+The RotamerConstructor Baseclass
--------------------------------------------------------------------------------
.. class:: RotamerConstructor
Abstract base class that cannot be initialized from Python. It builds
- an interface implemented by energy function specific constructors
+ an interface implemented by scoring function specific constructors
(e.g. :class:`SCWRL4RotamerConstructor`).
.. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib,\
@@ -213,6 +213,10 @@ Constructing Rotamers and Frame Residues
+Scoring Function Specific RotamerConstructors
+--------------------------------------------------------------------------------
+
+
.. class:: SCWRL4RotamerConstructor(cb_in_sidechain)
This object implements the full interface defined in
@@ -306,3 +310,180 @@ Constructing Rotamers and Frame Residues
:type psi: :class:`float`
:type n_ter: :class:`bool`
:type c_ter: :class:`bool`
+
+
+
+
+.. class:: SCWRL3RotamerConstructor(cb_in_sidechain)
+
+ This object implements the full interface defined in
+ :class:`RotamerConstructor` and constructs rotamers and frame residues that
+ are parametrized according to the SCWRL3 method. They contain only heavy atoms.
+
+ :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:: AssignInternalEnergies(rot_group, id, residue_index, \
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False])
+
+ Overrides the method defined in :class:`RotamerConstructor`.
+ Takes the rotamer group and assigns every single rotamer its internal
+ energy based on the probabilistic approach used by SCWRL3.
+ => -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
+ rotamer specific and max_p is the maximum probablity of any of the rotamers
+ in **rot_group**. If you construct a rotamer group by the
+ ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
+ is already called at construction and the energies are properly assigned.
+
+ :param rot_group: containing all rotamers for which internal energies have
+ to be assigned
+ :param id: Identifies the sidechain
+ :param residue_index: The index of the residue which is represented by
+ *rot_group*
+ :param phi: The dihedral angle of the current residue
+ :param psi: The dihedral angle of the current residue
+ :param n_ter: Whether the residue is n-terminal
+ :param c_ter: Whether the residue is c-terminal
+
+ :type rot_group: :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
+ :type id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+ :type n_ter: :class:`bool`
+ :type c_ter: :class:`bool`
+
+
+.. class:: VINARotamerConstructor(cb_in_sidechain)
+
+ This object implements the full interface defined in
+ :class:`RotamerConstructor` and constructs rotamers and frame residues that
+ are parametrized according to the VINA method. They contain only heavy atoms.
+
+ :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:: AssignInternalEnergies(rot_group, id, residue_index, \
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False])
+
+ Overrides the method defined in :class:`RotamerConstructor`.
+ Takes the rotamer group and assigns every single rotamer its internal
+ energy based on the probabilistic approach used by SCWRL3/SCWRL4.
+ => -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
+ rotamer specific and max_p is the maximum probablity of any of the rotamers
+ in **rot_group**. If you construct a rotamer group by the
+ ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
+ is already called at construction and the energies are properly assigned.
+
+ :param rot_group: containing all rotamers for which internal energies have
+ to be assigned
+ :param id: Identifies the sidechain
+ :param residue_index: The index of the residue which is represented by
+ *rot_group*
+ :param phi: The dihedral angle of the current residue
+ :param psi: The dihedral angle of the current residue
+ :param n_ter: Whether the residue is n-terminal
+ :param c_ter: Whether the residue is c-terminal
+
+ :type rot_group: :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
+ :type id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+ :type n_ter: :class:`bool`
+ :type c_ter: :class:`bool`
+
+
+ .. method:: ConstructFrameResidueHeuristic(res, res_idx)
+
+ Constructs a :class:`FrameResidue` from a :class:`ost.mol.ResidueHandle` using
+ a heuristic treatment of the atoms. It is important that the residue has
+ proper bonds assigned, as they influence the atom typing procedure.
+ Furthermore, you need hydrogens to automatically estimate the correct
+ atom type for oxygens and nitrogens (hydrogen bond donor/acceptor).
+ Alternatively you can assign generic properties to oxygens and nitrogens
+ to circumvent the requirement of hydrogens. This is further described for
+ the case of oxygen.
+
+ * Carbon is assigned C_VINAParticle :class:`VINAParticleType` if its only
+ bound to other carbons or hydrogens (and deuterium). All other carbons are
+ assigned C_P_VINAParticle :class:`VINAParticleType`.
+ * In case of oxygen, the heuristic first checks for set generic properties.
+ If the atom has the bool properties "is_hbond_acceptor" AND
+ "is_hbond_donor" set, it decides between the according oxygen types
+ in :class:`VINAParticleType`. If the generic properties are not set,
+ every oxygen is assumed to be an hbond acceptor. But only an hbond donor
+ if its bound to a hydrogen (or deuterium). You can set the generic
+ properties for an :class:`ost.mol.AtomHandle` by calling
+ at.SetBoolProp("is_hbond_donor", False) and
+ at.SetBoolProp("is_hbond_acceptor", True). An oxygen with those
+ generic properties is assigned O_A_VINAParticle :class:`VINAParticleType`.
+ * In case of nitrogen, the heuristic again first checks for set generic
+ properties.
+ If the atom has the bool properties "is_hbond_acceptor" AND
+ "is_hbond_donor" set, it decides between the according nitrogen types
+ in :class:`VINAParticleType`. If not, nitrogen is expected to be an
+ hbond donor if it is bound to a hydrogen (or deuterium) and
+ an hbond acceptor if it is bound to less than 3 other atoms (sounds
+ horrible but works surprisingly well).
+ * Atoms of elements ["MG", "MN", "ZN", "CA", "FE"] are assigned
+ M_VINAParticle :class:`VINAParticleType`.
+ * Atoms of elements ["S", "P", "F", "CL", "BR", "I"] are assigned their
+ corresponding :class:`VINAParticleType`.
+ * All other atoms are neglected and not added to the returned
+ :class:`FrameResidue`.
+
+ :param res: Residue from which to create the
+ :class:`FrameResidue`
+ :param res_idx: Index that is set in :class:`FrameResidue`
+ :type res: :class:`ost.mol.ResidueHandle`
+ :type res_idx: :class:`int`
+ :rtype: :class:`FrameResidue`
+
+
+ .. method:: ConstructRRMRotamerHeuristic(res)
+
+ Construct a :class:`RRMRotamer` with the atom typing heuristic
+ as in the :meth:`ConstructFrameResidueHeuristic` method.
+
+ :param res: Residue from which to create the
+ :class:`RRMRotamer`
+ :type res: :class:`ost.mol.ResidueHandle`
+ :rtype: :class:`RRMRotamer`
+
+
+ .. method:: ConstructFRMRotamerHeuristic(res)
+
+ Construct a :class:`FRMRotamer` with the atom typing heuristic
+ as in the :meth:`ConstructFrameResidueHeuristic` method. The
+ constructed :class:`FRMRotamer` only contains one subrotamer that
+ contains the atoms from *residue*.
+
+ :param res: Residue from which to create the
+ :class:`FRMRotamer`
+ :type res: :class:`ost.mol.ResidueHandle`
+ :rtype: :class:`FRMRotamer`
diff --git a/doc/html/_sources/sidechain/rotamer_id.txt b/doc/html/_sources/sidechain/rotamer_id.txt
deleted file mode 100644
index 746a51641352c7295152567a742eda8befedc803..0000000000000000000000000000000000000000
--- a/doc/html/_sources/sidechain/rotamer_id.txt
+++ /dev/null
@@ -1,108 +0,0 @@
-.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
-.. Biozentrum - University of Basel
-..
-.. Licensed under the Apache License, Version 2.0 (the "License");
-.. you may not use this file except in compliance with the License.
-.. You may obtain a copy of the License at
-..
-.. http://www.apache.org/licenses/LICENSE-2.0
-..
-.. Unless required by applicable law or agreed to in writing, software
-.. distributed under the License is distributed on an "AS IS" BASIS,
-.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-.. See the License for the specific language governing permissions and
-.. limitations under the License.
-
-
-RotamerID
-================================================================================
-
-.. currentmodule:: promod3.sidechain
-
-The sidechain module has its own definition of amino acids to satisfy custom
-requirements for the implemented sidechain construction algorithms.
-As an example there are histidine in two possible protonation states,
-that affect the hbond term or different versions of proline/cysteine.
-
-
-The RotamerID
---------------------------------------------------------------------------------
-
-.. class:: RotamerID
-
- Enumerates the amino acids. Possible values:
-
- .. hlist::
- :columns: 2
-
- * ARG - Arginine
- * ASN - Asparagine
- * ASP - Aspartate
- * GLN - Glutamine
- * GLU - Glutamate
- * LYS - Lysine
- * SER - Serine
- * CYS - Cystein
- * CYH - "free" Cystein
- * CYD - disulfid bonded Cystein
- * MET - Methionine
- * TRP - Tryptophane
- * TYR - Tyrosine
- * THR - Threonine
- * VAL - Valine
- * ILE - Isoleucine
- * LEU - Leucine
- * PRO - Proline
- * CPR - cis-Proline
- * TPR - trans-Proline
- * HIS - Histidine
- * HSD - d-protonated Histidine
- * HSE - e-protonated Histidine
- * PHE - Phenylalanine
- * GLY - Glycine
- * ALA - Alanine
- * XXX - Invalid
-
- The RotamerID enum can be accessed either directly as ``promod3.sidechain.ARG``
- or as ``promod3.sidechain.RotamerID.ARG``.
-
-
-How can I get an ID?
---------------------------------------------------------------------------------
-The RotamerID enum can directly be accessed from Python. Two convenient
-functions exist to get RotamerIDs from the :class:`ost.conop.AminoAcid` enum
-or from amino acid three letter codes.
-
-.. method:: TLCToRotID(tlc)
-
- Directly translates the three letter code into a RotamerID. Following
- exactly the naming convention defined above.
-
- :param tlc: Three letter code of amino acid
- :type tlc: :class:`str`
-
- :returns: :class:`RotamerID`, XXX if **tlc** cannot be recoginzed.
-
-
-.. method:: AAToRotID(aa)
-
- Directly translates **aa** 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 :class:`ost.conop.AminoAcid`
-
- :param aa: AA enum of amino acid
- :type aa: :class:`ost.conop.AminoAcid`
-
- :returns: :class:`RotamerID`, XXX if **aa** is invalid.
-
-
-
-
-
-
-
-
-
-
-
diff --git a/doc/html/actions/index.html b/doc/html/actions/index.html
index b8d6aa5a8c57bcc6cec7e372194809a028e7efde..22ca5ecdc00fdc3793c2328a87a2226bb4617d45 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 2.0.0 documentation</title>
+ <title>ProMod3 Actions — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -112,7 +112,7 @@ 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="https://www.openstructure.org/docs/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.9.0)"><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/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.10.0)"><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
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
@@ -139,7 +139,7 @@ to the corresponding target sequences. This has an impact on loop scoring with
the database approach.
The profiles can be provided as plain files or gzipped. Following file
extensions are understood: .hhm, .hhm.gz, .pssm, .pssm.gz.
-Consider to use <a class="reference external" href="https://www.openstructure.org/docs/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a
+Consider to use <a class="reference external" href="https://www.openstructure.org/docs/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a
file in a3m format at hand.</p>
<ul class="simple">
<li>The profiles are mapped based on exact matches towards the gapless
@@ -194,7 +194,7 @@ detects and models disulfid bonds and reconstructs all sidechains with the
flexible rotamer model. The result is stored as <code class="file docutils literal"><span class="pre">out.pdb</span></code>.
The output filename can be controlled with the <code class="docutils literal"><span class="pre">-o</span></code> flag.</p>
<p>A structure 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="https://www.openstructure.org/docs/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.9.0)"><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/io/io/#ost.io.LoadEntity" title="(in OpenStructure v1.10.0)"><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
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>.</p>
<p>Several flags control the modelling behaviour:</p>
@@ -287,7 +287,7 @@ supported by <a class="reference internal" href="../modelling/sidechain_reconstr
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/actions/index_dev.html b/doc/html/actions/index_dev.html
index 38817d23f9ff466370ec6d216532bb39f123df27..4da2b7382d8d688f3df5c57f972f272b8d0c9690 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 2.0.0 documentation</title>
+ <title>test_actions - Testing Actions — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -194,7 +194,7 @@ 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="https://www.OpenStructure.org">OST</a>‘s <a class="reference external" href="https://www.openstructure.org/docs/base/testutils/#module-ost.testutils" title="(in OpenStructure v1.9.0)"><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/base/testutils/#module-ost.testutils" title="(in OpenStructure v1.10.0)"><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-default"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre>13
@@ -411,7 +411,7 @@ file (also complains if a directory is found instead).</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/buildsystem.html b/doc/html/buildsystem.html
index fa8c0e469b4a5eb6c7390314fa906edb0abd5421..8a84acd090055744040cee4e433f39edb1fc5fce 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 2.0.0 documentation</title>
+ <title>Building ProMod3 — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Users" href="users.html" />
<link rel="next" title="ProMod3 and Containers" href="container/index.html" />
<link rel="prev" title="ProMod3 Actions" href="actions/index.html" />
@@ -47,20 +47,20 @@
<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="https://www.OpenStructure.org">OpenStructure</a> (OST), requiring at least version
-1.10.0. 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. The same
-versions of <a class="reference external" href="https://www.python.org/">Python</a> and <a class="reference external" href="https://www.boost.org/">Boost</a> are needed as used in OST. For <a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a>
-we need at least version 3.3.0. To build the documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> is
-required.</p>
+1.11.0. A C++11 compatible compiler is required. 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. The same versions of <a class="reference external" href="https://www.python.org/">Python</a> and <a class="reference external" href="https://www.boost.org/">Boost</a>
+are needed as used in OST. For <a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> we need at least version 3.3.0. To
+build the documentation, <a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> is required.</p>
<p>The currently preferred versions are:</p>
<ul class="simple">
-<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 1.10.0</li>
+<li><a class="reference external" href="https://www.OpenStructure.org">OST</a> 1.11.0</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="https://www.python.org/">Python</a> 2.7.11</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>
+<li><a class="reference external" href="http://eigen.tuxfamily.org/index.php?title=Main_Page">Eigen 3</a> 3.3.1</li>
+<li><a class="reference external" href="http://sphinx-doc.org/">Sphinx</a> 1.4.1</li>
</ul>
</div>
<div class="section" id="using-cmake">
@@ -204,7 +204,7 @@ safely delete the whole source folder.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/changelog.html b/doc/html/changelog.html
index 624bccd94e33f53368466218e89ad9391160b0ab..5a5229642a989f2bd592bbaf602a76587601f08f 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 2.0.0 documentation</title>
+ <title>Changelog — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="prev" title="References" href="references.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -42,6 +42,19 @@
<div class="section" id="changelog">
<h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
+<div class="section" id="release-2-1-0">
+<h2>Release 2.1.0<a class="headerlink" href="#release-2-1-0" title="Permalink to this headline">¶</a></h2>
+<ul class="simple">
+<li>This is expected to be the last release supporting Python 2.</li>
+<li>This project now requires a C++11 compatible compiler.</li>
+<li>Introduced VINA scoring function in the sidechain module. A scoring function
+specific RotamerConstructor is provided that comes with extensive heuristics
+to parametrize arbitrary compounds.</li>
+<li>Motif finding algorithm to identify objects in 3D space, e.g. binding sites.
+The algorithm is based on principles of geometric hashing.</li>
+<li>Several minor bug fixes, improvements, and speed-ups</li>
+</ul>
+</div>
<div class="section" id="release-2-0-0">
<h2>Release 2.0.0<a class="headerlink" href="#release-2-0-0" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
@@ -150,6 +163,7 @@ 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-2-1-0">Release 2.1.0</a></li>
<li><a class="reference internal" href="#release-2-0-0">Release 2.0.0</a></li>
<li><a class="reference internal" href="#release-1-3-0">Release 1.3.0</a></li>
<li><a class="reference internal" href="#release-1-2-0">Release 1.2.0</a></li>
@@ -188,7 +202,7 @@ selected loops, reconstruct hydrogens and minimize energy with MM</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/cmake/index.html b/doc/html/cmake/index.html
index dbdb850375223b71efa895b6a0829191f86ef661..f1be147fee04b09b4bae608526b985cdff0642b2 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 2.0.0 documentation</title>
+ <title>ProMod3‘s Share Of CMake — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -373,7 +373,7 @@ target has to be created <strong>before</strong> any action may be attached to i
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/container/docker.html b/doc/html/container/docker.html
index aabd7220fa7648ca54682b5ecbab4d03828b924e..361df7199becb9d60af6d90f347e332504fb75a2 100644
--- a/doc/html/container/docker.html
+++ b/doc/html/container/docker.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Docker — ProMod3 2.0.0 documentation</title>
+ <title>Docker — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="ProMod3 and Containers" href="index.html" />
<link rel="next" title="Singularity" href="singularity.html" />
<link rel="prev" title="ProMod3 and Containers" href="index.html" />
@@ -76,7 +76,7 @@ provide the (relative) path to the script and (relative) path to the file eg:</p
</div>
<div class="section" id="the-compound-library">
<span id="docker-compound-lib"></span><h2>The Compound Library<a class="headerlink" href="#the-compound-library" title="Permalink to this headline">¶</a></h2>
-<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">CompoundLib</span></code></a> is generated.
+<p>At build time of the container, a <a class="reference external" href="https://www.openstructure.org/docs/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">CompoundLib</span></code></a> is generated.
Compound libraries contain information on chemical compounds, such as their
connectivity, chemical class and one-letter-code. The compound library has
several uses, but the most important one is to provide the connectivy
@@ -175,7 +175,7 @@ output when running a Python script with following code in the container:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/container/index.html b/doc/html/container/index.html
index db0c08685d4d1f055c795f795d7b5ce3553746d3..57ed423f9c5cf4397850c3e32fd12918bebb204a 100644
--- a/doc/html/container/index.html
+++ b/doc/html/container/index.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ProMod3 and Containers — ProMod3 2.0.0 documentation</title>
+ <title>ProMod3 and Containers — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Docker" href="docker.html" />
<link rel="prev" title="Building ProMod3" href="../buildsystem.html" />
@@ -94,7 +94,7 @@ some sugar on top.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/container/singularity.html b/doc/html/container/singularity.html
index 1940dd077a6abb6bbd4ec67cd9215e20136d11c2..e6ef2d40ea1dfcb5ac2d6e7457ef5edd730c25d6 100644
--- a/doc/html/container/singularity.html
+++ b/doc/html/container/singularity.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Singularity — ProMod3 2.0.0 documentation</title>
+ <title>Singularity — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="ProMod3 and Containers" href="index.html" />
<link rel="next" title="modelling - Protein Modelling" href="../modelling/index.html" />
<link rel="prev" title="Docker" href="docker.html" />
@@ -57,7 +57,9 @@ sudo docker tag promod localhost:5000/promod
sudo docker push localhost:5000/promod
</pre></div>
</div>
-<p>Make sure, that on top of your Singularity recipe you have something like:</p>
+<p>If port 5000 is already taken on your machine, use a different <code class="docutils literal"><span class="pre"><PORT></span></code> by
+using the flag <code class="docutils literal"><span class="pre">-p</span> <span class="pre"><PORT>:5000</span></code> and <code class="docutils literal"><span class="pre">localhost:<PORT></span></code> in these commands.
+Make sure, that on top of your Singularity recipe you have something like:</p>
<div class="highlight-bash"><div class="highlight"><pre><span></span>BootStrap: docker
Registry: http://localhost:5000
Namespace:
@@ -81,7 +83,22 @@ E.g. to run scripts with pm:</p>
</div>
<p>The jupyter notebook is setup as an app in the container.
To get help on how to run it:</p>
-<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity run --app Notebook <IMAGE> --help
+<div class="highlight-bash"><div class="highlight"><pre><span></span>singularity <span class="nb">help</span> --app Notebook <IMAGE>
+</pre></div>
+</div>
+<p>Within the notebook you can test OST, ProMod3 and nglview as follows:</p>
+<div class="highlight-python"><div class="highlight"><pre><span></span><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="kn">import</span> <span class="nn">nglview</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="s2">"test.pdb"</span><span class="p">)</span>
+
+<span class="c1"># display stored file</span>
+<span class="n">view</span> <span class="o">=</span> <span class="n">nglview</span><span class="o">.</span><span class="n">show_file</span><span class="p">(</span><span class="s2">"test.pdb"</span><span class="p">)</span>
+<span class="n">view</span>
</pre></div>
</div>
</div>
@@ -162,7 +179,7 @@ in the Docker documentation: <a class="reference internal" href="docker.html#doc
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/contributing.html b/doc/html/contributing.html
index 6ba9fbd7067c5142f04d98e093072d0ddd560810..4cb717b7e531fa33b942add272bf1df27d613f33 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 2.0.0 documentation</title>
+ <title>Contributing — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -660,7 +660,7 @@ contributions to web pages using ProMod3.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/geometry.html b/doc/html/core/geometry.html
index d19a2ef9b2d9b9add2b2947d20380f58001ba1ad..6d4e9ca68f9e82a8513a6cc33fe50cf513e75cc2 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 2.0.0 documentation</title>
+ <title>Geometry functions — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -56,14 +56,14 @@
<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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -79,16 +79,16 @@
<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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -105,9 +105,9 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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>
@@ -117,7 +117,7 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -134,16 +134,16 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -160,8 +160,8 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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>
@@ -169,7 +169,7 @@ 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="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat4</span></code></a></p>
</td>
</tr>
</tbody>
@@ -186,7 +186,7 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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>
@@ -194,7 +194,7 @@ 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="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v1.9.0)"><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/geom/mat/#ost.geom.Mat3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Mat3</span></code></a></p>
</td>
</tr>
</tbody>
@@ -211,7 +211,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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>
<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>
@@ -230,7 +230,7 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a></td>
</tr>
</tbody>
</table>
@@ -347,7 +347,7 @@ angles and one distance and is used in the fragment database for fast lookups.</
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/graph_minimizer.html b/doc/html/core/graph_minimizer.html
index d68b21c165fc6019713bed993ea39f8cb2f4253b..e95c19333fd51a6f95e8d9086c3be91731f7eefc 100644
--- a/doc/html/core/graph_minimizer.html
+++ b/doc/html/core/graph_minimizer.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Graph Minimizer — ProMod3 2.0.0 documentation</title>
+ <title>Graph Minimizer — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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="prev" title="Runtime profiling" href="runtime_profiling.html" />
@@ -373,7 +373,7 @@ The second element is the according energy value.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 87148791bae5e46800b3e711aab3997235ee5fa9..6690837afb52ef67ca60356b4aea1e1696e5f210 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 2.0.0 documentation</title>
+ <title>helper - Shared Functionality For the Everything — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -247,7 +247,7 @@ script will terminate if a gzip file is found.</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index 8b6e7db3867d73c6e293926c7fe4559efc646622..c99853589643093ceb89fc0dad473b51d1bdb52a 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 2.0.0 documentation</title>
+ <title>core - ProMod3 Core Functionality — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -105,7 +105,7 @@ modeling per se but cover standard programming issues.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index 5a2053814b6e1a22491d37f93af21b4ec0d7e876..b7d2472f0af8cbe3c684eec4d42083337b8b5996 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 2.0.0 documentation</title>
+ <title>pm3argparse - Parsing Command Lines — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -252,7 +252,7 @@ input is post processed and checked in <a class="reference internal" href="#prom
by the <code class="xref py py-meth docutils literal"><span class="pre">ost.io.LoadSequenceProfile()</span></code> method. Format is chosen by
file ending. Recognized file extensions: .hhm, .hhm.gz, .pssm,
.pssm.gz. Consider to use
-<a class="reference external" href="https://www.openstructure.org/docs/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a file
+<a class="reference external" href="https://www.openstructure.org/docs/bindings/hhblits/#ost.bindings.hhblits.HHblits.A3MToProfile" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.bindings.hhblits.HHblits.A3MToProfile()</span></code></a> if you have a file
in a3m format at hand.</li>
</ul>
<p>Notes:</p>
@@ -266,7 +266,7 @@ target sequences</li>
</ul>
<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">profiles</span></code> - <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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
+<li><code class="xref py py-attr docutils literal"><span class="pre">profiles</span></code> - <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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>,
ordered to match the target sequences.</li>
</ul>
<p>Exit codes related to profile input:</p>
@@ -424,7 +424,7 @@ and with the right constraints.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/runtime_profiling.html b/doc/html/core/runtime_profiling.html
index b1d223150b95f9bf449b761943880311ae222d14..1e93da67dc60315f1a49e184805ebc77dec5a60a 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 2.0.0 documentation</title>
+ <title>Runtime profiling — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="Graph Minimizer" href="graph_minimizer.html" />
<link rel="prev" title="Geometry functions" href="geometry.html" />
@@ -201,7 +201,7 @@ will fail miserably if timers are currently running.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/core/setcompoundschemlib.html b/doc/html/core/setcompoundschemlib.html
index 7fb563f83c914e52745443e88ba9a11993a702eb..0e9ebf7b873cf65e2a459594f701123ab045d1af 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 2.0.0 documentation</title>
+ <title>SetCompoundsChemlib() — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="Documentation For Users" href="../users.html" />
<link rel="next" title="Contributing" href="../user_contributions.html" />
<link rel="prev" title="Graph Minimizer" href="graph_minimizer.html" />
@@ -106,7 +106,7 @@ enabled globally.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/dev_setup.html b/doc/html/dev_setup.html
index 81c008ef7ec5ac3abde06e4c93516bdf3c8f12bd..b1f9b94e87b2209d1bac373e274593f0ea7978b0 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 2.0.0 documentation</title>
+ <title>ProMod3 Setup — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -293,7 +293,7 @@ modules from there, use the binaries from <code class="file docutils literal"><s
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/developers.html b/doc/html/developers.html
index df1b45e5ad8a04972c1e0e61aa33e038ea49b9d7..80e54edf05379533716d36261103e34b904250ba 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 2.0.0 documentation</title>
+ <title>Documentation For Developers — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="next" title="ProMod3 Setup" href="dev_setup.html" />
<link rel="prev" title="Contributing" href="user_contributions.html" />
@@ -125,7 +125,7 @@ new features.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index 8de63c6d8cfc5785d9b7876437a0251f12d01a0f..f0bf33a2b4a6e64aa4a8414a5fff8df4e452402b 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 2.0.0 documentation</title>
+ <title>Index — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -25,7 +25,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -66,6 +66,7 @@
| <a href="#S"><strong>S</strong></a>
| <a href="#T"><strong>T</strong></a>
| <a href="#U"><strong>U</strong></a>
+ | <a href="#V"><strong>V</strong></a>
</div>
<h2 id="Symbols">Symbols</h2>
@@ -244,7 +245,7 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="sidechain/rotamer_id.html#promod3.sidechain.AAToRotID">AAToRotID() (in module promod3.sidechain)</a>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.AAToRotID">AAToRotID() (in module promod3.sidechain)</a>
</dt>
@@ -414,6 +415,10 @@
</dt>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifMatch.alignment">alignment (promod3.modelling.MotifMatch attribute)</a>
+ </dt>
+
+
<dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_scorer">all_atom_scorer (promod3.modelling.ModellingHandle attribute)</a>
</dt>
@@ -421,12 +426,12 @@
<dt><a href="modelling/pipeline.html#promod3.modelling.ModellingHandle.all_atom_scorer_env">all_atom_scorer_env (promod3.modelling.ModellingHandle attribute)</a>
</dt>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<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>
@@ -583,9 +588,17 @@
<dd><dl>
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies">(promod3.sidechain.SCWRL3RotamerConstructor method)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL4RotamerConstructor.AssignInternalEnergies">(promod3.sidechain.SCWRL4RotamerConstructor method)</a>
</dt>
+
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.AssignInternalEnergies">(promod3.sidechain.VINARotamerConstructor method)</a>
+ </dt>
+
</dl></dd>
<dt><a href="core/graph_minimizer.html#promod3.core.GraphMinimizer.AStarSolve">AStarSolve() (promod3.core.GraphMinimizer method)</a>
@@ -632,7 +645,7 @@
</dt>
- <dt><a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">BackboneList() (promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[1]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[2]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[3]</a>
+ <dt><a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">BackboneList() (promod3.loop.BackboneList method)</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[1]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[2]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[3]</a>, <a href="loop/backbone.html#promod3.loop.BackboneList.BackboneList">[4]</a>
</dt>
@@ -837,8 +850,6 @@
<dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.ClearPos">ClearPos() (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.ClearResidue">ClearResidue() (promod3.loop.AllAtomPositions method)</a>
</dt>
@@ -881,6 +892,8 @@
</dt>
</dl></dd>
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
<dt><a href="modelling/pipeline.html#promod3.modelling.CloseGaps">CloseGaps() (in module promod3.modelling)</a>
</dt>
@@ -991,11 +1004,25 @@
<dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL4RotamerConstructor.ConstructFrameResidueHeuristic">ConstructFrameResidueHeuristic() (promod3.sidechain.SCWRL4RotamerConstructor method)</a>
</dt>
+ <dd><dl>
+
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic">(promod3.sidechain.VINARotamerConstructor method)</a>
+ </dt>
+
+ </dl></dd>
+
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic">ConstructFRMRotamerHeuristic() (promod3.sidechain.VINARotamerConstructor method)</a>
+ </dt>
+
<dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">ConstructRRMRotamerGroup() (promod3.sidechain.RotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">[1]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">[2]</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">[3]</a>
</dt>
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic">ConstructRRMRotamerHeuristic() (promod3.sidechain.VINARotamerConstructor method)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue">ConstructSidechainFrameResidue() (promod3.sidechain.RotamerConstructor method)</a>, <a href="sidechain/rotamer_constructor.html#promod3.sidechain.RotamerConstructor.ConstructSidechainFrameResidue">[1]</a>
</dt>
@@ -1083,10 +1110,18 @@
</dt>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.CreateSCWRL3Particle">CreateSCWRL3Particle() (in module promod3.sidechain)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer.html#promod3.sidechain.CreateSCWRL4Particle">CreateSCWRL4Particle() (in module promod3.sidechain)</a>
</dt>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.CreateVINAParticle">CreateVINAParticle() (in module promod3.sidechain)</a>
+ </dt>
+
+
<dt><a href="modelling/monte_carlo.html#promod3.modelling.CTerminalCloser">CTerminalCloser (class in promod3.modelling)</a>
</dt>
@@ -1391,6 +1426,10 @@
</dt>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.FindMotifs">FindMotifs() (in module promod3.modelling)</a>
+ </dt>
+
+
<dt><a href="loop/mm_system_creation.html#promod3.loop.ForcefieldBondInfo.force_constant">force_constant (promod3.loop.ForcefieldBondInfo attribute)</a>
</dt>
@@ -1811,6 +1850,10 @@
</dl></dd>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.GetIdentifiers">GetIdentifiers() (promod3.modelling.MotifQuery method)</a>
+ </dt>
+
+
<dt><a href="loop/all_atom.html#promod3.loop.AllAtomPositions.GetIndex">GetIndex() (promod3.loop.AllAtomPositions method)</a>
</dt>
@@ -1890,6 +1933,12 @@
<dt><a href="loop/backbone.html#promod3.loop.BackboneList.GetN">GetN() (promod3.loop.BackboneList method)</a>
</dt>
+ <dd><dl>
+
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.GetN">(promod3.modelling.MotifQuery method)</a>
+ </dt>
+
+ </dl></dd>
<dt><a href="sidechain/rotamer.html#promod3.sidechain.Particle.GetName">GetName() (promod3.sidechain.Particle method)</a>
</dt>
@@ -2007,6 +2056,10 @@
</dl></dd>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.GetPositions">GetPositions() (promod3.modelling.MotifQuery method)</a>
+ </dt>
+
+
<dt><a href="loop/structure_db.html#promod3.loop.PsipredPrediction.GetPrediction">GetPrediction() (promod3.loop.PsipredPrediction method)</a>
</dt>
@@ -2478,6 +2531,10 @@
</dt>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.Load">(promod3.modelling.MotifQuery static method)</a>
+ </dt>
+
+
<dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.Load">(promod3.scoring.AllAtomInteractionScorer static method)</a>
</dt>
@@ -2719,6 +2776,10 @@
</dl></dd>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifMatch.mat">mat (promod3.modelling.MotifMatch attribute)</a>
+ </dt>
+
+
<dt><a href="loop/structure_db.html#promod3.loop.FragDB.MaxFragLength">MaxFragLength() (promod3.loop.FragDB method)</a>
</dt>
@@ -2802,6 +2863,14 @@
</dl></dd>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifMatch">MotifMatch (class in promod3.modelling)</a>
+ </dt>
+
+
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery">MotifQuery (class in promod3.modelling)</a>
+ </dt>
+
+
<dt><a href="core/helper.html#promod3.core.helper.MsgErrorAndExit">MsgErrorAndExit() (in module promod3.core.helper)</a>
</dt>
@@ -3037,6 +3106,12 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifMatch.query_idx">query_idx (promod3.modelling.MotifMatch attribute)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
<dt><a href="sidechain/rotamer_lib.html#promod3.sidechain.BBDepRotamerLib.QueryLib">QueryLib() (promod3.sidechain.BBDepRotamerLib method)</a>
</dt>
@@ -3157,7 +3232,7 @@
</dt>
- <dt><a href="sidechain/rotamer_id.html#promod3.sidechain.RotamerID">RotamerID (class in promod3.sidechain)</a>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.RotamerID">RotamerID (class in promod3.sidechain)</a>
</dt>
@@ -3258,6 +3333,10 @@
</dt>
+ <dt><a href="modelling/algorithms.html#promod3.modelling.MotifQuery.Save">(promod3.modelling.MotifQuery method)</a>
+ </dt>
+
+
<dt><a href="scoring/all_atom_scorers.html#promod3.scoring.AllAtomInteractionScorer.Save">(promod3.scoring.AllAtomInteractionScorer method)</a>
</dt>
@@ -3393,6 +3472,10 @@
</dt>
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.SCWRL3RotamerConstructor">SCWRL3RotamerConstructor (class in promod3.sidechain)</a>
+ </dt>
+
+
<dt><a href="sidechain/rotamer.html#promod3.sidechain.SCWRL4ParticleType">SCWRL4ParticleType (class in promod3.sidechain)</a>
</dt>
@@ -3845,7 +3928,7 @@
</dt>
- <dt><a href="sidechain/rotamer_id.html#promod3.sidechain.TLCToRotID">TLCToRotID() (in module promod3.sidechain)</a>
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.TLCToRotID">TLCToRotID() (in module promod3.sidechain)</a>
</dt>
@@ -3920,6 +4003,22 @@
<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>
+</tr></table>
+
+<h2 id="V">V</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="sidechain/rotamer.html#promod3.sidechain.VINAParticleType">VINAParticleType (class in promod3.sidechain)</a>
+ </dt>
+
+ </dl></td>
+ <td style="width: 33%" valign="top"><dl>
+
+ <dt><a href="sidechain/rotamer_constructor.html#promod3.sidechain.VINARotamerConstructor">VINARotamerConstructor (class in promod3.sidechain)</a>
+ </dt>
+
</dl></td>
</tr></table>
@@ -3954,7 +4053,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/gettingstarted.html b/doc/html/gettingstarted.html
index 357e240355a9190825c5917add13b6acea6f2786..4d7ff9696487f382ec6af7b2464ebabc68f0302b 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 2.0.0 documentation</title>
+ <title>Getting Started — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -98,7 +98,7 @@ 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 <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.9.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> from OST)</li>
+(using <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.10.0)"><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
@@ -157,7 +157,7 @@ not set, 1 thread will be used by default.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/index.html b/doc/html/index.html
index 9d19520871229f8900a8a2009e90705197cff8b1..9e798617816b8b47ed902271e0e3a065ae188aff 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>ProMod3 — ProMod3 2.0.0 documentation</title>
+ <title>ProMod3 — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="#" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="#" />
<link rel="next" title="Documentation For Users" href="users.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -122,7 +122,7 @@ algorithms.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/license.html b/doc/html/license.html
index 1841fd40a92b860fdbde8c9c1062f3075492e7c4..6f42206198fb624746da8fa674b391171a756099 100644
--- a/doc/html/license.html
+++ b/doc/html/license.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>License — ProMod3 2.0.0 documentation</title>
+ <title>License — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="next" title="References" href="references.html" />
<link rel="prev" title="Using Binary Files In ProMod3" href="portableIO.html" />
@@ -293,7 +293,7 @@ doc/Copyright_cmake.py.txt
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/all_atom.html b/doc/html/loop/all_atom.html
index d0aee5addf9fffd6386651ec4a1f6c3c229451c8..4b0276cb78dbd9046716cf9f4cd696d99abd22f1 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 2.0.0 documentation</title>
+ <title>Handling All Atom Positions — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -91,8 +91,8 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><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
chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
</tr>
</tbody>
@@ -114,7 +114,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</td>
</tr>
@@ -144,7 +144,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><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>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>
@@ -221,7 +221,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -355,7 +355,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue providing atoms</li>
</ul>
</td>
</tr>
@@ -401,7 +401,7 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Set position to <em>pos</em>.</li>
</ul>
</td>
</tr>
@@ -451,7 +451,7 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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>
@@ -555,7 +555,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
@@ -834,9 +834,9 @@ 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 <a class="reference external" href="https://www.openstructure.org/docs/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.HeuristicProcessor</span></code></a>.</td>
+Connectivity resolved with <a class="reference external" href="https://www.openstructure.org/docs/conop/connectivity/#ost.conop.HeuristicProcessor" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -856,8 +856,8 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResNum</span></code></a>) – Residue number for the inserted residue</li>
</ul>
</td>
</tr>
@@ -950,7 +950,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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
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">
@@ -963,7 +963,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -985,7 +985,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
@@ -1015,7 +1015,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
@@ -1044,7 +1044,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
@@ -1072,7 +1072,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
@@ -1096,7 +1096,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -1128,7 +1128,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">AminoAcid</span></code></a>) – Amino acid type</td>
</tr>
</tbody>
</table>
@@ -1161,7 +1161,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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">
@@ -1255,7 +1255,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
@@ -1279,7 +1279,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
@@ -1343,7 +1343,7 @@ when residue is N terminal.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
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diff --git a/doc/html/loop/backbone.html b/doc/html/loop/backbone.html
index f44cf2070cf736fde687d7cbeff88cf77e357bb7..5bc7e7738c7a762b3140782249f5ec57f9593d6b 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 2.0.0 documentation</title>
+ <title>Representing Loops — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="loop - Loop Handling" href="index.html" />
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@@ -47,7 +47,7 @@
<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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a>.</p>
+converted from, to, or inserted to a <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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>
@@ -150,6 +150,28 @@ code which is not one of the 20 default amino acids or if
</table>
</dd></dl>
+<dl class="method">
+<dt>
+<code class="descname">BackboneList</code><span class="sig-paren">(</span><em>residues</em><span class="sig-paren">)</span></dt>
+<dd><p>Creates a BackboneList with positions and sequence extracted from
+<em>residues</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"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> objects from
+which the backbone positions and one letter codes
+are extracted.</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 a residue in <em>residues</em>
+contains a one letter code which is not one of the 20 default
+amino acids or when there is a residue not providing all
+required positions.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
<dl class="method">
<dt>
<code class="descname">BackboneList</code><span class="sig-paren">(</span><em>sequence</em>, <em>residues</em><span class="sig-paren">)</span></dt>
@@ -161,7 +183,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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>
@@ -185,7 +207,7 @@ 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="https://www.openstructure.org/docs/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.9.0)"><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/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.img.ImageHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -195,7 +217,7 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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>
@@ -214,7 +236,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -231,8 +253,8 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><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>
</ul>
</td>
</tr>
@@ -248,7 +270,7 @@ 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="https://www.openstructure.org/docs/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.9.0)"><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/img/base/img/#ost.img.ImageHandle" title="(in OpenStructure v1.10.0)"><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>
@@ -267,7 +289,7 @@ 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="https://www.openstructure.org/docs/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v1.9.0)"><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/geom/composite/#ost.geom.AlignedCuboid" title="(in OpenStructure v1.10.0)"><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>
@@ -371,7 +393,7 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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>
@@ -396,7 +418,7 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Vec3</span></code></a>) – Set position of nitrogen / alpha carbon / beta carbon / carbon
/ oxygen atom to this.</li>
</ul>
</td>
@@ -448,7 +470,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
@@ -465,7 +487,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
</ul>
</td>
</tr>
@@ -491,12 +513,12 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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>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>
@@ -566,12 +588,12 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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>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>
@@ -635,7 +657,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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
element of this backbone list)</td>
</tr>
</tbody>
@@ -652,7 +674,7 @@ 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="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
</ul>
</td>
</tr>
@@ -672,7 +694,7 @@ 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="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</li>
</ul>
</td>
</tr>
@@ -688,7 +710,7 @@ 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="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Mat4</span></code></a>) – The transformation</td>
</tr>
</tbody>
</table>
@@ -708,12 +730,12 @@ 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="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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>
@@ -733,7 +755,7 @@ 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="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><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>
@@ -1005,7 +1027,7 @@ backbone list.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/index.html b/doc/html/loop/index.html
index 58b98b7aa4ff3f8e0be5b7e561bd02f62d6661b0..b5c82a2904e1141b2be11b0c06de3e1e21e7952a 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 2.0.0 documentation</title>
+ <title>loop - Loop Handling — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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="Other Scoring Functions" href="../scoring/other_scoring_functions.html" />
@@ -163,7 +163,7 @@ loops. The following example should give you an idea of what can be done:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/load_loop_objects.html b/doc/html/loop/load_loop_objects.html
index ce2e37a473c1447a33f8ba8679fed9dd2ece6047..862906c9a062de9f3447fbff595aaf1f20d50956 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 2.0.0 documentation</title>
+ <title>Loading Precomputed Objects — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -204,7 +204,7 @@ returned by <a class="reference internal" href="#promod3.loop.LoadStructureDB" t
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/mm_system_creation.html b/doc/html/loop/mm_system_creation.html
index 8dfaaaec37aec2fb0da5bfca21607687e1e8147f..a46f522fd8fab7a5f592707b11e5d2d8676db5a8 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 2.0.0 documentation</title>
+ <title>Generate ost.mol.mm systems — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -43,8 +43,8 @@
<div class="body" role="main">
<div class="section" id="generate-ost-mol-mm-systems">
-<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.9.0)"><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/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.9.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> / OpenMM simulations for loops in
+<h1>Generate <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.10.0)"><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/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.10.0)"><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>
@@ -289,7 +289,7 @@ 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="https://www.openstructure.org/docs/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.9.0)"><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/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.mm.Simulation</span></code></a></td>
</tr>
</tbody>
</table>
@@ -436,7 +436,7 @@ 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="https://www.openstructure.org/docs/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.9.0)"><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/mol/mm/simulation/#ost.mol.mm.Simulation" title="(in OpenStructure v1.10.0)"><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
@@ -549,7 +549,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
@@ -665,7 +665,7 @@ 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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v1.9.0)"><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/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeLJ" title="(in OpenStructure v1.10.0)"><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>
@@ -681,7 +681,7 @@ 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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v1.9.0)"><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/mol/mm/topology/#ost.mol.mm.Topology.SetFudgeQQ" title="(in OpenStructure v1.10.0)"><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>
@@ -696,7 +696,7 @@ 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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v1.9.0)"><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/mol/mm/topology/#ost.mol.mm.Topology.SetMasses" title="(in OpenStructure v1.10.0)"><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>
@@ -720,7 +720,7 @@ 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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v1.9.0)"><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/mol/mm/topology/#ost.mol.mm.Topology.SetCharges" title="(in OpenStructure v1.10.0)"><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>
@@ -745,7 +745,7 @@ 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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v1.9.0)"><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/mol/mm/topology/#ost.mol.mm.Topology.SetSigmas" title="(in OpenStructure v1.10.0)"><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>
@@ -770,7 +770,7 @@ 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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v1.9.0)"><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/mol/mm/topology/#ost.mol.mm.Topology.SetEpsilons" title="(in OpenStructure v1.10.0)"><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>
@@ -916,7 +916,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
@@ -933,7 +933,7 @@ 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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v1.9.0)"><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/mol/mm/topology/#ost.mol.mm.Topology" title="(in OpenStructure v1.10.0)"><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
@@ -1043,7 +1043,7 @@ 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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v1.9.0)"><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/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicBond" title="(in OpenStructure v1.10.0)"><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>
@@ -1105,7 +1105,7 @@ 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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v1.9.0)"><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/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicAngle" title="(in OpenStructure v1.10.0)"><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>
@@ -1182,7 +1182,7 @@ 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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v1.9.0)"><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/mol/mm/topology/#ost.mol.mm.Topology.AddUreyBradleyAngle" title="(in OpenStructure v1.10.0)"><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>
@@ -1287,8 +1287,8 @@ 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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v1.9.0)"><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/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicDihedral" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddPeriodicImproper" title="(in OpenStructure v1.10.0)"><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>
@@ -1392,7 +1392,7 @@ 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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v1.9.0)"><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/mol/mm/topology/#ost.mol.mm.Topology.AddHarmonicImproper" title="(in OpenStructure v1.10.0)"><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>
@@ -1482,7 +1482,7 @@ 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="https://www.openstructure.org/docs/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v1.9.0)"><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/mol/mm/topology/#ost.mol.mm.Topology.AddLJPair" title="(in OpenStructure v1.10.0)"><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>
@@ -1593,7 +1593,7 @@ False, False)</em>.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/structure_db.html b/doc/html/loop/structure_db.html
index 0b6af0659d3cd5399ce7aa1a943d430a83e6bd49..e9187bffffdf6c3282227c9959f929dfb75e07de 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 2.0.0 documentation</title>
+ <title>Structural Data — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -126,7 +126,7 @@ stuff to the structure db. (<a class="reference external" href="https://docs.pyt
<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. (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
+structural information in db. (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>)</p>
</dd></dl>
</dd></dl>
@@ -243,16 +243,9 @@ and fill it with content.</p>
<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="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="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">i</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">i</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>
@@ -275,7 +268,7 @@ database, you might want to consider two things:</p>
<ol class="arabic simple">
<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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.ProfileDB" title="(in OpenStructure v1.10.0)"><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">
@@ -284,14 +277,15 @@ running in parallel</li>
<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.
+For the bare minimum (only backbone coordinates and sequence), use Minimal.
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 <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>). 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>
+<p>Minimal, All, Dihedrals, SolventAccessibilities, ResidueDepths, DSSP,
+AAFrequencies, AAFrequenciesStruct</p>
</dd></dl>
<dl class="class">
@@ -409,10 +403,11 @@ in the according <a class="reference internal" href="#promod3.loop.CoordInfo" ti
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><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
+<li><strong>ent</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.EntityHandle</span></code></a> /
+<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for the chain with name
+<li><strong>seqres</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><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
@@ -526,12 +521,17 @@ the database.</td>
<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>
<dt>
-<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>fragment</em>, <em>sequence</em><span class="sig-paren">)</span></dt>
+<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>fragment</em>, <em>sequence=""</em><span class="sig-paren">)</span></dt>
+<dt>
+<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>coord_idx</em>, <em>sequence=""</em><span class="sig-paren">)</span></dt>
+<dt>
+<code class="descname">GetBackboneList</code><span class="sig-paren">(</span><em>n_stem</em>, <em>c_stem</em>, <em>coord_idx</em>, <em>sequence=""</em><span class="sig-paren">)</span></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">Backbone list with positions extracted from <em>fragment</em>.</p>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Backbone list with positions extracted from <em>fragment</em> or
+full entry at <em>coord_idx</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 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></p>
@@ -539,18 +539,23 @@ the database.</td>
</tr>
<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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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>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>) – Idx of entry 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 of the returned backbone list. If not
+set, the original sequence at specified location in the
+database is used.</li>
+<li><strong>n_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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
superposed onto.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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
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 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>
+<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 length of <em>sequence</em> does
+not match with the desired backbone list, if <em>sequence</em> contains
+a character which does not belong to the 20 proteinogenic amino
+acids or if <em>fragment</em> or <em>coord_idx</em> is invalid. Fragment can
+be invalid when it does not fully fit into one of the connected
+stretches of residues in the database.</p>
</td>
</tr>
</tbody>
@@ -560,19 +565,28 @@ code which is not one of the 20 default amino acids.</p>
<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>
+<dt>
+<code class="descname">GetSequence</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></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 sequence of <em>fragment</em></td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The sequence of <em>fragment</em> or full entry at <em>coord_idx</em></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/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 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#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></p>
+</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.</td>
+<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 the sequence.</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>) – Idx of entry from which to extract the sequence</li>
+</ul>
+</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
-the case when the fragment does not fully fit into one of the
-connected stretches of residues in the database.</td>
+<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 or coord_idx is
+invalid. Fragment can be invalid when it does not fully fit into
+one of the connected stretches of residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -581,20 +595,29 @@ connected stretches of residues in the database.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetDSSPStates">
<code class="descname">GetDSSPStates</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetDSSPStates" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">GetDSSPStates</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></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 dssp states of <em>fragment</em></td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The dssp states of <em>fragment</em> or full entry at <em>coord_idx</em></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/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 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#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a></p>
+</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 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 the states.</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>) – Idx of entry from which to extract the dssp states</li>
+</ul>
+</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 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
-connected stretches of residues in the database.</td>
+<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 database does not contain dssp
+data or if fragment/ coord_idx is invalid. Fragment can be invalid
+when it does not fully fit into one of the connected stretches of
+residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -603,20 +626,30 @@ connected stretches of residues in the database.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetDihedralAngles">
<code class="descname">GetDihedralAngles</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetDihedralAngles" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">GetDihedralAngles</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></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 phi and psi dihedral angles of every residue of <em>fragment</em></td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The phi and psi dihedral angles of every residue of <em>fragment</em>
+or full entry at <em>coord_idx</em></p>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><code class="xref py py-class docutils literal"><span class="pre">list</span></code> of pairs (<code class="xref py py-class docutils literal"><span class="pre">tuple</span></code>)</td>
+<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 pairs (<code class="xref py py-class docutils literal"><span class="pre">tuple</span></code>)</p>
+</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 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 the dihedrals.</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>) – Idx of entry from which to extract the dihedral angles</li>
+</ul>
+</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 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
-connected stretches of residues in the database.</td>
+<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 database does not contain
+dihedral angle data or if fragment/ coord_idx is invalid.
+Fragment can be invalid when it does not fully fit into one of the
+connected stretches of residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -625,21 +658,31 @@ connected stretches of residues in the database.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetResidueDepths">
<code class="descname">GetResidueDepths</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetResidueDepths" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">GetResidueDepths</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></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">Residue depth for each residue of <em>fragment</em>.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Residue depth for each residue of <em>fragment</em> or full entry
+at <em>coord_idx</em></p>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return 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://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"><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-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 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 the residue
+depths</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>) – Idx of entry from which to extract the residue depths</li>
+</ul>
+</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 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
-connected stretches of residues in the database.</td>
+<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 database does not contain
+residue depth data or if fragment/ coord_idx is invalid.
+Fragment can be invalid when it does not fully fit into one of the
+connected stretches of residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -648,23 +691,34 @@ connected stretches of residues in the database.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSolventAccessibilitites">
<code class="descname">GetSolventAccessibilitites</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSolventAccessibilitites" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">GetSolventAccessibilitites</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></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">Solvent accessibility for each residue of <em>fragment</em> in square A
-as calculated by <a class="reference external" href="https://www.openstructure.org/docs/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">Accessibility()</span></code></a> when adding
-the structure to the database.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">Solvent accessibility for each residue of <em>fragment</em> or full entry
+at <em>coord_idx</em> in square A as calculated by
+<a class="reference external" href="https://www.openstructure.org/docs/mol/alg/molalg/#ost.mol.alg.Accessibility" title="(in OpenStructure v1.10.0)"><code class="xref py py-meth docutils literal"><span class="pre">Accessibility()</span></code></a> when adding the structure to
+the database.</p>
+</td>
</tr>
-<tr class="field-even field"><th class="field-name">Return 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://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"><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-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 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 the solvent
+accessibilities</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>) – Idx of entry from which to extract the solvent
+accessibilities</li>
+</ul>
+</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 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
-connected stretches of residues in the database.</td>
+<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 database does not contain
+solvent accessibility data or if fragment/ coord_idx is invalid.
+Fragment can be invalid when it does not fully fit into one of the
+connected stretches of residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -673,22 +727,32 @@ connected stretches of residues in the database.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetSequenceProfile">
<code class="descname">GetSequenceProfile</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetSequenceProfile" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">GetSequenceProfile</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></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 sequence profile for the residues defined by <em>fragment</em> with
-the BLOSUM62 probabilities as NULL model.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The sequence profile for the residues defined by <em>fragment</em> or
+full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
+model.</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://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><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"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+</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 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 the sequence
+profile</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>) – Idx of entry from which to extract the sequence profile</li>
+</ul>
+</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 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
-connected stretches of residues in the database.</td>
+<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 database does not contain
+sequence profile data or if fragment/ coord_idx is invalid.
+Fragment can be invalid when it does not fully fit into one of the
+connected stretches of residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -697,22 +761,32 @@ connected stretches of residues in the database.</td>
<dl class="method">
<dt id="promod3.loop.StructureDB.GetStructureProfile">
<code class="descname">GetStructureProfile</code><span class="sig-paren">(</span><em>fragment</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.loop.StructureDB.GetStructureProfile" title="Permalink to this definition">¶</a></dt>
+<dt>
+<code class="descname">GetStructureProfile</code><span class="sig-paren">(</span><em>coord_idx</em><span class="sig-paren">)</span></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 structure profile for the residues defined by <em>fragment</em> with
-the BLOSUM62 probabilities as NULL model.</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">The structure profile for the residues defined by <em>fragment</em> or
+full entry at <em>coord_idx</em> with the BLOSUM62 probabilities as NULL
+model.</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://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><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"><p class="first"><a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></p>
+</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 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 the structure
+profile</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>) – Idx of entry from which to extract the structure profile</li>
+</ul>
+</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 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
-connected stretches of residues in the database.</td>
+<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 database does not contain
+structure profile data or if fragment/ coord_idx is invalid.
+Fragment can be invalid when it does not fully fit into one of the
+connected stretches of residues in the database.</p>
+</td>
</tr>
</tbody>
</table>
@@ -739,12 +813,12 @@ containing that data.</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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><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, when their size is 0
-or when database does not contain aa frequencies struct data.</p>
+or when database does not contain residue depth data.</p>
</td>
</tr>
</tbody>
@@ -761,7 +835,7 @@ frequencies in entry with <em>coord_idx</em></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>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li>
+<li><strong>prof</strong> (<a class="reference external" href="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Source of profile frequencies</li>
<li><strong>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>
@@ -1064,8 +1138,8 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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
@@ -1289,7 +1363,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
</ul>
</td>
</tr>
@@ -1307,7 +1381,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile for the fraggers target_sequence</li>
</ul>
</td>
</tr>
@@ -1761,7 +1835,7 @@ to <strong>to</strong>, not including <strong>to</strong> itself</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/loop/torsion_sampler.html b/doc/html/loop/torsion_sampler.html
index 08cab65299b62467bf9c559ccbd086ddf997ad52..c30bb37417d8f8e58ddb80d0d2aea8dcfd0b2bdd 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 2.0.0 documentation</title>
+ <title>Sampling Dihedral Angles — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -139,7 +139,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><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>
</tbody>
</table>
@@ -211,9 +211,9 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
</ul>
</td>
</tr>
@@ -253,9 +253,9 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>
</ul>
</td>
</tr>
@@ -291,9 +291,9 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>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>
@@ -335,9 +335,9 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>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>
@@ -379,9 +379,9 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>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>
@@ -425,9 +425,9 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>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>
@@ -449,9 +449,9 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>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>
@@ -590,7 +590,7 @@ standard amino acid</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/algorithms.html b/doc/html/modelling/algorithms.html
index 2070e317cc6919e6a68be9f020fbbf14782dab0b..bbcc316494931d4b60b9c3bcbe702bf53fa1972b 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 2.0.0 documentation</title>
+ <title>Modelling Algorithms — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -95,7 +95,7 @@ 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="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><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>
@@ -113,7 +113,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><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>
@@ -134,9 +134,9 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><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>
@@ -173,7 +173,7 @@ 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="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><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>
@@ -236,8 +236,8 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><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>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
@@ -329,7 +329,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><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
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>
@@ -360,6 +360,267 @@ with the keys of the scores in <strong>scorer</strong></li>
</table>
</dd></dl>
+</div>
+<div class="section" id="motif-finder">
+<h2>Motif Finder<a class="headerlink" href="#motif-finder" title="Permalink to this headline">¶</a></h2>
+<p>Distinct spatial arrangements of atoms or functional groups are key for protein
+function. For their detection, ProMod3 implements the MotifFinder algorithm
+which is based on geometric hashing as described by Nussinov and Wolfson
+<a class="reference internal" href="../references.html#nussinov1991" id="id1">[nussinov1991]</a>. The algorithm consists of a learning stage, a detection stage
+and a refinement stage.</p>
+<p>Learning Stage: A motif (query) is represented by a set of coordinates. Triplets
+(p1, p2, p3) of coordinates are selected that define triangles. For each
+triangle one can define an orthogonal vector basis
+(in our case v1 = norm(p2-p1), v3 = norm(cross(v1,p3-p1),
+v2 = norm(cross(v1,v3)))). For each coordinate not in [p1,p2,p3], we add the
+identity of the query/triangle as value to a hash map.
+The corresponding key consists of discretized values describing the edge lengths
+of the triangle, as well as the coordinate transformed into the triangle
+specific orthogonal vector basis. That’s 6 numbers in total.</p>
+<p>Detection Stage: The goal is to identify one or several subsets of target
+coordinates that resemble an input query.
+We first setup an accumulator containing a counter for each triangle observed
+in the input query. We then iterate over each possible triangle with vertices
+p1, p2 and p3 in the target coordinates. At the beginning of each iteration,
+all counters in the accumulator are set to zero. Again, we build a vector basis
+given that triangle and transform all coordinates not in [p1,p2,p3] into that
+vector space. For each transformed coordinate we obtain a key for the query hash
+map. If there is one or several values at that location in the hash map,
+we increment the corresponding locations in the accumulator.
+Once all coordinates are processed, we search for high counts in the
+accumulator. Given <em>N</em> query coordinates, we keep a solution for further
+refinement if count/(<em>N</em>-3) >= <em>hash_tresh</em>. This is repeated until all
+triangles in the target are processed. One key problem with this approach is
+the discretization of floating point numbers that give raise to the hash map
+keys. Two extremely close values might end up in different bins just because
+they are close to the bin boundaries. For each of the 6 relevant numbers
+we estimate the actual bin as well as the closest neighbouring bin. Processing
+all possible combinations results in 64 hash map lookups instead of only one.</p>
+<p>Refinement Stage: Every potential solution identified in the detection stage is
+further refined based on the <em>distance_thresh</em> and <em>refine_thresh</em> parameters.
+A potential solution found in the detection stage is a pair of triangles, one
+in the query and one in the target, for which we find many matching coordinates
+in their respective vector space. We start with a coordinate mapping based on
+the triangle vertices from the query and the target (3 pairs).
+This coordinate mapping is iteratively updated by estimating the minimum RMSD
+superposition of the mapped query coordinates onto the target, apply that
+superposition on the query, find the closest target coordinate for each
+coordinate in the query and redo the mapping by including all pairs with
+minimum distance < <em>distance_thresh</em>. Iteration stops if nothing changes
+anymore. The solution is returned to the user if the final fraction of mapped
+query coordinates is larger or equal <em>refine_thresh</em>.
+The larger the mapping, the more accurate the superposition. As we start with
+only the three triangle vertices, <em>distance_thresh</em> is doubled for the initial
+iteration.</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Example script that loads protein structures that contain ATP and</span>
+<span class="c1"># generates motif queries describing their binding pockets.</span>
+<span class="c1"># In a second step, those pockets are matched against a protein </span>
+<span class="c1"># structure that only contains an ATP analog. The ATP from every </span>
+<span class="c1"># match is transformed and stored to disk for further processing.</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="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="n">files</span> <span class="o">=</span> <span class="p">[</span><span class="s1">'data/1E2Q.pdb'</span><span class="p">,</span> <span class="s1">'data/1KO5.pdb'</span><span class="p">,</span> <span class="s1">'data/2IYW.pdb'</span><span class="p">]</span>
+
+<span class="n">atp_list</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+<span class="n">query_list</span> <span class="o">=</span> <span class="nb">list</span><span class="p">()</span>
+
+<span class="k">for</span> <span class="n">f</span> <span class="ow">in</span> <span class="n">files</span><span class="p">:</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">f</span><span class="p">)</span>
+ <span class="n">peptide_sel</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">"peptide=true"</span><span class="p">)</span>
+ <span class="n">atp_sel</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">"rname=ATP"</span><span class="p">)</span>
+
+ <span class="c1"># generate a single query for each ATP pocket</span>
+ <span class="k">for</span> <span class="n">atp_idx</span><span class="p">,</span> <span class="n">atp_r</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">atp_sel</span><span class="o">.</span><span class="n">residues</span><span class="p">):</span>
+ <span class="n">pocket_view</span> <span class="o">=</span> <span class="n">peptide_sel</span><span class="o">.</span><span class="n">CreateEmptyView</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">atp_at</span> <span class="ow">in</span> <span class="n">atp_r</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span>
+ <span class="n">close_at</span> <span class="o">=</span> <span class="n">peptide_sel</span><span class="o">.</span><span class="n">FindWithin</span><span class="p">(</span><span class="n">atp_at</span><span class="o">.</span><span class="n">GetPos</span><span class="p">(),</span> <span class="mf">4.5</span><span class="p">)</span>
+ <span class="k">for</span> <span class="n">at</span> <span class="ow">in</span> <span class="n">close_at</span><span class="p">:</span>
+ <span class="n">r</span> <span class="o">=</span> <span class="n">at</span><span class="o">.</span><span class="n">handle</span><span class="o">.</span><span class="n">GetResidue</span><span class="p">()</span>
+ <span class="n">add_flag</span> <span class="o">=</span> <span class="n">mol</span><span class="o">.</span><span class="n">INCLUDE_ATOMS</span> <span class="o">|</span> <span class="n">mol</span><span class="o">.</span><span class="n">CHECK_DUPLICATES</span>
+ <span class="n">pocket_view</span><span class="o">.</span><span class="n">AddResidue</span><span class="p">(</span><span class="n">r</span><span class="p">,</span> <span class="n">add_flag</span><span class="p">)</span>
+
+ <span class="n">ca_positions</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">Vec3List</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">res</span> <span class="ow">in</span> <span class="n">pocket_view</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
+ <span class="n">ca_positions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">res</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="o">.</span><span class="n">GetPos</span><span class="p">())</span>
+ <span class="n">i</span> <span class="o">=</span> <span class="s2">"</span><span class="si">%s</span><span class="s2">_</span><span class="si">%i</span><span class="s2">"</span><span class="o">%</span><span class="p">(</span><span class="n">f</span><span class="p">,</span> <span class="n">atp_idx</span><span class="p">)</span>
+ <span class="n">query</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">MotifQuery</span><span class="p">(</span><span class="n">ca_positions</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="mf">4.0</span><span class="p">,</span> <span class="mf">9.0</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">)</span>
+ <span class="n">query_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">query</span><span class="p">)</span>
+
+ <span class="c1"># create an entity from atp for later use</span>
+ <span class="n">atp_view</span> <span class="o">=</span> <span class="n">prot</span><span class="o">.</span><span class="n">CreateEmptyView</span><span class="p">()</span>
+ <span class="n">atp_view</span><span class="o">.</span><span class="n">AddResidue</span><span class="p">(</span><span class="n">atp_r</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">atp_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">mol</span><span class="o">.</span><span class="n">CreateEntityFromView</span><span class="p">(</span><span class="n">atp_view</span><span class="p">,</span> <span class="kc">True</span><span class="p">))</span>
+
+<span class="c1"># That's it, let's combine the single queries</span>
+<span class="n">full_query</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">MotifQuery</span><span class="p">(</span><span class="n">query_list</span><span class="p">)</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="s2">"data/1AKE.pdb"</span><span class="p">)</span>
+<span class="n">peptide_sel</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">"peptide=true"</span><span class="p">)</span>
+<span class="n">ca_positions</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">Vec3List</span><span class="p">()</span>
+<span class="k">for</span> <span class="n">r</span> <span class="ow">in</span> <span class="n">peptide_sel</span><span class="o">.</span><span class="n">residues</span><span class="p">:</span>
+ <span class="n">ca_positions</span><span class="o">.</span><span class="n">append</span><span class="p">(</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="o">.</span><span class="n">GetPos</span><span class="p">())</span>
+
+<span class="c1"># search all matches, fetch the corresponding atps,</span>
+<span class="c1"># transform them onto the 1ake binding site and dump them to disk</span>
+<span class="n">matches</span> <span class="o">=</span> <span class="n">modelling</span><span class="o">.</span><span class="n">FindMotifs</span><span class="p">(</span><span class="n">full_query</span><span class="p">,</span> <span class="n">ca_positions</span><span class="p">)</span>
+<span class="k">for</span> <span class="n">m_idx</span><span class="p">,</span> <span class="n">m</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">matches</span><span class="p">):</span>
+ <span class="n">atp</span> <span class="o">=</span> <span class="n">atp_list</span><span class="p">[</span><span class="n">m</span><span class="o">.</span><span class="n">query_idx</span><span class="p">]</span><span class="o">.</span><span class="n">Copy</span><span class="p">()</span>
+ <span class="n">atp</span><span class="o">.</span><span class="n">EditXCS</span><span class="p">()</span><span class="o">.</span><span class="n">ApplyTransform</span><span class="p">(</span><span class="n">m</span><span class="o">.</span><span class="n">mat</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">atp</span><span class="p">,</span> <span class="s2">"m_</span><span class="si">%i</span><span class="s2">.pdb"</span><span class="o">%</span><span class="p">(</span><span class="n">m_idx</span><span class="p">))</span>
+
+</pre></div>
+</div>
+<dl class="class">
+<dt id="promod3.modelling.MotifQuery">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifQuery</code><span class="sig-paren">(</span><em>positions</em>, <em>identifier</em>, <em>min_triangle_edge_length</em>, <em>max_triangle_edge_length</em>, <em>bin_size</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery" title="Permalink to this definition">¶</a></dt>
+<dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifQuery</code><span class="sig-paren">(</span><em>positions</em>, <em>identifier</em>, <em>min_triangle_edge_length</em>, <em>max_triangle_edge_length</em>, <em>bin_size</em>, <em>flags</em><span class="sig-paren">)</span></dt>
+<dt>
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifQuery</code><span class="sig-paren">(</span><em>query_list</em><span class="sig-paren">)</span></dt>
+<dd><p>A single query or a container of queries.
+The constructor performs the learning stage of a single query or combines
+several queries, so they can be searched at once.</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>positions</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – Coordinates of the query</li>
+<li><strong>identifier</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>) – Descriptor of the query</li>
+<li><strong>min_triangle_edge_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>) – To avoid the full O(n^3) hell, triangles
+with any edge length below <em>min_triangle_edge_length</em>
+are skipped</li>
+<li><strong>max_triangle_edge_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>) – Same as <em>min_triangle_edge_length</em> but
+upper bound</li>
+<li><strong>bin_size</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>) – Bin size in A, relevant to generate hash map keys</li>
+<li><strong>flags</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>) – Flag in range [0,63] for every coordinate in <em>positions</em>.
+They’re also added to the hash map keys (default: 0).
+This means that additionally to having a matching
+relative position, the coordinates must also have a
+matching flag in the detection/refinement stage.
+If not provided (in the query and in the search),
+only coordinates matter.</li>
+<li><strong>query_list</strong> (<code class="xref py py-class docutils literal"><span class="pre">list</span></code> of <a class="reference internal" href="#promod3.modelling.MotifQuery" title="promod3.modelling.MotifQuery"><code class="xref py py-class docutils literal"><span class="pre">MotifQuery</span></code></a>) – E pluribus unum</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+<dl class="method">
+<dt id="promod3.modelling.MotifQuery.Save">
+<code class="descname">Save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.Save" title="Permalink to this definition">¶</a></dt>
+<dd><p>Saves the query down to disk</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>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>) – filename</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="staticmethod">
+<dt id="promod3.modelling.MotifQuery.Load">
+<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.modelling.MotifQuery.Load" title="Permalink to this definition">¶</a></dt>
+<dd><p>Load query from disk</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>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>) – filename</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.MotifQuery.GetPositions">
+<code class="descname">GetPositions</code><span class="sig-paren">(</span><em>query_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetPositions" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns coordinates of specified query</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>query_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>) – Query from which you want the positions</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.MotifQuery.GetIdentifiers">
+<code class="descname">GetIdentifiers</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetIdentifiers" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns a list of all query identifiers.</p>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.MotifQuery.GetN">
+<code class="descname">GetN</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.MotifQuery.GetN" title="Permalink to this definition">¶</a></dt>
+<dd><p>Returns the number of queries</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="promod3.modelling.MotifMatch">
+<em class="property">class </em><code class="descclassname">promod3.modelling.</code><code class="descname">MotifMatch</code><a class="headerlink" href="#promod3.modelling.MotifMatch" title="Permalink to this definition">¶</a></dt>
+<dd><p>Object that holds information about a match found in <a class="reference internal" href="#promod3.modelling.FindMotifs" title="promod3.modelling.FindMotifs"><code class="xref py py-meth docutils literal"><span class="pre">FindMotifs()</span></code></a></p>
+<dl class="attribute">
+<dt id="promod3.modelling.MotifMatch.query_idx">
+<code class="descname">query_idx</code><a class="headerlink" href="#promod3.modelling.MotifMatch.query_idx" title="Permalink to this definition">¶</a></dt>
+<dd><p>Index of matching query</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.modelling.MotifMatch.mat">
+<code class="descname">mat</code><a class="headerlink" href="#promod3.modelling.MotifMatch.mat" title="Permalink to this definition">¶</a></dt>
+<dd><p>Transformation matrix to superpose matching query onto target</p>
+</dd></dl>
+
+<dl class="attribute">
+<dt id="promod3.modelling.MotifMatch.alignment">
+<code class="descname">alignment</code><a class="headerlink" href="#promod3.modelling.MotifMatch.alignment" title="Permalink to this definition">¶</a></dt>
+<dd><p>List of tuples which define matching pairs of query/target coordinates</p>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.modelling.FindMotifs">
+<code class="descclassname">promod3.modelling.</code><code class="descname">FindMotifs</code><span class="sig-paren">(</span><em>query</em>, <em>target_positions</em>, <em>hash_tresh=0.4</em>, <em>distance_thresh=1.0</em>, <em>refine_thresh=0.7</em>, <em>flags=list()</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.modelling.FindMotifs" title="Permalink to this definition">¶</a></dt>
+<dd><p>Performs the detection and refinement stages of the geometric hashing
+algorithm.</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>query</strong> – Query to be searched</li>
+<li><strong>target_positions</strong> – Coordinates of the target</li>
+<li><strong>hash_thresh</strong> – Parameter relevant for detection stage</li>
+<li><strong>distance_thresh</strong> – Parameter relevant for refinement stage</li>
+<li><strong>refine_thresh</strong> – Parameter relevant for refinement stage</li>
+<li><strong>flags</strong> – Equivalent to <em>flags</em> in <a class="reference internal" href="#promod3.modelling.MotifQuery" title="promod3.modelling.MotifQuery"><code class="xref py py-class docutils literal"><span class="pre">MotifQuery</span></code></a>
+constructor. If you didn’t provide anything there,
+this can be ignored. Only the actual coordinates
+matter in this case.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">All found matches</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 internal" href="#promod3.modelling.MotifMatch" title="promod3.modelling.MotifMatch"><code class="xref py py-class docutils literal"><span class="pre">MotifMatch</span></code></a></p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</div>
</div>
@@ -374,6 +635,7 @@ with the keys of the scores in <strong>scorer</strong></li>
<li><a class="reference internal" href="#">Modelling Algorithms</a><ul>
<li><a class="reference internal" href="#rigid-blocks">Rigid Blocks</a></li>
<li><a class="reference internal" href="#de-novo-modelling">De Novo Modelling</a></li>
+<li><a class="reference internal" href="#motif-finder">Motif Finder</a></li>
</ul>
</li>
</ul>
@@ -412,7 +674,7 @@ with the keys of the scores in <strong>scorer</strong></li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/gap_handling.html b/doc/html/modelling/gap_handling.html
index 5d52d66e2f53f35fe5e372accb51963bceef9d14..856ed3a388cb7915ae2d01dab313469d5e6c2824 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 2.0.0 documentation</title>
+ <title>Handling Gaps — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -61,8 +61,8 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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>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>
@@ -117,7 +117,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ChainHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ChainHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -268,13 +268,13 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>)</p>
</dd></dl>
<dl class="attribute">
@@ -319,7 +319,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><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>
</ul>
</td>
</tr>
@@ -360,7 +360,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><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>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
@@ -413,7 +413,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><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>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>
@@ -653,7 +653,7 @@ gaps of different chains or an N-terminal gap with a C-terminal gap.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/index.html b/doc/html/modelling/index.html
index d23c5cba75446f74ed5ef10605a6c07b8e44f214..4d1d100b5b554a0b27e792d8f223784866bc4aac 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 2.0.0 documentation</title>
+ <title>modelling - Protein Modelling — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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="Singularity" href="../container/singularity.html" />
@@ -114,6 +114,7 @@ a model fully automatically as follows:</p>
<li class="toctree-l1"><a class="reference internal" href="algorithms.html">Modelling Algorithms</a><ul>
<li class="toctree-l2"><a class="reference internal" href="algorithms.html#rigid-blocks">Rigid Blocks</a></li>
<li class="toctree-l2"><a class="reference internal" href="algorithms.html#de-novo-modelling">De Novo Modelling</a></li>
+<li class="toctree-l2"><a class="reference internal" href="algorithms.html#motif-finder">Motif Finder</a></li>
</ul>
</li>
</ul>
@@ -158,7 +159,7 @@ a model fully automatically as follows:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/loop_candidates.html b/doc/html/modelling/loop_candidates.html
index 2c2ed901ea6407d3f0c1662efa8e1052550ff6e1..82e51fce4011104f6a35012c2e1d73417da3b4b4 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 2.0.0 documentation</title>
+ <title>Handling Loop Candidates — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -133,8 +133,8 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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>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>
@@ -245,9 +245,9 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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
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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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
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
@@ -289,9 +289,9 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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
should match</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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
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>
@@ -365,7 +365,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.ProfileHandle.GetAverageScore" title="(in OpenStructure v1.10.0)"><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>
@@ -381,7 +381,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a>) – Profile information for target.</li>
<li><strong>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>
@@ -413,8 +413,8 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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>
</ul>
</td>
</tr>
@@ -1140,7 +1140,7 @@ scoring routines, <a class="reference internal" href="#promod3.modelling.ScoreCo
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/loop_closing.html b/doc/html/modelling/loop_closing.html
index b80eab62447dcba8e7a6a7fce292eb359a5eb063..7c104e3051826856a67092851e155c422174f8a3 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 2.0.0 documentation</title>
+ <title>Fitting Loops Into Gaps — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -84,11 +84,11 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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>
@@ -125,8 +125,8 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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>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>
@@ -327,7 +327,7 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>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>
@@ -349,7 +349,7 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>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>
@@ -372,7 +372,7 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>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>
@@ -394,7 +394,7 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>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>
@@ -416,7 +416,7 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – Restraint Position (in Angstrom)</li>
<li><strong>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>
@@ -643,7 +643,7 @@ the one given in the constructor.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/model_checking.html b/doc/html/modelling/model_checking.html
index 7c4a7a84be245178429a9b27b181b29da09d76a2..b944116fa0366bf0023ddaa88572d819f5cd94f3 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 2.0.0 documentation</title>
+ <title>Model Checking — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -58,14 +58,14 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/composite/#ost.geom.Plane" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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/geom/composite/#ost.geom.Plane" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>).</td>
</tr>
</tbody>
</table>
@@ -81,11 +81,11 @@ residue (<a class="reference external" href="https://www.openstructure.org/docs/
<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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a>) which
have a punched ring.</p>
</td>
</tr>
@@ -104,7 +104,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><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>
@@ -129,7 +129,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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>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>
@@ -194,7 +194,7 @@ 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="https://www.openstructure.org/docs/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v1.9.0)"><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/base/settings/#ost.settings.FileNotFound" title="(in OpenStructure v1.10.0)"><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>
@@ -211,7 +211,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a>) – OST entity on which to do analysis.</td>
</tr>
</tbody>
</table>
@@ -283,7 +283,7 @@ executable is not found.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/monte_carlo.html b/doc/html/modelling/monte_carlo.html
index 36c37e6adae99ef01fc1e36b383ca6cc525e14b3..e10a1bfadccc3282e33e6e99a11a4ba2272e5154 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 2.0.0 documentation</title>
+ <title>Generating Loops De Novo — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -506,9 +506,9 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should 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>
@@ -556,9 +556,9 @@ dihedral angles as it is the case for the <a class="reference internal" href="#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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation
should adapt.</li>
</ul>
</td>
@@ -598,9 +598,9 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</li>
-<li><strong>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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>c_stem</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</li>
<li><strong>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 for internal random generators.</li>
</ul>
@@ -639,7 +639,7 @@ superposing 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</td>
</tr>
</tbody>
@@ -677,7 +677,7 @@ superposing 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Defining stem positions the closed conformation should
adapt.</td>
</tr>
</tbody>
@@ -940,7 +940,7 @@ internal counter to 0</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/pipeline.html b/doc/html/modelling/pipeline.html
index 70a70284b31c5fa1fe17ea2b1acd9290dfda5763..33215e8bfb81487a015e272515314a80690fa0ee 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 2.0.0 documentation</title>
+ <title>Modelling Pipeline — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -118,7 +118,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">EntityHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -144,13 +144,13 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -159,7 +159,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><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
@@ -168,7 +168,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.ProfileHandle</span></code></a></td>
</tr>
</tbody>
</table>
@@ -355,7 +355,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityView" title="(in OpenStructure v1.10.0)"><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
@@ -383,7 +383,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.10.0)"><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
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
@@ -409,7 +409,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.AlignmentHandle.SetSequenceOffset" title="(in OpenStructure v1.10.0)"><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>
@@ -453,12 +453,12 @@ 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="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v1.9.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
-and <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v1.9.0)"><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/mol/mm/forcefield/#ost.mol.mm.LoadAMBERForcefield" title="(in OpenStructure v1.10.0)"><code class="xref py py-func docutils literal"><span class="pre">ost.mol.mm.LoadAMBERForcefield()</span></code></a>
+and <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.LoadCHARMMForcefield" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.9.0)"><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/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.10.0)"><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
(ligand) residue cannot be parametrized with the
default force field. The force fields are tried
in the order as given and ligands without an
@@ -479,7 +479,7 @@ limited. Termini of length 1 won’t be modelled.</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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
</td>
</tr>
</tbody>
@@ -654,7 +654,7 @@ 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="https://www.openstructure.org/docs/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.9.0)"><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/geom/mat/#ost.geom.Mat4" title="(in OpenStructure v1.10.0)"><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
they’re copied over</li>
</ul>
</td>
@@ -685,7 +685,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.ProfileHandle" title="(in OpenStructure v1.10.0)"><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>
@@ -842,7 +842,7 @@ 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="https://www.openstructure.org/docs/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v1.9.0)"><code class="xref py py-meth docutils literal"><span class="pre">ost.mol.alg.AssignSecStruct()</span></code></a>).</li>
+<a class="reference external" href="https://www.openstructure.org/docs/mol/alg/molalg/#ost.mol.alg.AssignSecStruct" title="(in OpenStructure v1.10.0)"><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
@@ -913,7 +913,7 @@ 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>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><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=None</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="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
@@ -946,7 +946,8 @@ This function cannot fill gaps at C- or N-terminal.</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>) – Modelling handle on which to apply change.</li>
<li><strong>fragment_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>) – A fragment database coupled to the <em>structure_db</em>.</li>
<li><strong>structure_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>) – Backbone/profile data.</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>) – A sampler for torsion angles.</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>) – A sampler for torsion angles. A default one is
+loaded if None.</li>
<li><strong>max_loops_to_search</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>) – Define how many candidates are ‘enough’ to be
evaluated per loop. The actual found candidates
may be more (if we found ‘enough’) or less (if
@@ -1015,7 +1016,7 @@ loops.</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>, <em>length_dep_weights=False</em><span class="sig-paren">)</span><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=None</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="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>.
@@ -1049,7 +1050,8 @@ is only used if the gap length is >= the length of fragments stored.</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>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>) – Modelling handle on which to apply change.</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>) – A sampler for torsion angles.</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>) – A sampler for torsion angles. A default one is
+loaded if None.</li>
<li><strong>max_loops_to_search</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>) – Define how many candidates are ‘enough’ to be
evaluated per loop.</li>
<li><strong>max_extension</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 gap extension steps to perform
@@ -1211,7 +1213,7 @@ one is loaded 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="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 <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.9.0)"><code class="xref py py-mod docutils literal"><span class="pre">ost.mol.mm</span></code></a> to perform energy minimization.
+<p>Uses <a class="reference external" href="https://www.openstructure.org/docs/mol/mm/molmm/#module-ost.mol.mm" title="(in OpenStructure v1.10.0)"><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>
@@ -1239,7 +1241,7 @@ minimization is aborted. This issue is logged and added as a major issue to
<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="https://www.openstructure.org/docs/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.9.0)"><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/mol/mm/forcefield/#ost.mol.mm.Forcefield" title="(in OpenStructure v1.10.0)"><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
<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>
@@ -1247,7 +1249,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">Entity</span></code></a></p>
</td>
</tr>
</tbody>
@@ -1335,8 +1337,8 @@ set to True, if the problem affects backbone atoms.</li>
<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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a> /
-<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueView</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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueHandle</span></code></a> /
+<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueView" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ResidueView</span></code></a></td>
</tr>
</tbody>
</table>
@@ -1453,7 +1455,7 @@ attribute yet, it is added.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/modelling/sidechain_reconstruction.html b/doc/html/modelling/sidechain_reconstruction.html
index 58ac0f35df0c576c780fb241eb008d389dba9dcc..0a2b09ea8c269e3a61396bf576b543c5f59cf734 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 2.0.0 documentation</title>
+ <title>Sidechain Reconstruction — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -47,7 +47,7 @@
<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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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>
@@ -102,7 +102,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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
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
@@ -214,7 +214,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><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>
@@ -441,7 +441,7 @@ in the environment (same length as <em>env_pos.res_indices</em>)</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 01a546df33de2546098bf5872f811a54f33353fe..02ecc00e655c54dada0b5e1e709b33f23e845db2 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 b1fbc6e8a0374ebe94ecc2eaa2d0ee2f8623c101..807daaeef51b0813f61a4e40407916889de0aa02 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 2.0.0 documentation</title>
+ <title>Using Binary Files In ProMod3 — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="up" title="Documentation For Developers" href="developers.html" />
<link rel="next" title="License" href="license.html" />
<link rel="prev" title="ProMod3‘s Share Of CMake" href="cmake/index.html" />
@@ -478,7 +478,7 @@ in the <code class="file docutils literal"><span class="pre">extras/data_generat
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/py-modindex.html b/doc/html/py-modindex.html
index 47841194a7a87d9425151bf3bb96d3332b3d75cb..8382e9e26c6f32c6bdb0bac184c676e330cf50fd 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 2.0.0 documentation</title>
+ <title>Python Module Index — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
@@ -132,7 +132,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/references.html b/doc/html/references.html
index d0836ee0a3ecb34c9bc50de14cb86f68f3ce9c47..cee6d5434a8074eff00e925c919d771815a4f10d 100644
--- a/doc/html/references.html
+++ b/doc/html/references.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>References — ProMod3 2.0.0 documentation</title>
+ <title>References — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="next" title="Changelog" href="changelog.html" />
<link rel="prev" title="License" href="license.html" />
@@ -132,6 +132,14 @@ Exploring the conformational space of protein side chains using
dead-end elimination and the A* algorithm. Proteins.</td></tr>
</tbody>
</table>
+<table class="docutils citation" frame="void" id="nussinov1991" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[nussinov1991]</td><td>Nussinov R and Wolfson HJ (1991).
+Efficient detection of three-dimensional structural motifs in
+biological macromolecules by computer vision techniques. PNAS.</td></tr>
+</tbody>
+</table>
<table class="docutils citation" frame="void" id="shapovalov2011" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
@@ -157,6 +165,14 @@ potentials and threading score functions using information
maximization. Proteins.</td></tr>
</tbody>
</table>
+<table class="docutils citation" frame="void" id="trott2010" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
+<tr><td class="label">[trott2010]</td><td>Trott O, Olson AJ (2010). AutoDock Vina: improving the speed and
+accuracy of docking with a new scoring function, efficient
+optimization and multithreading. J Comput Chem</td></tr>
+</tbody>
+</table>
<table class="docutils citation" frame="void" id="zhou2005" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
@@ -204,7 +220,7 @@ Fragments. Proteins.</td></tr>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/all_atom_scorers.html b/doc/html/scoring/all_atom_scorers.html
index 9c9f58223d159cc67c8941f0301d9412442629be..2c1ceae1ca06c0417fd24bbe814e340ccb68e694 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 2.0.0 documentation</title>
+ <title>All Atom Scorers — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="../index.html" />
<link rel="up" title="scoring - Loop Scoring" href="index.html" />
<link rel="next" title="Other Scoring Functions" href="other_scoring_functions.html" />
<link rel="prev" title="Backbone Scorers" href="backbone_scorers.html" />
@@ -672,7 +672,7 @@ of residues in the input loop. True by default.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/backbone_score_env.html b/doc/html/scoring/backbone_score_env.html
index 6235608ccb7f65b630125f4963999b8efe227e07..4102971fd221d81757841b4e3daa61f0d0a36a4b 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 2.0.0 documentation</title>
+ <title>Backbone Score Environment — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -69,8 +69,8 @@ task.</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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><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
chain). Whenever setting structural data, consistency with this SEQRES is enforced.</td>
</tr>
</tbody>
@@ -107,7 +107,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.EntityHandle" title="(in OpenStructure v1.10.0)"><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
in <em>env_structure</em> are expected to be in the same
order as the SEQRES items provided in constructor.</td>
</tr>
@@ -131,7 +131,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResNum" title="(in OpenStructure v1.10.0)"><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>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>
@@ -280,7 +280,7 @@ providing lists of integers.</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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.SequenceList" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.SequenceList</span></code></a></td>
</tr>
</tbody>
</table>
@@ -387,7 +387,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.SequenceHandle" title="(in OpenStructure v1.10.0)"><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>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>
@@ -402,7 +402,7 @@ 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="https://www.openstructure.org/docs/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.9.0)"><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/seq/base/seq/#ost.seq.AlignmentHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.seq.AlignmentHandle</span></code></a>) – Alignment, where first sequence represent the initial
SEQRES and the second sequence the actual structural
info. The second sequence must have a view attached.</td>
</tr>
@@ -508,7 +508,7 @@ inconsistent with SEQRES you initialized the DiscoContainer with</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/backbone_scorers.html b/doc/html/scoring/backbone_scorers.html
index 7b8ad9e7b4e2f9a759ccd41078a13c8d9cb4cf1a..5787bc4c9307fa8d0716f96a6d7593a821b593ea 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 2.0.0 documentation</title>
+ <title>Backbone Scorers — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -381,7 +381,7 @@ 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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>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>
@@ -515,8 +515,8 @@ SetEnergy(aa2, aa1, bin, energy).</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>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>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>
@@ -695,8 +695,8 @@ SetEnergy(aa2, aa1, dist_bin, beta_bin, alpha_bin, energy).</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>aa1</strong> (<a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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>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>
@@ -1388,7 +1388,7 @@ of residues to be scored. True by default.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/index.html b/doc/html/scoring/index.html
index f56b23ba357753d48b79c1708a60c2c588312afe..c4a6177e14b51adb45f06bd050d16a21184d1994 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 2.0.0 documentation</title>
+ <title>scoring - Loop Scoring — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -152,7 +152,7 @@ scorers to it and finally score some loops:</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/scoring/other_scoring_functions.html b/doc/html/scoring/other_scoring_functions.html
index 57c6c16db63043d18557fa5de92e3348e1fc74b0..b639d4f79929726ca22d0eb2ff8a075318326e28 100644
--- a/doc/html/scoring/other_scoring_functions.html
+++ b/doc/html/scoring/other_scoring_functions.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Other Scoring Functions — ProMod3 2.0.0 documentation</title>
+ <title>Other Scoring Functions — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -159,7 +159,7 @@ construction algorithm <a class="reference internal" href="../references.html#ca
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/search.html b/doc/html/search.html
index 4eb4082b859a1ecc68b3dd78a53e83b6061b6eb1..874ca440df26a4aac33d1d09769355e081d5c63a 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 2.0.0 documentation</title>
+ <title>Search — ProMod3 2.1.0 documentation</title>
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<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '2.0.0',
+ VERSION: '2.1.0',
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FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -25,7 +25,7 @@
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<script type="text/javascript" src="_static/searchtools.js"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<script type="text/javascript">
jQuery(function() { Search.loadIndex("searchindex.js"); });
</script>
@@ -87,7 +87,7 @@
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
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index 7b6f6337667fa0eb0c3269740f31f593b2cd9106..0526fe4e70ec80cc440a08f0b2f0c0139e787535 100644
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+++ b/doc/html/searchindex.js
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urs:8,coutsia:38,coutsias2005:[32,38],cover:[0,1,8,12,13,14,21,25,26,28,30,34,35],coverag:[0,3,35],cparticl:49,cpp:4,cpr:[51,52],cpu:[18,25,35],cpu_platform_support:25,crambin:[26,31,34],crash:47,createalign:[31,35],createentityfromview:[36,47],createfromfrmlist:[46,47],createfromrrmlist:46,createfullview:[30,31,35],createscwrl4particl:49,createsequ:[26,31,35],creation:[25,32,49],creator:[25,32],criteria:36,criterion:[10,34],criterium:31,croak:16,cross:20,crucial:8,crude:[0,35],cryst:38,cterminalclos:34,cumul:50,current:[2,4,5,8,10,14,16,21,22,25,26,31,34,35,37,40,41,42,49,50,53],custom:[8,26,34,35,36,37,48,51],customari:20,cutoff:[24,25,31,32,36,39,41],cycl:29,cyclic:[31,32,38],cyd:[51,52],cyh:[51,52],cys_hb3:21,cys_sg:21,cystein:[25,36,44,47,51],d_bin:41,dai:11,damag:20,dampen:25,danc:38,dare:4,dat:[26,37],data1:4,data2:4,data:[0,1,3,4,8,16,17,21,23,24,25],data_:37,data_gener:[3,37,48],data_to_stor:26,data_typ:26,databas:[0,9,23,24],databs:26,datatyp:26,date:[5,7,16,20],davi:38,davis2006:[22,38],dbg:8,dcmake_install_prefix:2,deactiv:10,dead:[10,38],deal:[35,36],debug:[8,10,21],decent:15,decid:[3,8,32],decis:27,declar:[4,8,16],decod:13,decompos:[3,10],decomposit:[10,28,46],decreas:34,dedic:[4,8,16],dee:10,deep:[22,35],def:[1,8,21,35],def_angl:21,defend:20,defin:[1,4,8,9,13,14,15,20,21,22,23,24,25],definem:8,degre:[22,26,27],delet:[0,2,8,22,35,49],deliber:20,deliv:[1,26,34,35],delta_scor:34,demand:35,demonstr:26,denovoclos:34,densiti:[22,32,38],dep1:4,dep2:4,dep:4,depend:0,dependency1:4,dependency2:4,depends_on:4,depth:[26,38],deriv:[1,20,26,38,43,44],descend:35,descent:[31,32,38],describ:[0,4,7,8,10,11,17,20,21,22,26,29,30,32,33,37,39,41,44,47,48,49,52,55],descript:[0,5,13,16,20,34,35,52],descriptor:26,descsrib:10,design:[1,3,19,20],desir:[9,18,25,31,32,34,35,39,40,41],despit:3,detail:[0,9,13,16,20,25,26,27,31,33,34,35,39,41,48,52],detect:[0,11,28,30],determin:[8,11,20,25,26,31,34,40,41],determinist:28,deuterium:35,develop:[1,3,8,16],deviat:[22,33,34,52],devot:12,dict:[4,28,31,33,34,39,41],dictionari:[4,5,13,15,33,38],did:[8,26,31,35],didn:7,didnt:5,differ:[1,2,4,8,10,15,16,20,21,26,28,29,31,35,39,41,47,51,52],differenti:49,dihedr:[9,18,22,23,25,26],dihedral_angl:22,dihedral_bin:41,dihedral_idx:52,dihedral_pair:27,dihedralconfigur:52,dill:38,dimens:27,dir:[4,8,18],direct:[8,20,22,24,26,41,49,50],directli:[8,10,18,26,31,35,36,40,44,49,51,52,54],directori:[1,2,4,5,7,8],dirti:1,dirtyccdclos:34,disabl:[1,16],disable_doctest:2,disable_document:2,disable_linkcheck:2,discard:26,disclaim:20,discocontain:40,disconnect:3,discret:[39,41],discuss:[20,26],disk:[8,25,28,39,41,52],displai:[11,13,14,20],dissimilar:28,dist:41,dist_bin:41,dist_bin_s:26,distanc:[9,22,26,28,31,35,36,39,40,41,43,49],distance_thresh:28,distant:40,distinct:[21,36,52],distinguish:3,distribut:[1,8,20,25,26,27,34,37,39,41,48,52],disulfid:[0,25,32,36,43],disulfid_bridg:[25,36],disulfid_score_thresh:36,disulfidscor:[36,44],dive:[16,35],diverg:8,divers:[26,28],dng:18,do_it:[39,41],doc:[2,4,8,16,20],docker:3,dockerfil:[5,7],docstr:13,doctest:[2,8,16],document:[1,2],doe:[1,3,4,8,9,10,11,13,15,16,20,22,26,30,31,34,35,37,40,48],doesn:[8,16,29,32,34,35,52],doesnt:52,doexternalscor:[39,41],dointernalscor:[39,41],domain:28,domin:10,don:[2,10,20,31,35,50],done:[1,8,11,13,16,23,25,27,31,34,35,37],donor:41,donorm:[39,41],dont:[0,34],dont_write_bytecod:1,dost_root:2,doubt:13,down:[13,22,26,34],download:5,dpm3_runtime_profiling_level:14,draw:[22,27,34],drawback:8,drawn:[27,34],drawphigivenpsi:27,drawpsigivenphi:27,drop:8,dssp:[3,26,41],dssp_state:41,due:[0,26,31,32,35,44],dump:52,dunbrack:[3,38,48],duplic:6,dure:[1,21,32,35,37,45,52],dynam:52,dynamicspatialorgan:3,e_cut:10,e_thresh:[10,35],e_tresh:10,each:[0,8,10,13,14,20,21,22,25,26,27,28,29,31,32,33,34,35,36,37,39,41],earli:3,earlier:2,easi:8,easier:[1,8,20],easili:[4,16,35],echo:8,edg:10,edge_idx:10,editor:1,editori:20,educ:8,effect:[4,8,10,25,36,44],effici:[21,28,34,38,42],egg:26,eigen3_include_dir:2,eigen:[2,3],either:[0,8,13,16,20,21,22,27,29,31,32,34,35,36,37,39,40,41,45,49,51,52],elabor:[8,20],electron:20,electrostat:[25,32],element:[1,10,21,22,26,28,31,33,37,40,44],elimin:[10,38],els:[8,16,36,37],emerg:1,empir:[43,44],emploi:16,empti:[8,11,13,22,26,28,31,35,49],enabl:[1,2,3,11,13,15,25,26],enable_mm:2,enable_ss:2,enclos:[20,29,35],encod:0,encount:[29,34],end:[0,1,2,4,8,10,11,13,16,20,21,22,26,28,29,31,35,38],end_resnum:35,end_transl:4,endian:37,energi:[0,3,8,10,18,25,32,34,35,36,39,41,44,45,46,47,49,50,53],energy_funct:[0,36],enforc:[0,3,21,31,34,35,36,39,40,41],engin:19,enough:[8,16,25,26,35,37],ensur:[2,8,18,31,35,37],ent:[0,13,21,25,26,33,36,42],ent_seq:42,enter:[35,45],entiti:[8,13,14,20,21,22,26,33,35,42,47],entityhandl:[13,21,22,33,35,36,40],entityview:[26,27,28,33,35],entri:[0,3,8,14,25,26,31,32,33,36,41,47,50],enumer:[8,10,21,25,26,31,35,40,47,50,51,52],env:[8,18,21,25,28,32,33,35,36,39,40,41,42],env_po:[32,36],env_structur:[21,40],environ:[1,3,8,21,28,29,31,32,34,35,36,37,39],epsilon:[10,25,36,5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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","Docker","ProMod3 and Containers","Singularity","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","ProMod3","License","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","References","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 - The Rigid Part","Rotamer Graph","<code class=\"docutils literal\"><span class=\"pre\">sidechain</span></code> - Sidechain Modelling","Loading Rotamer Libraries","Representing Sidechains - Rotamers & Co.","Rotamer Constructor","Rotamer Library","Subrotamer Optimization","Contributing","Documentation For Users"],titleterms:{"class":[21,22,26,27,29,31,36,39,40,41],"default":35,"function":[4,9,11,12,29,36,40,43,49,50],acid:[21,25,27],action:[0,1,4,5,7,8],actiontestcas:1,algorithm:28,all:[21,32,39],allatomclashscor:39,allatomenv:21,allatomenvposit:21,allatominteractionscor:39,allatomoverallscor:39,allatompackingscor:39,allatomposit:21,allatomscor:39,amino:[21,25,27],angl:27,api:1,argument:13,atom:[21,32,39],backbon:[32,40,41,51],backbonelist:22,backboneoverallscor:41,backbonescor:41,backbonescoreenv:40,base:[26,39,41],baseclass:50,binari:37,block:[28,49],bond:44,branch:16,build:[0,2,5,7,35,49],can:49,candid:31,cbetascor:41,cbpackingscor:41,ccd:32,chain:26,changelog:3,check:33,clashscor:41,closer:34,cmake:[1,2,4,16],code:37,command:13,compound:[5,7],configur:51,construct:40,constructor:50,contain:6,contribut:[8,53],conveni:40,cooler:34,core:12,creat:[1,25],data:[26,37],databas:26,defin:[26,27],definit:4,depend:[2,51],detect:33,develop:17,dihedr:27,directori:16,distinguish:21,disulfid:44,docker:5,document:[4,8,17,19,54],entri:51,environ:40,evalu:44,everyth:11,exampl:[31,37],execut:1,exisit:37,extend:29,featur:[8,26],file:[11,37],find:26,finder:28,fit:32,forcefield:25,fragment:26,frame:45,from:43,gap:[29,32],gener:[25,34],geometr:26,geometri:9,get:[18,49],git:16,graph:[10,46],group:49,handl:[21,23,29,31,35],have:1,hbondscor:41,header:37,helper:11,hook:16,how:[8,49],imag:[5,7],instal:2,integr:1,introduct:[4,11,13],issu:8,keep:31,kic:32,librari:[5,7,48,51],licens:[8,20],line:13,load:[24,48],lookup:25,loop:[22,23,25,31,32,34,42],loopcandid:31,mainten:4,make:[1,2],messag:11,minim:10,model:[0,18,28,30,31,33,35,47],modul:[4,8],mol:25,molprob:33,motif:28,must:1,non:51,novo:[28,34],object:[24,34,45],optim:52,ost:[5,7,25],other:43,output:1,own:8,pairwis:40,pairwisescor:41,pars:13,parser:13,part:45,parti:8,particl:49,pipelin:[18,35],pm3argpars:13,portabl:37,posit:21,precomput:24,profil:14,promod3:[0,2,4,6,8,12,16,18,19,37],protein:30,psipredpredict:26,punch:33,quick:8,raw:35,reconstruct:36,reducedscor:41,refer:38,relax:32,releas:3,repres:[22,49],rigid:[28,45],ring:33,rotam:[46,48,49,50,51],rotamerconstructor:50,rotamerid:49,run:[1,2,5,7,18],runtim:14,sampl:27,sampler:[27,34],score:[31,40,42,43,49,50],scorer:[8,34,39,41],script:[1,5,7,8],scwrl3:[43,49],scwrl4:49,sequenc:26,setcompoundschemlib:15,setup:16,share:[4,8,11],sidechain:[0,36,47,49],sidechainreconstructiondata:36,sidechainreconstructor:36,singular:7,smallest:49,specif:50,ssagreementscor:41,stage:16,start:[8,18],step:35,structur:[16,26],subclass:1,subrotam:52,system:25,test:[1,4,8,11],test_act:1,third:8,torsion:27,torsionscor:41,track:31,triplet:27,type:51,unit:[1,4,8],user:54,vina:49,write:8,your:8}})
\ No newline at end of file
diff --git a/doc/html/sidechain/disulfid.html b/doc/html/sidechain/disulfid.html
index 9e47ea4c753400b53429b567c94e62517f6bbdd1..934027fea20063d03c090c1936b0fd653d078932 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 2.0.0 documentation</title>
+ <title>Disulfid Bond Evaluation — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -77,10 +77,10 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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>
@@ -113,8 +113,8 @@ 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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><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>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
@@ -180,7 +180,7 @@ describe the optimal rotamers in the according rotamer groups.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/frame.html b/doc/html/sidechain/frame.html
index a40d117535fa22c6b4ee6610509f3ec34afffdde..b754527088d1cbe230c678d2500463cb3ffa54dd 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 2.0.0 documentation</title>
+ <title>Frame - The Rigid Part — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,10 +24,10 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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="next" title="Rotamer Constructor" href="rotamer_constructor.html" />
+ <link rel="prev" title="Representing Sidechains - Rotamers & Co." href="rotamer.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -42,8 +42,8 @@
<div class="bodywrapper">
<div class="body" role="main">
- <div class="section" id="frame">
-<h1>Frame<a class="headerlink" href="#frame" title="Permalink to this headline">¶</a></h1>
+ <div class="section" id="frame-the-rigid-part">
+<h1>Frame - The Rigid Part<a class="headerlink" href="#frame-the-rigid-part" title="Permalink to this headline">¶</a></h1>
<p>In contrast to the rotamers, the frame is a rigid object. It either
represents the protein backbone or sidechains kept rigid during the
sidechain modelling process. Regions, that should not be occupied by
@@ -129,7 +129,7 @@ can be passed to rotamer groups for calculating frame energies.</p>
<div class="sphinxsidebarwrapper">
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
-<li><a class="reference internal" href="#">Frame</a><ul>
+<li><a class="reference internal" href="#">Frame - The Rigid Part</a><ul>
<li><a class="reference internal" href="#the-frame-objects">The Frame Objects</a></li>
</ul>
</li>
@@ -140,8 +140,8 @@ can be passed to rotamer groups for calculating frame energies.</p>
<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">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="rotamer.html" title="previous chapter">Rotamers</a></li>
- <li>Next: <a href="rotamer_lib.html" title="next chapter">Rotamer Library</a></li>
+ <li>Previous: <a href="rotamer.html" title="previous chapter">Representing Sidechains - Rotamers & Co.</a></li>
+ <li>Next: <a href="rotamer_constructor.html" title="next chapter">Rotamer Constructor</a></li>
</ul></li>
</ul></li>
</ul></li>
@@ -169,7 +169,7 @@ can be passed to rotamer groups for calculating frame energies.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/graph.html b/doc/html/sidechain/graph.html
index e843e0a687a79b945b82600f3087b3f90451be9a..03f601c9b5ab3462fc42aafdac4f90b0e57546c1 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 2.0.0 documentation</title>
+ <title>Rotamer Graph — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,10 +24,10 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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="prev" title="Rotamer Library" href="rotamer_lib.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -91,7 +91,7 @@ conformations for every amino acid position.</td>
<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">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="rotamer_constructor.html" title="previous chapter">Rotamer Constructor</a></li>
+ <li>Previous: <a href="rotamer_lib.html" title="previous chapter">Rotamer Library</a></li>
<li>Next: <a href="disulfid.html" title="next chapter">Disulfid Bond Evaluation</a></li>
</ul></li>
</ul></li>
@@ -120,7 +120,7 @@ conformations for every amino acid position.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/index.html b/doc/html/sidechain/index.html
index 1f48d7131a1c4e1b7064a8ebd8f819e8300316f5..57f8e3d4ae42ec76cedc4fab30b4402a7e32d8a3 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 2.0.0 documentation</title>
+ <title>sidechain - Sidechain Modelling — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,9 +24,9 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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="next" title="Representing Sidechains - Rotamers & Co." href="rotamer.html" />
<link rel="prev" title="Modelling Algorithms" href="../modelling/algorithms.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -145,22 +145,22 @@ pipelines available in the modelling module.</p>
<p>Contents:</p>
<div class="toctree-wrapper compound">
<ul>
-<li class="toctree-l1"><a class="reference internal" href="rotamer_id.html">RotamerID</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="rotamer_id.html#the-rotamerid">The RotamerID</a></li>
-<li class="toctree-l2"><a class="reference internal" href="rotamer_id.html#how-can-i-get-an-id">How can I get an ID?</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="rotamer.html">Rotamers</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="rotamer.html">Representing Sidechains - Rotamers & Co.</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="rotamer.html#rotamerid">RotamerID</a></li>
<li class="toctree-l2"><a class="reference internal" href="rotamer.html#the-smallest-building-block-the-particle">The Smallest Building Block - The Particle</a></li>
-<li class="toctree-l2"><a class="reference internal" href="rotamer.html#the-scwrl4-scoring-function">The SCWRL4 scoring function</a></li>
-<li class="toctree-l2"><a class="reference internal" href="rotamer.html#id1">Rotamers</a></li>
+<li class="toctree-l2"><a class="reference internal" href="rotamer.html#rotamers">Rotamers</a></li>
<li class="toctree-l2"><a class="reference internal" href="rotamer.html#rotamer-groups">Rotamer Groups</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="frame.html">Frame</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="frame.html">Frame - The Rigid Part</a><ul>
<li class="toctree-l2"><a class="reference internal" href="frame.html#the-frame-objects">The Frame Objects</a></li>
</ul>
</li>
+<li class="toctree-l1"><a class="reference internal" href="rotamer_constructor.html">Rotamer Constructor</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="rotamer_constructor.html#the-rotamerconstructor-baseclass">The RotamerConstructor Baseclass</a></li>
+<li class="toctree-l2"><a class="reference internal" href="rotamer_constructor.html#scoring-function-specific-rotamerconstructors">Scoring Function Specific RotamerConstructors</a></li>
+</ul>
+</li>
<li class="toctree-l1"><a class="reference internal" href="rotamer_lib.html">Rotamer Library</a><ul>
<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#the-non-backbone-dependent-rotamer-library">The Non Backbone Dependent Rotamer Library</a></li>
<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#the-backbone-dependent-rotamer-library">The Backbone Dependent Rotamer Library</a></li>
@@ -168,10 +168,6 @@ pipelines available in the modelling module.</p>
<li class="toctree-l2"><a class="reference internal" href="rotamer_lib.html#rotamer-configurations">Rotamer Configurations</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="rotamer_constructor.html">Rotamer Constructor</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="rotamer_constructor.html#constructing-rotamers-and-frame-residues">Constructing Rotamers and Frame Residues</a></li>
-</ul>
-</li>
<li class="toctree-l1"><a class="reference internal" href="graph.html">Rotamer Graph</a></li>
<li class="toctree-l1"><a class="reference internal" href="disulfid.html">Disulfid Bond Evaluation</a></li>
<li class="toctree-l1"><a class="reference internal" href="loading.html">Loading Rotamer Libraries</a></li>
@@ -191,7 +187,7 @@ pipelines available in the modelling module.</p>
<li><a href="../index.html">Documentation overview</a><ul>
<li><a href="../users.html">Documentation For Users</a><ul>
<li>Previous: <a href="../modelling/algorithms.html" title="previous chapter">Modelling Algorithms</a></li>
- <li>Next: <a href="rotamer_id.html" title="next chapter">RotamerID</a></li>
+ <li>Next: <a href="rotamer.html" title="next chapter">Representing Sidechains - Rotamers & Co.</a></li>
</ul></li>
</ul></li>
</ul>
@@ -218,7 +214,7 @@ pipelines available in the modelling module.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/loading.html b/doc/html/sidechain/loading.html
index 1e7bc1857b82f08787f9391ab628bbf4b25680de..1cd38b191475013d7c8f3f9386a78dc28747c80d 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 2.0.0 documentation</title>
+ <title>Loading Rotamer Libraries — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -159,7 +159,7 @@ incomplete if the last problem gets triggered.</td>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/rotamer.html b/doc/html/sidechain/rotamer.html
index e91619bdea34caade0bbe9f581575b1ef222ce51..74427adf1f6b560313d9863e8ee20eb13ec118e4 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 2.0.0 documentation</title>
+ <title>Representing Sidechains - Rotamers & Co. — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,10 +24,10 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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="next" title="Frame - The Rigid Part" href="frame.html" />
+ <link rel="prev" title="sidechain - Sidechain Modelling" href="index.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -42,18 +42,104 @@
<div class="bodywrapper">
<div class="body" role="main">
- <div class="section" id="rotamers">
-<h1>Rotamers<a class="headerlink" href="#rotamers" title="Permalink to this headline">¶</a></h1>
-<p>A rotamer represents an amino acid sidechain and is basically a set of
-<a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> objects. There exist two types. The <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> and
-<a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>.
-To gather all possible rotamers for one particular sidechain position,
+ <div class="section" id="representing-sidechains-rotamers-co">
+<h1>Representing Sidechains - Rotamers & Co.<a class="headerlink" href="#representing-sidechains-rotamers-co" title="Permalink to this headline">¶</a></h1>
+<p>A rotamer represents an amino acid sidechain identified by a <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>
+and is a set of <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> objects.
+Two types of rotamers exist. The <a class="reference internal" href="#promod3.sidechain.RRMRotamer" title="promod3.sidechain.RRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamer</span></code></a> and <a class="reference internal" href="#promod3.sidechain.FRMRotamer" title="promod3.sidechain.FRMRotamer"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamer</span></code></a>.
+To gather all possible rotamers for one location,
ProMod3 offers the <a class="reference internal" href="#promod3.sidechain.RRMRotamerGroup" title="promod3.sidechain.RRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">RRMRotamerGroup</span></code></a> and <a class="reference internal" href="#promod3.sidechain.FRMRotamerGroup" title="promod3.sidechain.FRMRotamerGroup"><code class="xref py py-class docutils literal"><span class="pre">FRMRotamerGroup</span></code></a>.
-Pairwise interactions between particles give raise to pairwise energies between
-rotamers. Nevertheless, the energy calculation itself happens on the level
-of RotamerGroups and is mostly hidden away in the construction of the
-the <a class="reference internal" href="graph.html#promod3.sidechain.RotamerGraph" title="promod3.sidechain.RotamerGraph"><code class="xref py py-class docutils literal"><span class="pre">RotamerGraph</span></code></a>. If you’re too lazy to build up your rotamers
-by hand, you might be interested in the <a class="reference internal" href="rotamer_constructor.html#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a>.</p>
+All parts of the structure that are kept rigid can be represented by
+a <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> object.</p>
+<div class="section" id="rotamerid">
+<h2>RotamerID<a class="headerlink" href="#rotamerid" title="Permalink to this headline">¶</a></h2>
+<p>The sidechain module has its own definition of amino acids to satisfy custom
+requirements for the implemented sidechain construction algorithms.
+As an example there are histidine in two possible protonation states,
+that affect the hbond term or different versions of proline/cysteine.</p>
+<dl class="class">
+<dt id="promod3.sidechain.RotamerID">
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerID</code><a class="headerlink" href="#promod3.sidechain.RotamerID" title="Permalink to this definition">¶</a></dt>
+<dd><p>Enumerates the amino acids. Possible values:</p>
+<table class="hlist"><tr><td><ul class="simple">
+<li>ARG - Arginine</li>
+<li>ASN - Asparagine</li>
+<li>ASP - Aspartate</li>
+<li>GLN - Glutamine</li>
+<li>GLU - Glutamate</li>
+<li>LYS - Lysine</li>
+<li>SER - Serine</li>
+<li>CYS - Cystein</li>
+<li>CYH - “free” Cystein</li>
+<li>CYD - disulfid bonded Cystein</li>
+<li>MET - Methionine</li>
+<li>TRP - Tryptophane</li>
+<li>TYR - Tyrosine</li>
+<li>THR - Threonine</li>
+</ul>
+</td><td><ul class="simple">
+<li>VAL - Valine</li>
+<li>ILE - Isoleucine</li>
+<li>LEU - Leucine</li>
+<li>PRO - Proline</li>
+<li>CPR - cis-Proline</li>
+<li>TPR - trans-Proline</li>
+<li>HIS - Histidine</li>
+<li>HSD - d-protonated Histidine</li>
+<li>HSE - e-protonated Histidine</li>
+<li>PHE - Phenylalanine</li>
+<li>GLY - Glycine</li>
+<li>ALA - Alanine</li>
+<li>XXX - Invalid</li>
+</ul>
+</td></tr></table>
+<p>The RotamerID enum can be accessed either directly as <code class="docutils literal"><span class="pre">promod3.sidechain.ARG</span></code>
+or as <code class="docutils literal"><span class="pre">promod3.sidechain.RotamerID.ARG</span></code>.</p>
+</dd></dl>
+
+<div class="section" id="how-can-i-get-an-id">
+<h3>How can I get an ID?<a class="headerlink" href="#how-can-i-get-an-id" title="Permalink to this headline">¶</a></h3>
+<p>The RotamerID enum can directly be accessed from Python. Two convenient
+functions exist to get RotamerIDs from the <a class="reference external" href="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">TLCToRotID</code><span class="sig-paren">(</span><em>tlc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.TLCToRotID" title="Permalink to this definition">¶</a></dt>
+<dd><p>Directly translates the three letter code into a RotamerID. Following
+exactly the naming convention defined above.</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>tlc</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>) – Three letter code 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>tlc</strong> cannot be recoginzed.</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.AAToRotID">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">AAToRotID</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.AAToRotID" title="Permalink to this definition">¶</a></dt>
+<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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td>
+</tr>
+<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>
+</tbody>
+</table>
+</dd></dl>
+
+</div>
+</div>
<div class="section" id="the-smallest-building-block-the-particle">
<h2>The Smallest Building Block - The Particle<a class="headerlink" href="#the-smallest-building-block-the-particle" title="Permalink to this headline">¶</a></h2>
<p>Particles give raise to more complex objects such as rotamers and frame
@@ -65,7 +151,9 @@ function.</p>
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">PScoringFunction</code><a class="headerlink" href="#promod3.sidechain.PScoringFunction" title="Permalink to this definition">¶</a></dt>
<dd><p>The available scoring functions between <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> objects</p>
<ul class="simple">
-<li>SCWRL4</li>
+<li>SCWRL4 - <a class="reference internal" href="#scwrl4-scoring-function"><span class="std std-ref">The SCWRL4 scoring function</span></a></li>
+<li>SCWRL3 - <a class="reference internal" href="#scwrl3-scoring-function"><span class="std std-ref">The SCWRL3 scoring function</span></a></li>
+<li>VINA - <a class="reference internal" href="#vina-scoring-function"><span class="std std-ref">The VINA scoring function</span></a></li>
</ul>
</dd></dl>
@@ -140,7 +228,7 @@ evaluated by the underlying scoring function.</td>
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">The position of the particle</td>
</tr>
-<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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><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/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a></td>
</tr>
</tbody>
</table>
@@ -163,13 +251,16 @@ evaluated by the underlying scoring function.</td>
</dd></dl>
-</div>
<div class="section" id="the-scwrl4-scoring-function">
-<h2>The SCWRL4 scoring function<a class="headerlink" href="#the-scwrl4-scoring-function" title="Permalink to this headline">¶</a></h2>
+<span id="scwrl4-scoring-function"></span><h3>The SCWRL4 scoring function<a class="headerlink" href="#the-scwrl4-scoring-function" title="Permalink to this headline">¶</a></h3>
+<p>The SCWRL4 scoring function combines a Lennard-Jones style term with
+a hydrogen bond term. Details can be found in the relevant publication
+<a class="reference internal" href="../references.html#krivov2009" id="id1">[krivov2009]</a>.</p>
<dl class="class">
<dt id="promod3.sidechain.SCWRL4ParticleType">
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRL4ParticleType</code><a class="headerlink" href="#promod3.sidechain.SCWRL4ParticleType" title="Permalink to this definition">¶</a></dt>
-<dd><p>The SCWRL4 energy function differentiates between following particle types</p>
+<dd><p>The SCWRL4 energy function differentiates between following particle types
+that define the behaviour of the Lennard-Jones style term:</p>
<ul class="simple">
<li>HParticle - represents hydrogen</li>
<li>CParticle - default representation of a carbon</li>
@@ -195,13 +286,21 @@ function</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<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>) – The name of the particle</li>
<li><strong>particle_type</strong> (<a class="reference internal" href="#promod3.sidechain.SCWRL4ParticleType" title="promod3.sidechain.SCWRL4ParticleType"><code class="xref py py-class docutils literal"><span class="pre">SCWRL4ParticleType</span></code></a>) – The type of the particle</li>
-<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the 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>) – The charge of the particle, relevant for the hydrogen
bond term</li>
<li><strong>lone_pairs</strong> (<code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3List</span></code>) – Direction of all possible lone pairs of the particle,
-relevant for the hydrogen bond term</li>
-<li><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
-relevant for the hdrogen bond term</li>
+relevant for the hydrogen bond term. If set, the
+particle is a potential hydrogen bond acceptor.
+An example would be the Serine OG atom, where you can
+represent the two lone pairs with vectors pointing
+from the OG position towards the lone pair centers.</li>
+<li><strong>polar_direction</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The polar direction of the particle,
+relevant for the hydrogen bond term. If set, the
+particle is a potential hydrogen bond donor. An
+example would be the Serine HG hydrogen. The
+<em>polar_direction</em> would be a vector
+estimated as follows: hg_pos-og_pos.</li>
</ul>
</td>
</tr>
@@ -210,8 +309,93 @@ relevant for the hdrogen bond term</li>
</dd></dl>
</div>
-<div class="section" id="id1">
-<h2>Rotamers<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="the-scwrl3-scoring-function">
+<span id="scwrl3-scoring-function"></span><h3>The SCWRL3 scoring function<a class="headerlink" href="#the-scwrl3-scoring-function" title="Permalink to this headline">¶</a></h3>
+<p>The SCWRL3 scoring function implements a simple repulsion term that depends on
+the hard-sphere radius of the involved particles.
+Details can be found in the relevant publication <a class="reference internal" href="../references.html#canutescu2003" id="id2">[canutescu2003]</a>.</p>
+<dl class="method">
+<dt id="promod3.sidechain.CreateSCWRL3Particle">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">CreateSCWRL3Particle</code><span class="sig-paren">(</span><em>name</em>, <em>radius</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateSCWRL3Particle" title="Permalink to this definition">¶</a></dt>
+<dd><p>Creates and returns a <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> that can evaluate the SCWRL3 scoring
+function</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>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>) – The name of the particle</li>
+<li><strong>radius</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 hard-sphere radius of the particle, relevant for the
+repulsion term.</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</div>
+<div class="section" id="the-vina-scoring-function">
+<span id="vina-scoring-function"></span><h3>The VINA scoring function<a class="headerlink" href="#the-vina-scoring-function" title="Permalink to this headline">¶</a></h3>
+<p>The VINA scoring function is a combination of scores that are named
+gaussian1, gaussian2, repulsion, hydrophobic and hbond in the Autodock Vina
+software <a class="reference internal" href="../references.html#trott2010" id="id3">[trott2010]</a>. VINA only evaluates heavy atoms. Gaussian1, gaussian2
+and repulsion are evaluated for all pairs of particles. Hydrophobic is only
+evaluated between C_VINAParticle <a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a> and hbond is
+evaluated between hydrogen bond donor/acceptor pairs. While SCWRL3 and SCWRL4
+are intended to evaluate sidechain-sidechain interactions in proteins,
+VINA is mainly targeted at interactions between sidechains and ligands.</p>
+<p>The VINA scoring function differentiates between the following particle types:</p>
+<dl class="class">
+<dt id="promod3.sidechain.VINAParticleType">
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">VINAParticleType</code><a class="headerlink" href="#promod3.sidechain.VINAParticleType" title="Permalink to this definition">¶</a></dt>
+<dd><ul class="simple">
+<li>O_D_VINAParticle - Oxygen that can be a hydrogen bond donor</li>
+<li>N_D_VINAParticle - Nitrogen that can be a hydrogen bond donor</li>
+<li>O_A_VINAParticle - Oxygen that can be a hydrogen bond acceptor</li>
+<li>N_A_VINAParticle - Nitrogen that can be a hydrogen bond acceptor</li>
+<li>O_AD_VINAParticle - Oxygen that can be a hydrogen bond donor and acceptor</li>
+<li>N_AD_VINAParticle - Nitrogen that can be a hydrogen bond donor and acceptor</li>
+<li>O_VINAParticle - Oxygen</li>
+<li>N_VINAParticle - Nitrogen</li>
+<li>S_VINAParticle - Sulfur</li>
+<li>P_VINAParticle - Phosphorus</li>
+<li>C_P_VINAParticle - Polar carbon that is covalently bound to a charged atom</li>
+<li>C_VINAParticle - Hydrophobic carbon that is only bound to other carbons or hydrogens</li>
+<li>F_VINAParticle - Fluorine</li>
+<li>Cl_VINAParticle - Chlorine</li>
+<li>Br_VINAParticle - Bromine</li>
+<li>I_VINAParticle - Iodine</li>
+<li>M_VINAParticle - Metals</li>
+<li>INVALID_VINAParticle - Invalid particle...</li>
+</ul>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.CreateVINAParticle">
+<code class="descclassname">promod3.sidechain.</code><code class="descname">CreateVINAParticle</code><span class="sig-paren">(</span><em>name</em>, <em>particle_type</em>, <em>pos</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.CreateVINAParticle" title="Permalink to this definition">¶</a></dt>
+<dd><p>Creates and returns a <a class="reference internal" href="#promod3.sidechain.Particle" title="promod3.sidechain.Particle"><code class="xref py py-class docutils literal"><span class="pre">Particle</span></code></a> that can evaluate the VINA scoring
+function</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>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>) – The name of the particle</li>
+<li><strong>radius</strong> (<a class="reference internal" href="#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>) – The type of the particle</li>
+<li><strong>pos</strong> (<a class="reference external" href="https://www.openstructure.org/docs/geom/vec/#ost.geom.Vec3" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.geom.Vec3</span></code></a>) – The position of the particle</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</div>
+</div>
+<div class="section" id="rotamers">
+<h2>Rotamers<a class="headerlink" href="#rotamers" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.RRMRotamer">
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RRMRotamer</code><span class="sig-paren">(</span><em>particles</em>, <em>probability</em>, <em>internal_e_prefactor</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RRMRotamer" title="Permalink to this definition">¶</a></dt>
@@ -278,7 +462,7 @@ in this process.</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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>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
@@ -554,7 +738,7 @@ No atoms are removed from <strong>res</strong> in this process.</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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>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
@@ -954,7 +1138,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>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
@@ -1088,7 +1272,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue to be reconstructed</li>
<li><strong>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
@@ -1170,10 +1354,18 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<div class="sphinxsidebarwrapper">
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
-<li><a class="reference internal" href="#">Rotamers</a><ul>
-<li><a class="reference internal" href="#the-smallest-building-block-the-particle">The Smallest Building Block - The Particle</a></li>
+<li><a class="reference internal" href="#">Representing Sidechains - Rotamers & Co.</a><ul>
+<li><a class="reference internal" href="#rotamerid">RotamerID</a><ul>
+<li><a class="reference internal" href="#how-can-i-get-an-id">How can I get an ID?</a></li>
+</ul>
+</li>
+<li><a class="reference internal" href="#the-smallest-building-block-the-particle">The Smallest Building Block - The Particle</a><ul>
<li><a class="reference internal" href="#the-scwrl4-scoring-function">The SCWRL4 scoring function</a></li>
-<li><a class="reference internal" href="#id1">Rotamers</a></li>
+<li><a class="reference internal" href="#the-scwrl3-scoring-function">The SCWRL3 scoring function</a></li>
+<li><a class="reference internal" href="#the-vina-scoring-function">The VINA scoring function</a></li>
+</ul>
+</li>
+<li><a class="reference internal" href="#rotamers">Rotamers</a></li>
<li><a class="reference internal" href="#rotamer-groups">Rotamer Groups</a></li>
</ul>
</li>
@@ -1184,8 +1376,8 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<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">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="rotamer_id.html" title="previous chapter">RotamerID</a></li>
- <li>Next: <a href="frame.html" title="next chapter">Frame</a></li>
+ <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
+ <li>Next: <a href="frame.html" title="next chapter">Frame - The Rigid Part</a></li>
</ul></li>
</ul></li>
</ul></li>
@@ -1213,7 +1405,7 @@ rotamers with <em>self_energy</em> > <em>l_e</em> + <em>thresh</em></p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/rotamer_constructor.html b/doc/html/sidechain/rotamer_constructor.html
index 992881a63c466cf6e9dad28c2276f87bd8837b6b..cc1e1e8a80f21e51d9942ba7a60803771bfd5835 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 2.0.0 documentation</title>
+ <title>Rotamer Constructor — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,10 +24,10 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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="next" title="Rotamer Library" href="rotamer_lib.html" />
+ <link rel="prev" title="Frame - The Rigid Part" href="frame.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -44,15 +44,15 @@
<div class="section" id="rotamer-constructor">
<h1>Rotamer Constructor<a class="headerlink" href="#rotamer-constructor" title="Permalink to this headline">¶</a></h1>
-<p>Instead of creating rotamers by yourself, you can simply use the convenient
-functionality provided by ProMod3.</p>
-<div class="section" id="constructing-rotamers-and-frame-residues">
-<h2>Constructing Rotamers and Frame Residues<a class="headerlink" href="#constructing-rotamers-and-frame-residues" title="Permalink to this headline">¶</a></h2>
+<p>Instead of creating rotamers or frame residues by yourself, you can use the
+convenient functionality provided by ProMod3.</p>
+<div class="section" id="the-rotamerconstructor-baseclass">
+<h2>The RotamerConstructor Baseclass<a class="headerlink" href="#the-rotamerconstructor-baseclass" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.RotamerConstructor">
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerConstructor</code><a class="headerlink" href="#promod3.sidechain.RotamerConstructor" title="Permalink to this definition">¶</a></dt>
<dd><p>Abstract base class that cannot be initialized from Python. It builds
-an interface implemented by energy function specific constructors
+an interface implemented by scoring function specific constructors
(e.g. <a class="reference internal" href="#promod3.sidechain.SCWRL4RotamerConstructor" title="promod3.sidechain.SCWRL4RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">SCWRL4RotamerConstructor</span></code></a>).</p>
<dl class="method">
<dt id="promod3.sidechain.RotamerConstructor.ConstructRRMRotamerGroup">
@@ -79,11 +79,11 @@ an interface implemented by energy function specific constructors
<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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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 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>id</strong> (<a class="reference internal" href="rotamer.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
energy of the sidechain particles towards particles
@@ -134,11 +134,11 @@ don’t show up in a rotamer).</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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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>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>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>id</strong> (<a class="reference internal" href="rotamer.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
energy of the sidechain particles towards particles
@@ -177,11 +177,11 @@ you observe in a rotamer).</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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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>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>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>id</strong> (<a class="reference internal" href="rotamer.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
energy of the sidechain particles towards particles
@@ -219,7 +219,7 @@ to the energy function specific constructors to override that behaviour.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>rot_group</strong> (<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> / <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>) – containing all rotamers for which internal energies have
to be assigned</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>id</strong> (<a class="reference internal" href="rotamer.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>) – The index of the residue which is represented by
<em>rot_group</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>) – The dihedral angle of the current residue</li>
@@ -235,6 +235,9 @@ to be assigned</li>
</dd></dl>
+</div>
+<div class="section" id="scoring-function-specific-rotamerconstructors">
+<h2>Scoring Function Specific RotamerConstructors<a class="headerlink" href="#scoring-function-specific-rotamerconstructors" title="Permalink to this headline">¶</a></h2>
<dl class="class">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor">
<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRL4RotamerConstructor</code><span class="sig-paren">(</span><em>cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL4RotamerConstructor" title="Permalink to this definition">¶</a></dt>
@@ -262,7 +265,7 @@ any rotamers for ALA and GLY.</td>
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.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.SCWRL4RotamerConstructor.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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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 heavy
atoms of the residue will be represented as carbons and hydrogens are
@@ -272,7 +275,7 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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
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>
@@ -288,7 +291,7 @@ construct a <a class="reference internal" href="frame.html#promod3.sidechain.Fra
<dl class="method">
<dt id="promod3.sidechain.SCWRL4RotamerConstructor.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.SCWRL4RotamerConstructor.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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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.SCWRL4RotamerConstructor.ConstructFrameResidue" title="promod3.sidechain.SCWRL4RotamerConstructor.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
@@ -306,10 +309,10 @@ as in the <code class="xref py py-class docutils literal"><span class="pre">Side
<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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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
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="https://www.openstructure.org/docs/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.9.0)"><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/conop/compoundlib/#ost.conop.CompoundLib" title="(in OpenStructure v1.10.0)"><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>
@@ -338,7 +341,121 @@ is already called at construction and the energies are properly assigned.</p>
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>rot_group</strong> (<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> / <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>) – containing all rotamers for which internal energies have
to be assigned</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>id</strong> (<a class="reference internal" href="rotamer.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>) – The index of the residue which is represented by
+<em>rot_group</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>) – The dihedral angle of the current residue</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>) – The dihedral angle of the current residue</li>
+<li><strong>n_ter</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 residue is n-terminal</li>
+<li><strong>c_ter</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 residue is c-terminal</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="promod3.sidechain.SCWRL3RotamerConstructor">
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">SCWRL3RotamerConstructor</code><span class="sig-paren">(</span><em>cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL3RotamerConstructor" title="Permalink to this definition">¶</a></dt>
+<dd><p>This object implements the full interface defined in
+<a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a> and constructs rotamers and frame residues that
+are parametrized according to the SCWRL3 method. They contain only heavy atoms.</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.SCWRL3RotamerConstructor.AssignInternalEnergies">
+<code class="descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em>rot_group</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.SCWRL3RotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<dd><p>Overrides the method defined in <a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a>.
+Takes the rotamer group and assigns every single rotamer its internal
+energy based on the probabilistic approach used by SCWRL3.
+=> -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
+rotamer specific and max_p is the maximum probablity of any of the rotamers
+in <strong>rot_group</strong>. If you construct a rotamer group by the
+ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
+is already called at construction and the energies are properly assigned.</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>rot_group</strong> (<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> / <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>) – containing all rotamers for which internal energies have
+to be assigned</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.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>) – The index of the residue which is represented by
+<em>rot_group</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>) – The dihedral angle of the current residue</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>) – The dihedral angle of the current residue</li>
+<li><strong>n_ter</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 residue is n-terminal</li>
+<li><strong>c_ter</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 residue is c-terminal</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="class">
+<dt id="promod3.sidechain.VINARotamerConstructor">
+<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">VINARotamerConstructor</code><span class="sig-paren">(</span><em>cb_in_sidechain</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor" title="Permalink to this definition">¶</a></dt>
+<dd><p>This object implements the full interface defined in
+<a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a> and constructs rotamers and frame residues that
+are parametrized according to the VINA method. They contain only heavy atoms.</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.VINARotamerConstructor.AssignInternalEnergies">
+<code class="descname">AssignInternalEnergies</code><span class="sig-paren">(</span><em>rot_group</em>, <em>id</em>, <em>residue_index</em><span class="optional">[</span>, <em>phi = -1.0472</em>, <em>psi = -0.7854</em>, <em>n_ter = False</em>, <em>c_ter = False</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.AssignInternalEnergies" title="Permalink to this definition">¶</a></dt>
+<dd><p>Overrides the method defined in <a class="reference internal" href="#promod3.sidechain.RotamerConstructor" title="promod3.sidechain.RotamerConstructor"><code class="xref py py-class docutils literal"><span class="pre">RotamerConstructor</span></code></a>.
+Takes the rotamer group and assigns every single rotamer its internal
+energy based on the probabilistic approach used by SCWRL3/SCWRL4.
+=> -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
+rotamer specific and max_p is the maximum probablity of any of the rotamers
+in <strong>rot_group</strong>. If you construct a rotamer group by the
+ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
+is already called at construction and the energies are properly assigned.</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>rot_group</strong> (<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> / <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>) – containing all rotamers for which internal energies have
+to be assigned</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.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>) – The index of the residue which is represented by
<em>rot_group</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>) – The dihedral angle of the current residue</li>
@@ -352,6 +469,102 @@ to be assigned</li>
</table>
</dd></dl>
+<dl class="method">
+<dt id="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic">
+<code class="descname">ConstructFrameResidueHeuristic</code><span class="sig-paren">(</span><em>res</em>, <em>res_idx</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a> using
+a heuristic treatment of the atoms. It is important that the residue has
+proper bonds assigned, as they influence the atom typing procedure.
+Furthermore, you need hydrogens to automatically estimate the correct
+atom type for oxygens and nitrogens (hydrogen bond donor/acceptor).
+Alternatively you can assign generic properties to oxygens and nitrogens
+to circumvent the requirement of hydrogens. This is further described for
+the case of oxygen.</p>
+<ul class="simple">
+<li>Carbon is assigned C_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a> if its only
+bound to other carbons or hydrogens (and deuterium). All other carbons are
+assigned C_P_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>.</li>
+<li>In case of oxygen, the heuristic first checks for set generic properties.
+If the atom has the bool properties “is_hbond_acceptor” AND
+“is_hbond_donor” set, it decides between the according oxygen types
+in <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>. If the generic properties are not set,
+every oxygen is assumed to be an hbond acceptor. But only an hbond donor
+if its bound to a hydrogen (or deuterium). You can set the generic
+properties for an <a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.AtomHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.AtomHandle</span></code></a> by calling
+at.SetBoolProp(“is_hbond_donor”, False) and
+at.SetBoolProp(“is_hbond_acceptor”, True). An oxygen with those
+generic properties is assigned O_A_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>.</li>
+<li>In case of nitrogen, the heuristic again first checks for set generic
+properties.
+If the atom has the bool properties “is_hbond_acceptor” AND
+“is_hbond_donor” set, it decides between the according nitrogen types
+in <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>. If not, nitrogen is expected to be an
+hbond donor if it is bound to a hydrogen (or deuterium) and
+an hbond acceptor if it is bound to less than 3 other atoms (sounds
+horrible but works surprisingly well).</li>
+<li>Atoms of elements [“MG”, “MN”, “ZN”, “CA”, “FE”] are assigned
+M_VINAParticle <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>.</li>
+<li>Atoms of elements [“S”, “P”, “F”, “CL”, “BR”, “I”] are assigned their
+corresponding <a class="reference internal" href="rotamer.html#promod3.sidechain.VINAParticleType" title="promod3.sidechain.VINAParticleType"><code class="xref py py-class docutils literal"><span class="pre">VINAParticleType</span></code></a>.</li>
+<li>All other atoms are neglected and not added to the returned
+<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>
+</ul>
+<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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create 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></li>
+<li><strong>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 that is set in <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>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><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></p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic">
+<code class="descname">ConstructRRMRotamerHeuristic</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructRRMRotamerHeuristic" title="Permalink to this definition">¶</a></dt>
+<dd><p>Construct a <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> with the atom typing heuristic
+as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic"><code class="xref py py-meth docutils literal"><span class="pre">ConstructFrameResidueHeuristic()</span></code></a> method.</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>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<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></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><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></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic">
+<code class="descname">ConstructFRMRotamerHeuristic</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.VINARotamerConstructor.ConstructFRMRotamerHeuristic" title="Permalink to this definition">¶</a></dt>
+<dd><p>Construct 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> with the atom typing heuristic
+as in the <a class="reference internal" href="#promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic" title="promod3.sidechain.VINARotamerConstructor.ConstructFrameResidueHeuristic"><code class="xref py py-meth docutils literal"><span class="pre">ConstructFrameResidueHeuristic()</span></code></a> method. The
+constructed <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> only contains one subrotamer that
+contains the atoms from <em>residue</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"><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Residue from which to create the
+<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></td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><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></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</dd></dl>
</div>
@@ -366,7 +579,8 @@ to be assigned</li>
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Rotamer Constructor</a><ul>
-<li><a class="reference internal" href="#constructing-rotamers-and-frame-residues">Constructing Rotamers and Frame Residues</a></li>
+<li><a class="reference internal" href="#the-rotamerconstructor-baseclass">The RotamerConstructor Baseclass</a></li>
+<li><a class="reference internal" href="#scoring-function-specific-rotamerconstructors">Scoring Function Specific RotamerConstructors</a></li>
</ul>
</li>
</ul>
@@ -376,8 +590,8 @@ to be assigned</li>
<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">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="rotamer_lib.html" title="previous chapter">Rotamer Library</a></li>
- <li>Next: <a href="graph.html" title="next chapter">Rotamer Graph</a></li>
+ <li>Previous: <a href="frame.html" title="previous chapter">Frame - The Rigid Part</a></li>
+ <li>Next: <a href="rotamer_lib.html" title="next chapter">Rotamer Library</a></li>
</ul></li>
</ul></li>
</ul></li>
@@ -405,7 +619,7 @@ to be assigned</li>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/rotamer_id.html b/doc/html/sidechain/rotamer_id.html
deleted file mode 100644
index 80e2b6832047a2ac820f8d5dd21d16cc6b4e7e57..0000000000000000000000000000000000000000
--- a/doc/html/sidechain/rotamer_id.html
+++ /dev/null
@@ -1,202 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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-
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- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>RotamerID — ProMod3 2.0.0 documentation</title>
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- <link rel="up" title="sidechain - Sidechain Modelling" href="index.html" />
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-
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- <div class="documentwrapper">
- <div class="bodywrapper">
- <div class="body" role="main">
-
- <div class="section" id="rotamerid">
-<h1>RotamerID<a class="headerlink" href="#rotamerid" title="Permalink to this headline">¶</a></h1>
-<p>The sidechain module has its own definition of amino acids to satisfy custom
-requirements for the implemented sidechain construction algorithms.
-As an example there are histidine in two possible protonation states,
-that affect the hbond term or different versions of proline/cysteine.</p>
-<div class="section" id="the-rotamerid">
-<h2>The RotamerID<a class="headerlink" href="#the-rotamerid" title="Permalink to this headline">¶</a></h2>
-<dl class="class">
-<dt id="promod3.sidechain.RotamerID">
-<em class="property">class </em><code class="descclassname">promod3.sidechain.</code><code class="descname">RotamerID</code><a class="headerlink" href="#promod3.sidechain.RotamerID" title="Permalink to this definition">¶</a></dt>
-<dd><p>Enumerates the amino acids. Possible values:</p>
-<table class="hlist"><tr><td><ul class="simple">
-<li>ARG - Arginine</li>
-<li>ASN - Asparagine</li>
-<li>ASP - Aspartate</li>
-<li>GLN - Glutamine</li>
-<li>GLU - Glutamate</li>
-<li>LYS - Lysine</li>
-<li>SER - Serine</li>
-<li>CYS - Cystein</li>
-<li>CYH - “free” Cystein</li>
-<li>CYD - disulfid bonded Cystein</li>
-<li>MET - Methionine</li>
-<li>TRP - Tryptophane</li>
-<li>TYR - Tyrosine</li>
-<li>THR - Threonine</li>
-</ul>
-</td><td><ul class="simple">
-<li>VAL - Valine</li>
-<li>ILE - Isoleucine</li>
-<li>LEU - Leucine</li>
-<li>PRO - Proline</li>
-<li>CPR - cis-Proline</li>
-<li>TPR - trans-Proline</li>
-<li>HIS - Histidine</li>
-<li>HSD - d-protonated Histidine</li>
-<li>HSE - e-protonated Histidine</li>
-<li>PHE - Phenylalanine</li>
-<li>GLY - Glycine</li>
-<li>ALA - Alanine</li>
-<li>XXX - Invalid</li>
-</ul>
-</td></tr></table>
-<p>The RotamerID enum can be accessed either directly as <code class="docutils literal"><span class="pre">promod3.sidechain.ARG</span></code>
-or as <code class="docutils literal"><span class="pre">promod3.sidechain.RotamerID.ARG</span></code>.</p>
-</dd></dl>
-
-</div>
-<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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">TLCToRotID</code><span class="sig-paren">(</span><em>tlc</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.TLCToRotID" title="Permalink to this definition">¶</a></dt>
-<dd><p>Directly translates the three letter code into a RotamerID. Following
-exactly the naming convention defined above.</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>tlc</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>) – Three letter code 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>tlc</strong> cannot be recoginzed.</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="promod3.sidechain.AAToRotID">
-<code class="descclassname">promod3.sidechain.</code><code class="descname">AAToRotID</code><span class="sig-paren">(</span><em>aa</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.AAToRotID" title="Permalink to this definition">¶</a></dt>
-<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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><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="https://www.openstructure.org/docs/conop/aminoacid/#ost.conop.AminoAcid" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.conop.AminoAcid</span></code></a>) – AA enum of amino acid</td>
-</tr>
-<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>
-</tbody>
-</table>
-</dd></dl>
-
-</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="#">RotamerID</a><ul>
-<li><a class="reference internal" href="#the-rotamerid">The RotamerID</a></li>
-<li><a class="reference internal" href="#how-can-i-get-an-id">How can I get an ID?</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">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="index.html" title="previous chapter"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a></li>
- <li>Next: <a href="rotamer.html" title="next chapter">Rotamers</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/sidechain/rotamer_id.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">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
-
- |
- 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"
- rel="nofollow">Page source</a>
- </div>
-
-
-
-
- </body>
-</html>
\ No newline at end of file
diff --git a/doc/html/sidechain/rotamer_lib.html b/doc/html/sidechain/rotamer_lib.html
index ea9eb17d345a9d27780d4c12a5e80198cfbc9698..9d52fdcf96927e184234973507f62579c7bdc3b2 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 2.0.0 documentation</title>
+ <title>Rotamer Library — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,10 +24,10 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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="next" title="Rotamer Graph" href="graph.html" />
+ <link rel="prev" title="Rotamer Constructor" href="rotamer_constructor.html" />
<link rel="stylesheet" href="../_static/custom.css" type="text/css" />
@@ -115,7 +115,7 @@ 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>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>) – Identity of rotamer to be added</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</li>
<li><strong>rotamer</strong> (<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>) – the rotamer to be added</li>
</ul>
</td>
@@ -144,7 +144,7 @@ special <em>id</em> requests.</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>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>) – Identity of rotamer of interest</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</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 <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> of nonzero
probability sorted by their probability</td>
@@ -237,7 +237,7 @@ 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>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>) – Identity of rotamer to be added</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer to be added</li>
<li><strong>r1</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>) – Configuration of chi1</li>
<li><strong>r2</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>) – Configuration of chi2</li>
<li><strong>r3</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>) – Configuration of chi3</li>
@@ -284,7 +284,7 @@ special <em>id</em> requests.</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>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>) – Identity of rotamer of interest</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer of interest</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 backbone dihedral angle in range [-pi,pi[</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 backbone dihedral angle in range [-pi,pi[</li>
</ul>
@@ -308,11 +308,11 @@ found</p>
<dd><p>Once all rotamers are added, the library can be made static to become readable
and ready for io. Several things get checked during this process</p>
<ul class="simple">
-<li>For every phi/psi bin combination of a particular <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>,
+<li>For every phi/psi bin combination of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>,
the same number of rotamers must have been added</li>
<li>All configuration combinations of the added rotamers in one phi/psi bin
-of a particular <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> must be unique</li>
-<li>The configuration combinations of a particular <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> must
+of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> must be unique</li>
+<li>The configuration combinations of a particular <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> must
be consistent across all phi/psi bins</li>
</ul>
<table class="docutils field-list" frame="void" rules="none">
@@ -436,7 +436,7 @@ functionalities.</p>
<dt id="promod3.sidechain.RotamerLibEntry.FromResidue">
<em class="property">static </em><code class="descname">FromResidue</code><span class="sig-paren">(</span><em>res</em><span class="sig-paren">)</span><a class="headerlink" href="#promod3.sidechain.RotamerLibEntry.FromResidue" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates a <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> from the given <em>res</em>.
-The function tries to automatically identify the <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> based
+The function tries to automatically identify the <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> based
on the residue name. The probability and standard deviations are set to 0.0,
all not required chi angles with their corresponding standard deviations to
NaN.</p>
@@ -444,12 +444,12 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><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/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><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>
<tr class="field-odd 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 residue name cannot be
-translated to <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> or when not all required atoms
+translated to <a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a> or when not all required atoms
are present in <em>res</em>.</td>
</tr>
</tbody>
@@ -468,8 +468,8 @@ 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="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.9.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li>
-<li><strong>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>
+<li><strong>res</strong> (<a class="reference external" href="https://www.openstructure.org/docs/mol/base/entity/#ost.mol.ResidueHandle" title="(in OpenStructure v1.10.0)"><code class="xref py py-class docutils literal"><span class="pre">ost.mol.ResidueHandle</span></code></a>) – Source of dihedral angles</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.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>
</tr>
@@ -528,7 +528,7 @@ the chi2 is checked for its actual value, but also for its flipped state.</p>
<li><strong>other</strong> (<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>) – The Entry you want to compare with</li>
<li><strong>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>) – The max difference between two dihedrals to be
considered similar</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>) – Identity of the entries to be compared</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</li>
</ul>
</td>
</tr>
@@ -586,7 +586,7 @@ for its actual value, but also for its flipped state.</p>
(0 for chi1, 3 for chi4)</li>
<li><strong>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>) – The max difference between two dihedrals to be
considered similar</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>) – Identity of the entries to be compared</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of the entries to be compared</li>
</ul>
</td>
</tr>
@@ -652,7 +652,7 @@ to also return NON_ROTAMERIC (e.g. chi2 for ASN).</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>entry</strong> (<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>) – Sidechain dihedral angle comes from here</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>) – Identity of rotamer</li>
+<li><strong>id</strong> (<a class="reference internal" href="rotamer.html#promod3.sidechain.RotamerID" title="promod3.sidechain.RotamerID"><code class="xref py py-class docutils literal"><span class="pre">RotamerID</span></code></a>) – Identity of rotamer</li>
<li><strong>dihedral_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 angle (0 => chi1, ..., 3 => chi4)</li>
</ul>
</td>
@@ -691,8 +691,8 @@ valid and non rotameric, INVALID otherwise.</p>
<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">sidechain</span></code> - Sidechain Modelling</a><ul>
- <li>Previous: <a href="frame.html" title="previous chapter">Frame</a></li>
- <li>Next: <a href="rotamer_constructor.html" title="next chapter">Rotamer Constructor</a></li>
+ <li>Previous: <a href="rotamer_constructor.html" title="previous chapter">Rotamer Constructor</a></li>
+ <li>Next: <a href="graph.html" title="next chapter">Rotamer Graph</a></li>
</ul></li>
</ul></li>
</ul></li>
@@ -720,7 +720,7 @@ valid and non rotameric, INVALID otherwise.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/sidechain/subrotamer_optimizer.html b/doc/html/sidechain/subrotamer_optimizer.html
index 866eab60f7473aaddc35597e20ac9bcd3a9a08ab..4919ec5cd562a672a8c5dd640d7c6a18e2ad2140 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 2.0.0 documentation</title>
+ <title>Subrotamer Optimization — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="../index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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" />
@@ -126,7 +126,7 @@ internal <a class="reference internal" href="graph.html#promod3.sidechain.Rotame
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/user_contributions.html b/doc/html/user_contributions.html
index ee0f7551b808e93fd74f67b2d31d813b6809ce8c..df6d3a8e13a6c45f1862db56f6eaeda2cddfa4ce 100644
--- a/doc/html/user_contributions.html
+++ b/doc/html/user_contributions.html
@@ -6,7 +6,7 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Contributing — ProMod3 2.0.0 documentation</title>
+ <title>Contributing — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 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="SetCompoundsChemlib()" href="core/setcompoundschemlib.html" />
@@ -92,7 +92,7 @@ information on that matter in the developer section of the documentation
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/html/users.html b/doc/html/users.html
index e576c73592ed54aaec6a4e2db6c99ad4bbd635ea..dc1a92438ecea83e3e810dbb99cfc865e9503e94 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 2.0.0 documentation</title>
+ <title>Documentation For Users — ProMod3 2.1.0 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: '2.0.0',
+ VERSION: '2.1.0',
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="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-MML-AM_CHTML"></script>
- <link rel="top" title="ProMod3 2.0.0 documentation" href="index.html" />
+ <link rel="top" title="ProMod3 2.1.0 documentation" href="index.html" />
<link rel="next" title="Getting Started" href="gettingstarted.html" />
<link rel="prev" title="ProMod3" href="index.html" />
@@ -82,11 +82,10 @@ scripts using the functionality of this library.</p>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="sidechain/index.html"><code class="docutils literal"><span class="pre">sidechain</span></code> - Sidechain Modelling</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_id.html">RotamerID</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer.html">Rotamers</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/frame.html">Frame</a></li>
-<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_lib.html">Rotamer Library</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer.html">Representing Sidechains - Rotamers & Co.</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/frame.html">Frame - The Rigid Part</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_constructor.html">Rotamer Constructor</a></li>
+<li class="toctree-l2"><a class="reference internal" href="sidechain/rotamer_lib.html">Rotamer Library</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/graph.html">Rotamer Graph</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/disulfid.html">Disulfid Bond Evaluation</a></li>
<li class="toctree-l2"><a class="reference internal" href="sidechain/loading.html">Loading Rotamer Libraries</a></li>
@@ -159,7 +158,7 @@ scripts using the functionality of this library.</p>
<div class="clearer"></div>
</div>
<div class="footer">
- ©2013-2019, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
+ ©2013-2020, SIB - Swiss Institute of Bioinformatics and Biozentrum - University of Basel.
|
Powered by <a href="http://sphinx-doc.org/">Sphinx 1.4.1</a>
diff --git a/doc/references.rst b/doc/references.rst
index 927de6ddbad6c032f0f760c17384e977d1ed31e9..18a5a3b25ba4779ccd336b9bbfdae278f04735ab 100644
--- a/doc/references.rst
+++ b/doc/references.rst
@@ -62,6 +62,10 @@ References
Exploring the conformational space of protein side chains using
dead-end elimination and the A* algorithm. Proteins.
+.. [nussinov1991] Nussinov R and Wolfson HJ (1991).
+ Efficient detection of three-dimensional structural motifs in
+ biological macromolecules by computer vision techniques. PNAS.
+
.. [shapovalov2011] Shapovalov MV and Dunbrack RL Jr. (2011).
A smoothed backbone-dependent rotamer library for proteins
derived from adaptive kernel density estimates and
@@ -75,6 +79,10 @@ References
potentials and threading score functions using information
maximization. Proteins.
+.. [trott2010] Trott O, Olson AJ (2010). AutoDock Vina: improving the speed and
+ accuracy of docking with a new scoring function, efficient
+ optimization and multithreading. J Comput Chem
+
.. [zhou2005] Zhou H, Zhou Y (2005).
Fold Recognition by Combining Sequence Profiles Derived From
Evolution and From Depth-Dependent Structural Alignment of
diff --git a/doc/tests/CMakeLists.txt b/doc/tests/CMakeLists.txt
index 15ba86032f016e1d9f83003f3ef7afdd6f946511..f484a2f1cb868a492ef7e29e5437c870b460c123 100644
--- a/doc/tests/CMakeLists.txt
+++ b/doc/tests/CMakeLists.txt
@@ -13,6 +13,10 @@ set(DOC_TEST_DATA
data/1eye_rec.pdb
data/gly.pdb
data/port_str_db.dat
+ data/1AKE.pdb
+ data/1E2Q.pdb
+ data/1KO5.pdb
+ data/2IYW.pdb
)
set (DOC_TEST_SCRIPTS
@@ -50,6 +54,7 @@ set (DOC_TEST_SCRIPTS
scripts/modelling_reconstruct_sidechains.py
scripts/modelling_sidechain_reconstructor.py
scripts/modelling_allatomrelaxer.py
+ scripts/modelling_motif_finder.py
scripts/sidechain_steps.py
)
diff --git a/doc/tests/data/1AKE.pdb b/doc/tests/data/1AKE.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..32cb897a31436dbf606e885629f5e61f13324aa0
--- /dev/null
+++ b/doc/tests/data/1AKE.pdb
@@ -0,0 +1,3933 @@
+ATOM 1 N MET A 1 26.981 53.977 40.085 1.00 40.83 N
+ATOM 2 CA MET A 1 26.091 52.849 39.889 1.00 37.14 C
+ATOM 3 C MET A 1 26.679 52.163 38.675 1.00 30.15 C
+ATOM 4 O MET A 1 27.020 52.865 37.715 1.00 27.59 O
+ATOM 5 CB MET A 1 24.677 53.310 39.580 1.00 38.06 C
+ATOM 6 CG MET A 1 23.624 52.189 39.442 1.00 46.67 C
+ATOM 7 SD MET A 1 21.917 52.816 39.301 1.00 61.54 S
+ATOM 8 CE MET A 1 21.930 53.926 37.910 1.00 51.17 C
+ATOM 9 N ARG A 2 26.861 50.841 38.803 1.00 28.23 N
+ATOM 10 CA ARG A 2 27.437 49.969 37.786 1.00 25.76 C
+ATOM 11 C ARG A 2 26.336 48.959 37.429 1.00 25.85 C
+ATOM 12 O ARG A 2 25.745 48.313 38.312 1.00 25.74 O
+ATOM 13 CB ARG A 2 28.653 49.266 38.349 1.00 21.92 C
+ATOM 14 CG ARG A 2 29.870 50.188 38.416 1.00 39.05 C
+ATOM 15 CD ARG A 2 31.033 49.532 39.173 1.00 51.33 C
+ATOM 16 NE ARG A 2 32.318 50.244 39.125 1.00 59.73 N
+ATOM 17 CZ ARG A 2 33.462 49.750 39.679 1.00 58.78 C
+ATOM 18 NH1 ARG A 2 33.522 48.572 40.308 1.00 58.56 N
+ATOM 19 NH2 ARG A 2 34.610 50.427 39.597 1.00 59.20 N
+ATOM 20 N ILE A 3 26.039 48.836 36.139 1.00 21.59 N
+ATOM 21 CA ILE A 3 24.961 47.988 35.671 1.00 23.90 C
+ATOM 22 C ILE A 3 25.374 47.080 34.537 1.00 21.12 C
+ATOM 23 O ILE A 3 26.029 47.614 33.642 1.00 24.59 O
+ATOM 24 CB ILE A 3 23.802 48.880 35.202 1.00 23.84 C
+ATOM 25 CG1 ILE A 3 23.317 49.724 36.378 1.00 26.14 C
+ATOM 26 CG2 ILE A 3 22.660 48.010 34.642 1.00 19.29 C
+ATOM 27 CD1 ILE A 3 22.436 50.890 35.992 1.00 24.97 C
+ATOM 28 N ILE A 4 25.062 45.774 34.541 1.00 20.44 N
+ATOM 29 CA ILE A 4 25.194 44.925 33.360 1.00 17.83 C
+ATOM 30 C ILE A 4 23.804 44.715 32.751 1.00 18.42 C
+ATOM 31 O ILE A 4 22.824 44.536 33.484 1.00 16.35 O
+ATOM 32 CB ILE A 4 25.789 43.561 33.720 1.00 16.64 C
+ATOM 33 CG1 ILE A 4 27.206 43.753 34.233 1.00 17.27 C
+ATOM 34 CG2 ILE A 4 25.829 42.650 32.463 1.00 21.39 C
+ATOM 35 CD1 ILE A 4 27.967 42.486 34.621 1.00 15.61 C
+ATOM 36 N LEU A 5 23.655 44.874 31.424 1.00 19.74 N
+ATOM 37 CA LEU A 5 22.428 44.503 30.712 1.00 19.86 C
+ATOM 38 C LEU A 5 22.668 43.134 30.012 1.00 18.50 C
+ATOM 39 O LEU A 5 23.614 42.932 29.232 1.00 17.64 O
+ATOM 40 CB LEU A 5 22.088 45.547 29.675 1.00 22.23 C
+ATOM 41 CG LEU A 5 22.076 47.021 30.069 1.00 27.37 C
+ATOM 42 CD1 LEU A 5 21.735 47.848 28.817 1.00 19.28 C
+ATOM 43 CD2 LEU A 5 21.088 47.249 31.193 1.00 24.82 C
+ATOM 44 N LEU A 6 21.787 42.178 30.248 1.00 14.28 N
+ATOM 45 CA LEU A 6 21.933 40.811 29.752 1.00 21.75 C
+ATOM 46 C LEU A 6 20.711 40.529 28.870 1.00 23.97 C
+ATOM 47 O LEU A 6 19.602 40.977 29.220 1.00 19.19 O
+ATOM 48 CB LEU A 6 21.919 39.891 30.945 1.00 27.49 C
+ATOM 49 CG LEU A 6 22.847 38.789 31.103 1.00 31.51 C
+ATOM 50 CD1 LEU A 6 24.254 39.345 31.210 1.00 34.32 C
+ATOM 51 CD2 LEU A 6 22.465 38.042 32.355 1.00 24.54 C
+ATOM 52 N GLY A 7 20.800 39.799 27.764 1.00 18.09 N
+ATOM 53 CA GLY A 7 19.604 39.512 26.973 1.00 20.21 C
+ATOM 54 C GLY A 7 19.959 39.035 25.585 1.00 14.48 C
+ATOM 55 O GLY A 7 21.049 39.324 25.122 1.00 15.84 O
+ATOM 56 N ALA A 8 19.117 38.232 24.936 1.00 19.71 N
+ATOM 57 CA ALA A 8 19.324 37.742 23.567 1.00 16.92 C
+ATOM 58 C ALA A 8 19.530 38.886 22.568 1.00 17.35 C
+ATOM 59 O ALA A 8 19.158 40.013 22.889 1.00 15.41 O
+ATOM 60 CB ALA A 8 18.092 36.960 23.169 1.00 15.12 C
+ATOM 61 N PRO A 9 20.069 38.660 21.359 1.00 20.54 N
+ATOM 62 CA PRO A 9 20.108 39.651 20.294 1.00 17.47 C
+ATOM 63 C PRO A 9 18.750 40.300 20.095 1.00 21.25 C
+ATOM 64 O PRO A 9 17.760 39.552 20.084 1.00 17.47 O
+ATOM 65 CB PRO A 9 20.574 38.908 19.047 1.00 19.04 C
+ATOM 66 CG PRO A 9 20.687 37.425 19.450 1.00 25.54 C
+ATOM 67 CD PRO A 9 20.695 37.403 20.958 1.00 17.37 C
+ATOM 68 N GLY A 10 18.697 41.656 20.019 1.00 21.90 N
+ATOM 69 CA GLY A 10 17.487 42.426 19.756 1.00 18.35 C
+ATOM 70 C GLY A 10 16.476 42.449 20.905 1.00 19.36 C
+ATOM 71 O GLY A 10 15.311 42.745 20.642 1.00 18.88 O
+ATOM 72 N ALA A 11 16.899 42.259 22.187 1.00 16.83 N
+ATOM 73 CA ALA A 11 15.960 42.201 23.284 1.00 18.31 C
+ATOM 74 C ALA A 11 15.625 43.630 23.738 1.00 17.96 C
+ATOM 75 O ALA A 11 14.821 43.804 24.675 1.00 22.53 O
+ATOM 76 CB ALA A 11 16.528 41.416 24.561 1.00 15.72 C
+ATOM 77 N GLY A 12 16.317 44.646 23.192 1.00 15.75 N
+ATOM 78 CA GLY A 12 16.082 46.035 23.547 1.00 20.57 C
+ATOM 79 C GLY A 12 17.115 46.628 24.499 1.00 19.31 C
+ATOM 80 O GLY A 12 16.847 47.654 25.139 1.00 18.99 O
+ATOM 81 N LYS A 13 18.320 46.036 24.586 1.00 15.72 N
+ATOM 82 CA LYS A 13 19.303 46.427 25.595 1.00 14.56 C
+ATOM 83 C LYS A 13 19.811 47.802 25.236 1.00 23.49 C
+ATOM 84 O LYS A 13 19.666 48.712 26.068 1.00 17.44 O
+ATOM 85 CB LYS A 13 20.485 45.442 25.661 1.00 14.39 C
+ATOM 86 CG LYS A 13 20.219 44.133 26.392 1.00 16.06 C
+ATOM 87 CD LYS A 13 21.297 43.055 26.321 1.00 14.28 C
+ATOM 88 CE LYS A 13 21.965 42.761 24.960 1.00 16.79 C
+ATOM 89 NZ LYS A 13 21.056 42.207 23.991 1.00 14.14 N
+ATOM 90 N GLY A 14 20.270 47.997 23.985 1.00 17.69 N
+ATOM 91 CA GLY A 14 20.816 49.254 23.528 1.00 17.87 C
+ATOM 92 C GLY A 14 19.793 50.385 23.631 1.00 22.90 C
+ATOM 93 O GLY A 14 20.196 51.500 24.037 1.00 23.43 O
+ATOM 94 N THR A 15 18.498 50.132 23.306 1.00 17.68 N
+ATOM 95 CA THR A 15 17.421 51.124 23.373 1.00 11.87 C
+ATOM 96 C THR A 15 17.273 51.590 24.830 1.00 21.09 C
+ATOM 97 O THR A 15 17.270 52.795 25.123 1.00 17.30 O
+ATOM 98 CB THR A 15 16.120 50.501 22.872 1.00 15.41 C
+ATOM 99 OG1 THR A 15 16.372 50.206 21.494 1.00 17.67 O
+ATOM 100 CG2 THR A 15 14.890 51.418 22.995 1.00 16.41 C
+ATOM 101 N GLN A 16 17.226 50.671 25.798 1.00 18.86 N
+ATOM 102 CA GLN A 16 17.135 51.071 27.210 1.00 24.63 C
+ATOM 103 C GLN A 16 18.402 51.664 27.843 1.00 28.08 C
+ATOM 104 O GLN A 16 18.310 52.464 28.793 1.00 21.17 O
+ATOM 105 CB GLN A 16 16.681 49.884 28.037 1.00 22.62 C
+ATOM 106 CG GLN A 16 15.323 49.406 27.525 1.00 28.34 C
+ATOM 107 CD GLN A 16 14.227 50.459 27.630 1.00 26.24 C
+ATOM 108 OE1 GLN A 16 13.285 50.464 26.849 1.00 28.75 O
+ATOM 109 NE2 GLN A 16 14.220 51.378 28.575 1.00 21.97 N
+ATOM 110 N ALA A 17 19.571 51.282 27.302 1.00 21.47 N
+ATOM 111 CA ALA A 17 20.821 51.825 27.722 1.00 21.29 C
+ATOM 112 C ALA A 17 20.827 53.331 27.452 1.00 24.27 C
+ATOM 113 O ALA A 17 21.287 54.060 28.335 1.00 21.39 O
+ATOM 114 CB ALA A 17 21.915 51.150 26.941 1.00 19.10 C
+ATOM 115 N GLN A 18 20.335 53.865 26.299 1.00 23.09 N
+ATOM 116 CA GLN A 18 20.249 55.314 26.080 1.00 35.13 C
+ATOM 117 C GLN A 18 19.380 55.998 27.161 1.00 30.93 C
+ATOM 118 O GLN A 18 19.805 57.033 27.660 1.00 29.17 O
+ATOM 119 CB GLN A 18 19.663 55.642 24.704 1.00 39.96 C
+ATOM 120 CG GLN A 18 20.470 55.251 23.446 1.00 56.33 C
+ATOM 121 CD GLN A 18 19.589 55.276 22.173 1.00 66.12 C
+ATOM 122 OE1 GLN A 18 19.597 54.383 21.297 1.00 60.71 O
+ATOM 123 NE2 GLN A 18 18.775 56.322 22.023 1.00 58.49 N
+ATOM 124 N PHE A 19 18.249 55.451 27.639 1.00 30.18 N
+ATOM 125 CA PHE A 19 17.474 56.050 28.712 1.00 29.68 C
+ATOM 126 C PHE A 19 18.238 56.003 30.023 1.00 28.43 C
+ATOM 127 O PHE A 19 18.209 56.994 30.747 1.00 30.45 O
+ATOM 128 CB PHE A 19 16.077 55.343 28.905 1.00 29.03 C
+ATOM 129 CG PHE A 19 15.536 55.268 30.366 1.00 42.14 C
+ATOM 130 CD1 PHE A 19 15.100 56.407 31.053 1.00 42.90 C
+ATOM 131 CD2 PHE A 19 15.580 54.062 31.054 1.00 44.87 C
+ATOM 132 CE1 PHE A 19 14.735 56.359 32.386 1.00 37.82 C
+ATOM 133 CE2 PHE A 19 15.213 54.022 32.386 1.00 42.62 C
+ATOM 134 CZ PHE A 19 14.799 55.160 33.050 1.00 43.84 C
+ATOM 135 N ILE A 20 18.869 54.909 30.422 1.00 23.09 N
+ATOM 136 CA ILE A 20 19.532 54.877 31.696 1.00 23.96 C
+ATOM 137 C ILE A 20 20.645 55.887 31.681 1.00 29.63 C
+ATOM 138 O ILE A 20 20.846 56.617 32.663 1.00 32.83 O
+ATOM 139 CB ILE A 20 20.070 53.459 31.980 1.00 27.73 C
+ATOM 140 CG1 ILE A 20 18.829 52.589 32.155 1.00 24.67 C
+ATOM 141 CG2 ILE A 20 20.994 53.376 33.235 1.00 26.89 C
+ATOM 142 CD1 ILE A 20 19.248 51.106 32.066 1.00 25.96 C
+ATOM 143 N MET A 21 21.352 55.962 30.577 1.00 22.68 N
+ATOM 144 CA MET A 21 22.441 56.903 30.479 1.00 32.34 C
+ATOM 145 C MET A 21 21.963 58.344 30.645 1.00 36.61 C
+ATOM 146 O MET A 21 22.537 59.094 31.451 1.00 35.98 O
+ATOM 147 CB MET A 21 23.126 56.713 29.136 1.00 34.45 C
+ATOM 148 CG MET A 21 23.987 57.889 28.770 1.00 47.17 C
+ATOM 149 SD MET A 21 24.666 57.634 27.140 1.00 58.05 S
+ATOM 150 CE MET A 21 26.316 57.426 27.691 1.00 46.92 C
+ATOM 151 N GLU A 22 20.892 58.740 29.957 1.00 35.15 N
+ATOM 152 CA GLU A 22 20.467 60.117 30.020 1.00 35.34 C
+ATOM 153 C GLU A 22 19.853 60.448 31.354 1.00 41.37 C
+ATOM 154 O GLU A 22 20.085 61.541 31.858 1.00 49.63 O
+ATOM 155 CB GLU A 22 19.479 60.433 28.914 1.00 42.27 C
+ATOM 156 CG GLU A 22 18.092 59.796 28.979 1.00 68.08 C
+ATOM 157 CD GLU A 22 17.103 60.339 27.946 1.00 82.33 C
+ATOM 158 OE1 GLU A 22 17.363 60.191 26.740 1.00 86.19 O
+ATOM 159 OE2 GLU A 22 16.077 60.905 28.360 1.00 89.10 O
+ATOM 160 N LYS A 23 19.160 59.507 31.983 1.00 40.77 N
+ATOM 161 CA LYS A 23 18.497 59.710 33.252 1.00 35.64 C
+ATOM 162 C LYS A 23 19.376 59.568 34.467 1.00 42.07 C
+ATOM 163 O LYS A 23 19.054 60.110 35.524 1.00 51.32 O
+ATOM 164 CB LYS A 23 17.349 58.727 33.381 1.00 39.75 C
+ATOM 165 CG LYS A 23 16.112 59.315 34.008 1.00 41.63 C
+ATOM 166 CD LYS A 23 15.916 58.649 35.332 1.00 47.22 C
+ATOM 167 CE LYS A 23 14.562 59.056 35.858 1.00 50.81 C
+ATOM 168 NZ LYS A 23 14.238 58.262 37.026 1.00 52.24 N
+ATOM 169 N TYR A 24 20.432 58.765 34.406 1.00 46.00 N
+ATOM 170 CA TYR A 24 21.269 58.502 35.566 1.00 38.91 C
+ATOM 171 C TYR A 24 22.706 58.970 35.378 1.00 39.17 C
+ATOM 172 O TYR A 24 23.565 58.695 36.216 1.00 40.96 O
+ATOM 173 CB TYR A 24 21.239 57.011 35.866 1.00 41.58 C
+ATOM 174 CG TYR A 24 19.834 56.522 36.193 1.00 45.68 C
+ATOM 175 CD1 TYR A 24 19.324 56.640 37.474 1.00 43.85 C
+ATOM 176 CD2 TYR A 24 19.065 55.950 35.192 1.00 51.33 C
+ATOM 177 CE1 TYR A 24 18.047 56.180 37.751 1.00 53.35 C
+ATOM 178 CE2 TYR A 24 17.787 55.490 35.459 1.00 52.15 C
+ATOM 179 CZ TYR A 24 17.283 55.607 36.743 1.00 54.96 C
+ATOM 180 OH TYR A 24 16.010 55.128 36.994 1.00 56.26 O
+ATOM 181 N GLY A 25 22.969 59.641 34.252 1.00 34.82 N
+ATOM 182 CA GLY A 25 24.253 60.217 33.938 1.00 29.00 C
+ATOM 183 C GLY A 25 25.410 59.236 33.969 1.00 43.54 C
+ATOM 184 O GLY A 25 26.527 59.669 34.253 1.00 44.35 O
+ATOM 185 N ILE A 26 25.220 57.924 33.751 1.00 47.69 N
+ATOM 186 CA ILE A 26 26.346 56.989 33.707 1.00 36.55 C
+ATOM 187 C ILE A 26 26.607 56.614 32.249 1.00 35.98 C
+ATOM 188 O ILE A 26 25.682 56.499 31.427 1.00 30.67 O
+ATOM 189 CB ILE A 26 26.052 55.747 34.560 1.00 36.41 C
+ATOM 190 CG1 ILE A 26 24.746 55.087 34.229 1.00 41.45 C
+ATOM 191 CG2 ILE A 26 26.001 56.219 36.017 1.00 39.77 C
+ATOM 192 CD1 ILE A 26 24.439 53.923 35.198 1.00 48.36 C
+ATOM 193 N PRO A 27 27.875 56.500 31.841 1.00 34.73 N
+ATOM 194 CA PRO A 27 28.231 56.198 30.472 1.00 28.83 C
+ATOM 195 C PRO A 27 27.891 54.763 30.180 1.00 23.60 C
+ATOM 196 O PRO A 27 28.027 53.875 31.033 1.00 27.00 O
+ATOM 197 CB PRO A 27 29.693 56.494 30.393 1.00 28.89 C
+ATOM 198 CG PRO A 27 30.135 56.089 31.760 1.00 35.46 C
+ATOM 199 CD PRO A 27 29.069 56.668 32.663 1.00 33.80 C
+ATOM 200 N GLN A 28 27.439 54.643 28.939 1.00 27.50 N
+ATOM 201 CA GLN A 28 27.118 53.394 28.303 1.00 27.15 C
+ATOM 202 C GLN A 28 28.433 52.911 27.659 1.00 30.41 C
+ATOM 203 O GLN A 28 28.996 53.606 26.809 1.00 31.73 O
+ATOM 204 CB GLN A 28 26.069 53.601 27.214 1.00 27.04 C
+ATOM 205 CG GLN A 28 25.883 52.370 26.246 1.00 33.40 C
+ATOM 206 CD GLN A 28 24.954 52.485 25.024 1.00 35.82 C
+ATOM 207 OE1 GLN A 28 24.659 53.643 24.452 1.00 40.26 O
+ATOM 208 NE2 GLN A 28 24.463 51.483 24.505 1.00 36.86 N
+ATOM 209 N ILE A 29 28.954 51.735 28.010 1.00 28.81 N
+ATOM 210 CA ILE A 29 30.122 51.105 27.381 1.00 30.28 C
+ATOM 211 C ILE A 29 29.558 49.951 26.533 1.00 27.89 C
+ATOM 212 O ILE A 29 29.160 48.912 27.052 1.00 25.04 O
+ATOM 213 CB ILE A 29 31.060 50.660 28.537 1.00 26.02 C
+ATOM 214 CG1 ILE A 29 31.505 51.927 29.291 1.00 20.27 C
+ATOM 215 CG2 ILE A 29 32.195 49.761 27.969 1.00 23.69 C
+ATOM 216 CD1 ILE A 29 32.357 51.636 30.507 1.00 32.49 C
+ATOM 217 N SER A 30 29.386 50.098 25.234 1.00 24.91 N
+ATOM 218 CA SER A 30 28.780 49.070 24.408 1.00 28.13 C
+ATOM 219 C SER A 30 29.856 48.513 23.484 1.00 27.39 C
+ATOM 220 O SER A 30 30.450 49.195 22.628 1.00 21.34 O
+ATOM 221 CB SER A 30 27.641 49.674 23.614 1.00 21.93 C
+ATOM 222 OG SER A 30 27.393 49.012 22.382 1.00 29.69 O
+ATOM 223 N THR A 31 30.102 47.225 23.695 1.00 23.11 N
+ATOM 224 CA THR A 31 31.156 46.587 22.987 1.00 19.90 C
+ATOM 225 C THR A 31 30.787 46.464 21.542 1.00 18.73 C
+ATOM 226 O THR A 31 31.720 46.622 20.766 1.00 19.30 O
+ATOM 227 CB THR A 31 31.489 45.205 23.617 1.00 20.48 C
+ATOM 228 OG1 THR A 31 30.313 44.530 23.975 1.00 21.10 O
+ATOM 229 CG2 THR A 31 32.316 45.409 24.879 1.00 20.87 C
+ATOM 230 N GLY A 32 29.544 46.231 21.122 1.00 16.33 N
+ATOM 231 CA GLY A 32 29.191 46.253 19.704 1.00 21.95 C
+ATOM 232 C GLY A 32 29.525 47.627 19.099 1.00 22.83 C
+ATOM 233 O GLY A 32 30.121 47.705 18.019 1.00 17.51 O
+ATOM 234 N ASP A 33 29.237 48.726 19.826 1.00 23.46 N
+ATOM 235 CA ASP A 33 29.487 50.042 19.273 1.00 25.07 C
+ATOM 236 C ASP A 33 30.983 50.250 19.161 1.00 22.43 C
+ATOM 237 O ASP A 33 31.454 50.638 18.077 1.00 25.43 O
+ATOM 238 CB ASP A 33 28.914 51.173 20.141 1.00 20.81 C
+ATOM 239 CG ASP A 33 27.419 51.446 19.994 1.00 34.20 C
+ATOM 240 OD1 ASP A 33 26.816 50.961 19.027 1.00 28.19 O
+ATOM 241 OD2 ASP A 33 26.880 52.176 20.852 1.00 37.34 O
+ATOM 242 N MET A 34 31.738 49.947 20.223 1.00 16.91 N
+ATOM 243 CA MET A 34 33.184 50.074 20.161 1.00 16.15 C
+ATOM 244 C MET A 34 33.787 49.222 19.073 1.00 17.63 C
+ATOM 245 O MET A 34 34.703 49.685 18.386 1.00 23.65 O
+ATOM 246 CB MET A 34 33.832 49.679 21.452 1.00 17.88 C
+ATOM 247 CG MET A 34 33.464 50.634 22.545 1.00 28.29 C
+ATOM 248 SD MET A 34 34.415 50.284 24.035 1.00 37.95 S
+ATOM 249 CE MET A 34 33.371 49.008 24.702 1.00 31.80 C
+ATOM 250 N LEU A 35 33.336 48.008 18.816 1.00 14.18 N
+ATOM 251 CA LEU A 35 33.940 47.195 17.763 1.00 18.35 C
+ATOM 252 C LEU A 35 33.532 47.687 16.374 1.00 22.21 C
+ATOM 253 O LEU A 35 34.397 47.686 15.499 1.00 23.14 O
+ATOM 254 CB LEU A 35 33.538 45.702 17.921 1.00 14.38 C
+ATOM 255 CG LEU A 35 34.178 44.933 19.144 1.00 22.42 C
+ATOM 256 CD1 LEU A 35 33.426 43.634 19.487 1.00 22.66 C
+ATOM 257 CD2 LEU A 35 35.633 44.683 18.796 1.00 21.21 C
+ATOM 258 N ARG A 36 32.291 48.095 16.040 1.00 25.04 N
+ATOM 259 CA ARG A 36 31.961 48.619 14.693 1.00 21.19 C
+ATOM 260 C ARG A 36 32.777 49.890 14.437 1.00 20.98 C
+ATOM 261 O ARG A 36 33.328 50.113 13.362 1.00 22.82 O
+ATOM 262 CB ARG A 36 30.469 48.931 14.605 1.00 15.77 C
+ATOM 263 CG ARG A 36 29.578 47.699 14.429 1.00 19.41 C
+ATOM 264 CD ARG A 36 28.058 47.971 14.453 1.00 15.24 C
+ATOM 265 NE ARG A 36 27.555 48.398 15.764 1.00 17.70 N
+ATOM 266 CZ ARG A 36 27.064 47.570 16.706 1.00 14.08 C
+ATOM 267 NH1 ARG A 36 27.106 46.256 16.575 1.00 20.01 N
+ATOM 268 NH2 ARG A 36 26.547 48.043 17.839 1.00 15.42 N
+ATOM 269 N ALA A 37 32.963 50.707 15.460 1.00 17.17 N
+ATOM 270 CA ALA A 37 33.778 51.895 15.373 1.00 27.13 C
+ATOM 271 C ALA A 37 35.212 51.490 15.060 1.00 28.62 C
+ATOM 272 O ALA A 37 35.775 51.983 14.083 1.00 27.31 O
+ATOM 273 CB ALA A 37 33.764 52.668 16.691 1.00 24.59 C
+ATOM 274 N ALA A 38 35.832 50.581 15.801 1.00 23.95 N
+ATOM 275 CA ALA A 38 37.207 50.146 15.498 1.00 28.55 C
+ATOM 276 C ALA A 38 37.350 49.607 14.071 1.00 23.97 C
+ATOM 277 O ALA A 38 38.315 49.935 13.355 1.00 26.96 O
+ATOM 278 CB ALA A 38 37.658 49.037 16.499 1.00 23.72 C
+ATOM 279 N VAL A 39 36.370 48.833 13.594 1.00 20.08 N
+ATOM 280 CA VAL A 39 36.426 48.279 12.266 1.00 21.10 C
+ATOM 281 C VAL A 39 36.378 49.421 11.306 1.00 33.75 C
+ATOM 282 O VAL A 39 37.180 49.428 10.380 1.00 40.93 O
+ATOM 283 CB VAL A 39 35.264 47.365 12.049 1.00 22.86 C
+ATOM 284 CG1 VAL A 39 35.016 47.117 10.563 1.00 26.70 C
+ATOM 285 CG2 VAL A 39 35.625 46.029 12.675 1.00 19.03 C
+ATOM 286 N LYS A 40 35.526 50.417 11.553 1.00 36.34 N
+ATOM 287 CA LYS A 40 35.384 51.553 10.650 1.00 38.88 C
+ATOM 288 C LYS A 40 36.590 52.492 10.671 1.00 39.37 C
+ATOM 289 O LYS A 40 36.908 53.028 9.605 1.00 39.37 O
+ATOM 290 CB LYS A 40 34.110 52.246 11.044 1.00 46.46 C
+ATOM 291 CG LYS A 40 33.417 53.311 10.207 1.00 55.86 C
+ATOM 292 CD LYS A 40 32.105 53.543 10.986 1.00 68.28 C
+ATOM 293 CE LYS A 40 32.307 53.985 12.477 1.00 76.27 C
+ATOM 294 NZ LYS A 40 31.158 53.781 13.360 1.00 74.69 N
+ATOM 295 N SER A 41 37.272 52.721 11.806 1.00 30.04 N
+ATOM 296 CA SER A 41 38.507 53.491 11.905 1.00 33.63 C
+ATOM 297 C SER A 41 39.777 52.736 11.541 1.00 34.75 C
+ATOM 298 O SER A 41 40.837 53.367 11.412 1.00 43.02 O
+ATOM 299 CB SER A 41 38.784 53.990 13.294 1.00 31.94 C
+ATOM 300 OG SER A 41 37.700 54.780 13.703 1.00 53.72 O
+ATOM 301 N GLY A 42 39.746 51.404 11.382 1.00 39.50 N
+ATOM 302 CA GLY A 42 40.955 50.617 11.185 1.00 29.51 C
+ATOM 303 C GLY A 42 41.822 50.731 12.450 1.00 28.13 C
+ATOM 304 O GLY A 42 43.052 50.709 12.332 1.00 31.99 O
+ATOM 305 N SER A 43 41.232 50.910 13.656 1.00 24.66 N
+ATOM 306 CA SER A 43 41.976 50.997 14.916 1.00 29.21 C
+ATOM 307 C SER A 43 42.661 49.644 15.134 1.00 31.46 C
+ATOM 308 O SER A 43 42.039 48.580 14.922 1.00 25.60 O
+ATOM 309 CB SER A 43 41.035 51.263 16.084 1.00 29.99 C
+ATOM 310 OG SER A 43 40.232 52.405 15.825 1.00 44.89 O
+ATOM 311 N GLU A 44 43.932 49.643 15.550 1.00 31.16 N
+ATOM 312 CA GLU A 44 44.618 48.368 15.772 1.00 33.01 C
+ATOM 313 C GLU A 44 43.907 47.521 16.842 1.00 28.72 C
+ATOM 314 O GLU A 44 43.847 46.298 16.691 1.00 30.36 O
+ATOM 315 CB GLU A 44 46.104 48.609 16.173 1.00 33.07 C
+ATOM 316 CG GLU A 44 46.901 47.312 16.527 1.00 49.76 C
+ATOM 317 CD GLU A 44 46.976 46.124 15.533 1.00 56.05 C
+ATOM 318 OE1 GLU A 44 46.829 46.355 14.334 1.00 64.47 O
+ATOM 319 OE2 GLU A 44 47.197 44.971 15.941 1.00 42.68 O
+ATOM 320 N LEU A 45 43.369 48.073 17.935 1.00 21.36 N
+ATOM 321 CA LEU A 45 42.604 47.255 18.836 1.00 20.92 C
+ATOM 322 C LEU A 45 41.154 47.218 18.387 1.00 22.01 C
+ATOM 323 O LEU A 45 40.358 48.129 18.639 1.00 25.70 O
+ATOM 324 CB LEU A 45 42.682 47.763 20.285 1.00 21.03 C
+ATOM 325 CG LEU A 45 42.073 46.942 21.452 1.00 23.72 C
+ATOM 326 CD1 LEU A 45 42.721 45.578 21.647 1.00 21.19 C
+ATOM 327 CD2 LEU A 45 42.367 47.680 22.716 1.00 29.45 C
+ATOM 328 N GLY A 46 40.826 46.179 17.622 1.00 18.13 N
+ATOM 329 CA GLY A 46 39.438 45.942 17.303 1.00 17.17 C
+ATOM 330 C GLY A 46 39.168 45.842 15.824 1.00 23.73 C
+ATOM 331 O GLY A 46 38.144 45.232 15.468 1.00 24.40 O
+ATOM 332 N LYS A 47 39.996 46.362 14.895 1.00 23.50 N
+ATOM 333 CA LYS A 47 39.679 46.226 13.467 1.00 25.84 C
+ATOM 334 C LYS A 47 39.573 44.757 13.054 1.00 22.74 C
+ATOM 335 O LYS A 47 38.879 44.398 12.105 1.00 24.12 O
+ATOM 336 CB LYS A 47 40.745 46.915 12.592 1.00 27.57 C
+ATOM 337 CG LYS A 47 42.100 46.284 12.693 1.00 29.81 C
+ATOM 338 CD LYS A 47 43.176 46.843 11.807 1.00 39.67 C
+ATOM 339 CE LYS A 47 44.309 45.903 12.225 1.00 49.23 C
+ATOM 340 NZ LYS A 47 45.613 46.363 11.795 1.00 59.26 N
+ATOM 341 N GLN A 48 40.174 43.863 13.838 1.00 23.23 N
+ATOM 342 CA GLN A 48 40.193 42.426 13.556 1.00 29.80 C
+ATOM 343 C GLN A 48 38.799 41.803 13.641 1.00 28.52 C
+ATOM 344 O GLN A 48 38.628 40.680 13.160 1.00 24.52 O
+ATOM 345 CB GLN A 48 41.091 41.651 14.550 1.00 28.39 C
+ATOM 346 CG GLN A 48 42.545 42.077 14.615 1.00 16.98 C
+ATOM 347 CD GLN A 48 42.764 43.318 15.409 1.00 21.22 C
+ATOM 348 OE1 GLN A 48 41.872 43.870 16.081 1.00 26.23 O
+ATOM 349 NE2 GLN A 48 43.995 43.740 15.370 1.00 23.03 N
+ATOM 350 N ALA A 49 37.806 42.475 14.253 1.00 21.21 N
+ATOM 351 CA ALA A 49 36.488 41.903 14.418 1.00 16.89 C
+ATOM 352 C ALA A 49 35.659 41.895 13.161 1.00 19.52 C
+ATOM 353 O ALA A 49 34.709 41.109 13.072 1.00 23.10 O
+ATOM 354 CB ALA A 49 35.759 42.659 15.487 1.00 22.58 C
+ATOM 355 N LYS A 50 36.097 42.602 12.125 1.00 17.73 N
+ATOM 356 CA LYS A 50 35.308 42.759 10.917 1.00 24.66 C
+ATOM 357 C LYS A 50 34.650 41.524 10.384 1.00 30.87 C
+ATOM 358 O LYS A 50 33.426 41.471 10.278 1.00 36.65 O
+ATOM 359 CB LYS A 50 36.143 43.316 9.800 1.00 34.17 C
+ATOM 360 CG LYS A 50 35.224 43.799 8.664 1.00 45.95 C
+ATOM 361 CD LYS A 50 36.154 44.209 7.561 1.00 56.17 C
+ATOM 362 CE LYS A 50 35.425 44.373 6.250 1.00 66.66 C
+ATOM 363 NZ LYS A 50 36.415 44.386 5.180 1.00 79.68 N
+ATOM 364 N ASP A 51 35.416 40.493 10.111 1.00 28.37 N
+ATOM 365 CA ASP A 51 34.849 39.271 9.552 1.00 35.62 C
+ATOM 366 C ASP A 51 34.045 38.338 10.448 1.00 25.22 C
+ATOM 367 O ASP A 51 33.120 37.663 10.011 1.00 30.31 O
+ATOM 368 CB ASP A 51 35.989 38.504 8.921 1.00 43.20 C
+ATOM 369 CG ASP A 51 36.454 39.059 7.573 1.00 50.07 C
+ATOM 370 OD1 ASP A 51 35.853 40.016 7.050 1.00 46.59 O
+ATOM 371 OD2 ASP A 51 37.423 38.492 7.051 1.00 57.73 O
+ATOM 372 N ILE A 52 34.418 38.333 11.713 1.00 22.79 N
+ATOM 373 CA ILE A 52 33.759 37.591 12.753 1.00 23.52 C
+ATOM 374 C ILE A 52 32.335 38.163 12.892 1.00 20.34 C
+ATOM 375 O ILE A 52 31.372 37.397 12.769 1.00 22.10 O
+ATOM 376 CB ILE A 52 34.522 37.749 14.102 1.00 22.08 C
+ATOM 377 CG1 ILE A 52 36.035 37.435 13.963 1.00 26.19 C
+ATOM 378 CG2 ILE A 52 33.881 36.769 15.110 1.00 21.64 C
+ATOM 379 CD1 ILE A 52 36.841 37.512 15.303 1.00 33.11 C
+ATOM 380 N MET A 53 32.175 39.479 13.080 1.00 19.44 N
+ATOM 381 CA MET A 53 30.854 40.075 13.253 1.00 23.37 C
+ATOM 382 C MET A 53 29.979 39.860 12.019 1.00 24.24 C
+ATOM 383 O MET A 53 28.783 39.588 12.107 1.00 26.60 O
+ATOM 384 CB MET A 53 30.924 41.555 13.495 1.00 15.23 C
+ATOM 385 CG MET A 53 31.597 41.967 14.781 1.00 17.79 C
+ATOM 386 SD MET A 53 31.472 43.709 15.259 1.00 23.09 S
+ATOM 387 CE MET A 53 32.499 44.502 14.091 1.00 24.41 C
+ATOM 388 N ASP A 54 30.589 39.897 10.843 1.00 29.99 N
+ATOM 389 CA ASP A 54 29.903 39.620 9.595 1.00 34.41 C
+ATOM 390 C ASP A 54 29.341 38.234 9.548 1.00 34.53 C
+ATOM 391 O ASP A 54 28.271 38.002 8.980 1.00 27.93 O
+ATOM 392 CB ASP A 54 30.846 39.759 8.427 1.00 53.31 C
+ATOM 393 CG ASP A 54 30.564 41.029 7.641 1.00 70.87 C
+ATOM 394 OD1 ASP A 54 29.567 41.055 6.910 1.00 79.36 O
+ATOM 395 OD2 ASP A 54 31.337 41.984 7.762 1.00 76.90 O
+ATOM 396 N ALA A 55 30.099 37.277 10.090 1.00 34.64 N
+ATOM 397 CA ALA A 55 29.654 35.907 10.111 1.00 25.96 C
+ATOM 398 C ALA A 55 28.643 35.688 11.231 1.00 30.04 C
+ATOM 399 O ALA A 55 27.968 34.667 11.178 1.00 28.03 O
+ATOM 400 CB ALA A 55 30.846 34.979 10.311 1.00 30.79 C
+ATOM 401 N GLY A 56 28.424 36.586 12.210 1.00 27.41 N
+ATOM 402 CA GLY A 56 27.438 36.396 13.278 1.00 16.79 C
+ATOM 403 C GLY A 56 28.029 35.715 14.500 1.00 19.84 C
+ATOM 404 O GLY A 56 27.354 35.184 15.394 1.00 20.05 O
+ATOM 405 N LYS A 57 29.353 35.725 14.527 1.00 19.78 N
+ATOM 406 CA LYS A 57 30.045 35.011 15.563 1.00 20.20 C
+ATOM 407 C LYS A 57 30.554 35.895 16.685 1.00 16.98 C
+ATOM 408 O LYS A 57 30.776 37.065 16.459 1.00 15.79 O
+ATOM 409 CB LYS A 57 31.199 34.244 14.906 1.00 29.82 C
+ATOM 410 CG LYS A 57 30.657 32.925 14.399 1.00 40.46 C
+ATOM 411 CD LYS A 57 31.789 32.009 13.997 1.00 62.41 C
+ATOM 412 CE LYS A 57 31.195 30.661 13.561 1.00 79.19 C
+ATOM 413 NZ LYS A 57 32.082 29.917 12.671 1.00 88.79 N
+ATOM 414 N LEU A 58 30.876 35.344 17.855 1.00 20.88 N
+ATOM 415 CA LEU A 58 31.439 36.126 18.922 1.00 23.72 C
+ATOM 416 C LEU A 58 32.927 36.378 18.633 1.00 31.20 C
+ATOM 417 O LEU A 58 33.598 35.546 18.015 1.00 18.63 O
+ATOM 418 CB LEU A 58 31.221 35.381 20.215 1.00 16.70 C
+ATOM 419 CG LEU A 58 29.766 35.311 20.615 1.00 21.10 C
+ATOM 420 CD1 LEU A 58 29.660 34.685 22.003 1.00 21.80 C
+ATOM 421 CD2 LEU A 58 29.175 36.702 20.724 1.00 19.30 C
+ATOM 422 N VAL A 59 33.396 37.616 18.899 1.00 30.29 N
+ATOM 423 CA VAL A 59 34.805 38.036 18.787 1.00 23.29 C
+ATOM 424 C VAL A 59 35.544 37.378 20.008 1.00 21.99 C
+ATOM 425 O VAL A 59 34.935 37.144 21.071 1.00 21.43 O
+ATOM 426 CB VAL A 59 34.761 39.591 18.806 1.00 19.93 C
+ATOM 427 CG1 VAL A 59 36.142 40.223 18.968 1.00 18.47 C
+ATOM 428 CG2 VAL A 59 34.130 40.031 17.478 1.00 20.27 C
+ATOM 429 N THR A 60 36.865 37.120 19.939 1.00 21.24 N
+ATOM 430 CA THR A 60 37.608 36.412 20.972 1.00 25.23 C
+ATOM 431 C THR A 60 37.527 37.208 22.258 1.00 18.79 C
+ATOM 432 O THR A 60 37.609 38.459 22.254 1.00 21.05 O
+ATOM 433 CB THR A 60 39.117 36.197 20.509 1.00 33.74 C
+ATOM 434 OG1 THR A 60 39.753 37.453 20.343 1.00 39.83 O
+ATOM 435 CG2 THR A 60 39.207 35.549 19.155 1.00 33.28 C
+ATOM 436 N ASP A 61 37.436 36.473 23.370 1.00 17.01 N
+ATOM 437 CA ASP A 61 37.300 37.089 24.665 1.00 19.81 C
+ATOM 438 C ASP A 61 38.471 37.991 24.925 1.00 17.79 C
+ATOM 439 O ASP A 61 38.270 39.110 25.380 1.00 20.11 O
+ATOM 440 CB ASP A 61 37.283 36.074 25.778 1.00 24.12 C
+ATOM 441 CG ASP A 61 36.119 35.113 25.728 1.00 23.83 C
+ATOM 442 OD1 ASP A 61 35.028 35.471 25.285 1.00 23.79 O
+ATOM 443 OD2 ASP A 61 36.303 34.003 26.173 1.00 28.74 O
+ATOM 444 N GLU A 62 39.673 37.506 24.610 1.00 20.66 N
+ATOM 445 CA GLU A 62 40.905 38.219 24.879 1.00 19.00 C
+ATOM 446 C GLU A 62 40.846 39.627 24.225 1.00 19.84 C
+ATOM 447 O GLU A 62 41.185 40.658 24.843 1.00 19.50 O
+ATOM 448 CB GLU A 62 41.978 37.216 24.370 1.00 23.93 C
+ATOM 449 CG GLU A 62 43.314 37.871 24.232 1.00 32.16 C
+ATOM 450 CD GLU A 62 44.432 37.171 23.444 1.00 24.91 C
+ATOM 451 OE1 GLU A 62 44.232 36.601 22.375 1.00 22.63 O
+ATOM 452 OE2 GLU A 62 45.550 37.294 23.917 1.00 24.05 O
+ATOM 453 N LEU A 63 40.288 39.759 23.018 1.00 20.30 N
+ATOM 454 CA LEU A 63 40.206 41.060 22.376 1.00 20.21 C
+ATOM 455 C LEU A 63 39.236 42.029 23.037 1.00 24.42 C
+ATOM 456 O LEU A 63 39.556 43.177 23.403 1.00 26.47 O
+ATOM 457 CB LEU A 63 39.820 40.866 20.937 1.00 22.40 C
+ATOM 458 CG LEU A 63 39.963 41.979 19.870 1.00 31.71 C
+ATOM 459 CD1 LEU A 63 41.386 42.539 19.788 1.00 29.21 C
+ATOM 460 CD2 LEU A 63 39.567 41.359 18.551 1.00 28.31 C
+ATOM 461 N VAL A 64 38.042 41.515 23.278 1.00 19.19 N
+ATOM 462 CA VAL A 64 36.989 42.314 23.858 1.00 22.62 C
+ATOM 463 C VAL A 64 37.317 42.711 25.310 1.00 18.33 C
+ATOM 464 O VAL A 64 37.064 43.855 25.724 1.00 18.42 O
+ATOM 465 CB VAL A 64 35.727 41.422 23.626 1.00 27.94 C
+ATOM 466 CG1 VAL A 64 34.666 41.782 24.563 1.00 28.09 C
+ATOM 467 CG2 VAL A 64 35.186 41.635 22.200 1.00 21.84 C
+ATOM 468 N ILE A 65 37.932 41.831 26.118 1.00 15.64 N
+ATOM 469 CA ILE A 65 38.291 42.205 27.487 1.00 21.40 C
+ATOM 470 C ILE A 65 39.308 43.361 27.450 1.00 18.81 C
+ATOM 471 O ILE A 65 39.185 44.270 28.275 1.00 22.15 O
+ATOM 472 CB ILE A 65 38.880 40.988 28.218 1.00 21.60 C
+ATOM 473 CG1 ILE A 65 37.768 39.982 28.459 1.00 24.64 C
+ATOM 474 CG2 ILE A 65 39.518 41.397 29.563 1.00 19.09 C
+ATOM 475 CD1 ILE A 65 38.290 38.529 28.684 1.00 33.45 C
+ATOM 476 N ALA A 66 40.247 43.371 26.490 1.00 22.49 N
+ATOM 477 CA ALA A 66 41.229 44.428 26.326 1.00 23.47 C
+ATOM 478 C ALA A 66 40.556 45.752 26.050 1.00 27.14 C
+ATOM 479 O ALA A 66 40.889 46.691 26.771 1.00 22.25 O
+ATOM 480 CB ALA A 66 42.154 44.098 25.181 1.00 26.83 C
+ATOM 481 N LEU A 67 39.598 45.847 25.096 1.00 22.67 N
+ATOM 482 CA LEU A 67 38.822 47.067 24.857 1.00 23.20 C
+ATOM 483 C LEU A 67 38.087 47.631 26.094 1.00 23.28 C
+ATOM 484 O LEU A 67 38.032 48.833 26.366 1.00 22.63 O
+ATOM 485 CB LEU A 67 37.710 46.875 23.851 1.00 25.15 C
+ATOM 486 CG LEU A 67 37.953 46.957 22.398 1.00 32.06 C
+ATOM 487 CD1 LEU A 67 36.584 47.044 21.775 1.00 30.24 C
+ATOM 488 CD2 LEU A 67 38.687 48.217 21.983 1.00 37.55 C
+ATOM 489 N VAL A 68 37.431 46.744 26.840 1.00 27.54 N
+ATOM 490 CA VAL A 68 36.653 47.149 28.003 1.00 20.21 C
+ATOM 491 C VAL A 68 37.537 47.626 29.102 1.00 19.66 C
+ATOM 492 O VAL A 68 37.203 48.612 29.736 1.00 30.83 O
+ATOM 493 CB VAL A 68 35.831 45.965 28.478 1.00 26.49 C
+ATOM 494 CG1 VAL A 68 34.940 46.335 29.616 1.00 31.37 C
+ATOM 495 CG2 VAL A 68 34.898 45.539 27.352 1.00 31.66 C
+ATOM 496 N LYS A 69 38.667 46.995 29.384 1.00 22.78 N
+ATOM 497 CA LYS A 69 39.562 47.475 30.424 1.00 25.90 C
+ATOM 498 C LYS A 69 40.090 48.852 30.080 1.00 24.97 C
+ATOM 499 O LYS A 69 40.097 49.753 30.915 1.00 31.23 O
+ATOM 500 CB LYS A 69 40.700 46.501 30.600 1.00 28.00 C
+ATOM 501 CG LYS A 69 40.167 45.297 31.338 1.00 30.21 C
+ATOM 502 CD LYS A 69 41.270 44.299 31.635 1.00 36.61 C
+ATOM 503 CE LYS A 69 40.783 43.298 32.706 1.00 31.99 C
+ATOM 504 NZ LYS A 69 41.758 42.233 32.928 1.00 42.55 N
+ATOM 505 N GLU A 70 40.397 49.079 28.816 1.00 33.07 N
+ATOM 506 CA GLU A 70 40.826 50.385 28.390 1.00 30.58 C
+ATOM 507 C GLU A 70 39.776 51.431 28.654 1.00 35.74 C
+ATOM 508 O GLU A 70 40.061 52.492 29.219 1.00 40.89 O
+ATOM 509 CB GLU A 70 41.137 50.372 26.925 1.00 36.86 C
+ATOM 510 CG GLU A 70 42.419 49.619 26.569 1.00 68.88 C
+ATOM 511 CD GLU A 70 43.756 50.224 27.053 1.00 81.97 C
+ATOM 512 OE1 GLU A 70 44.192 51.213 26.452 1.00 91.43 O
+ATOM 513 OE2 GLU A 70 44.377 49.696 27.992 1.00 83.01 O
+ATOM 514 N ARG A 71 38.530 51.127 28.314 1.00 34.88 N
+ATOM 515 CA ARG A 71 37.492 52.114 28.408 1.00 28.25 C
+ATOM 516 C ARG A 71 37.148 52.412 29.843 1.00 29.75 C
+ATOM 517 O ARG A 71 36.991 53.574 30.227 1.00 34.73 O
+ATOM 518 CB ARG A 71 36.343 51.567 27.618 1.00 34.66 C
+ATOM 519 CG ARG A 71 35.168 52.512 27.514 1.00 40.53 C
+ATOM 520 CD ARG A 71 35.377 53.828 26.770 1.00 43.80 C
+ATOM 521 NE ARG A 71 34.191 54.670 26.914 1.00 44.89 N
+ATOM 522 CZ ARG A 71 33.973 55.394 28.021 1.00 48.53 C
+ATOM 523 NH1 ARG A 71 34.867 55.374 29.010 1.00 57.90 N
+ATOM 524 NH2 ARG A 71 32.869 56.143 28.147 1.00 51.00 N
+ATOM 525 N ILE A 72 37.112 51.388 30.683 1.00 25.93 N
+ATOM 526 CA ILE A 72 36.751 51.628 32.046 1.00 37.60 C
+ATOM 527 C ILE A 72 37.787 52.553 32.685 1.00 44.26 C
+ATOM 528 O ILE A 72 37.427 53.302 33.600 1.00 48.70 O
+ATOM 529 CB ILE A 72 36.610 50.224 32.696 1.00 41.40 C
+ATOM 530 CG1 ILE A 72 35.159 49.850 32.530 1.00 39.96 C
+ATOM 531 CG2 ILE A 72 36.972 50.163 34.165 1.00 42.22 C
+ATOM 532 CD1 ILE A 72 34.812 48.546 33.232 1.00 37.38 C
+ATOM 533 N ALA A 73 39.030 52.562 32.162 1.00 43.97 N
+ATOM 534 CA ALA A 73 40.118 53.390 32.667 1.00 44.66 C
+ATOM 535 C ALA A 73 40.006 54.893 32.371 1.00 52.90 C
+ATOM 536 O ALA A 73 40.631 55.700 33.076 1.00 55.40 O
+ATOM 537 CB ALA A 73 41.427 52.868 32.102 1.00 46.54 C
+ATOM 538 N GLN A 74 39.183 55.305 31.395 1.00 52.56 N
+ATOM 539 CA GLN A 74 38.879 56.700 31.105 1.00 54.46 C
+ATOM 540 C GLN A 74 38.149 57.337 32.249 1.00 61.22 C
+ATOM 541 O GLN A 74 37.207 56.740 32.781 1.00 54.31 O
+ATOM 542 CB GLN A 74 37.966 56.863 29.913 1.00 63.60 C
+ATOM 543 CG GLN A 74 38.663 57.055 28.588 1.00 72.57 C
+ATOM 544 CD GLN A 74 39.765 56.027 28.429 1.00 79.14 C
+ATOM 545 OE1 GLN A 74 40.864 56.177 28.960 1.00 83.90 O
+ATOM 546 NE2 GLN A 74 39.490 54.937 27.738 1.00 82.91 N
+ATOM 547 N GLU A 75 38.475 58.612 32.497 1.00 77.77 N
+ATOM 548 CA GLU A 75 37.942 59.347 33.644 1.00 91.10 C
+ATOM 549 C GLU A 75 36.415 59.360 33.749 1.00 93.91 C
+ATOM 550 O GLU A 75 35.879 59.633 34.819 1.00 95.86 O
+ATOM 551 CB GLU A 75 38.425 60.829 33.654 1.00 98.26 C
+ATOM 552 CG GLU A 75 38.526 61.372 35.113 1.00103.87 C
+ATOM 553 CD GLU A 75 38.185 62.829 35.468 1.00104.80 C
+ATOM 554 OE1 GLU A 75 37.004 63.210 35.441 1.00102.97 O
+ATOM 555 OE2 GLU A 75 39.105 63.564 35.839 1.00104.78 O
+ATOM 556 N ASP A 76 35.616 59.078 32.718 1.00 93.76 N
+ATOM 557 CA ASP A 76 34.169 59.072 32.914 1.00 92.02 C
+ATOM 558 C ASP A 76 33.706 57.854 33.711 1.00 89.07 C
+ATOM 559 O ASP A 76 32.676 57.919 34.384 1.00 91.58 O
+ATOM 560 CB ASP A 76 33.458 59.100 31.568 1.00 93.17 C
+ATOM 561 CG ASP A 76 33.882 57.975 30.644 1.00 95.09 C
+ATOM 562 OD1 ASP A 76 33.457 56.847 30.869 1.00 93.80 O
+ATOM 563 OD2 ASP A 76 34.641 58.228 29.711 1.00 98.66 O
+ATOM 564 N CYS A 77 34.453 56.748 33.687 1.00 83.80 N
+ATOM 565 CA CYS A 77 34.023 55.549 34.377 1.00 86.85 C
+ATOM 566 C CYS A 77 34.310 55.413 35.882 1.00 86.06 C
+ATOM 567 O CYS A 77 33.851 54.454 36.538 1.00 76.52 O
+ATOM 568 CB CYS A 77 34.601 54.387 33.587 1.00 91.50 C
+ATOM 569 SG CYS A 77 33.687 54.075 32.043 1.00 97.16 S
+ATOM 570 N ARG A 78 35.006 56.403 36.489 1.00 86.24 N
+ATOM 571 CA ARG A 78 35.295 56.377 37.930 1.00 80.21 C
+ATOM 572 C ARG A 78 34.070 56.504 38.817 1.00 76.65 C
+ATOM 573 O ARG A 78 34.124 56.054 39.971 1.00 66.30 O
+ATOM 574 CB ARG A 78 36.300 57.470 38.328 1.00 76.97 C
+ATOM 575 CG ARG A 78 36.332 58.732 37.505 1.00 83.24 C
+ATOM 576 CD ARG A 78 35.130 59.641 37.680 1.00 90.01 C
+ATOM 577 NE ARG A 78 35.264 60.191 39.007 1.00 95.96 N
+ATOM 578 CZ ARG A 78 35.993 61.277 39.249 1.00 99.10 C
+ATOM 579 NH1 ARG A 78 36.520 62.025 38.277 1.00100.61 N
+ATOM 580 NH2 ARG A 78 36.144 61.646 40.515 1.00106.26 N
+ATOM 581 N ASN A 79 32.968 57.042 38.246 1.00 72.42 N
+ATOM 582 CA ASN A 79 31.688 57.065 38.942 1.00 68.72 C
+ATOM 583 C ASN A 79 30.547 56.203 38.348 1.00 60.44 C
+ATOM 584 O ASN A 79 29.333 56.432 38.474 1.00 59.20 O
+ATOM 585 CB ASN A 79 31.248 58.516 39.083 1.00 76.33 C
+ATOM 586 CG ASN A 79 31.876 59.229 40.281 1.00 84.78 C
+ATOM 587 OD1 ASN A 79 32.717 58.723 41.031 1.00 81.21 O
+ATOM 588 ND2 ASN A 79 31.493 60.483 40.481 1.00 95.47 N
+ATOM 589 N GLY A 80 30.893 55.065 37.766 1.00 50.24 N
+ATOM 590 CA GLY A 80 29.874 54.162 37.301 1.00 42.01 C
+ATOM 591 C GLY A 80 29.876 54.131 35.806 1.00 40.97 C
+ATOM 592 O GLY A 80 30.481 54.954 35.108 1.00 42.41 O
+ATOM 593 N PHE A 81 29.175 53.126 35.339 1.00 30.61 N
+ATOM 594 CA PHE A 81 29.106 52.875 33.933 1.00 27.69 C
+ATOM 595 C PHE A 81 28.054 51.772 33.789 1.00 29.03 C
+ATOM 596 O PHE A 81 27.708 51.011 34.721 1.00 30.28 O
+ATOM 597 CB PHE A 81 30.488 52.437 33.455 1.00 23.62 C
+ATOM 598 CG PHE A 81 31.144 51.301 34.244 1.00 31.29 C
+ATOM 599 CD1 PHE A 81 30.709 49.987 34.151 1.00 32.67 C
+ATOM 600 CD2 PHE A 81 32.177 51.582 35.106 1.00 37.49 C
+ATOM 601 CE1 PHE A 81 31.276 48.981 34.900 1.00 36.53 C
+ATOM 602 CE2 PHE A 81 32.753 50.572 35.859 1.00 40.77 C
+ATOM 603 CZ PHE A 81 32.307 49.275 35.761 1.00 43.61 C
+ATOM 604 N LEU A 82 27.572 51.677 32.576 1.00 22.96 N
+ATOM 605 CA LEU A 82 26.566 50.720 32.180 1.00 23.06 C
+ATOM 606 C LEU A 82 27.232 49.795 31.129 1.00 23.88 C
+ATOM 607 O LEU A 82 27.737 50.305 30.120 1.00 22.70 O
+ATOM 608 CB LEU A 82 25.443 51.611 31.676 1.00 24.66 C
+ATOM 609 CG LEU A 82 24.393 51.169 30.711 1.00 35.91 C
+ATOM 610 CD1 LEU A 82 23.487 50.154 31.356 1.00 38.55 C
+ATOM 611 CD2 LEU A 82 23.647 52.397 30.272 1.00 36.65 C
+ATOM 612 N LEU A 83 27.322 48.468 31.312 1.00 22.35 N
+ATOM 613 CA LEU A 83 27.916 47.525 30.373 1.00 21.98 C
+ATOM 614 C LEU A 83 26.790 46.979 29.510 1.00 15.68 C
+ATOM 615 O LEU A 83 25.890 46.273 29.957 1.00 20.27 O
+ATOM 616 CB LEU A 83 28.647 46.397 31.158 1.00 21.31 C
+ATOM 617 CG LEU A 83 29.913 46.836 31.911 1.00 22.33 C
+ATOM 618 CD1 LEU A 83 30.399 45.707 32.742 1.00 23.77 C
+ATOM 619 CD2 LEU A 83 30.969 47.306 30.942 1.00 21.58 C
+ATOM 620 N ASP A 84 26.821 47.301 28.234 1.00 21.73 N
+ATOM 621 CA ASP A 84 25.834 46.813 27.329 1.00 18.60 C
+ATOM 622 C ASP A 84 26.538 45.908 26.331 1.00 19.76 C
+ATOM 623 O ASP A 84 27.279 46.353 25.444 1.00 26.97 O
+ATOM 624 CB ASP A 84 25.219 48.071 26.753 1.00 20.18 C
+ATOM 625 CG ASP A 84 24.284 47.851 25.579 1.00 26.66 C
+ATOM 626 OD1 ASP A 84 23.727 46.759 25.479 1.00 20.63 O
+ATOM 627 OD2 ASP A 84 24.147 48.769 24.756 1.00 25.38 O
+ATOM 628 N GLY A 85 26.338 44.610 26.441 1.00 18.28 N
+ATOM 629 CA GLY A 85 26.933 43.697 25.483 1.00 20.17 C
+ATOM 630 C GLY A 85 28.144 42.984 25.997 1.00 20.42 C
+ATOM 631 O GLY A 85 28.746 42.135 25.324 1.00 24.43 O
+ATOM 632 N PHE A 86 28.474 43.263 27.270 1.00 19.63 N
+ATOM 633 CA PHE A 86 29.653 42.677 27.895 1.00 15.06 C
+ATOM 634 C PHE A 86 29.300 42.433 29.357 1.00 16.02 C
+ATOM 635 O PHE A 86 28.662 43.281 29.948 1.00 17.35 O
+ATOM 636 CB PHE A 86 30.850 43.633 27.792 1.00 16.51 C
+ATOM 637 CG PHE A 86 32.110 43.083 28.429 1.00 19.92 C
+ATOM 638 CD1 PHE A 86 32.380 43.279 29.780 1.00 19.32 C
+ATOM 639 CD2 PHE A 86 32.982 42.320 27.685 1.00 18.32 C
+ATOM 640 CE1 PHE A 86 33.516 42.701 30.345 1.00 23.56 C
+ATOM 641 CE2 PHE A 86 34.127 41.744 28.271 1.00 24.09 C
+ATOM 642 CZ PHE A 86 34.396 41.931 29.608 1.00 23.30 C
+ATOM 643 N PRO A 87 29.637 41.373 30.042 1.00 17.31 N
+ATOM 644 CA PRO A 87 30.201 40.135 29.493 1.00 14.20 C
+ATOM 645 C PRO A 87 29.220 39.423 28.586 1.00 15.84 C
+ATOM 646 O PRO A 87 28.004 39.540 28.685 1.00 15.08 O
+ATOM 647 CB PRO A 87 30.562 39.298 30.721 1.00 17.79 C
+ATOM 648 CG PRO A 87 29.514 39.755 31.754 1.00 19.99 C
+ATOM 649 CD PRO A 87 29.467 41.275 31.506 1.00 22.58 C
+ATOM 650 N ARG A 88 29.801 38.654 27.722 1.00 16.01 N
+ATOM 651 CA ARG A 88 29.055 37.920 26.723 1.00 23.07 C
+ATOM 652 C ARG A 88 29.382 36.436 26.897 1.00 20.65 C
+ATOM 653 O ARG A 88 28.787 35.564 26.251 1.00 16.57 O
+ATOM 654 CB ARG A 88 29.526 38.549 25.414 1.00 19.25 C
+ATOM 655 CG ARG A 88 28.725 38.490 24.178 1.00 21.95 C
+ATOM 656 CD ARG A 88 27.454 39.281 24.359 1.00 23.84 C
+ATOM 657 NE ARG A 88 26.873 39.298 23.031 1.00 28.56 N
+ATOM 658 CZ ARG A 88 26.792 40.409 22.295 1.00 28.06 C
+ATOM 659 NH1 ARG A 88 27.107 41.605 22.798 1.00 21.46 N
+ATOM 660 NH2 ARG A 88 26.328 40.311 21.053 1.00 22.33 N
+ATOM 661 N THR A 89 30.404 36.096 27.685 1.00 17.94 N
+ATOM 662 CA THR A 89 30.715 34.709 27.886 1.00 20.36 C
+ATOM 663 C THR A 89 31.195 34.573 29.346 1.00 15.20 C
+ATOM 664 O THR A 89 31.458 35.571 30.025 1.00 14.40 O
+ATOM 665 CB THR A 89 31.822 34.210 26.905 1.00 19.18 C
+ATOM 666 OG1 THR A 89 32.985 34.981 27.240 1.00 24.39 O
+ATOM 667 CG2 THR A 89 31.513 34.326 25.412 1.00 17.68 C
+ATOM 668 N ILE A 90 31.283 33.344 29.853 1.00 16.73 N
+ATOM 669 CA ILE A 90 31.743 33.110 31.221 1.00 25.76 C
+ATOM 670 C ILE A 90 33.216 33.563 31.349 1.00 21.33 C
+ATOM 671 O ILE A 90 33.497 34.260 32.324 1.00 22.19 O
+ATOM 672 CB ILE A 90 31.625 31.590 31.611 1.00 26.68 C
+ATOM 673 CG1 ILE A 90 30.193 31.055 31.591 1.00 28.19 C
+ATOM 674 CG2 ILE A 90 32.227 31.450 33.022 1.00 26.35 C
+ATOM 675 CD1 ILE A 90 29.211 31.631 32.634 1.00 26.66 C
+ATOM 676 N PRO A 91 34.212 33.299 30.483 1.00 16.51 N
+ATOM 677 CA PRO A 91 35.535 33.921 30.568 1.00 17.02 C
+ATOM 678 C PRO A 91 35.502 35.437 30.711 1.00 24.68 C
+ATOM 679 O PRO A 91 36.288 35.971 31.495 1.00 24.46 O
+ATOM 680 CB PRO A 91 36.242 33.526 29.317 1.00 20.92 C
+ATOM 681 CG PRO A 91 35.677 32.159 29.063 1.00 23.66 C
+ATOM 682 CD PRO A 91 34.181 32.354 29.365 1.00 18.59 C
+ATOM 683 N GLN A 92 34.624 36.171 29.974 1.00 16.06 N
+ATOM 684 CA GLN A 92 34.575 37.605 30.140 1.00 13.71 C
+ATOM 685 C GLN A 92 34.007 37.921 31.517 1.00 15.94 C
+ATOM 686 O GLN A 92 34.421 38.926 32.116 1.00 20.24 O
+ATOM 687 CB GLN A 92 33.734 38.195 29.024 1.00 18.99 C
+ATOM 688 CG GLN A 92 34.303 37.956 27.594 1.00 15.80 C
+ATOM 689 CD GLN A 92 33.377 38.444 26.478 1.00 15.95 C
+ATOM 690 OE1 GLN A 92 32.493 39.288 26.669 1.00 14.11 O
+ATOM 691 NE2 GLN A 92 33.519 37.974 25.252 1.00 14.69 N
+ATOM 692 N ALA A 93 33.089 37.118 32.100 1.00 17.91 N
+ATOM 693 CA ALA A 93 32.541 37.446 33.423 1.00 23.88 C
+ATOM 694 C ALA A 93 33.605 37.178 34.477 1.00 16.87 C
+ATOM 695 O ALA A 93 33.790 37.986 35.396 1.00 18.41 O
+ATOM 696 CB ALA A 93 31.308 36.594 33.760 1.00 23.17 C
+ATOM 697 N ASP A 94 34.311 36.050 34.355 1.00 19.98 N
+ATOM 698 CA ASP A 94 35.444 35.776 35.246 1.00 26.72 C
+ATOM 699 C ASP A 94 36.510 36.853 35.215 1.00 28.05 C
+ATOM 700 O ASP A 94 36.945 37.281 36.287 1.00 24.29 O
+ATOM 701 CB ASP A 94 36.128 34.487 34.895 1.00 27.71 C
+ATOM 702 CG ASP A 94 35.301 33.302 35.338 1.00 36.49 C
+ATOM 703 OD1 ASP A 94 34.611 33.382 36.374 1.00 29.94 O
+ATOM 704 OD2 ASP A 94 35.361 32.307 34.623 1.00 38.04 O
+ATOM 705 N ALA A 95 36.870 37.362 34.022 1.00 21.73 N
+ATOM 706 CA ALA A 95 37.851 38.413 33.908 1.00 22.58 C
+ATOM 707 C ALA A 95 37.456 39.643 34.695 1.00 23.08 C
+ATOM 708 O ALA A 95 38.316 40.287 35.305 1.00 22.24 O
+ATOM 709 CB ALA A 95 38.030 38.801 32.439 1.00 30.84 C
+ATOM 710 N MET A 96 36.171 40.029 34.687 1.00 25.96 N
+ATOM 711 CA MET A 96 35.660 41.143 35.472 1.00 24.51 C
+ATOM 712 C MET A 96 35.829 40.881 36.968 1.00 31.22 C
+ATOM 713 O MET A 96 36.231 41.756 37.735 1.00 30.31 O
+ATOM 714 CB MET A 96 34.193 41.341 35.189 1.00 29.30 C
+ATOM 715 CG MET A 96 33.874 42.444 34.199 1.00 40.35 C
+ATOM 716 SD MET A 96 32.075 42.465 33.950 1.00 42.93 S
+ATOM 717 CE MET A 96 31.495 43.419 35.312 1.00 34.49 C
+ATOM 718 N LYS A 97 35.579 39.630 37.360 1.00 37.96 N
+ATOM 719 CA LYS A 97 35.733 39.148 38.737 1.00 45.23 C
+ATOM 720 C LYS A 97 37.192 39.350 39.141 1.00 39.73 C
+ATOM 721 O LYS A 97 37.472 40.257 39.920 1.00 35.21 O
+ATOM 722 CB LYS A 97 35.355 37.656 38.817 1.00 47.93 C
+ATOM 723 CG LYS A 97 34.564 37.502 40.078 1.00 60.44 C
+ATOM 724 CD LYS A 97 33.783 36.222 40.196 1.00 65.76 C
+ATOM 725 CE LYS A 97 33.050 36.502 41.498 1.00 74.61 C
+ATOM 726 NZ LYS A 97 32.365 35.323 41.977 1.00 81.01 N
+ATOM 727 N GLU A 98 38.122 38.596 38.530 1.00 38.69 N
+ATOM 728 CA GLU A 98 39.569 38.768 38.720 1.00 38.07 C
+ATOM 729 C GLU A 98 40.078 40.206 38.835 1.00 37.47 C
+ATOM 730 O GLU A 98 40.993 40.501 39.623 1.00 39.85 O
+ATOM 731 CB GLU A 98 40.337 38.096 37.566 1.00 35.66 C
+ATOM 732 CG GLU A 98 40.135 36.609 37.434 1.00 35.33 C
+ATOM 733 CD GLU A 98 40.527 35.822 38.674 1.00 51.96 C
+ATOM 734 OE1 GLU A 98 39.691 35.639 39.568 1.00 52.83 O
+ATOM 735 OE2 GLU A 98 41.678 35.379 38.736 1.00 63.50 O
+ATOM 736 N ALA A 99 39.495 41.100 38.025 1.00 39.23 N
+ATOM 737 CA ALA A 99 39.899 42.490 37.999 1.00 36.97 C
+ATOM 738 C ALA A 99 39.206 43.370 39.028 1.00 30.71 C
+ATOM 739 O ALA A 99 39.436 44.578 39.006 1.00 36.58 O
+ATOM 740 CB ALA A 99 39.670 43.086 36.578 1.00 33.85 C
+ATOM 741 N GLY A 100 38.375 42.922 39.962 1.00 36.48 N
+ATOM 742 CA GLY A 100 37.775 43.860 40.924 1.00 35.17 C
+ATOM 743 C GLY A 100 36.680 44.765 40.354 1.00 36.37 C
+ATOM 744 O GLY A 100 36.431 45.866 40.852 1.00 39.36 O
+ATOM 745 N ILE A 101 35.985 44.319 39.280 1.00 36.15 N
+ATOM 746 CA ILE A 101 34.864 45.066 38.723 1.00 37.83 C
+ATOM 747 C ILE A 101 33.614 44.296 39.115 1.00 39.43 C
+ATOM 748 O ILE A 101 33.219 43.281 38.517 1.00 41.33 O
+ATOM 749 CB ILE A 101 34.865 45.177 37.170 1.00 37.52 C
+ATOM 750 CG1 ILE A 101 36.173 45.753 36.598 1.00 30.53 C
+ATOM 751 CG2 ILE A 101 33.628 46.042 36.841 1.00 28.64 C
+ATOM 752 CD1 ILE A 101 36.469 45.273 35.166 1.00 33.83 C
+ATOM 753 N ASN A 102 33.039 44.800 40.182 1.00 40.13 N
+ATOM 754 CA ASN A 102 31.793 44.278 40.733 1.00 43.69 C
+ATOM 755 C ASN A 102 30.685 45.229 40.224 1.00 40.71 C
+ATOM 756 O ASN A 102 30.982 46.365 39.806 1.00 34.57 O
+ATOM 757 CB ASN A 102 31.854 44.260 42.290 1.00 39.88 C
+ATOM 758 CG ASN A 102 32.154 45.659 42.838 1.00 53.51 C
+ATOM 759 OD1 ASN A 102 33.249 46.185 42.565 1.00 51.52 O
+ATOM 760 ND2 ASN A 102 31.246 46.346 43.552 1.00 57.38 N
+ATOM 761 N VAL A 103 29.399 44.824 40.159 1.00 34.58 N
+ATOM 762 CA VAL A 103 28.372 45.707 39.643 1.00 29.14 C
+ATOM 763 C VAL A 103 27.271 45.729 40.658 1.00 25.58 C
+ATOM 764 O VAL A 103 27.144 44.832 41.501 1.00 26.58 O
+ATOM 765 CB VAL A 103 27.780 45.248 38.259 1.00 32.44 C
+ATOM 766 CG1 VAL A 103 28.899 45.246 37.269 1.00 25.15 C
+ATOM 767 CG2 VAL A 103 27.146 43.894 38.301 1.00 29.59 C
+ATOM 768 N ASP A 104 26.464 46.759 40.530 1.00 25.82 N
+ATOM 769 CA ASP A 104 25.332 46.877 41.404 1.00 24.56 C
+ATOM 770 C ASP A 104 24.124 46.100 40.979 1.00 28.20 C
+ATOM 771 O ASP A 104 23.498 45.493 41.846 1.00 21.75 O
+ATOM 772 CB ASP A 104 24.986 48.303 41.522 1.00 29.61 C
+ATOM 773 CG ASP A 104 26.128 49.007 42.261 1.00 39.01 C
+ATOM 774 OD1 ASP A 104 26.394 48.723 43.441 1.00 40.49 O
+ATOM 775 OD2 ASP A 104 26.773 49.834 41.630 1.00 31.93 O
+ATOM 776 N TYR A 105 23.831 46.089 39.678 1.00 19.14 N
+ATOM 777 CA TYR A 105 22.614 45.492 39.142 1.00 25.20 C
+ATOM 778 C TYR A 105 22.931 44.745 37.883 1.00 25.41 C
+ATOM 779 O TYR A 105 23.764 45.224 37.097 1.00 27.61 O
+ATOM 780 CB TYR A 105 21.548 46.495 38.715 1.00 32.67 C
+ATOM 781 CG TYR A 105 20.839 47.286 39.803 1.00 43.56 C
+ATOM 782 CD1 TYR A 105 21.434 48.446 40.274 1.00 52.04 C
+ATOM 783 CD2 TYR A 105 19.604 46.881 40.304 1.00 46.91 C
+ATOM 784 CE1 TYR A 105 20.809 49.220 41.239 1.00 55.58 C
+ATOM 785 CE2 TYR A 105 18.972 47.644 41.280 1.00 49.41 C
+ATOM 786 CZ TYR A 105 19.583 48.816 41.737 1.00 57.41 C
+ATOM 787 OH TYR A 105 18.989 49.616 42.708 1.00 63.15 O
+ATOM 788 N VAL A 106 22.320 43.572 37.739 1.00 19.65 N
+ATOM 789 CA VAL A 106 22.348 42.878 36.473 1.00 19.27 C
+ATOM 790 C VAL A 106 20.870 42.849 36.044 1.00 21.52 C
+ATOM 791 O VAL A 106 19.967 42.515 36.823 1.00 21.79 O
+ATOM 792 CB VAL A 106 22.942 41.493 36.681 1.00 14.46 C
+ATOM 793 CG1 VAL A 106 22.901 40.759 35.332 1.00 17.52 C
+ATOM 794 CG2 VAL A 106 24.412 41.568 37.146 1.00 21.05 C
+ATOM 795 N LEU A 107 20.543 43.290 34.837 1.00 19.73 N
+ATOM 796 CA LEU A 107 19.163 43.331 34.358 1.00 20.88 C
+ATOM 797 C LEU A 107 19.072 42.441 33.134 1.00 23.74 C
+ATOM 798 O LEU A 107 19.839 42.522 32.166 1.00 20.53 O
+ATOM 799 CB LEU A 107 18.781 44.770 34.012 1.00 25.86 C
+ATOM 800 CG LEU A 107 19.037 45.845 35.123 1.00 26.90 C
+ATOM 801 CD1 LEU A 107 18.745 47.167 34.547 1.00 23.91 C
+ATOM 802 CD2 LEU A 107 18.136 45.687 36.346 1.00 28.78 C
+ATOM 803 N GLU A 108 18.168 41.477 33.207 1.00 22.08 N
+ATOM 804 CA GLU A 108 17.976 40.535 32.145 1.00 18.27 C
+ATOM 805 C GLU A 108 16.739 41.024 31.406 1.00 20.53 C
+ATOM 806 O GLU A 108 15.736 41.348 32.022 1.00 24.69 O
+ATOM 807 CB GLU A 108 17.795 39.197 32.772 1.00 17.12 C
+ATOM 808 CG GLU A 108 17.479 38.112 31.769 1.00 23.19 C
+ATOM 809 CD GLU A 108 16.878 36.862 32.373 1.00 29.16 C
+ATOM 810 OE1 GLU A 108 16.949 36.652 33.582 1.00 26.95 O
+ATOM 811 OE2 GLU A 108 16.327 36.092 31.607 1.00 28.40 O
+ATOM 812 N PHE A 109 16.860 41.159 30.095 1.00 16.76 N
+ATOM 813 CA PHE A 109 15.795 41.545 29.219 1.00 16.96 C
+ATOM 814 C PHE A 109 15.347 40.241 28.577 1.00 20.60 C
+ATOM 815 O PHE A 109 16.033 39.691 27.704 1.00 21.91 O
+ATOM 816 CB PHE A 109 16.303 42.506 28.144 1.00 19.38 C
+ATOM 817 CG PHE A 109 16.534 43.943 28.597 1.00 29.84 C
+ATOM 818 CD1 PHE A 109 17.292 44.250 29.712 1.00 28.76 C
+ATOM 819 CD2 PHE A 109 15.962 44.982 27.878 1.00 39.45 C
+ATOM 820 CE1 PHE A 109 17.484 45.555 30.122 1.00 21.86 C
+ATOM 821 CE2 PHE A 109 16.160 46.290 28.294 1.00 37.45 C
+ATOM 822 CZ PHE A 109 16.916 46.586 29.411 1.00 29.73 C
+ATOM 823 N ASP A 110 14.196 39.690 28.948 1.00 18.29 N
+ATOM 824 CA ASP A 110 13.724 38.460 28.356 1.00 21.38 C
+ATOM 825 C ASP A 110 12.796 38.645 27.163 1.00 17.73 C
+ATOM 826 O ASP A 110 11.750 39.309 27.235 1.00 19.51 O
+ATOM 827 CB ASP A 110 13.057 37.683 29.461 1.00 20.74 C
+ATOM 828 CG ASP A 110 12.395 36.407 28.943 1.00 39.61 C
+ATOM 829 OD1 ASP A 110 13.069 35.651 28.223 1.00 44.65 O
+ATOM 830 OD2 ASP A 110 11.211 36.195 29.261 1.00 42.80 O
+ATOM 831 N VAL A 111 13.115 38.026 26.066 1.00 13.74 N
+ATOM 832 CA VAL A 111 12.261 38.125 24.898 1.00 18.33 C
+ATOM 833 C VAL A 111 12.190 36.725 24.317 1.00 23.62 C
+ATOM 834 O VAL A 111 13.216 36.063 24.352 1.00 27.92 O
+ATOM 835 CB VAL A 111 12.903 39.113 23.915 1.00 26.33 C
+ATOM 836 CG1 VAL A 111 12.176 39.180 22.613 1.00 33.87 C
+ATOM 837 CG2 VAL A 111 12.652 40.546 24.393 1.00 27.91 C
+ATOM 838 N PRO A 112 11.100 36.192 23.795 1.00 18.89 N
+ATOM 839 CA PRO A 112 11.073 34.932 23.064 1.00 23.18 C
+ATOM 840 C PRO A 112 11.931 34.951 21.804 1.00 22.44 C
+ATOM 841 O PRO A 112 11.936 35.964 21.097 1.00 24.36 O
+ATOM 842 CB PRO A 112 9.604 34.695 22.743 1.00 19.78 C
+ATOM 843 CG PRO A 112 8.875 35.631 23.655 1.00 20.79 C
+ATOM 844 CD PRO A 112 9.794 36.808 23.854 1.00 18.21 C
+ATOM 845 N ASP A 113 12.616 33.862 21.441 1.00 21.33 N
+ATOM 846 CA ASP A 113 13.347 33.748 20.186 1.00 21.15 C
+ATOM 847 C ASP A 113 12.584 34.097 18.926 1.00 20.23 C
+ATOM 848 O ASP A 113 13.097 34.687 18.000 1.00 16.45 O
+ATOM 849 CB ASP A 113 13.861 32.342 19.980 1.00 32.08 C
+ATOM 850 CG ASP A 113 15.006 31.883 20.899 1.00 36.08 C
+ATOM 851 OD1 ASP A 113 15.672 32.736 21.459 1.00 28.01 O
+ATOM 852 OD2 ASP A 113 15.240 30.674 21.052 1.00 46.72 O
+ATOM 853 N GLU A 114 11.311 33.801 18.881 1.00 21.14 N
+ATOM 854 CA GLU A 114 10.481 34.000 17.694 1.00 21.97 C
+ATOM 855 C GLU A 114 10.252 35.458 17.333 1.00 23.20 C
+ATOM 856 O GLU A 114 9.862 35.766 16.207 1.00 23.38 O
+ATOM 857 CB GLU A 114 9.111 33.311 17.908 1.00 20.25 C
+ATOM 858 CG GLU A 114 9.285 31.800 18.061 1.00 16.29 C
+ATOM 859 CD GLU A 114 9.575 31.249 19.445 1.00 27.80 C
+ATOM 860 OE1 GLU A 114 9.790 31.988 20.409 1.00 25.25 O
+ATOM 861 OE2 GLU A 114 9.547 30.034 19.574 1.00 35.12 O
+ATOM 862 N LEU A 115 10.447 36.399 18.260 1.00 18.48 N
+ATOM 863 CA LEU A 115 10.260 37.817 17.934 1.00 22.63 C
+ATOM 864 C LEU A 115 11.520 38.459 17.358 1.00 17.14 C
+ATOM 865 O LEU A 115 11.445 39.577 16.853 1.00 22.09 O
+ATOM 866 CB LEU A 115 9.894 38.618 19.183 1.00 16.50 C
+ATOM 867 CG LEU A 115 8.447 38.724 19.632 1.00 26.94 C
+ATOM 868 CD1 LEU A 115 7.704 37.409 19.736 1.00 22.97 C
+ATOM 869 CD2 LEU A 115 8.535 39.366 21.024 1.00 19.62 C
+ATOM 870 N ILE A 116 12.688 37.820 17.416 1.00 13.97 N
+ATOM 871 CA ILE A 116 13.933 38.508 17.208 1.00 9.74 C
+ATOM 872 C ILE A 116 14.128 38.875 15.783 1.00 15.70 C
+ATOM 873 O ILE A 116 14.512 40.022 15.543 1.00 18.13 O
+ATOM 874 CB ILE A 116 15.118 37.648 17.676 1.00 16.67 C
+ATOM 875 CG1 ILE A 116 15.038 37.342 19.166 1.00 25.20 C
+ATOM 876 CG2 ILE A 116 16.410 38.405 17.515 1.00 20.38 C
+ATOM 877 CD1 ILE A 116 14.720 38.497 20.100 1.00 34.08 C
+ATOM 878 N VAL A 117 13.897 37.966 14.832 1.00 16.33 N
+ATOM 879 CA VAL A 117 14.225 38.291 13.469 1.00 16.71 C
+ATOM 880 C VAL A 117 13.446 39.514 12.993 1.00 21.91 C
+ATOM 881 O VAL A 117 14.126 40.388 12.436 1.00 28.27 O
+ATOM 882 CB VAL A 117 13.999 37.013 12.648 1.00 21.49 C
+ATOM 883 CG1 VAL A 117 13.955 37.307 11.153 1.00 26.80 C
+ATOM 884 CG2 VAL A 117 15.191 36.083 12.902 1.00 22.62 C
+ATOM 885 N ASP A 118 12.133 39.750 13.252 1.00 27.52 N
+ATOM 886 CA ASP A 118 11.453 40.992 12.840 1.00 26.18 C
+ATOM 887 C ASP A 118 11.855 42.240 13.570 1.00 33.69 C
+ATOM 888 O ASP A 118 11.803 43.327 12.976 1.00 32.99 O
+ATOM 889 CB ASP A 118 9.956 40.872 12.967 1.00 40.16 C
+ATOM 890 CG ASP A 118 9.362 39.878 11.975 1.00 52.51 C
+ATOM 891 OD1 ASP A 118 9.972 39.579 10.941 1.00 60.07 O
+ATOM 892 OD2 ASP A 118 8.263 39.402 12.240 1.00 65.46 O
+ATOM 893 N ARG A 119 12.271 42.147 14.844 1.00 24.50 N
+ATOM 894 CA ARG A 119 12.823 43.313 15.486 1.00 30.39 C
+ATOM 895 C ARG A 119 14.023 43.741 14.703 1.00 32.84 C
+ATOM 896 O ARG A 119 14.076 44.882 14.235 1.00 43.09 O
+ATOM 897 CB ARG A 119 13.349 43.091 16.885 1.00 24.69 C
+ATOM 898 CG ARG A 119 12.147 43.270 17.709 1.00 17.45 C
+ATOM 899 CD ARG A 119 12.614 43.243 19.102 1.00 16.60 C
+ATOM 900 NE ARG A 119 11.421 43.252 19.890 1.00 12.44 N
+ATOM 901 CZ ARG A 119 11.441 43.334 21.207 1.00 16.89 C
+ATOM 902 NH1 ARG A 119 12.549 43.550 21.878 1.00 14.06 N
+ATOM 903 NH2 ARG A 119 10.279 43.260 21.851 1.00 25.25 N
+ATOM 904 N ILE A 120 14.928 42.797 14.446 1.00 26.70 N
+ATOM 905 CA ILE A 120 16.144 43.201 13.823 1.00 22.95 C
+ATOM 906 C ILE A 120 15.993 43.613 12.372 1.00 21.07 C
+ATOM 907 O ILE A 120 16.753 44.515 12.019 1.00 20.97 O
+ATOM 908 CB ILE A 120 17.173 42.082 14.081 1.00 23.49 C
+ATOM 909 CG1 ILE A 120 17.584 42.257 15.571 1.00 26.12 C
+ATOM 910 CG2 ILE A 120 18.409 42.194 13.267 1.00 20.91 C
+ATOM 911 CD1 ILE A 120 18.641 41.390 16.229 1.00 29.96 C
+ATOM 912 N VAL A 121 15.022 43.213 11.561 1.00 17.44 N
+ATOM 913 CA VAL A 121 14.990 43.687 10.181 1.00 25.51 C
+ATOM 914 C VAL A 121 14.486 45.127 10.063 1.00 27.87 C
+ATOM 915 O VAL A 121 14.749 45.831 9.069 1.00 29.46 O
+ATOM 916 CB VAL A 121 14.109 42.771 9.195 1.00 29.84 C
+ATOM 917 CG1 VAL A 121 14.722 41.392 9.259 1.00 31.89 C
+ATOM 918 CG2 VAL A 121 12.609 42.770 9.486 1.00 29.22 C
+ATOM 919 N GLY A 122 13.725 45.594 11.052 1.00 23.01 N
+ATOM 920 CA GLY A 122 13.285 46.970 11.062 1.00 20.28 C
+ATOM 921 C GLY A 122 14.309 47.830 11.795 1.00 22.81 C
+ATOM 922 O GLY A 122 14.030 49.017 11.944 1.00 19.95 O
+ATOM 923 N ARG A 123 15.453 47.336 12.286 1.00 16.72 N
+ATOM 924 CA ARG A 123 16.370 48.198 12.993 1.00 16.86 C
+ATOM 925 C ARG A 123 17.171 49.081 12.041 1.00 20.28 C
+ATOM 926 O ARG A 123 17.626 48.652 10.981 1.00 20.03 O
+ATOM 927 CB ARG A 123 17.314 47.379 13.834 1.00 12.78 C
+ATOM 928 CG ARG A 123 18.432 48.166 14.505 1.00 13.69 C
+ATOM 929 CD ARG A 123 19.062 47.450 15.704 1.00 19.15 C
+ATOM 930 NE ARG A 123 19.820 46.254 15.332 1.00 18.77 N
+ATOM 931 CZ ARG A 123 20.399 45.419 16.211 1.00 20.69 C
+ATOM 932 NH1 ARG A 123 20.319 45.627 17.515 1.00 23.25 N
+ATOM 933 NH2 ARG A 123 21.068 44.353 15.795 1.00 17.61 N
+ATOM 934 N ARG A 124 17.329 50.354 12.446 1.00 20.44 N
+ATOM 935 CA ARG A 124 18.075 51.418 11.759 1.00 21.94 C
+ATOM 936 C ARG A 124 18.848 52.144 12.874 1.00 16.05 C
+ATOM 937 O ARG A 124 18.380 52.374 14.014 1.00 19.24 O
+ATOM 938 CB ARG A 124 17.102 52.390 11.080 1.00 21.22 C
+ATOM 939 CG ARG A 124 16.056 51.719 10.134 1.00 19.93 C
+ATOM 940 CD ARG A 124 16.756 51.250 8.837 1.00 25.72 C
+ATOM 941 NE ARG A 124 15.849 50.731 7.802 1.00 26.35 N
+ATOM 942 CZ ARG A 124 15.457 49.451 7.820 1.00 31.92 C
+ATOM 943 NH1 ARG A 124 15.860 48.603 8.760 1.00 24.37 N
+ATOM 944 NH2 ARG A 124 14.671 48.979 6.874 1.00 28.82 N
+ATOM 945 N VAL A 125 20.088 52.483 12.559 1.00 18.98 N
+ATOM 946 CA VAL A 125 20.966 53.077 13.531 1.00 20.59 C
+ATOM 947 C VAL A 125 21.605 54.366 12.987 1.00 20.40 C
+ATOM 948 O VAL A 125 21.692 54.631 11.783 1.00 18.82 O
+ATOM 949 CB VAL A 125 22.074 52.053 13.931 1.00 19.00 C
+ATOM 950 CG1 VAL A 125 21.467 50.733 14.377 1.00 22.11 C
+ATOM 951 CG2 VAL A 125 22.950 51.736 12.737 1.00 23.07 C
+ATOM 952 N HIS A 126 21.928 55.220 13.949 1.00 17.05 N
+ATOM 953 CA HIS A 126 22.804 56.339 13.735 1.00 21.64 C
+ATOM 954 C HIS A 126 24.189 55.862 14.226 1.00 19.30 C
+ATOM 955 O HIS A 126 24.537 55.932 15.416 1.00 23.61 O
+ATOM 956 CB HIS A 126 22.295 57.498 14.554 1.00 21.63 C
+ATOM 957 CG HIS A 126 23.213 58.665 14.288 1.00 26.08 C
+ATOM 958 ND1 HIS A 126 23.867 59.380 15.198 1.00 22.48 N
+ATOM 959 CD2 HIS A 126 23.473 59.169 13.019 1.00 22.91 C
+ATOM 960 CE1 HIS A 126 24.521 60.319 14.545 1.00 21.17 C
+ATOM 961 NE2 HIS A 126 24.272 60.172 13.258 1.00 28.56 N
+ATOM 962 N ALA A 127 25.066 55.475 13.319 1.00 24.92 N
+ATOM 963 CA ALA A 127 26.322 54.841 13.688 1.00 27.42 C
+ATOM 964 C ALA A 127 27.277 55.648 14.511 1.00 35.22 C
+ATOM 965 O ALA A 127 27.802 55.137 15.509 1.00 40.67 O
+ATOM 966 CB ALA A 127 27.041 54.387 12.447 1.00 26.91 C
+ATOM 967 N PRO A 128 27.458 56.954 14.262 1.00 40.32 N
+ATOM 968 CA PRO A 128 28.355 57.764 15.058 1.00 35.72 C
+ATOM 969 C PRO A 128 27.943 57.745 16.524 1.00 39.27 C
+ATOM 970 O PRO A 128 28.805 57.752 17.407 1.00 46.54 O
+ATOM 971 CB PRO A 128 28.277 59.143 14.438 1.00 36.83 C
+ATOM 972 CG PRO A 128 27.812 58.895 13.050 1.00 36.86 C
+ATOM 973 CD PRO A 128 26.822 57.781 13.235 1.00 36.44 C
+ATOM 974 N SER A 129 26.656 57.667 16.849 1.00 35.27 N
+ATOM 975 CA SER A 129 26.333 57.776 18.239 1.00 23.47 C
+ATOM 976 C SER A 129 25.926 56.464 18.824 1.00 32.54 C
+ATOM 977 O SER A 129 25.808 56.334 20.061 1.00 35.53 O
+ATOM 978 CB SER A 129 25.223 58.760 18.417 1.00 30.16 C
+ATOM 979 OG SER A 129 24.044 58.377 17.705 1.00 35.12 O
+ATOM 980 N GLY A 130 25.612 55.532 17.923 1.00 26.18 N
+ATOM 981 CA GLY A 130 25.086 54.264 18.402 1.00 31.57 C
+ATOM 982 C GLY A 130 23.598 54.425 18.751 1.00 32.35 C
+ATOM 983 O GLY A 130 23.027 53.495 19.323 1.00 34.98 O
+ATOM 984 N ARG A 131 22.885 55.539 18.455 1.00 30.74 N
+ATOM 985 CA ARG A 131 21.452 55.561 18.766 1.00 23.71 C
+ATOM 986 C ARG A 131 20.753 54.602 17.792 1.00 24.28 C
+ATOM 987 O ARG A 131 21.124 54.515 16.607 1.00 21.25 O
+ATOM 988 CB ARG A 131 20.834 56.943 18.600 1.00 22.87 C
+ATOM 989 CG ARG A 131 21.186 57.787 19.786 1.00 25.33 C
+ATOM 990 CD ARG A 131 20.561 59.179 19.746 1.00 31.06 C
+ATOM 991 NE ARG A 131 21.221 59.976 18.723 1.00 30.64 N
+ATOM 992 CZ ARG A 131 22.354 60.630 18.959 1.00 29.68 C
+ATOM 993 NH1 ARG A 131 22.938 60.617 20.160 1.00 30.29 N
+ATOM 994 NH2 ARG A 131 22.908 61.281 17.947 1.00 23.08 N
+ATOM 995 N VAL A 132 19.743 53.897 18.296 1.00 24.42 N
+ATOM 996 CA VAL A 132 18.996 52.896 17.538 1.00 19.01 C
+ATOM 997 C VAL A 132 17.477 53.158 17.515 1.00 13.30 C
+ATOM 998 O VAL A 132 16.814 53.564 18.478 1.00 14.89 O
+ATOM 999 CB VAL A 132 19.419 51.464 18.159 1.00 27.21 C
+ATOM 1000 CG1 VAL A 132 19.165 51.388 19.655 1.00 27.91 C
+ATOM 1001 CG2 VAL A 132 18.586 50.364 17.565 1.00 24.25 C
+ATOM 1002 N TYR A 133 16.916 52.890 16.343 1.00 15.85 N
+ATOM 1003 CA TYR A 133 15.513 53.093 16.026 1.00 21.52 C
+ATOM 1004 C TYR A 133 14.915 51.820 15.394 1.00 20.47 C
+ATOM 1005 O TYR A 133 15.625 50.920 14.954 1.00 18.64 O
+ATOM 1006 CB TYR A 133 15.433 54.267 15.027 1.00 25.21 C
+ATOM 1007 CG TYR A 133 16.013 55.579 15.528 1.00 27.60 C
+ATOM 1008 CD1 TYR A 133 15.224 56.455 16.286 1.00 25.53 C
+ATOM 1009 CD2 TYR A 133 17.316 55.908 15.188 1.00 22.73 C
+ATOM 1010 CE1 TYR A 133 15.785 57.673 16.667 1.00 30.03 C
+ATOM 1011 CE2 TYR A 133 17.887 57.132 15.588 1.00 24.54 C
+ATOM 1012 CZ TYR A 133 17.104 58.005 16.323 1.00 24.88 C
+ATOM 1013 OH TYR A 133 17.628 59.229 16.733 1.00 25.95 O
+ATOM 1014 N HIS A 134 13.592 51.753 15.260 1.00 20.27 N
+ATOM 1015 CA HIS A 134 12.920 50.671 14.575 1.00 19.40 C
+ATOM 1016 C HIS A 134 11.872 51.327 13.699 1.00 18.72 C
+ATOM 1017 O HIS A 134 11.007 52.053 14.215 1.00 17.83 O
+ATOM 1018 CB HIS A 134 12.210 49.730 15.557 1.00 15.32 C
+ATOM 1019 CG HIS A 134 11.706 48.501 14.821 1.00 21.13 C
+ATOM 1020 ND1 HIS A 134 10.556 48.276 14.167 1.00 22.51 N
+ATOM 1021 CD2 HIS A 134 12.468 47.369 14.712 1.00 18.02 C
+ATOM 1022 CE1 HIS A 134 10.613 47.062 13.668 1.00 22.98 C
+ATOM 1023 NE2 HIS A 134 11.757 46.532 13.999 1.00 24.90 N
+ATOM 1024 N VAL A 135 11.820 50.979 12.420 1.00 21.45 N
+ATOM 1025 CA VAL A 135 10.854 51.600 11.529 1.00 24.32 C
+ATOM 1026 C VAL A 135 9.394 51.546 11.945 1.00 32.49 C
+ATOM 1027 O VAL A 135 8.615 52.427 11.555 1.00 33.83 O
+ATOM 1028 CB VAL A 135 10.957 51.010 10.116 1.00 24.25 C
+ATOM 1029 CG1 VAL A 135 12.323 51.398 9.568 1.00 29.33 C
+ATOM 1030 CG2 VAL A 135 10.715 49.521 10.097 1.00 26.30 C
+ATOM 1031 N LYS A 136 9.031 50.478 12.695 1.00 33.22 N
+ATOM 1032 CA LYS A 136 7.667 50.304 13.237 1.00 34.28 C
+ATOM 1033 C LYS A 136 7.568 50.589 14.724 1.00 30.05 C
+ATOM 1034 O LYS A 136 6.735 51.363 15.188 1.00 32.74 O
+ATOM 1035 CB LYS A 136 7.130 48.860 13.071 1.00 33.43 C
+ATOM 1036 CG LYS A 136 7.245 48.246 11.697 1.00 45.05 C
+ATOM 1037 CD LYS A 136 6.950 46.762 11.781 1.00 55.68 C
+ATOM 1038 CE LYS A 136 6.657 46.207 10.383 1.00 62.38 C
+ATOM 1039 NZ LYS A 136 6.469 44.763 10.438 1.00 70.97 N
+ATOM 1040 N PHE A 137 8.501 50.023 15.507 1.00 27.80 N
+ATOM 1041 CA PHE A 137 8.263 49.977 16.941 1.00 23.96 C
+ATOM 1042 C PHE A 137 8.764 51.187 17.679 1.00 23.18 C
+ATOM 1043 O PHE A 137 8.381 51.422 18.832 1.00 27.47 O
+ATOM 1044 CB PHE A 137 8.914 48.710 17.552 1.00 22.50 C
+ATOM 1045 CG PHE A 137 8.346 47.450 16.934 1.00 32.69 C
+ATOM 1046 CD1 PHE A 137 6.992 47.346 16.631 1.00 36.01 C
+ATOM 1047 CD2 PHE A 137 9.194 46.386 16.624 1.00 36.10 C
+ATOM 1048 CE1 PHE A 137 6.489 46.191 16.029 1.00 37.80 C
+ATOM 1049 CE2 PHE A 137 8.688 45.235 16.023 1.00 35.51 C
+ATOM 1050 CZ PHE A 137 7.333 45.131 15.713 1.00 32.08 C
+ATOM 1051 N ASN A 138 9.642 51.947 17.056 1.00 20.34 N
+ATOM 1052 CA ASN A 138 10.221 53.056 17.749 1.00 23.14 C
+ATOM 1053 C ASN A 138 10.871 53.923 16.696 1.00 25.33 C
+ATOM 1054 O ASN A 138 12.104 54.056 16.622 1.00 24.22 O
+ATOM 1055 CB ASN A 138 11.246 52.544 18.729 1.00 25.40 C
+ATOM 1056 CG ASN A 138 11.698 53.585 19.740 1.00 30.80 C
+ATOM 1057 OD1 ASN A 138 12.777 53.462 20.329 1.00 31.43 O
+ATOM 1058 ND2 ASN A 138 10.944 54.633 20.051 1.00 31.30 N
+ATOM 1059 N PRO A 139 10.068 54.516 15.808 1.00 25.18 N
+ATOM 1060 CA PRO A 139 10.584 55.204 14.637 1.00 26.60 C
+ATOM 1061 C PRO A 139 11.249 56.549 14.973 1.00 28.04 C
+ATOM 1062 O PRO A 139 10.957 57.118 16.053 1.00 20.41 O
+ATOM 1063 CB PRO A 139 9.361 55.282 13.743 1.00 24.06 C
+ATOM 1064 CG PRO A 139 8.226 55.412 14.673 1.00 25.14 C
+ATOM 1065 CD PRO A 139 8.622 54.613 15.916 1.00 25.14 C
+ATOM 1066 N PRO A 140 12.156 57.097 14.143 1.00 21.89 N
+ATOM 1067 CA PRO A 140 12.639 58.484 14.325 1.00 24.94 C
+ATOM 1068 C PRO A 140 11.489 59.513 14.106 1.00 32.79 C
+ATOM 1069 O PRO A 140 10.477 59.167 13.475 1.00 33.82 O
+ATOM 1070 CB PRO A 140 13.777 58.555 13.334 1.00 14.35 C
+ATOM 1071 CG PRO A 140 13.249 57.750 12.177 1.00 18.38 C
+ATOM 1072 CD PRO A 140 12.651 56.529 12.894 1.00 22.17 C
+ATOM 1073 N LYS A 141 11.577 60.786 14.571 1.00 33.28 N
+ATOM 1074 CA LYS A 141 10.533 61.820 14.450 1.00 28.49 C
+ATOM 1075 C LYS A 141 10.428 62.236 13.006 1.00 20.79 C
+ATOM 1076 O LYS A 141 9.377 62.640 12.524 1.00 34.52 O
+ATOM 1077 CB LYS A 141 10.883 63.022 15.357 1.00 28.74 C
+ATOM 1078 CG LYS A 141 10.754 62.565 16.817 1.00 28.76 C
+ATOM 1079 CD LYS A 141 11.473 63.536 17.715 1.00 39.32 C
+ATOM 1080 CE LYS A 141 11.519 63.023 19.151 1.00 53.53 C
+ATOM 1081 NZ LYS A 141 12.323 63.885 20.020 1.00 60.63 N
+ATOM 1082 N VAL A 142 11.505 62.114 12.251 1.00 20.02 N
+ATOM 1083 CA VAL A 142 11.505 62.370 10.828 1.00 28.18 C
+ATOM 1084 C VAL A 142 12.110 61.082 10.227 1.00 31.10 C
+ATOM 1085 O VAL A 142 13.252 60.661 10.498 1.00 27.90 O
+ATOM 1086 CB VAL A 142 12.377 63.646 10.539 1.00 28.28 C
+ATOM 1087 CG1 VAL A 142 12.325 63.850 9.046 1.00 29.42 C
+ATOM 1088 CG2 VAL A 142 11.957 64.872 11.407 1.00 26.80 C
+ATOM 1089 N GLU A 143 11.321 60.416 9.410 1.00 31.49 N
+ATOM 1090 CA GLU A 143 11.718 59.172 8.801 1.00 41.64 C
+ATOM 1091 C GLU A 143 13.096 59.198 8.139 1.00 41.12 C
+ATOM 1092 O GLU A 143 13.448 60.073 7.340 1.00 44.60 O
+ATOM 1093 CB GLU A 143 10.606 58.810 7.824 1.00 53.24 C
+ATOM 1094 CG GLU A 143 10.749 57.508 7.007 1.00 73.66 C
+ATOM 1095 CD GLU A 143 9.483 57.011 6.281 1.00 82.01 C
+ATOM 1096 OE1 GLU A 143 8.626 57.820 5.890 1.00 83.52 O
+ATOM 1097 OE2 GLU A 143 9.362 55.790 6.107 1.00 87.59 O
+ATOM 1098 N GLY A 144 13.927 58.251 8.571 1.00 38.69 N
+ATOM 1099 CA GLY A 144 15.260 58.064 8.028 1.00 23.85 C
+ATOM 1100 C GLY A 144 16.320 58.957 8.633 1.00 24.25 C
+ATOM 1101 O GLY A 144 17.474 58.897 8.193 1.00 25.77 O
+ATOM 1102 N LYS A 145 16.033 59.770 9.638 1.00 26.01 N
+ATOM 1103 CA LYS A 145 17.037 60.722 10.089 1.00 28.67 C
+ATOM 1104 C LYS A 145 17.154 60.573 11.575 1.00 27.94 C
+ATOM 1105 O LYS A 145 16.188 60.303 12.293 1.00 28.01 O
+ATOM 1106 CB LYS A 145 16.659 62.186 9.822 1.00 27.19 C
+ATOM 1107 CG LYS A 145 16.244 62.558 8.408 1.00 27.14 C
+ATOM 1108 CD LYS A 145 17.425 62.505 7.529 1.00 24.35 C
+ATOM 1109 CE LYS A 145 16.816 62.743 6.193 1.00 28.27 C
+ATOM 1110 NZ LYS A 145 17.869 62.607 5.232 1.00 23.85 N
+ATOM 1111 N ASP A 146 18.354 60.773 12.087 1.00 26.12 N
+ATOM 1112 CA ASP A 146 18.527 60.716 13.497 1.00 28.76 C
+ATOM 1113 C ASP A 146 17.902 61.992 14.096 1.00 30.04 C
+ATOM 1114 O ASP A 146 18.118 63.080 13.573 1.00 34.21 O
+ATOM 1115 CB ASP A 146 20.019 60.587 13.695 1.00 23.57 C
+ATOM 1116 CG ASP A 146 20.437 60.730 15.135 1.00 28.55 C
+ATOM 1117 OD1 ASP A 146 20.070 59.919 15.991 1.00 28.50 O
+ATOM 1118 OD2 ASP A 146 21.164 61.676 15.393 1.00 31.43 O
+ATOM 1119 N ASP A 147 17.190 61.879 15.213 1.00 30.22 N
+ATOM 1120 CA ASP A 147 16.517 62.933 15.961 1.00 35.16 C
+ATOM 1121 C ASP A 147 17.370 64.106 16.391 1.00 41.54 C
+ATOM 1122 O ASP A 147 16.985 65.266 16.259 1.00 47.42 O
+ATOM 1123 CB ASP A 147 15.898 62.337 17.210 1.00 28.79 C
+ATOM 1124 CG ASP A 147 14.693 61.426 16.990 1.00 26.78 C
+ATOM 1125 OD1 ASP A 147 14.242 61.247 15.880 1.00 26.62 O
+ATOM 1126 OD2 ASP A 147 14.187 60.871 17.943 1.00 33.87 O
+ATOM 1127 N VAL A 148 18.572 63.785 16.853 1.00 38.44 N
+ATOM 1128 CA VAL A 148 19.530 64.752 17.344 1.00 35.46 C
+ATOM 1129 C VAL A 148 20.308 65.445 16.239 1.00 32.92 C
+ATOM 1130 O VAL A 148 20.359 66.663 16.142 1.00 41.42 O
+ATOM 1131 CB VAL A 148 20.453 63.990 18.325 1.00 36.53 C
+ATOM 1132 CG1 VAL A 148 21.535 64.842 18.981 1.00 43.62 C
+ATOM 1133 CG2 VAL A 148 19.558 63.529 19.462 1.00 33.95 C
+ATOM 1134 N THR A 149 20.915 64.727 15.344 1.00 29.89 N
+ATOM 1135 CA THR A 149 21.763 65.360 14.392 1.00 28.74 C
+ATOM 1136 C THR A 149 21.109 65.528 13.059 1.00 33.15 C
+ATOM 1137 O THR A 149 21.721 66.135 12.166 1.00 33.44 O
+ATOM 1138 CB THR A 149 23.067 64.545 14.212 1.00 27.75 C
+ATOM 1139 OG1 THR A 149 22.740 63.377 13.487 1.00 29.08 O
+ATOM 1140 CG2 THR A 149 23.714 64.169 15.499 1.00 23.53 C
+ATOM 1141 N GLY A 150 19.955 64.916 12.789 1.00 30.36 N
+ATOM 1142 CA GLY A 150 19.389 65.023 11.444 1.00 26.99 C
+ATOM 1143 C GLY A 150 20.135 64.251 10.365 1.00 25.62 C
+ATOM 1144 O GLY A 150 19.877 64.351 9.159 1.00 29.50 O
+ATOM 1145 N GLU A 151 21.081 63.418 10.801 1.00 30.76 N
+ATOM 1146 CA GLU A 151 21.826 62.570 9.898 1.00 31.74 C
+ATOM 1147 C GLU A 151 21.047 61.311 9.535 1.00 29.22 C
+ATOM 1148 O GLU A 151 20.270 60.766 10.319 1.00 26.44 O
+ATOM 1149 CB GLU A 151 23.117 62.205 10.560 1.00 35.83 C
+ATOM 1150 CG GLU A 151 24.145 63.317 10.561 1.00 42.57 C
+ATOM 1151 CD GLU A 151 25.317 63.047 11.493 1.00 52.40 C
+ATOM 1152 OE1 GLU A 151 25.895 61.969 11.408 1.00 59.87 O
+ATOM 1153 OE2 GLU A 151 25.664 63.907 12.303 1.00 63.32 O
+ATOM 1154 N GLU A 152 21.328 60.861 8.327 1.00 29.78 N
+ATOM 1155 CA GLU A 152 20.683 59.723 7.720 1.00 40.41 C
+ATOM 1156 C GLU A 152 20.987 58.437 8.522 1.00 41.63 C
+ATOM 1157 O GLU A 152 22.117 58.203 9.003 1.00 47.05 O
+ATOM 1158 CB GLU A 152 21.194 59.697 6.283 1.00 39.69 C
+ATOM 1159 CG GLU A 152 20.390 58.891 5.261 1.00 52.14 C
+ATOM 1160 CD GLU A 152 19.048 59.446 4.773 1.00 56.13 C
+ATOM 1161 OE1 GLU A 152 18.109 59.534 5.550 1.00 54.04 O
+ATOM 1162 OE2 GLU A 152 18.918 59.765 3.590 1.00 67.86 O
+ATOM 1163 N LEU A 153 19.934 57.666 8.790 1.00 33.23 N
+ATOM 1164 CA LEU A 153 20.090 56.412 9.516 1.00 33.73 C
+ATOM 1165 C LEU A 153 20.514 55.309 8.534 1.00 37.08 C
+ATOM 1166 O LEU A 153 20.252 55.401 7.326 1.00 35.21 O
+ATOM 1167 CB LEU A 153 18.781 56.079 10.188 1.00 25.04 C
+ATOM 1168 CG LEU A 153 18.374 57.112 11.221 1.00 19.61 C
+ATOM 1169 CD1 LEU A 153 17.029 56.729 11.739 1.00 22.29 C
+ATOM 1170 CD2 LEU A 153 19.407 57.231 12.302 1.00 19.25 C
+ATOM 1171 N THR A 154 21.202 54.249 8.973 1.00 32.66 N
+ATOM 1172 CA THR A 154 21.658 53.190 8.095 1.00 25.57 C
+ATOM 1173 C THR A 154 21.204 51.862 8.721 1.00 28.71 C
+ATOM 1174 O THR A 154 20.647 51.837 9.850 1.00 22.81 O
+ATOM 1175 CB THR A 154 23.240 53.250 7.944 1.00 24.18 C
+ATOM 1176 OG1 THR A 154 23.887 53.318 9.212 1.00 25.95 O
+ATOM 1177 CG2 THR A 154 23.697 54.526 7.287 1.00 32.42 C
+ATOM 1178 N THR A 155 21.420 50.764 7.992 1.00 22.86 N
+ATOM 1179 CA THR A 155 21.171 49.444 8.553 1.00 29.13 C
+ATOM 1180 C THR A 155 22.511 48.807 8.882 1.00 23.46 C
+ATOM 1181 O THR A 155 23.544 49.124 8.298 1.00 33.84 O
+ATOM 1182 CB THR A 155 20.398 48.630 7.547 1.00 23.33 C
+ATOM 1183 OG1 THR A 155 21.165 48.608 6.369 1.00 36.29 O
+ATOM 1184 CG2 THR A 155 19.135 49.291 7.127 1.00 26.67 C
+ATOM 1185 N ARG A 156 22.602 47.980 9.890 1.00 24.19 N
+ATOM 1186 CA ARG A 156 23.818 47.270 10.158 1.00 29.74 C
+ATOM 1187 C ARG A 156 23.937 46.129 9.152 1.00 30.49 C
+ATOM 1188 O ARG A 156 22.965 45.487 8.692 1.00 25.60 O
+ATOM 1189 CB ARG A 156 23.770 46.767 11.585 1.00 29.92 C
+ATOM 1190 CG ARG A 156 24.197 47.879 12.528 1.00 29.70 C
+ATOM 1191 CD ARG A 156 24.163 47.484 13.977 1.00 32.72 C
+ATOM 1192 NE ARG A 156 24.554 46.097 14.182 1.00 23.91 N
+ATOM 1193 CZ ARG A 156 24.321 45.507 15.337 1.00 22.39 C
+ATOM 1194 NH1 ARG A 156 23.810 46.190 16.331 1.00 18.90 N
+ATOM 1195 NH2 ARG A 156 24.583 44.231 15.522 1.00 21.23 N
+ATOM 1196 N LYS A 157 25.209 45.893 8.840 1.00 30.14 N
+ATOM 1197 CA LYS A 157 25.618 44.885 7.852 1.00 36.32 C
+ATOM 1198 C LYS A 157 25.246 43.470 8.313 1.00 34.85 C
+ATOM 1199 O LYS A 157 24.904 42.622 7.505 1.00 29.40 O
+ATOM 1200 CB LYS A 157 27.139 44.916 7.632 1.00 45.21 C
+ATOM 1201 CG LYS A 157 27.925 46.171 7.166 1.00 66.21 C
+ATOM 1202 CD LYS A 157 27.832 47.491 7.978 1.00 69.30 C
+ATOM 1203 CE LYS A 157 28.295 47.435 9.433 1.00 67.90 C
+ATOM 1204 NZ LYS A 157 27.330 48.130 10.268 1.00 59.59 N
+ATOM 1205 N ASP A 158 25.330 43.207 9.631 1.00 27.72 N
+ATOM 1206 CA ASP A 158 25.037 41.923 10.230 1.00 22.58 C
+ATOM 1207 C ASP A 158 23.558 41.788 10.628 1.00 23.77 C
+ATOM 1208 O ASP A 158 23.137 40.888 11.347 1.00 23.52 O
+ATOM 1209 CB ASP A 158 26.023 41.808 11.400 1.00 18.63 C
+ATOM 1210 CG ASP A 158 25.801 42.776 12.548 1.00 25.36 C
+ATOM 1211 OD1 ASP A 158 25.283 43.851 12.308 1.00 23.75 O
+ATOM 1212 OD2 ASP A 158 26.141 42.476 13.699 1.00 22.19 O
+ATOM 1213 N ASP A 159 22.670 42.699 10.221 1.00 22.20 N
+ATOM 1214 CA ASP A 159 21.262 42.561 10.522 1.00 22.82 C
+ATOM 1215 C ASP A 159 20.494 42.016 9.332 1.00 33.97 C
+ATOM 1216 O ASP A 159 19.650 42.689 8.724 1.00 48.79 O
+ATOM 1217 CB ASP A 159 20.648 43.890 10.940 1.00 24.27 C
+ATOM 1218 CG ASP A 159 21.002 44.350 12.347 1.00 25.38 C
+ATOM 1219 OD1 ASP A 159 21.619 43.630 13.123 1.00 21.20 O
+ATOM 1220 OD2 ASP A 159 20.672 45.479 12.638 1.00 21.21 O
+ATOM 1221 N GLN A 160 20.899 40.828 8.874 1.00 44.86 N
+ATOM 1222 CA GLN A 160 20.054 40.082 7.944 1.00 46.67 C
+ATOM 1223 C GLN A 160 19.689 38.809 8.687 1.00 40.62 C
+ATOM 1224 O GLN A 160 20.435 38.358 9.585 1.00 30.26 O
+ATOM 1225 CB GLN A 160 20.728 39.640 6.676 1.00 58.15 C
+ATOM 1226 CG GLN A 160 21.152 40.744 5.745 1.00 71.86 C
+ATOM 1227 CD GLN A 160 22.649 40.914 5.852 1.00 83.20 C
+ATOM 1228 OE1 GLN A 160 23.385 40.029 6.315 1.00 85.76 O
+ATOM 1229 NE2 GLN A 160 23.142 42.076 5.456 1.00 94.35 N
+ATOM 1230 N GLU A 161 18.553 38.261 8.255 1.00 33.46 N
+ATOM 1231 CA GLU A 161 17.942 37.066 8.799 1.00 29.44 C
+ATOM 1232 C GLU A 161 18.925 35.929 9.092 1.00 30.28 C
+ATOM 1233 O GLU A 161 18.945 35.421 10.227 1.00 26.51 O
+ATOM 1234 CB GLU A 161 16.920 36.733 7.795 1.00 32.95 C
+ATOM 1235 CG GLU A 161 15.999 35.552 8.012 1.00 53.23 C
+ATOM 1236 CD GLU A 161 14.748 35.661 7.126 1.00 67.25 C
+ATOM 1237 OE1 GLU A 161 14.858 35.852 5.898 1.00 72.00 O
+ATOM 1238 OE2 GLU A 161 13.649 35.573 7.684 1.00 71.74 O
+ATOM 1239 N GLU A 162 19.847 35.559 8.181 1.00 25.87 N
+ATOM 1240 CA GLU A 162 20.712 34.443 8.506 1.00 25.40 C
+ATOM 1241 C GLU A 162 21.809 34.739 9.498 1.00 27.85 C
+ATOM 1242 O GLU A 162 22.129 33.853 10.290 1.00 26.83 O
+ATOM 1243 CB GLU A 162 21.297 33.885 7.242 1.00 38.07 C
+ATOM 1244 CG GLU A 162 20.162 33.253 6.378 1.00 66.76 C
+ATOM 1245 CD GLU A 162 19.068 32.377 7.051 1.00 77.76 C
+ATOM 1246 OE1 GLU A 162 19.372 31.314 7.615 1.00 76.86 O
+ATOM 1247 OE2 GLU A 162 17.891 32.766 6.989 1.00 82.71 O
+ATOM 1248 N THR A 163 22.382 35.951 9.529 1.00 24.33 N
+ATOM 1249 CA THR A 163 23.378 36.312 10.514 1.00 17.27 C
+ATOM 1250 C THR A 163 22.699 36.426 11.855 1.00 14.23 C
+ATOM 1251 O THR A 163 23.332 35.982 12.797 1.00 18.16 O
+ATOM 1252 CB THR A 163 24.024 37.637 10.229 1.00 22.22 C
+ATOM 1253 OG1 THR A 163 24.370 37.534 8.871 1.00 23.93 O
+ATOM 1254 CG2 THR A 163 25.227 37.972 11.077 1.00 18.66 C
+ATOM 1255 N VAL A 164 21.460 36.915 11.989 1.00 17.85 N
+ATOM 1256 CA VAL A 164 20.732 36.952 13.256 1.00 20.38 C
+ATOM 1257 C VAL A 164 20.535 35.509 13.773 1.00 18.27 C
+ATOM 1258 O VAL A 164 20.627 35.211 14.964 1.00 15.67 O
+ATOM 1259 CB VAL A 164 19.358 37.625 12.994 1.00 28.64 C
+ATOM 1260 CG1 VAL A 164 18.500 37.663 14.231 1.00 25.70 C
+ATOM 1261 CG2 VAL A 164 19.575 39.045 12.591 1.00 32.10 C
+ATOM 1262 N ARG A 165 20.189 34.559 12.910 1.00 18.98 N
+ATOM 1263 CA ARG A 165 20.001 33.162 13.347 1.00 21.55 C
+ATOM 1264 C ARG A 165 21.249 32.540 13.966 1.00 22.72 C
+ATOM 1265 O ARG A 165 21.232 31.882 15.043 1.00 23.45 O
+ATOM 1266 CB ARG A 165 19.529 32.365 12.146 1.00 28.98 C
+ATOM 1267 CG ARG A 165 18.077 32.631 12.181 1.00 42.85 C
+ATOM 1268 CD ARG A 165 17.291 31.953 11.104 1.00 62.01 C
+ATOM 1269 NE ARG A 165 15.902 32.196 11.468 1.00 80.24 N
+ATOM 1270 CZ ARG A 165 14.909 32.325 10.581 1.00 88.22 C
+ATOM 1271 NH1 ARG A 165 15.099 32.226 9.250 1.00 91.07 N
+ATOM 1272 NH2 ARG A 165 13.692 32.568 11.074 1.00 91.78 N
+ATOM 1273 N LYS A 166 22.365 32.880 13.294 1.00 16.12 N
+ATOM 1274 CA LYS A 166 23.644 32.450 13.793 1.00 19.19 C
+ATOM 1275 C LYS A 166 23.895 33.093 15.129 1.00 17.78 C
+ATOM 1276 O LYS A 166 24.266 32.386 16.088 1.00 17.47 O
+ATOM 1277 CB LYS A 166 24.755 32.828 12.834 1.00 32.39 C
+ATOM 1278 CG LYS A 166 24.691 31.972 11.575 1.00 44.21 C
+ATOM 1279 CD LYS A 166 25.711 32.369 10.502 1.00 56.21 C
+ATOM 1280 CE LYS A 166 25.353 31.635 9.208 1.00 67.75 C
+ATOM 1281 NZ LYS A 166 26.274 31.961 8.135 1.00 77.81 N
+ATOM 1282 N ARG A 167 23.637 34.403 15.257 1.00 14.61 N
+ATOM 1283 CA ARG A 167 23.859 35.071 16.525 1.00 15.89 C
+ATOM 1284 C ARG A 167 22.992 34.466 17.608 1.00 16.26 C
+ATOM 1285 O ARG A 167 23.486 34.362 18.729 1.00 16.68 O
+ATOM 1286 CB ARG A 167 23.527 36.558 16.451 1.00 20.63 C
+ATOM 1287 CG ARG A 167 24.499 37.362 15.615 1.00 19.15 C
+ATOM 1288 CD AARG A 167 24.502 38.811 16.129 0.50 24.49 C
+ATOM 1288 CD BARG A 167 24.690 38.671 16.294 0.50 23.17 C
+ATOM 1289 NE AARG A 167 23.377 39.692 15.806 0.50 23.32 N
+ATOM 1289 NE BARG A 167 23.697 39.706 16.111 0.50 24.59 N
+ATOM 1290 CZ AARG A 167 23.342 40.399 14.676 0.50 16.77 C
+ATOM 1290 CZ BARG A 167 23.245 40.509 17.085 0.50 23.03 C
+ATOM 1291 NH1AARG A 167 24.181 40.144 13.699 0.50 27.31 N
+ATOM 1291 NH1BARG A 167 23.482 40.319 18.402 0.50 27.91 N
+ATOM 1292 NH2AARG A 167 22.424 41.308 14.455 0.50 5.51 N
+ATOM 1292 NH2BARG A 167 22.409 41.488 16.714 0.50 18.45 N
+ATOM 1293 N LEU A 168 21.736 34.060 17.339 1.00 18.87 N
+ATOM 1294 CA LEU A 168 20.894 33.428 18.379 1.00 18.37 C
+ATOM 1295 C LEU A 168 21.418 32.111 18.964 1.00 15.26 C
+ATOM 1296 O LEU A 168 21.293 31.824 20.148 1.00 14.59 O
+ATOM 1297 CB LEU A 168 19.541 33.109 17.853 1.00 19.47 C
+ATOM 1298 CG LEU A 168 18.389 33.876 18.318 1.00 33.18 C
+ATOM 1299 CD1 LEU A 168 17.174 33.001 18.017 1.00 29.76 C
+ATOM 1300 CD2 LEU A 168 18.501 34.209 19.829 1.00 32.09 C
+ATOM 1301 N VAL A 169 21.925 31.249 18.094 1.00 26.09 N
+ATOM 1302 CA VAL A 169 22.603 29.993 18.470 1.00 30.51 C
+ATOM 1303 C VAL A 169 23.842 30.245 19.353 1.00 22.02 C
+ATOM 1304 O VAL A 169 24.011 29.553 20.374 1.00 25.50 O
+ATOM 1305 CB VAL A 169 23.019 29.242 17.160 1.00 27.97 C
+ATOM 1306 CG1 VAL A 169 23.878 28.046 17.490 1.00 25.96 C
+ATOM 1307 CG2 VAL A 169 21.780 28.769 16.406 1.00 23.43 C
+ATOM 1308 N GLU A 170 24.692 31.241 19.012 1.00 16.54 N
+ATOM 1309 CA GLU A 170 25.889 31.549 19.798 1.00 18.47 C
+ATOM 1310 C GLU A 170 25.434 32.130 21.117 1.00 16.07 C
+ATOM 1311 O GLU A 170 26.081 31.833 22.115 1.00 15.71 O
+ATOM 1312 CB GLU A 170 26.793 32.602 19.179 1.00 20.83 C
+ATOM 1313 CG GLU A 170 27.357 32.183 17.895 1.00 26.40 C
+ATOM 1314 CD GLU A 170 28.771 31.674 18.056 1.00 34.23 C
+ATOM 1315 OE1 GLU A 170 29.666 32.406 18.493 1.00 31.32 O
+ATOM 1316 OE2 GLU A 170 28.978 30.523 17.692 1.00 49.90 O
+ATOM 1317 N TYR A 171 24.354 32.925 21.145 1.00 14.06 N
+ATOM 1318 CA TYR A 171 23.794 33.424 22.374 1.00 11.70 C
+ATOM 1319 C TYR A 171 23.393 32.236 23.239 1.00 10.66 C
+ATOM 1320 O TYR A 171 23.705 32.182 24.426 1.00 15.53 O
+ATOM 1321 CB TYR A 171 22.586 34.304 22.076 1.00 8.79 C
+ATOM 1322 CG TYR A 171 21.855 34.686 23.358 1.00 12.93 C
+ATOM 1323 CD1 TYR A 171 22.379 35.655 24.198 1.00 15.64 C
+ATOM 1324 CD2 TYR A 171 20.712 34.037 23.753 1.00 15.73 C
+ATOM 1325 CE1 TYR A 171 21.813 35.981 25.410 1.00 17.39 C
+ATOM 1326 CE2 TYR A 171 20.127 34.341 24.992 1.00 19.42 C
+ATOM 1327 CZ TYR A 171 20.679 35.318 25.814 1.00 22.02 C
+ATOM 1328 OH TYR A 171 20.111 35.638 27.042 1.00 18.14 O
+ATOM 1329 N HIS A 172 22.676 31.248 22.763 1.00 16.23 N
+ATOM 1330 CA HIS A 172 22.188 30.172 23.627 1.00 18.45 C
+ATOM 1331 C HIS A 172 23.312 29.286 24.119 1.00 18.43 C
+ATOM 1332 O HIS A 172 23.372 28.883 25.294 1.00 18.10 O
+ATOM 1333 CB HIS A 172 21.136 29.341 22.873 1.00 17.33 C
+ATOM 1334 CG HIS A 172 19.759 29.989 22.906 1.00 15.22 C
+ATOM 1335 ND1 HIS A 172 18.953 30.156 23.953 1.00 25.05 N
+ATOM 1336 CD2 HIS A 172 19.144 30.562 21.809 1.00 19.89 C
+ATOM 1337 CE1 HIS A 172 17.891 30.813 23.549 1.00 27.06 C
+ATOM 1338 NE2 HIS A 172 18.026 31.049 22.258 1.00 23.50 N
+ATOM 1339 N GLN A 173 24.306 29.134 23.258 1.00 16.50 N
+ATOM 1340 CA GLN A 173 25.463 28.312 23.673 1.00 24.75 C
+ATOM 1341 C GLN A 173 26.378 28.959 24.688 1.00 17.73 C
+ATOM 1342 O GLN A 173 26.768 28.327 25.650 1.00 21.15 O
+ATOM 1343 CB GLN A 173 26.334 27.911 22.449 1.00 24.76 C
+ATOM 1344 CG GLN A 173 25.723 26.838 21.571 1.00 21.25 C
+ATOM 1345 CD GLN A 173 26.438 26.524 20.286 1.00 35.07 C
+ATOM 1346 OE1 GLN A 173 26.463 25.381 19.838 1.00 42.94 O
+ATOM 1347 NE2 GLN A 173 27.046 27.457 19.592 1.00 35.45 N
+ATOM 1348 N MET A 174 26.696 30.254 24.523 1.00 26.04 N
+ATOM 1349 CA MET A 174 27.780 30.924 25.231 1.00 16.63 C
+ATOM 1350 C MET A 174 27.350 31.962 26.189 1.00 14.52 C
+ATOM 1351 O MET A 174 28.031 32.138 27.194 1.00 19.50 O
+ATOM 1352 CB MET A 174 28.718 31.680 24.356 1.00 15.94 C
+ATOM 1353 CG MET A 174 29.289 31.050 23.072 1.00 38.68 C
+ATOM 1354 SD MET A 174 30.211 29.526 23.399 1.00 42.51 S
+ATOM 1355 CE MET A 174 31.373 30.185 24.584 1.00 45.74 C
+ATOM 1356 N THR A 175 26.232 32.646 25.930 1.00 15.93 N
+ATOM 1357 CA THR A 175 25.882 33.824 26.706 1.00 20.80 C
+ATOM 1358 C THR A 175 24.768 33.506 27.662 1.00 22.75 C
+ATOM 1359 O THR A 175 24.838 33.941 28.815 1.00 19.66 O
+ATOM 1360 CB THR A 175 25.427 35.010 25.806 1.00 15.05 C
+ATOM 1361 OG1 THR A 175 26.434 35.116 24.831 1.00 15.12 O
+ATOM 1362 CG2 THR A 175 25.209 36.343 26.547 1.00 13.66 C
+ATOM 1363 N ALA A 176 23.791 32.708 27.207 1.00 17.11 N
+ATOM 1364 CA ALA A 176 22.709 32.326 28.101 1.00 19.62 C
+ATOM 1365 C ALA A 176 23.182 31.802 29.462 1.00 18.00 C
+ATOM 1366 O ALA A 176 22.468 32.016 30.452 1.00 17.46 O
+ATOM 1367 CB ALA A 176 21.839 31.236 27.463 1.00 25.53 C
+ATOM 1368 N PRO A 177 24.354 31.136 29.583 1.00 18.68 N
+ATOM 1369 CA PRO A 177 24.840 30.655 30.859 1.00 22.56 C
+ATOM 1370 C PRO A 177 25.098 31.759 31.872 1.00 26.32 C
+ATOM 1371 O PRO A 177 25.183 31.459 33.070 1.00 25.97 O
+ATOM 1372 CB PRO A 177 26.070 29.871 30.484 1.00 22.51 C
+ATOM 1373 CG PRO A 177 25.742 29.241 29.117 1.00 20.39 C
+ATOM 1374 CD PRO A 177 25.070 30.405 28.505 1.00 16.87 C
+ATOM 1375 N LEU A 178 25.280 33.013 31.433 1.00 17.44 N
+ATOM 1376 CA LEU A 178 25.494 34.116 32.326 1.00 19.87 C
+ATOM 1377 C LEU A 178 24.251 34.374 33.171 1.00 22.27 C
+ATOM 1378 O LEU A 178 24.392 34.955 34.262 1.00 21.74 O
+ATOM 1379 CB LEU A 178 25.871 35.370 31.534 1.00 20.20 C
+ATOM 1380 CG LEU A 178 27.246 35.357 30.896 1.00 20.79 C
+ATOM 1381 CD1 LEU A 178 27.437 36.608 30.127 1.00 17.20 C
+ATOM 1382 CD2 LEU A 178 28.317 35.341 31.955 1.00 26.85 C
+ATOM 1383 N ILE A 179 23.041 33.926 32.787 1.00 20.11 N
+ATOM 1384 CA ILE A 179 21.847 34.121 33.617 1.00 20.22 C
+ATOM 1385 C ILE A 179 22.043 33.341 34.922 1.00 18.78 C
+ATOM 1386 O ILE A 179 21.829 33.929 35.978 1.00 25.03 O
+ATOM 1387 CB ILE A 179 20.563 33.642 32.860 1.00 19.24 C
+ATOM 1388 CG1 ILE A 179 20.330 34.577 31.655 1.00 19.48 C
+ATOM 1389 CG2 ILE A 179 19.359 33.621 33.820 1.00 15.26 C
+ATOM 1390 CD1 ILE A 179 19.363 34.061 30.604 1.00 26.50 C
+ATOM 1391 N GLY A 180 22.507 32.094 34.879 1.00 15.40 N
+ATOM 1392 CA GLY A 180 22.743 31.291 36.059 1.00 21.16 C
+ATOM 1393 C GLY A 180 23.936 31.788 36.861 1.00 26.48 C
+ATOM 1394 O GLY A 180 23.881 31.828 38.106 1.00 22.84 O
+ATOM 1395 N TYR A 181 25.001 32.215 36.144 1.00 24.74 N
+ATOM 1396 CA TYR A 181 26.209 32.813 36.742 1.00 22.13 C
+ATOM 1397 C TYR A 181 25.873 33.945 37.716 1.00 18.40 C
+ATOM 1398 O TYR A 181 26.193 33.901 38.911 1.00 22.35 O
+ATOM 1399 CB TYR A 181 27.140 33.355 35.625 1.00 21.69 C
+ATOM 1400 CG TYR A 181 28.489 33.927 36.089 1.00 23.52 C
+ATOM 1401 CD1 TYR A 181 28.603 35.224 36.552 1.00 19.96 C
+ATOM 1402 CD2 TYR A 181 29.618 33.116 36.045 1.00 26.38 C
+ATOM 1403 CE1 TYR A 181 29.825 35.728 36.976 1.00 29.06 C
+ATOM 1404 CE2 TYR A 181 30.840 33.617 36.468 1.00 26.56 C
+ATOM 1405 CZ TYR A 181 30.947 34.918 36.928 1.00 29.23 C
+ATOM 1406 OH TYR A 181 32.186 35.413 37.317 1.00 33.06 O
+ATOM 1407 N TYR A 182 25.194 34.979 37.221 1.00 27.88 N
+ATOM 1408 CA TYR A 182 24.857 36.175 37.960 1.00 20.66 C
+ATOM 1409 C TYR A 182 23.688 35.939 38.869 1.00 25.55 C
+ATOM 1410 O TYR A 182 23.566 36.705 39.814 1.00 22.46 O
+ATOM 1411 CB TYR A 182 24.536 37.293 36.986 1.00 18.15 C
+ATOM 1412 CG TYR A 182 25.815 37.884 36.435 1.00 23.80 C
+ATOM 1413 CD1 TYR A 182 26.753 38.411 37.316 1.00 25.62 C
+ATOM 1414 CD2 TYR A 182 26.071 37.822 35.075 1.00 20.65 C
+ATOM 1415 CE1 TYR A 182 27.950 38.888 36.826 1.00 23.86 C
+ATOM 1416 CE2 TYR A 182 27.282 38.286 34.588 1.00 22.91 C
+ATOM 1417 CZ TYR A 182 28.218 38.800 35.463 1.00 27.81 C
+ATOM 1418 OH TYR A 182 29.467 39.174 34.966 1.00 26.86 O
+ATOM 1419 N SER A 183 22.802 34.974 38.593 1.00 17.79 N
+ATOM 1420 CA SER A 183 21.773 34.685 39.550 1.00 22.82 C
+ATOM 1421 C SER A 183 22.498 34.117 40.779 1.00 24.33 C
+ATOM 1422 O SER A 183 22.192 34.532 41.892 1.00 28.47 O
+ATOM 1423 CB SER A 183 20.820 33.670 38.952 1.00 27.48 C
+ATOM 1424 OG SER A 183 19.962 34.251 37.970 1.00 36.61 O
+ATOM 1425 N LYS A 184 23.470 33.220 40.641 1.00 22.39 N
+ATOM 1426 CA LYS A 184 24.305 32.796 41.740 1.00 32.86 C
+ATOM 1427 C LYS A 184 25.041 33.947 42.441 1.00 36.64 C
+ATOM 1428 O LYS A 184 25.197 33.926 43.674 1.00 31.46 O
+ATOM 1429 CB LYS A 184 25.349 31.811 41.274 1.00 45.13 C
+ATOM 1430 CG LYS A 184 24.805 30.395 41.301 1.00 65.07 C
+ATOM 1431 CD LYS A 184 25.953 29.372 41.312 1.00 80.43 C
+ATOM 1432 CE LYS A 184 25.516 27.942 41.715 1.00 90.18 C
+ATOM 1433 NZ LYS A 184 25.133 27.852 43.121 1.00 95.35 N
+ATOM 1434 N GLU A 185 25.532 34.938 41.694 1.00 28.97 N
+ATOM 1435 CA GLU A 185 26.114 36.110 42.295 1.00 26.04 C
+ATOM 1436 C GLU A 185 25.074 36.823 43.129 1.00 29.58 C
+ATOM 1437 O GLU A 185 25.445 37.289 44.215 1.00 27.30 O
+ATOM 1438 CB GLU A 185 26.630 37.121 41.249 1.00 30.11 C
+ATOM 1439 CG GLU A 185 27.857 36.591 40.537 1.00 31.47 C
+ATOM 1440 CD GLU A 185 29.022 36.322 41.493 1.00 37.80 C
+ATOM 1441 OE1 GLU A 185 29.457 37.242 42.181 1.00 38.02 O
+ATOM 1442 OE2 GLU A 185 29.501 35.191 41.552 1.00 35.63 O
+ATOM 1443 N ALA A 186 23.799 36.967 42.704 1.00 22.47 N
+ATOM 1444 CA ALA A 186 22.815 37.702 43.488 1.00 20.60 C
+ATOM 1445 C ALA A 186 22.450 36.961 44.777 1.00 24.28 C
+ATOM 1446 O ALA A 186 22.235 37.529 45.854 1.00 25.34 O
+ATOM 1447 CB ALA A 186 21.568 37.882 42.680 1.00 19.02 C
+ATOM 1448 N GLU A 187 22.415 35.638 44.701 1.00 31.08 N
+ATOM 1449 CA GLU A 187 22.141 34.782 45.857 1.00 44.44 C
+ATOM 1450 C GLU A 187 23.150 34.955 46.976 1.00 40.98 C
+ATOM 1451 O GLU A 187 22.828 34.905 48.176 1.00 33.46 O
+ATOM 1452 CB GLU A 187 22.152 33.310 45.466 1.00 56.38 C
+ATOM 1453 CG GLU A 187 20.806 32.860 44.911 1.00 76.88 C
+ATOM 1454 CD GLU A 187 20.739 31.369 44.618 1.00 86.20 C
+ATOM 1455 OE1 GLU A 187 20.664 30.571 45.562 1.00 91.02 O
+ATOM 1456 OE2 GLU A 187 20.757 31.020 43.436 1.00 91.61 O
+ATOM 1457 N ALA A 188 24.399 35.166 46.536 1.00 30.39 N
+ATOM 1458 CA ALA A 188 25.497 35.366 47.468 1.00 35.28 C
+ATOM 1459 C ALA A 188 25.615 36.777 48.053 1.00 33.05 C
+ATOM 1460 O ALA A 188 26.471 37.056 48.894 1.00 38.47 O
+ATOM 1461 CB ALA A 188 26.798 34.962 46.745 1.00 31.61 C
+ATOM 1462 N GLY A 189 24.743 37.688 47.643 1.00 33.11 N
+ATOM 1463 CA GLY A 189 24.765 39.076 48.082 1.00 38.03 C
+ATOM 1464 C GLY A 189 25.738 40.009 47.310 1.00 39.17 C
+ATOM 1465 O GLY A 189 25.867 41.197 47.661 1.00 38.53 O
+ATOM 1466 N ASN A 190 26.374 39.541 46.221 1.00 32.23 N
+ATOM 1467 CA ASN A 190 27.363 40.312 45.461 1.00 28.46 C
+ATOM 1468 C ASN A 190 26.836 41.319 44.448 1.00 25.65 C
+ATOM 1469 O ASN A 190 27.599 42.167 44.016 1.00 32.64 O
+ATOM 1470 CB ASN A 190 28.307 39.357 44.735 1.00 34.00 C
+ATOM 1471 CG ASN A 190 29.016 38.341 45.616 1.00 34.48 C
+ATOM 1472 OD1 ASN A 190 29.153 38.496 46.827 1.00 33.98 O
+ATOM 1473 ND2 ASN A 190 29.479 37.218 45.112 1.00 35.91 N
+ATOM 1474 N THR A 191 25.556 41.263 44.069 1.00 26.13 N
+ATOM 1475 CA THR A 191 24.855 42.119 43.112 1.00 29.10 C
+ATOM 1476 C THR A 191 23.337 41.897 43.350 1.00 30.66 C
+ATOM 1477 O THR A 191 22.924 40.980 44.099 1.00 27.02 O
+ATOM 1478 CB THR A 191 25.234 41.732 41.612 1.00 26.13 C
+ATOM 1479 OG1 THR A 191 24.835 42.853 40.815 1.00 28.32 O
+ATOM 1480 CG2 THR A 191 24.563 40.464 41.070 1.00 26.95 C
+ATOM 1481 N LYS A 192 22.520 42.760 42.707 1.00 31.45 N
+ATOM 1482 CA LYS A 192 21.066 42.643 42.614 1.00 30.19 C
+ATOM 1483 C LYS A 192 20.766 42.082 41.200 1.00 26.48 C
+ATOM 1484 O LYS A 192 21.477 42.422 40.243 1.00 26.22 O
+ATOM 1485 CB LYS A 192 20.449 44.043 42.842 1.00 26.39 C
+ATOM 1486 CG LYS A 192 20.470 44.348 44.357 1.00 44.92 C
+ATOM 1487 CD LYS A 192 20.175 45.801 44.791 1.00 56.84 C
+ATOM 1488 CE LYS A 192 19.401 45.922 46.117 1.00 62.41 C
+ATOM 1489 NZ LYS A 192 17.996 45.547 45.934 1.00 71.82 N
+ATOM 1490 N TYR A 193 19.780 41.212 40.951 1.00 29.59 N
+ATOM 1491 CA TYR A 193 19.512 40.627 39.611 1.00 26.17 C
+ATOM 1492 C TYR A 193 18.078 41.014 39.353 1.00 22.39 C
+ATOM 1493 O TYR A 193 17.328 40.851 40.302 1.00 29.92 O
+ATOM 1494 CB TYR A 193 19.649 39.084 39.628 1.00 16.14 C
+ATOM 1495 CG TYR A 193 19.616 38.390 38.306 1.00 23.88 C
+ATOM 1496 CD1 TYR A 193 18.419 38.015 37.750 1.00 28.45 C
+ATOM 1497 CD2 TYR A 193 20.768 38.216 37.613 1.00 21.54 C
+ATOM 1498 CE1 TYR A 193 18.368 37.484 36.473 1.00 27.30 C
+ATOM 1499 CE2 TYR A 193 20.734 37.682 36.334 1.00 27.18 C
+ATOM 1500 CZ TYR A 193 19.534 37.328 35.772 1.00 22.84 C
+ATOM 1501 OH TYR A 193 19.490 36.855 34.496 1.00 23.98 O
+ATOM 1502 N ALA A 194 17.604 41.586 38.241 1.00 25.70 N
+ATOM 1503 CA ALA A 194 16.181 41.854 38.027 1.00 22.71 C
+ATOM 1504 C ALA A 194 15.867 41.433 36.601 1.00 24.56 C
+ATOM 1505 O ALA A 194 16.666 41.662 35.701 1.00 23.26 O
+ATOM 1506 CB ALA A 194 15.820 43.324 38.124 1.00 27.76 C
+ATOM 1507 N LYS A 195 14.803 40.679 36.385 1.00 22.73 N
+ATOM 1508 CA LYS A 195 14.390 40.266 35.066 1.00 23.39 C
+ATOM 1509 C LYS A 195 13.277 41.223 34.553 1.00 27.00 C
+ATOM 1510 O LYS A 195 12.415 41.677 35.322 1.00 29.46 O
+ATOM 1511 CB LYS A 195 13.973 38.819 35.238 1.00 21.78 C
+ATOM 1512 CG LYS A 195 13.755 38.186 33.909 1.00 29.40 C
+ATOM 1513 CD LYS A 195 13.211 36.799 34.127 1.00 38.23 C
+ATOM 1514 CE LYS A 195 12.745 36.343 32.751 1.00 39.99 C
+ATOM 1515 NZ LYS A 195 12.355 34.938 32.727 1.00 49.37 N
+ATOM 1516 N VAL A 196 13.287 41.732 33.311 1.00 20.78 N
+ATOM 1517 CA VAL A 196 12.218 42.589 32.815 1.00 23.44 C
+ATOM 1518 C VAL A 196 11.666 41.946 31.524 1.00 28.74 C
+ATOM 1519 O VAL A 196 12.321 41.203 30.767 1.00 21.38 O
+ATOM 1520 CB VAL A 196 12.717 44.035 32.521 1.00 32.45 C
+ATOM 1521 CG1 VAL A 196 13.508 44.521 33.736 1.00 37.45 C
+ATOM 1522 CG2 VAL A 196 13.623 44.112 31.315 1.00 31.23 C
+ATOM 1523 N ASP A 197 10.384 42.181 31.309 1.00 22.69 N
+ATOM 1524 CA ASP A 197 9.688 41.664 30.175 1.00 16.27 C
+ATOM 1525 C ASP A 197 10.000 42.516 28.963 1.00 21.71 C
+ATOM 1526 O ASP A 197 9.359 43.537 28.745 1.00 20.20 O
+ATOM 1527 CB ASP A 197 8.206 41.681 30.416 1.00 22.42 C
+ATOM 1528 CG ASP A 197 7.386 41.039 29.288 1.00 18.45 C
+ATOM 1529 OD1 ASP A 197 7.877 40.724 28.216 1.00 21.07 O
+ATOM 1530 OD2 ASP A 197 6.214 40.837 29.484 1.00 23.53 O
+ATOM 1531 N GLY A 198 10.921 42.068 28.123 1.00 16.61 N
+ATOM 1532 CA GLY A 198 11.316 42.835 26.964 1.00 21.26 C
+ATOM 1533 C GLY A 198 10.257 42.800 25.859 1.00 27.33 C
+ATOM 1534 O GLY A 198 10.499 43.434 24.830 1.00 21.75 O
+ATOM 1535 N THR A 199 9.094 42.109 25.950 1.00 23.59 N
+ATOM 1536 CA THR A 199 8.045 42.211 24.904 1.00 24.67 C
+ATOM 1537 C THR A 199 7.121 43.430 25.058 1.00 26.11 C
+ATOM 1538 O THR A 199 6.469 43.835 24.074 1.00 31.06 O
+ATOM 1539 CB THR A 199 7.149 40.904 24.823 1.00 20.04 C
+ATOM 1540 OG1 THR A 199 6.307 40.816 25.949 1.00 20.89 O
+ATOM 1541 CG2 THR A 199 8.016 39.649 24.778 1.00 20.89 C
+ATOM 1542 N LYS A 200 7.171 44.113 26.224 1.00 23.64 N
+ATOM 1543 CA LYS A 200 6.346 45.271 26.476 1.00 19.12 C
+ATOM 1544 C LYS A 200 6.785 46.344 25.533 1.00 24.01 C
+ATOM 1545 O LYS A 200 7.861 46.304 24.939 1.00 22.82 O
+ATOM 1546 CB LYS A 200 6.509 45.758 27.894 1.00 22.39 C
+ATOM 1547 CG LYS A 200 5.870 44.746 28.839 1.00 18.31 C
+ATOM 1548 CD LYS A 200 5.898 45.383 30.175 1.00 26.54 C
+ATOM 1549 CE LYS A 200 5.474 44.334 31.116 1.00 24.03 C
+ATOM 1550 NZ LYS A 200 5.688 44.892 32.400 1.00 28.94 N
+ATOM 1551 N PRO A 201 5.945 47.296 25.281 1.00 25.29 N
+ATOM 1552 CA PRO A 201 6.324 48.459 24.505 1.00 23.26 C
+ATOM 1553 C PRO A 201 7.525 49.152 25.131 1.00 21.27 C
+ATOM 1554 O PRO A 201 7.674 49.071 26.368 1.00 22.64 O
+ATOM 1555 CB PRO A 201 5.022 49.240 24.502 1.00 29.11 C
+ATOM 1556 CG PRO A 201 3.940 48.167 24.515 1.00 26.68 C
+ATOM 1557 CD PRO A 201 4.511 47.257 25.583 1.00 33.70 C
+ATOM 1558 N VAL A 202 8.368 49.799 24.296 1.00 24.14 N
+ATOM 1559 CA VAL A 202 9.572 50.527 24.721 1.00 21.75 C
+ATOM 1560 C VAL A 202 9.234 51.377 25.959 1.00 24.15 C
+ATOM 1561 O VAL A 202 9.796 51.162 27.026 1.00 29.61 O
+ATOM 1562 CB VAL A 202 10.094 51.474 23.582 1.00 20.87 C
+ATOM 1563 CG1 VAL A 202 11.238 52.354 24.054 1.00 17.93 C
+ATOM 1564 CG2 VAL A 202 10.665 50.653 22.471 1.00 22.03 C
+ATOM 1565 N ALA A 203 8.262 52.286 25.965 1.00 26.44 N
+ATOM 1566 CA ALA A 203 8.001 53.132 27.123 1.00 24.59 C
+ATOM 1567 C ALA A 203 7.638 52.381 28.370 1.00 24.66 C
+ATOM 1568 O ALA A 203 7.981 52.795 29.484 1.00 26.00 O
+ATOM 1569 CB ALA A 203 6.872 54.099 26.846 1.00 34.37 C
+ATOM 1570 N GLU A 204 6.959 51.252 28.190 1.00 28.00 N
+ATOM 1571 CA GLU A 204 6.592 50.429 29.321 1.00 27.26 C
+ATOM 1572 C GLU A 204 7.818 49.739 29.914 1.00 31.42 C
+ATOM 1573 O GLU A 204 7.951 49.646 31.138 1.00 23.09 O
+ATOM 1574 CB GLU A 204 5.587 49.382 28.900 1.00 36.46 C
+ATOM 1575 CG GLU A 204 4.144 49.866 28.988 1.00 44.61 C
+ATOM 1576 CD GLU A 204 3.138 48.709 28.884 1.00 48.97 C
+ATOM 1577 OE1 GLU A 204 2.993 47.948 29.851 1.00 52.39 O
+ATOM 1578 OE2 GLU A 204 2.506 48.562 27.836 1.00 51.56 O
+ATOM 1579 N VAL A 205 8.729 49.235 29.080 1.00 31.86 N
+ATOM 1580 CA VAL A 205 9.958 48.634 29.563 1.00 22.63 C
+ATOM 1581 C VAL A 205 10.665 49.763 30.292 1.00 21.22 C
+ATOM 1582 O VAL A 205 11.202 49.541 31.373 1.00 18.70 O
+ATOM 1583 CB VAL A 205 10.851 48.117 28.381 1.00 24.22 C
+ATOM 1584 CG1 VAL A 205 12.176 47.554 28.946 1.00 19.79 C
+ATOM 1585 CG2 VAL A 205 10.157 47.007 27.589 1.00 17.92 C
+ATOM 1586 N ARG A 206 10.676 50.985 29.748 1.00 23.27 N
+ATOM 1587 CA ARG A 206 11.381 52.102 30.354 1.00 26.40 C
+ATOM 1588 C ARG A 206 10.866 52.395 31.765 1.00 29.43 C
+ATOM 1589 O ARG A 206 11.653 52.530 32.704 1.00 32.42 O
+ATOM 1590 CB ARG A 206 11.196 53.246 29.421 1.00 26.38 C
+ATOM 1591 CG ARG A 206 11.935 54.435 29.920 1.00 49.92 C
+ATOM 1592 CD ARG A 206 11.129 55.634 29.476 1.00 67.93 C
+ATOM 1593 NE ARG A 206 11.566 56.767 30.264 1.00 84.85 N
+ATOM 1594 CZ ARG A 206 12.176 57.834 29.727 1.00 93.86 C
+ATOM 1595 NH1 ARG A 206 12.338 57.978 28.402 1.00 92.58 N
+ATOM 1596 NH2 ARG A 206 12.607 58.797 30.557 1.00100.35 N
+ATOM 1597 N ALA A 207 9.544 52.377 31.942 1.00 26.47 N
+ATOM 1598 CA ALA A 207 8.907 52.492 33.247 1.00 31.60 C
+ATOM 1599 C ALA A 207 9.202 51.350 34.241 1.00 38.53 C
+ATOM 1600 O ALA A 207 9.309 51.604 35.465 1.00 38.74 O
+ATOM 1601 CB ALA A 207 7.414 52.565 33.084 1.00 26.98 C
+ATOM 1602 N ASP A 208 9.362 50.072 33.834 1.00 34.71 N
+ATOM 1603 CA ASP A 208 9.716 48.993 34.790 1.00 29.57 C
+ATOM 1604 C ASP A 208 11.108 49.181 35.354 1.00 23.15 C
+ATOM 1605 O ASP A 208 11.374 49.013 36.553 1.00 27.89 O
+ATOM 1606 CB ASP A 208 9.597 47.611 34.097 1.00 28.86 C
+ATOM 1607 CG ASP A 208 8.157 47.235 33.726 1.00 36.94 C
+ATOM 1608 OD1 ASP A 208 7.226 47.532 34.481 1.00 38.17 O
+ATOM 1609 OD2 ASP A 208 7.946 46.649 32.669 1.00 43.37 O
+ATOM 1610 N LEU A 209 11.976 49.631 34.439 1.00 29.55 N
+ATOM 1611 CA LEU A 209 13.339 49.966 34.772 1.00 30.90 C
+ATOM 1612 C LEU A 209 13.384 51.107 35.751 1.00 30.94 C
+ATOM 1613 O LEU A 209 14.199 50.983 36.656 1.00 31.15 O
+ATOM 1614 CB LEU A 209 14.144 50.369 33.555 1.00 22.64 C
+ATOM 1615 CG LEU A 209 14.484 49.203 32.619 1.00 32.03 C
+ATOM 1616 CD1 LEU A 209 15.195 49.765 31.380 1.00 30.31 C
+ATOM 1617 CD2 LEU A 209 15.357 48.179 33.319 1.00 27.70 C
+ATOM 1618 N GLU A 210 12.618 52.198 35.657 1.00 29.77 N
+ATOM 1619 CA GLU A 210 12.663 53.230 36.684 1.00 32.29 C
+ATOM 1620 C GLU A 210 12.246 52.665 38.009 1.00 37.37 C
+ATOM 1621 O GLU A 210 12.926 52.974 38.982 1.00 37.57 O
+ATOM 1622 CB GLU A 210 11.762 54.334 36.399 1.00 30.94 C
+ATOM 1623 CG GLU A 210 12.483 55.212 35.433 1.00 46.47 C
+ATOM 1624 CD GLU A 210 11.646 56.411 35.024 1.00 59.35 C
+ATOM 1625 OE1 GLU A 210 11.393 57.236 35.902 1.00 73.54 O
+ATOM 1626 OE2 GLU A 210 11.248 56.534 33.859 1.00 55.93 O
+ATOM 1627 N LYS A 211 11.260 51.747 38.076 1.00 40.32 N
+ATOM 1628 CA LYS A 211 10.927 51.111 39.364 1.00 46.86 C
+ATOM 1629 C LYS A 211 12.078 50.386 40.001 1.00 44.48 C
+ATOM 1630 O LYS A 211 12.239 50.401 41.213 1.00 53.79 O
+ATOM 1631 CB LYS A 211 9.840 50.063 39.295 1.00 49.66 C
+ATOM 1632 CG LYS A 211 8.532 50.780 39.159 1.00 66.99 C
+ATOM 1633 CD LYS A 211 7.786 50.219 37.961 1.00 79.45 C
+ATOM 1634 CE LYS A 211 6.678 51.165 37.481 1.00 83.43 C
+ATOM 1635 NZ LYS A 211 6.007 50.590 36.327 1.00 85.04 N
+ATOM 1636 N ILE A 212 12.897 49.723 39.210 1.00 43.75 N
+ATOM 1637 CA ILE A 212 14.037 48.992 39.744 1.00 41.73 C
+ATOM 1638 C ILE A 212 15.155 49.961 40.162 1.00 40.35 C
+ATOM 1639 O ILE A 212 15.751 49.755 41.216 1.00 44.48 O
+ATOM 1640 CB ILE A 212 14.508 47.961 38.630 1.00 38.89 C
+ATOM 1641 CG1 ILE A 212 13.375 46.935 38.326 1.00 38.67 C
+ATOM 1642 CG2 ILE A 212 15.806 47.281 39.075 1.00 33.58 C
+ATOM 1643 CD1 ILE A 212 13.602 46.019 37.091 1.00 32.12 C
+ATOM 1644 N LEU A 213 15.456 51.032 39.420 1.00 40.42 N
+ATOM 1645 CA LEU A 213 16.624 51.868 39.661 1.00 49.31 C
+ATOM 1646 C LEU A 213 16.440 53.187 40.423 1.00 54.79 C
+ATOM 1647 O LEU A 213 17.458 53.704 40.904 1.00 53.77 O
+ATOM 1648 CB LEU A 213 17.321 52.160 38.292 1.00 37.29 C
+ATOM 1649 CG LEU A 213 17.772 50.963 37.443 1.00 35.90 C
+ATOM 1650 CD1 LEU A 213 18.238 51.457 36.081 1.00 37.96 C
+ATOM 1651 CD2 LEU A 213 18.910 50.230 38.104 1.00 30.51 C
+ATOM 1652 N GLY A 214 15.248 53.773 40.555 1.00 60.83 N
+ATOM 1653 CA GLY A 214 15.055 55.001 41.318 1.00 66.76 C
+ATOM 1654 C GLY A 214 14.400 56.086 40.466 1.00 77.41 C
+ATOM 1655 O GLY A 214 13.852 57.041 41.020 1.00 81.95 O
+ATOM 1656 OXT GLY A 214 14.430 55.983 39.238 1.00 80.44 O
+TER 1657 GLY A 214
+HETATM 1658 PA AP5 A 215 18.089 46.955 20.531 1.00 17.77 P
+HETATM 1659 O1A AP5 A 215 17.885 47.954 21.576 1.00 16.47 O
+HETATM 1660 O2A AP5 A 215 18.847 47.325 19.359 1.00 15.16 O
+HETATM 1661 O3A AP5 A 215 18.390 45.546 21.247 1.00 19.11 O
+HETATM 1662 PB AP5 A 215 19.799 44.954 21.708 1.00 16.65 P
+HETATM 1663 O1B AP5 A 215 19.334 44.008 22.760 1.00 15.25 O
+HETATM 1664 O2B AP5 A 215 20.626 46.063 22.136 1.00 17.16 O
+HETATM 1665 O3B AP5 A 215 20.354 44.137 20.429 1.00 15.96 O
+HETATM 1666 PG AP5 A 215 21.897 43.758 20.174 1.00 19.71 P
+HETATM 1667 O1GAAP5 A 215 21.897 42.507 19.181 0.50 18.18 O
+HETATM 1667 O1GBAP5 A 215 22.628 44.918 19.622 0.50 22.41 O
+HETATM 1668 O2G AP5 A 215 22.353 43.229 21.474 1.00 30.10 O
+HETATM 1669 O3GAAP5 A 215 22.628 44.918 19.622 0.50 22.41 O
+HETATM 1669 O3GBAP5 A 215 21.897 42.507 19.181 0.50 18.18 O
+HETATM 1670 PD AAP5 A 215 23.797 45.114 18.528 0.50 37.05 P
+HETATM 1670 PD BAP5 A 215 23.334 42.002 18.604 0.50 32.08 P
+HETATM 1671 O1DAAP5 A 215 23.854 46.581 18.294 0.50 43.58 O
+HETATM 1671 O1DBAP5 A 215 23.291 40.533 18.837 0.50 25.40 O
+HETATM 1672 O2DAAP5 A 215 23.326 44.324 17.361 0.50 43.58 O
+HETATM 1672 O2DBAP5 A 215 23.442 42.412 17.183 0.50 32.78 O
+HETATM 1673 O3DAAP5 A 215 25.870 44.772 18.892 0.50 36.10 O
+HETATM 1673 O3DBAP5 A 215 24.469 42.554 19.660 0.50 34.55 O
+HETATM 1674 PE AP5 A 215 25.829 43.456 19.553 1.00 25.81 P
+HETATM 1675 O1EAAP5 A 215 24.469 42.554 19.660 0.50 34.55 O
+HETATM 1675 O1EBAP5 A 215 25.870 44.772 18.892 0.50 36.10 O
+HETATM 1676 O2E AP5 A 215 26.407 43.595 20.903 1.00 31.63 O
+HETATM 1677 O5F AP5 A 215 16.664 46.579 19.961 1.00 19.72 O
+HETATM 1678 C5F AP5 A 215 16.543 45.843 18.766 1.00 15.12 C
+HETATM 1679 C4F AP5 A 215 15.520 46.464 17.814 1.00 20.75 C
+HETATM 1680 O4F AP5 A 215 14.167 46.347 18.313 1.00 17.34 O
+HETATM 1681 C3F AP5 A 215 15.758 47.986 17.508 1.00 14.48 C
+HETATM 1682 O3F AP5 A 215 15.239 48.274 16.227 1.00 13.13 O
+HETATM 1683 C2F AP5 A 215 14.853 48.663 18.549 1.00 15.06 C
+HETATM 1684 O2F AP5 A 215 14.344 49.927 18.068 1.00 18.78 O
+HETATM 1685 C1F AP5 A 215 13.766 47.596 18.882 1.00 12.64 C
+HETATM 1686 N9A AP5 A 215 13.106 47.571 20.171 1.00 16.08 N
+HETATM 1687 C8A AP5 A 215 13.724 47.823 21.374 1.00 15.47 C
+HETATM 1688 N7A AP5 A 215 12.929 47.661 22.405 1.00 18.45 N
+HETATM 1689 C5A AP5 A 215 11.690 47.264 21.916 1.00 19.01 C
+HETATM 1690 C6A AP5 A 215 10.452 46.992 22.534 1.00 17.84 C
+HETATM 1691 N6A AP5 A 215 10.265 47.142 23.846 1.00 16.43 N
+HETATM 1692 N1A AP5 A 215 9.421 46.705 21.718 1.00 18.69 N
+HETATM 1693 C2A AP5 A 215 9.647 46.591 20.416 1.00 17.51 C
+HETATM 1694 N3A AP5 A 215 10.750 46.812 19.701 1.00 17.03 N
+HETATM 1695 C4A AP5 A 215 11.799 47.190 20.490 1.00 19.52 C
+HETATM 1696 O5J AP5 A 215 26.954 42.555 18.868 1.00 26.97 O
+HETATM 1697 C5J AP5 A 215 27.043 42.291 17.471 1.00 17.15 C
+HETATM 1698 C4J AP5 A 215 28.387 41.590 17.248 1.00 20.83 C
+HETATM 1699 O4J AP5 A 215 29.446 42.276 17.982 1.00 21.77 O
+HETATM 1700 C3J AP5 A 215 28.351 40.164 17.844 1.00 18.19 C
+HETATM 1701 O3J AP5 A 215 27.754 39.232 16.913 1.00 16.22 O
+HETATM 1702 C2J AP5 A 215 29.838 39.895 18.106 1.00 18.14 C
+HETATM 1703 O2J AP5 A 215 30.514 39.703 16.874 1.00 19.73 O
+HETATM 1704 C1J AP5 A 215 30.173 41.289 18.687 1.00 14.80 C
+HETATM 1705 N9B AP5 A 215 30.420 41.506 20.099 1.00 18.44 N
+HETATM 1706 C8B AP5 A 215 29.899 42.503 20.829 1.00 14.07 C
+HETATM 1707 N7B AP5 A 215 30.217 42.424 22.086 1.00 17.74 N
+HETATM 1708 C5B AP5 A 215 30.966 41.318 22.252 1.00 15.06 C
+HETATM 1709 C6B AP5 A 215 31.484 40.713 23.388 1.00 18.26 C
+HETATM 1710 N6B AP5 A 215 31.368 41.238 24.626 1.00 15.83 N
+HETATM 1711 N1B AP5 A 215 32.095 39.556 23.160 1.00 13.73 N
+HETATM 1712 C2B AP5 A 215 32.310 39.150 21.918 1.00 14.83 C
+HETATM 1713 N3B AP5 A 215 31.828 39.596 20.774 1.00 13.67 N
+HETATM 1714 C4B AP5 A 215 31.109 40.715 20.989 1.00 13.30 C
+HETATM 1715 O HOH A 301 25.596 36.586 22.522 1.00 16.28 O
+HETATM 1716 O HOH A 302 25.457 36.154 20.002 1.00 15.85 O
+HETATM 1717 O HOH A 303 27.360 39.954 14.345 1.00 17.20 O
+HETATM 1718 O HOH A 304 15.282 51.799 19.712 1.00 22.17 O
+HETATM 1719 O HOH A 305 13.020 48.007 25.085 1.00 22.52 O
+HETATM 1720 O HOH A 306 12.773 45.390 25.482 1.00 21.76 O
+HETATM 1721 O HOH A 307 27.132 45.881 22.539 1.00 21.21 O
+HETATM 1722 O HOH A 308 30.510 31.136 28.189 1.00 25.89 O
+HETATM 1723 O HOH A 309 16.207 36.004 28.983 1.00 21.26 O
+HETATM 1724 O HOH A 310 14.242 62.088 13.362 1.00 17.64 O
+HETATM 1725 O HOH A 311 25.813 40.978 27.818 1.00 27.01 O
+HETATM 1726 O HOH A 312 9.008 43.719 33.343 1.00 28.03 O
+HETATM 1727 O HOH A 313 16.543 37.340 26.353 1.00 22.43 O
+HETATM 1728 O HOH A 314 3.939 42.513 26.204 1.00 25.60 O
+HETATM 1729 O HOH A 315 31.576 39.129 37.011 1.00 32.36 O
+HETATM 1730 O HOH A 316 25.175 47.132 20.346 1.00 29.77 O
+HETATM 1731 O HOH A 317 28.278 45.144 11.548 1.00 27.88 O
+HETATM 1732 O HOH A 318 33.867 35.301 22.895 1.00 28.20 O
+HETATM 1733 O HOH A 319 34.234 31.923 25.442 1.00 31.89 O
+HETATM 1734 O HOH A 320 21.619 48.040 19.533 1.00 19.81 O
+HETATM 1735 O HOH A 321 13.043 35.071 15.348 1.00 27.40 O
+HETATM 1736 O HOH A 322 23.568 39.008 23.839 1.00 33.01 O
+HETATM 1737 O HOH A 323 13.437 39.589 38.710 1.00 37.96 O
+HETATM 1738 O HOH A 324 13.211 55.614 9.722 1.00 34.98 O
+HETATM 1739 O HOH A 325 23.669 39.156 27.032 1.00 36.61 O
+HETATM 1740 O HOH A 326 16.156 56.578 19.719 1.00 48.18 O
+HETATM 1741 O HOH A 327 29.598 51.295 11.870 1.00 35.73 O
+HETATM 1742 O HOH A 328 17.432 34.051 27.206 1.00 54.06 O
+HETATM 1743 O HOH A 329 27.504 36.286 17.940 1.00 29.59 O
+HETATM 1744 O HOH A 330 30.017 52.340 16.042 1.00 35.74 O
+HETATM 1745 O HOH A 331 10.768 37.243 14.268 1.00 38.68 O
+HETATM 1746 O HOH A 332 30.339 52.486 24.065 1.00 35.78 O
+HETATM 1747 O HOH A 333 8.972 37.962 30.845 1.00 41.23 O
+HETATM 1748 O HOH A 334 8.802 62.000 8.672 1.00 39.15 O
+HETATM 1749 O HOH A 335 24.368 50.514 17.180 1.00 41.79 O
+HETATM 1750 O HOH A 336 31.297 48.990 11.275 1.00 42.39 O
+HETATM 1751 O HOH A 337 10.452 55.084 10.299 1.00 50.01 O
+HETATM 1752 O HOH A 338 42.937 38.041 28.710 1.00 49.55 O
+HETATM 1753 O HOH A 339 25.481 50.887 9.641 1.00 41.11 O
+HETATM 1754 O HOH A 340 26.141 43.595 28.875 1.00 57.69 O
+HETATM 1755 O HOH A 341 22.519 48.492 17.070 1.00 36.60 O
+HETATM 1756 O HOH A 342 13.806 52.080 5.412 1.00 53.46 O
+HETATM 1757 O HOH A 343 36.713 51.518 19.206 1.00 42.97 O
+HETATM 1758 O HOH A 344 38.718 36.798 11.750 1.00 55.46 O
+HETATM 1759 O HOH A 345 27.412 51.920 16.472 1.00 44.19 O
+HETATM 1760 O HOH A 346 32.573 36.131 7.752 1.00 51.02 O
+HETATM 1761 O HOH A 347 43.113 40.868 26.644 1.00 41.86 O
+HETATM 1762 O HOH A 348 26.339 61.999 17.029 1.00 43.95 O
+HETATM 1763 O HOH A 349 13.085 32.354 24.356 1.00 53.20 O
+HETATM 1764 O HOH A 350 35.015 54.871 14.423 1.00 48.99 O
+HETATM 1765 O HOH A 351 14.074 55.114 22.273 1.00 55.09 O
+HETATM 1766 O HOH A 352 11.836 59.991 25.928 1.00 58.11 O
+HETATM 1767 O HOH A 353 22.433 36.589 28.809 1.00 63.91 O
+HETATM 1768 O HOH A 354 40.246 59.186 36.182 1.00 47.64 O
+HETATM 1769 O HOH A 355 23.218 41.004 22.097 1.00 55.72 O
+HETATM 1770 O HOH A 356 16.131 34.762 35.353 1.00 39.37 O
+HETATM 1771 O HOH A 357 29.009 54.557 19.783 1.00 54.35 O
+HETATM 1772 O HOH A 358 45.595 38.998 26.142 1.00 19.77 O
+HETATM 1773 O HOH A 359 28.191 44.453 14.475 1.00 23.31 O
+HETATM 1774 O HOH A 360 9.204 38.029 28.270 1.00 25.00 O
+HETATM 1775 O HOH A 361 6.832 45.766 22.116 1.00 27.78 O
+HETATM 1776 O HOH A 362 23.337 46.533 22.599 1.00 22.31 O
+HETATM 1777 O HOH A 363 40.003 34.189 23.836 1.00 30.38 O
+HETATM 1778 O HOH A 364 3.660 41.393 29.054 1.00 29.88 O
+HETATM 1779 O HOH A 365 7.251 50.670 21.366 1.00 28.72 O
+HETATM 1780 O HOH A 366 25.488 29.039 34.559 1.00 44.50 O
+HETATM 1781 O HOH A 367 27.100 25.500 17.068 1.00 37.14 O
+HETATM 1782 O HOH A 368 23.774 32.874 49.923 1.00 28.18 O
+HETATM 1783 O HOH A 369 24.846 55.706 10.567 1.00 34.26 O
+HETATM 1784 O HOH A 370 26.922 50.280 11.984 1.00 39.27 O
+HETATM 1785 O HOH A 371 40.994 39.834 34.542 1.00 34.86 O
+HETATM 1786 O HOH A 372 38.928 35.051 31.559 1.00 31.59 O
+HETATM 1787 O HOH A 373 12.123 59.041 17.847 1.00 34.27 O
+HETATM 1788 O HOH A 374 8.733 65.027 8.110 1.00 48.29 O
+HETATM 1789 O HOH A 375 9.836 44.826 11.104 1.00 40.54 O
+HETATM 1790 O HOH A 376 18.036 39.059 1.106 1.00 47.03 O
+HETATM 1791 O HOH A 377 20.124 47.545 11.089 1.00 38.59 O
+HETATM 1792 O HOH A 378 15.531 34.707 23.250 1.00 32.99 O
+HETATM 1793 O HOH A 379 6.615 43.506 5.938 1.00 37.23 O
+HETATM 1794 O HOH A 380 15.327 60.252 4.773 1.00 41.60 O
+HETATM 1795 O HOH A 381 37.260 33.768 22.690 1.00 34.29 O
+HETATM 1796 O HOH A 382 5.123 47.906 20.867 1.00 43.95 O
+HETATM 1797 O HOH A 383 29.888 28.658 29.354 1.00 40.00 O
+HETATM 1798 O HOH A 384 41.993 49.212 7.143 1.00 67.55 O
+HETATM 1799 O HOH A 385 6.717 53.022 23.365 1.00 67.54 O
+HETATM 1800 O HOH A 386 32.244 32.066 19.403 1.00 44.86 O
+HETATM 1801 O HOH A 387 4.350 47.719 32.238 1.00 73.19 O
+HETATM 1802 O HOH A 388 29.481 42.062 41.990 1.00 45.85 O
+HETATM 1803 O HOH A 389 39.794 37.367 9.353 1.00 68.61 O
+HETATM 1804 O HOH A 390 6.029 45.540 19.504 1.00 53.50 O
+HETATM 1805 O HOH A 391 17.029 40.023 6.462 1.00 51.08 O
+HETATM 1806 O HOH A 392 26.848 43.689 47.205 1.00 43.70 O
+HETATM 1807 O HOH A 393 28.609 32.788 39.775 1.00 36.61 O
+HETATM 1808 O HOH A 394 17.425 66.489 13.506 1.00 43.52 O
+HETATM 1809 O HOH A 395 32.755 29.616 36.028 1.00 51.86 O
+HETATM 1810 O HOH A 396 12.148 30.004 16.579 1.00 51.18 O
+HETATM 1811 O HOH A 397 10.668 30.840 22.720 1.00 47.05 O
+HETATM 1812 O HOH A 398 39.381 44.374 9.252 1.00 67.50 O
+HETATM 1813 O HOH A 399 19.060 30.554 15.851 1.00 52.33 O
+HETATM 1814 O HOH A 400 45.137 52.638 15.714 1.00 57.15 O
+HETATM 1815 O HOH A 401 23.618 38.572 20.730 1.00 72.64 O
+HETATM 1816 O HOH A 402 41.685 37.298 33.804 1.00 43.42 O
+HETATM 1817 O HOH A 403 29.862 28.723 20.144 1.00 59.07 O
+HETATM 1818 O HOH A 404 15.870 65.078 19.427 1.00 51.65 O
+HETATM 1819 O HOH A 405 19.310 28.493 26.106 1.00 37.32 O
+HETATM 1820 O HOH A 406 49.509 46.617 12.088 1.00 62.48 O
+HETATM 1821 O HOH A 407 43.166 43.792 35.527 1.00 59.32 O
+HETATM 1822 O HOH A 408 6.848 42.517 34.221 1.00 44.62 O
+HETATM 1823 O HOH A 409 14.017 54.754 25.671 1.00 48.60 O
+HETATM 1824 O HOH A 410 11.552 37.836 7.900 1.00 59.57 O
+HETATM 1825 O HOH A 411 9.933 66.389 20.365 1.00 36.56 O
+HETATM 1826 O HOH A 412 43.474 51.060 18.443 1.00 49.42 O
+HETATM 1827 O HOH A 413 8.770 59.990 30.602 1.00 69.57 O
+HETATM 1828 O HOH A 414 9.320 60.011 19.492 1.00 53.90 O
+HETATM 1829 O HOH A 415 7.059 36.965 14.011 1.00 43.34 O
+HETATM 1830 O HOH A 416 38.160 34.328 12.917 1.00 66.53 O
+HETATM 1831 O HOH A 417 6.030 42.318 21.847 1.00 48.51 O
+HETATM 1832 O HOH A 418 4.807 40.626 31.711 1.00 41.24 O
+HETATM 1833 O HOH A 419 24.913 63.389 18.996 1.00 48.75 O
+HETATM 1834 O HOH A 420 37.961 34.219 16.864 1.00 43.46 O
+HETATM 1835 O HOH A 421 31.789 59.423 28.277 1.00 63.66 O
+HETATM 1836 O HOH A 422 7.038 38.920 5.927 1.00 47.84 O
+HETATM 1837 O HOH A 423 25.989 65.922 17.980 1.00 92.64 O
+HETATM 1838 O HOH A 424 7.137 55.109 30.794 1.00 51.46 O
+HETATM 1839 O HOH A 425 23.323 66.801 20.932 1.00 56.75 O
+HETATM 1840 O HOH A 426 29.627 39.761 40.789 1.00 43.36 O
+HETATM 1841 O HOH A 427 26.191 35.291 8.524 1.00 45.04 O
+HETATM 1842 O HOH A 428 11.817 41.950 38.134 1.00 47.91 O
+HETATM 1843 O HOH A 429 24.499 43.812 22.913 1.00 30.66 O
+HETATM 1844 O HOH A 430 21.594 29.250 39.195 1.00 51.34 O
+HETATM 1845 O HOH A 431 14.692 57.503 26.183 1.00 65.76 O
+HETATM 1846 O HOH A 432 21.776 30.228 32.723 1.00 49.54 O
+HETATM 1847 O HOH A 433 43.494 44.683 8.116 1.00 80.98 O
+HETATM 1848 O HOH A 434 17.764 32.952 36.707 1.00 55.46 O
+HETATM 1849 O HOH A 435 40.165 50.611 19.877 1.00 47.61 O
+HETATM 1850 O HOH A 436 41.546 48.772 33.202 1.00 53.83 O
+HETATM 1851 O HOH A 437 8.423 64.875 10.953 1.00 49.52 O
+HETATM 1852 O HOH A 438 32.402 54.455 24.269 1.00 55.06 O
+HETATM 1853 O HOH A 439 32.554 30.589 38.658 1.00 69.44 O
+HETATM 1854 O HOH A 440 19.782 29.447 35.543 1.00 77.94 O
+HETATM 1855 O HOH A 441 18.508 41.682 47.064 1.00 56.59 O
+HETATM 1856 O HOH A 442 23.527 67.385 10.336 1.00 73.49 O
+HETATM 1857 O HOH A 443 4.497 53.731 14.920 1.00 72.06 O
+HETATM 1858 O HOH A 444 10.239 45.411 39.661 1.00 79.81 O
+HETATM 1859 O HOH A 445 39.018 33.124 26.868 1.00 35.70 O
+HETATM 1860 O HOH A 446 26.791 30.572 14.383 1.00 44.60 O
+HETATM 1861 O HOH A 447 38.345 40.599 10.477 1.00 31.82 O
+HETATM 1862 O HOH A 448 10.577 66.628 6.955 1.00 53.04 O
+HETATM 1863 O HOH A 449 20.090 36.512 5.367 1.00 45.06 O
+HETATM 1864 O HOH A 450 10.885 27.784 21.584 1.00 59.57 O
+HETATM 1865 O HOH A 451 15.710 33.114 31.295 1.00 68.34 O
+HETATM 1866 O HOH A 452 22.392 42.836 1.924 1.00 92.57 O
+HETATM 1867 O HOH A 453 28.122 38.516 6.064 1.00 82.43 O
+HETATM 1868 O HOH A 454 15.216 64.740 12.755 1.00 35.20 O
+HETATM 1869 O HOH A 455 20.197 64.217 6.430 1.00 45.93 O
+HETATM 1870 O HOH A 456 25.812 38.728 18.933 1.00 59.25 O
+HETATM 1871 O HOH A 457 39.961 34.805 34.503 1.00 42.20 O
+HETATM 1872 O HOH A 458 4.337 43.965 13.243 1.00 58.81 O
+HETATM 1873 O HOH A 459 18.956 52.051 5.225 1.00 63.75 O
+HETATM 1874 O HOH A 460 14.161 33.114 34.250 1.00 97.69 O
+HETATM 1875 O HOH A 461 10.114 46.766 37.264 1.00 52.16 O
+HETATM 1876 O HOH A 462 24.067 67.933 18.552 1.00 85.10 O
+HETATM 1877 O HOH A 463 16.814 50.012 44.520 1.00 79.48 O
+HETATM 1878 O HOH A 464 27.818 59.760 30.349 1.00 59.18 O
+HETATM 1879 O HOH A 465 9.349 66.014 17.563 1.00 68.04 O
+HETATM 1880 O HOH A 466 37.570 53.233 17.287 1.00 46.75 O
+HETATM 1881 O HOH A 467 12.812 28.624 19.758 1.00 60.62 O
+HETATM 1882 O HOH A 468 10.086 46.232 8.712 1.00 45.81 O
+HETATM 1883 O HOH A 469 39.225 50.766 24.502 1.00 60.05 O
+HETATM 1884 O HOH A 470 30.789 46.239 11.591 1.00 64.20 O
+HETATM 1885 O HOH A 471 16.104 42.427 5.445 1.00 61.84 O
+HETATM 1886 O HOH A 472 42.535 42.337 10.717 1.00 55.32 O
+HETATM 1887 O HOH A 473 38.696 48.016 8.258 1.00 76.57 O
+HETATM 1888 O HOH A 474 2.855 52.242 25.858 1.00 65.77 O
+HETATM 1889 O HOH A 475 16.031 39.802 3.063 1.00 55.81 O
+HETATM 1890 O HOH A 476 24.310 61.583 30.610 1.00 55.63 O
+HETATM 1891 O HOH A 477 5.846 54.857 18.712 1.00 66.17 O
+HETATM 1892 O HOH A 478 21.605 58.126 23.468 1.00 84.99 O
+HETATM 1893 O HOH A 479 26.128 51.029 14.411 1.00 52.13 O
+HETATM 1894 O HOH A 480 21.290 62.495 0.905 1.00 71.24 O
+HETATM 1895 O HOH A 481 39.526 50.421 7.055 1.00 71.01 O
+HETATM 1896 O HOH A 482 30.262 60.358 31.669 1.00 69.26 O
+HETATM 1897 O HOH A 483 16.311 45.183 6.482 1.00 78.90 O
+HETATM 1898 O HOH A 484 43.655 46.627 28.150 1.00 62.22 O
+HETATM 1899 O HOH A 485 9.870 44.035 36.213 1.00 69.48 O
+HETATM 1900 O HOH A 486 32.269 44.152 10.518 1.00 74.47 O
+HETATM 1901 O HOH A 487 21.824 66.974 8.262 1.00 47.71 O
+HETATM 1902 O HOH A 488 21.598 44.267 6.261 1.00 58.62 O
+HETATM 1903 O HOH A 489 7.851 40.668 8.490 1.00 62.00 O
+HETATM 1904 O HOH A 490 43.182 43.002 38.713 1.00 42.41 O
+HETATM 1905 O HOH A 491 29.523 53.352 40.916 1.00 66.48 O
+HETATM 1906 O HOH A 492 6.567 62.652 5.125 1.00 56.38 O
+HETATM 1907 O HOH A 493 34.073 32.824 21.802 1.00 61.62 O
+HETATM 1908 O HOH A 494 46.746 48.998 12.977 1.00 63.98 O
+HETATM 1909 O HOH A 495 16.273 57.609 4.408 1.00 81.40 O
+HETATM 1910 O HOH A 496 29.717 43.275 9.808 1.00 47.90 O
+HETATM 1911 O HOH A 497 32.864 29.316 26.993 1.00 57.06 O
+HETATM 1912 O HOH A 498 27.420 52.904 8.999 1.00 52.15 O
+HETATM 1913 O HOH A 499 34.696 33.372 16.527 1.00 85.47 O
+HETATM 1914 O HOH A 500 31.284 41.355 38.672 1.00 60.84 O
+HETATM 1915 O HOH A 501 40.129 52.881 8.058 1.00 56.09 O
+HETATM 1916 O HOH A 502 11.530 31.821 14.592 1.00 59.89 O
+HETATM 1917 O HOH A 503 18.388 35.888 40.263 1.00 62.98 O
+HETATM 1918 O HOH A 504 24.624 37.008 5.996 1.00 60.08 O
+HETATM 1919 O HOH A 505 14.138 54.384 7.557 1.00 55.55 O
+HETATM 1920 O HOH A 506 20.876 30.493 9.653 1.00 62.57 O
+HETATM 1921 O HOH A 507 27.328 58.149 21.600 1.00 67.74 O
+HETATM 1922 O HOH A 508 44.148 48.327 31.469 1.00 62.63 O
+HETATM 1923 O HOH A 509 35.552 30.378 32.797 1.00 60.19 O
+HETATM 1924 O HOH A 510 45.321 44.866 40.838 1.00 49.33 O
+HETATM 1925 O HOH A 511 28.439 36.467 50.549 1.00 69.37 O
+HETATM 1926 O HOH A 512 21.371 62.014 3.596 1.00 49.98 O
+HETATM 1927 O HOH A 513 25.890 66.068 9.239 1.00 64.09 O
+HETATM 1928 O HOH A 514 45.734 51.886 12.941 1.00 87.03 O
+HETATM 1929 O HOH A 515 27.444 56.080 23.709 1.00 73.73 O
+HETATM 1930 O HOH A 516 28.445 27.443 27.536 1.00 55.49 O
+HETATM 1931 O HOH A 517 39.014 31.727 31.716 1.00 60.98 O
+HETATM 1932 O HOH A 518 30.469 58.394 36.070 1.00 61.00 O
+HETATM 1933 O HOH A 519 35.297 51.498 42.943 1.00 62.19 O
+HETATM 1934 O HOH A 520 25.252 31.535 45.433 1.00 60.86 O
+HETATM 1935 O HOH A 521 12.628 30.582 26.713 1.00 88.31 O
+HETATM 1936 O HOH A 522 10.907 56.239 26.269 1.00 78.48 O
+HETATM 1937 O HOH A 523 25.305 34.266 5.500 1.00 77.16 O
+HETATM 1938 O HOH A 524 29.666 56.430 11.280 1.00 82.31 O
+HETATM 1939 O HOH A 525 14.372 31.727 16.145 1.00 63.48 O
+HETATM 1940 O HOH A 526 36.595 56.088 41.181 1.00 68.21 O
+HETATM 1941 O HOH A 527 30.588 56.291 25.754 1.00 67.97 O
+HETATM 1942 O HOH A 528 23.820 45.463 45.863 1.00 71.02 O
+HETATM 1943 O HOH A 529 37.553 56.554 35.361 1.00 38.17 O
+HETATM 1944 O HOH A 530 40.463 61.999 38.163 1.00 59.25 O
+HETATM 1945 O HOH A 531 30.307 27.374 11.952 1.00 90.79 O
+HETATM 1946 O HOH A 534 11.176 48.839 6.067 1.00 82.53 O
+HETATM 1947 O HOH A 535 22.707 63.031 5.796 1.00 72.50 O
+HETATM 1948 O HOH A 536 30.118 54.769 17.243 1.00 61.10 O
+HETATM 1949 O HOH A 537 26.111 39.613 7.723 1.00 69.07 O
+HETATM 1950 O HOH A 538 9.208 45.673 30.600 1.00 56.63 O
+HETATM 1951 O HOH A 539 16.608 59.554 19.579 1.00 52.84 O
+HETATM 1952 O HOH A 540 28.975 53.951 22.347 1.00 65.19 O
+HETATM 1953 O HOH A 541 9.468 40.396 34.049 1.00 57.03 O
+HETATM 1954 O HOH A 542 29.298 60.386 34.180 1.00 82.76 O
+HETATM 1955 O HOH A 543 10.634 60.171 32.792 1.00 80.06 O
+ATOM 1956 N MET B 1 12.440 6.614 -1.137 1.00 84.71 N
+ATOM 1957 CA MET B 1 13.491 5.717 -0.668 1.00 76.22 C
+ATOM 1958 C MET B 1 13.148 5.442 0.796 1.00 71.67 C
+ATOM 1959 O MET B 1 12.868 6.366 1.556 1.00 63.59 O
+ATOM 1960 CB MET B 1 14.812 6.448 -0.874 1.00 75.77 C
+ATOM 1961 CG MET B 1 15.976 5.572 -1.280 1.00 71.66 C
+ATOM 1962 SD MET B 1 17.080 5.513 0.137 1.00 66.16 S
+ATOM 1963 CE MET B 1 18.072 6.943 -0.151 1.00 65.65 C
+ATOM 1964 N ARG B 2 13.034 4.158 1.147 1.00 68.59 N
+ATOM 1965 CA ARG B 2 12.484 3.732 2.434 1.00 67.43 C
+ATOM 1966 C ARG B 2 13.498 2.869 3.183 1.00 57.10 C
+ATOM 1967 O ARG B 2 14.114 1.992 2.555 1.00 53.89 O
+ATOM 1968 CB ARG B 2 11.195 2.956 2.146 1.00 72.67 C
+ATOM 1969 CG ARG B 2 10.165 3.697 1.313 1.00 72.08 C
+ATOM 1970 CD ARG B 2 9.624 2.850 0.185 1.00 73.99 C
+ATOM 1971 NE ARG B 2 8.201 3.110 0.140 1.00 84.42 N
+ATOM 1972 CZ ARG B 2 7.320 2.313 -0.472 1.00 87.12 C
+ATOM 1973 NH1 ARG B 2 7.700 1.235 -1.169 1.00 81.73 N
+ATOM 1974 NH2 ARG B 2 6.024 2.633 -0.378 1.00 89.07 N
+ATOM 1975 N ILE B 3 13.757 3.053 4.467 1.00 48.30 N
+ATOM 1976 CA ILE B 3 14.820 2.298 5.099 1.00 41.09 C
+ATOM 1977 C ILE B 3 14.372 2.025 6.524 1.00 46.91 C
+ATOM 1978 O ILE B 3 13.660 2.825 7.142 1.00 47.93 O
+ATOM 1979 CB ILE B 3 16.126 3.129 5.107 1.00 39.02 C
+ATOM 1980 CG1 ILE B 3 16.572 3.543 3.735 1.00 34.33 C
+ATOM 1981 CG2 ILE B 3 17.243 2.280 5.656 1.00 35.63 C
+ATOM 1982 CD1 ILE B 3 17.526 4.738 3.782 1.00 31.71 C
+ATOM 1983 N ILE B 4 14.732 0.846 7.026 1.00 49.38 N
+ATOM 1984 CA ILE B 4 14.527 0.452 8.416 1.00 49.63 C
+ATOM 1985 C ILE B 4 15.955 0.383 9.003 1.00 47.41 C
+ATOM 1986 O ILE B 4 16.934 0.000 8.324 1.00 43.23 O
+ATOM 1987 CB ILE B 4 13.839 -0.968 8.544 1.00 51.23 C
+ATOM 1988 CG1 ILE B 4 12.411 -0.962 8.018 1.00 59.00 C
+ATOM 1989 CG2 ILE B 4 13.787 -1.370 10.010 1.00 51.37 C
+ATOM 1990 CD1 ILE B 4 11.690 -2.343 8.025 1.00 60.42 C
+ATOM 1991 N LEU B 5 16.113 0.790 10.258 1.00 42.10 N
+ATOM 1992 CA LEU B 5 17.364 0.610 10.949 1.00 41.72 C
+ATOM 1993 C LEU B 5 17.066 -0.411 12.013 1.00 40.37 C
+ATOM 1994 O LEU B 5 16.071 -0.292 12.735 1.00 42.94 O
+ATOM 1995 CB LEU B 5 17.817 1.896 11.571 1.00 40.46 C
+ATOM 1996 CG LEU B 5 17.955 3.057 10.600 1.00 42.49 C
+ATOM 1997 CD1 LEU B 5 18.514 4.244 11.389 1.00 47.45 C
+ATOM 1998 CD2 LEU B 5 18.845 2.684 9.406 1.00 37.74 C
+ATOM 1999 N LEU B 6 17.961 -1.390 12.084 1.00 36.41 N
+ATOM 2000 CA LEU B 6 17.873 -2.565 12.933 1.00 40.19 C
+ATOM 2001 C LEU B 6 19.120 -2.684 13.799 1.00 39.44 C
+ATOM 2002 O LEU B 6 20.227 -2.447 13.301 1.00 42.64 O
+ATOM 2003 CB LEU B 6 17.758 -3.744 12.031 1.00 41.77 C
+ATOM 2004 CG LEU B 6 16.842 -4.871 12.331 1.00 48.66 C
+ATOM 2005 CD1 LEU B 6 15.402 -4.380 12.555 1.00 46.66 C
+ATOM 2006 CD2 LEU B 6 16.983 -5.852 11.167 1.00 49.02 C
+ATOM 2007 N GLY B 7 19.057 -3.003 15.080 1.00 44.76 N
+ATOM 2008 CA GLY B 7 20.272 -3.070 15.888 1.00 40.36 C
+ATOM 2009 C GLY B 7 19.954 -2.918 17.356 1.00 41.77 C
+ATOM 2010 O GLY B 7 18.844 -2.521 17.735 1.00 43.95 O
+ATOM 2011 N ALA B 8 20.929 -3.294 18.183 1.00 39.38 N
+ATOM 2012 CA ALA B 8 20.758 -3.337 19.621 1.00 35.60 C
+ATOM 2013 C ALA B 8 20.475 -1.974 20.190 1.00 27.31 C
+ATOM 2014 O ALA B 8 20.799 -0.992 19.522 1.00 33.53 O
+ATOM 2015 CB ALA B 8 22.035 -3.915 20.266 1.00 37.34 C
+ATOM 2016 N PRO B 9 19.946 -1.841 21.419 1.00 37.00 N
+ATOM 2017 CA PRO B 9 19.941 -0.573 22.161 1.00 29.14 C
+ATOM 2018 C PRO B 9 21.313 0.109 22.079 1.00 35.37 C
+ATOM 2019 O PRO B 9 22.304 -0.513 22.486 1.00 42.22 O
+ATOM 2020 CB PRO B 9 19.573 -1.010 23.539 1.00 33.91 C
+ATOM 2021 CG PRO B 9 18.671 -2.184 23.335 1.00 30.86 C
+ATOM 2022 CD PRO B 9 19.367 -2.929 22.219 1.00 33.98 C
+ATOM 2023 N GLY B 10 21.464 1.299 21.495 1.00 38.61 N
+ATOM 2024 CA GLY B 10 22.728 2.031 21.494 1.00 32.57 C
+ATOM 2025 C GLY B 10 23.612 1.650 20.330 1.00 30.37 C
+ATOM 2026 O GLY B 10 24.784 2.003 20.301 1.00 34.38 O
+ATOM 2027 N ALA B 11 23.098 0.947 19.342 1.00 34.02 N
+ATOM 2028 CA ALA B 11 23.890 0.547 18.190 1.00 33.03 C
+ATOM 2029 C ALA B 11 24.343 1.712 17.300 1.00 35.80 C
+ATOM 2030 O ALA B 11 25.245 1.535 16.462 1.00 43.03 O
+ATOM 2031 CB ALA B 11 23.091 -0.431 17.346 1.00 31.19 C
+ATOM 2032 N GLY B 12 23.720 2.893 17.440 1.00 33.35 N
+ATOM 2033 CA GLY B 12 24.077 4.056 16.658 1.00 30.37 C
+ATOM 2034 C GLY B 12 22.990 4.425 15.684 1.00 31.40 C
+ATOM 2035 O GLY B 12 23.215 5.330 14.878 1.00 40.02 O
+ATOM 2036 N LYS B 13 21.787 3.848 15.763 1.00 29.01 N
+ATOM 2037 CA LYS B 13 20.779 4.049 14.730 1.00 34.98 C
+ATOM 2038 C LYS B 13 20.288 5.485 14.599 1.00 33.86 C
+ATOM 2039 O LYS B 13 20.339 6.050 13.502 1.00 40.66 O
+ATOM 2040 CB LYS B 13 19.571 3.150 14.972 1.00 34.62 C
+ATOM 2041 CG LYS B 13 19.826 1.646 14.878 1.00 41.10 C
+ATOM 2042 CD LYS B 13 18.593 0.810 15.259 1.00 41.42 C
+ATOM 2043 CE LYS B 13 18.013 1.059 16.675 1.00 40.36 C
+ATOM 2044 NZ LYS B 13 18.879 0.536 17.689 1.00 33.42 N
+ATOM 2045 N GLY B 14 19.841 6.161 15.640 1.00 30.00 N
+ATOM 2046 CA GLY B 14 19.422 7.545 15.550 1.00 29.39 C
+ATOM 2047 C GLY B 14 20.566 8.450 15.119 1.00 38.09 C
+ATOM 2048 O GLY B 14 20.348 9.299 14.248 1.00 38.51 O
+ATOM 2049 N THR B 15 21.786 8.237 15.651 1.00 37.44 N
+ATOM 2050 CA THR B 15 22.940 9.041 15.293 1.00 33.43 C
+ATOM 2051 C THR B 15 23.058 8.991 13.791 1.00 32.89 C
+ATOM 2052 O THR B 15 23.175 10.044 13.166 1.00 30.84 O
+ATOM 2053 CB THR B 15 24.234 8.500 15.922 1.00 36.32 C
+ATOM 2054 OG1 THR B 15 24.090 8.662 17.329 1.00 38.15 O
+ATOM 2055 CG2 THR B 15 25.481 9.251 15.515 1.00 37.68 C
+ATOM 2056 N GLN B 16 22.914 7.843 13.158 1.00 32.92 N
+ATOM 2057 CA GLN B 16 23.052 7.821 11.715 1.00 36.52 C
+ATOM 2058 C GLN B 16 21.813 8.215 10.931 1.00 39.40 C
+ATOM 2059 O GLN B 16 21.889 8.729 9.816 1.00 42.84 O
+ATOM 2060 CB GLN B 16 23.502 6.458 11.302 1.00 32.86 C
+ATOM 2061 CG GLN B 16 24.868 6.174 11.887 1.00 34.60 C
+ATOM 2062 CD GLN B 16 25.969 7.091 11.400 1.00 34.87 C
+ATOM 2063 OE1 GLN B 16 26.979 7.292 12.064 1.00 36.99 O
+ATOM 2064 NE2 GLN B 16 25.870 7.644 10.208 1.00 40.19 N
+ATOM 2065 N ALA B 17 20.653 7.998 11.495 1.00 39.01 N
+ATOM 2066 CA ALA B 17 19.414 8.452 10.923 1.00 47.16 C
+ATOM 2067 C ALA B 17 19.407 9.931 10.549 1.00 43.52 C
+ATOM 2068 O ALA B 17 18.894 10.279 9.485 1.00 44.04 O
+ATOM 2069 CB ALA B 17 18.311 8.228 11.918 1.00 49.09 C
+ATOM 2070 N GLN B 18 19.997 10.805 11.370 1.00 44.22 N
+ATOM 2071 CA GLN B 18 20.001 12.242 11.128 1.00 48.06 C
+ATOM 2072 C GLN B 18 20.752 12.539 9.870 1.00 48.99 C
+ATOM 2073 O GLN B 18 20.228 13.295 9.050 1.00 49.18 O
+ATOM 2074 CB GLN B 18 20.651 13.030 12.231 1.00 52.01 C
+ATOM 2075 CG GLN B 18 19.844 13.002 13.529 1.00 64.20 C
+ATOM 2076 CD GLN B 18 20.717 13.009 14.801 1.00 76.47 C
+ATOM 2077 OE1 GLN B 18 20.261 12.589 15.863 1.00 80.71 O
+ATOM 2078 NE2 GLN B 18 21.988 13.408 14.870 1.00 76.58 N
+ATOM 2079 N PHE B 19 21.915 11.920 9.668 1.00 47.30 N
+ATOM 2080 CA PHE B 19 22.622 12.089 8.417 1.00 52.09 C
+ATOM 2081 C PHE B 19 21.761 11.614 7.227 1.00 52.15 C
+ATOM 2082 O PHE B 19 21.701 12.322 6.217 1.00 48.70 O
+ATOM 2083 CB PHE B 19 23.982 11.315 8.458 1.00 62.83 C
+ATOM 2084 CG PHE B 19 24.366 10.647 7.110 1.00 78.66 C
+ATOM 2085 CD1 PHE B 19 24.827 11.402 6.031 1.00 82.12 C
+ATOM 2086 CD2 PHE B 19 24.156 9.276 6.923 1.00 81.20 C
+ATOM 2087 CE1 PHE B 19 25.059 10.794 4.810 1.00 80.52 C
+ATOM 2088 CE2 PHE B 19 24.391 8.681 5.697 1.00 78.78 C
+ATOM 2089 CZ PHE B 19 24.835 9.443 4.648 1.00 80.40 C
+ATOM 2090 N ILE B 20 21.096 10.442 7.257 1.00 54.77 N
+ATOM 2091 CA ILE B 20 20.352 9.941 6.085 1.00 53.50 C
+ATOM 2092 C ILE B 20 19.277 10.955 5.691 1.00 55.71 C
+ATOM 2093 O ILE B 20 19.088 11.260 4.516 1.00 55.97 O
+ATOM 2094 CB ILE B 20 19.727 8.544 6.428 1.00 43.65 C
+ATOM 2095 CG1 ILE B 20 20.853 7.526 6.571 1.00 43.73 C
+ATOM 2096 CG2 ILE B 20 18.783 8.072 5.326 1.00 36.90 C
+ATOM 2097 CD1 ILE B 20 20.692 6.504 7.714 1.00 37.34 C
+ATOM 2098 N MET B 21 18.640 11.539 6.706 1.00 53.50 N
+ATOM 2099 CA MET B 21 17.584 12.511 6.566 1.00 55.59 C
+ATOM 2100 C MET B 21 18.019 13.768 5.786 1.00 63.26 C
+ATOM 2101 O MET B 21 17.646 14.000 4.619 1.00 54.67 O
+ATOM 2102 CB MET B 21 17.171 12.741 7.993 1.00 45.94 C
+ATOM 2103 CG MET B 21 16.117 13.778 8.216 1.00 59.65 C
+ATOM 2104 SD MET B 21 15.667 13.800 9.963 1.00 68.89 S
+ATOM 2105 CE MET B 21 17.230 14.160 10.717 1.00 65.04 C
+ATOM 2106 N GLU B 22 18.939 14.517 6.400 1.00 68.11 N
+ATOM 2107 CA GLU B 22 19.457 15.752 5.835 1.00 69.95 C
+ATOM 2108 C GLU B 22 20.054 15.548 4.462 1.00 61.74 C
+ATOM 2109 O GLU B 22 20.015 16.446 3.627 1.00 62.70 O
+ATOM 2110 CB GLU B 22 20.556 16.389 6.736 1.00 80.66 C
+ATOM 2111 CG GLU B 22 21.914 15.659 6.882 1.00 96.02 C
+ATOM 2112 CD GLU B 22 23.132 16.441 7.418 1.00103.95 C
+ATOM 2113 OE1 GLU B 22 23.305 16.504 8.643 1.00106.95 O
+ATOM 2114 OE2 GLU B 22 23.927 16.950 6.610 1.00106.47 O
+ATOM 2115 N LYS B 23 20.610 14.371 4.225 1.00 55.62 N
+ATOM 2116 CA LYS B 23 21.283 14.154 2.976 1.00 64.35 C
+ATOM 2117 C LYS B 23 20.345 13.533 1.962 1.00 66.14 C
+ATOM 2118 O LYS B 23 20.562 13.666 0.760 1.00 69.30 O
+ATOM 2119 CB LYS B 23 22.495 13.252 3.214 1.00 70.08 C
+ATOM 2120 CG LYS B 23 23.671 13.477 2.258 1.00 77.32 C
+ATOM 2121 CD LYS B 23 24.033 12.153 1.600 1.00 77.45 C
+ATOM 2122 CE LYS B 23 25.035 12.305 0.473 1.00 76.19 C
+ATOM 2123 NZ LYS B 23 25.206 11.005 -0.143 1.00 70.39 N
+ATOM 2124 N TYR B 24 19.288 12.836 2.336 1.00 65.86 N
+ATOM 2125 CA TYR B 24 18.518 12.180 1.304 1.00 66.45 C
+ATOM 2126 C TYR B 24 17.121 12.746 1.190 1.00 68.07 C
+ATOM 2127 O TYR B 24 16.349 12.397 0.290 1.00 63.72 O
+ATOM 2128 CB TYR B 24 18.537 10.672 1.616 1.00 67.20 C
+ATOM 2129 CG TYR B 24 19.927 10.040 1.444 1.00 65.48 C
+ATOM 2130 CD1 TYR B 24 20.337 9.705 0.176 1.00 66.90 C
+ATOM 2131 CD2 TYR B 24 20.777 9.794 2.509 1.00 65.22 C
+ATOM 2132 CE1 TYR B 24 21.572 9.134 -0.033 1.00 65.93 C
+ATOM 2133 CE2 TYR B 24 22.015 9.222 2.301 1.00 62.68 C
+ATOM 2134 CZ TYR B 24 22.406 8.896 1.020 1.00 59.30 C
+ATOM 2135 OH TYR B 24 23.642 8.343 0.766 1.00 55.27 O
+ATOM 2136 N GLY B 25 16.807 13.633 2.130 1.00 65.70 N
+ATOM 2137 CA GLY B 25 15.537 14.321 2.173 1.00 68.83 C
+ATOM 2138 C GLY B 25 14.372 13.599 2.839 1.00 69.97 C
+ATOM 2139 O GLY B 25 13.421 14.262 3.273 1.00 75.41 O
+ATOM 2140 N ILE B 26 14.388 12.268 2.923 1.00 68.22 N
+ATOM 2141 CA ILE B 26 13.304 11.475 3.522 1.00 59.20 C
+ATOM 2142 C ILE B 26 13.047 11.819 4.978 1.00 52.29 C
+ATOM 2143 O ILE B 26 14.011 12.185 5.640 1.00 59.87 O
+ATOM 2144 CB ILE B 26 13.627 9.977 3.429 1.00 56.62 C
+ATOM 2145 CG1 ILE B 26 15.003 9.610 3.977 1.00 54.45 C
+ATOM 2146 CG2 ILE B 26 13.497 9.635 1.979 1.00 48.49 C
+ATOM 2147 CD1 ILE B 26 15.252 8.104 4.018 1.00 62.43 C
+ATOM 2148 N PRO B 27 11.843 11.768 5.552 1.00 55.31 N
+ATOM 2149 CA PRO B 27 11.619 11.921 6.997 1.00 57.76 C
+ATOM 2150 C PRO B 27 11.911 10.709 7.912 1.00 59.90 C
+ATOM 2151 O PRO B 27 11.626 9.544 7.591 1.00 65.00 O
+ATOM 2152 CB PRO B 27 10.169 12.403 7.067 1.00 56.55 C
+ATOM 2153 CG PRO B 27 9.544 11.660 5.902 1.00 55.45 C
+ATOM 2154 CD PRO B 27 10.584 11.838 4.809 1.00 58.04 C
+ATOM 2155 N GLN B 28 12.496 10.968 9.087 1.00 59.88 N
+ATOM 2156 CA GLN B 28 12.800 9.945 10.086 1.00 61.78 C
+ATOM 2157 C GLN B 28 11.521 9.669 10.885 1.00 61.12 C
+ATOM 2158 O GLN B 28 10.899 10.585 11.427 1.00 64.12 O
+ATOM 2159 CB GLN B 28 13.937 10.449 11.024 1.00 60.26 C
+ATOM 2160 CG GLN B 28 14.373 9.546 12.192 1.00 65.40 C
+ATOM 2161 CD GLN B 28 15.089 10.216 13.380 1.00 70.59 C
+ATOM 2162 OE1 GLN B 28 15.294 11.528 13.541 1.00 70.04 O
+ATOM 2163 NE2 GLN B 28 15.483 9.498 14.298 1.00 75.58 N
+ATOM 2164 N ILE B 29 11.086 8.429 10.990 1.00 60.46 N
+ATOM 2165 CA ILE B 29 9.920 8.082 11.769 1.00 53.15 C
+ATOM 2166 C ILE B 29 10.517 7.211 12.854 1.00 46.16 C
+ATOM 2167 O ILE B 29 10.844 6.054 12.613 1.00 49.12 O
+ATOM 2168 CB ILE B 29 8.960 7.369 10.808 1.00 51.44 C
+ATOM 2169 CG1 ILE B 29 8.476 8.369 9.762 1.00 55.41 C
+ATOM 2170 CG2 ILE B 29 7.765 6.817 11.548 1.00 49.58 C
+ATOM 2171 CD1 ILE B 29 7.649 7.677 8.664 1.00 63.15 C
+ATOM 2172 N SER B 30 10.761 7.798 14.008 1.00 38.43 N
+ATOM 2173 CA SER B 30 11.332 7.135 15.151 1.00 41.27 C
+ATOM 2174 C SER B 30 10.293 6.883 16.240 1.00 47.30 C
+ATOM 2175 O SER B 30 9.831 7.812 16.932 1.00 50.43 O
+ATOM 2176 CB SER B 30 12.486 8.009 15.664 1.00 47.63 C
+ATOM 2177 OG SER B 30 12.863 7.872 17.046 1.00 52.30 O
+ATOM 2178 N THR B 31 9.905 5.621 16.468 1.00 43.77 N
+ATOM 2179 CA THR B 31 8.911 5.306 17.473 1.00 40.92 C
+ATOM 2180 C THR B 31 9.309 5.682 18.870 1.00 35.41 C
+ATOM 2181 O THR B 31 8.414 5.905 19.663 1.00 41.35 O
+ATOM 2182 CB THR B 31 8.583 3.831 17.460 1.00 45.07 C
+ATOM 2183 OG1 THR B 31 9.767 3.088 17.284 1.00 51.53 O
+ATOM 2184 CG2 THR B 31 7.681 3.521 16.314 1.00 47.35 C
+ATOM 2185 N GLY B 32 10.580 5.793 19.220 1.00 35.14 N
+ATOM 2186 CA GLY B 32 10.958 6.188 20.552 1.00 33.98 C
+ATOM 2187 C GLY B 32 10.749 7.689 20.740 1.00 46.60 C
+ATOM 2188 O GLY B 32 10.201 8.174 21.744 1.00 42.70 O
+ATOM 2189 N ASP B 33 11.152 8.457 19.730 1.00 47.09 N
+ATOM 2190 CA ASP B 33 10.994 9.894 19.767 1.00 51.78 C
+ATOM 2191 C ASP B 33 9.496 10.192 19.774 1.00 52.51 C
+ATOM 2192 O ASP B 33 9.056 11.057 20.535 1.00 54.04 O
+ATOM 2193 CB ASP B 33 11.707 10.528 18.538 1.00 60.32 C
+ATOM 2194 CG ASP B 33 13.263 10.632 18.532 1.00 66.90 C
+ATOM 2195 OD1 ASP B 33 13.922 10.356 19.548 1.00 62.29 O
+ATOM 2196 OD2 ASP B 33 13.828 11.004 17.487 1.00 67.91 O
+ATOM 2197 N MET B 34 8.671 9.451 19.020 1.00 52.93 N
+ATOM 2198 CA MET B 34 7.221 9.637 19.070 1.00 50.32 C
+ATOM 2199 C MET B 34 6.636 9.262 20.413 1.00 50.68 C
+ATOM 2200 O MET B 34 5.726 9.945 20.879 1.00 55.00 O
+ATOM 2201 CB MET B 34 6.461 8.809 18.056 1.00 44.43 C
+ATOM 2202 CG MET B 34 6.756 9.341 16.691 1.00 50.01 C
+ATOM 2203 SD MET B 34 5.799 8.544 15.390 1.00 66.03 S
+ATOM 2204 CE MET B 34 7.099 7.506 14.808 1.00 62.54 C
+ATOM 2205 N LEU B 35 7.104 8.194 21.055 1.00 55.68 N
+ATOM 2206 CA LEU B 35 6.569 7.770 22.340 1.00 52.31 C
+ATOM 2207 C LEU B 35 6.937 8.754 23.435 1.00 47.03 C
+ATOM 2208 O LEU B 35 6.074 9.184 24.198 1.00 44.69 O
+ATOM 2209 CB LEU B 35 7.097 6.375 22.686 1.00 50.83 C
+ATOM 2210 CG LEU B 35 6.388 5.204 22.029 1.00 48.18 C
+ATOM 2211 CD1 LEU B 35 7.211 3.945 22.230 1.00 47.33 C
+ATOM 2212 CD2 LEU B 35 4.986 5.061 22.624 1.00 39.86 C
+ATOM 2213 N ARG B 36 8.198 9.161 23.466 1.00 39.83 N
+ATOM 2214 CA ARG B 36 8.667 10.117 24.416 1.00 39.71 C
+ATOM 2215 C ARG B 36 7.979 11.474 24.392 1.00 43.36 C
+ATOM 2216 O ARG B 36 7.697 12.078 25.452 1.00 42.12 O
+ATOM 2217 CB ARG B 36 10.143 10.267 24.207 1.00 43.10 C
+ATOM 2218 CG ARG B 36 10.814 9.212 25.063 1.00 47.33 C
+ATOM 2219 CD ARG B 36 12.282 9.577 25.135 1.00 52.87 C
+ATOM 2220 NE ARG B 36 12.877 9.364 23.836 1.00 51.47 N
+ATOM 2221 CZ ARG B 36 13.272 8.150 23.436 1.00 61.11 C
+ATOM 2222 NH1 ARG B 36 13.234 7.081 24.267 1.00 56.72 N
+ATOM 2223 NH2 ARG B 36 13.729 8.029 22.179 1.00 58.02 N
+ATOM 2224 N ALA B 37 7.701 11.931 23.172 1.00 38.58 N
+ATOM 2225 CA ALA B 37 6.975 13.176 22.941 1.00 46.05 C
+ATOM 2226 C ALA B 37 5.509 13.082 23.384 1.00 51.87 C
+ATOM 2227 O ALA B 37 5.050 13.907 24.176 1.00 53.11 O
+ATOM 2228 CB ALA B 37 6.990 13.540 21.458 1.00 46.56 C
+ATOM 2229 N ALA B 38 4.775 12.045 22.956 1.00 54.55 N
+ATOM 2230 CA ALA B 38 3.400 11.801 23.354 1.00 47.35 C
+ATOM 2231 C ALA B 38 3.314 11.682 24.854 1.00 41.41 C
+ATOM 2232 O ALA B 38 2.391 12.202 25.447 1.00 44.57 O
+ATOM 2233 CB ALA B 38 2.875 10.516 22.745 1.00 44.78 C
+ATOM 2234 N VAL B 39 4.292 11.129 25.525 1.00 43.63 N
+ATOM 2235 CA VAL B 39 4.238 11.005 26.952 1.00 47.67 C
+ATOM 2236 C VAL B 39 4.357 12.370 27.603 1.00 60.59 C
+ATOM 2237 O VAL B 39 3.553 12.697 28.481 1.00 63.13 O
+ATOM 2238 CB VAL B 39 5.356 10.051 27.348 1.00 46.76 C
+ATOM 2239 CG1 VAL B 39 5.677 10.089 28.836 1.00 47.93 C
+ATOM 2240 CG2 VAL B 39 4.877 8.665 26.992 1.00 41.86 C
+ATOM 2241 N LYS B 40 5.289 13.199 27.126 1.00 66.45 N
+ATOM 2242 CA LYS B 40 5.546 14.510 27.721 1.00 74.18 C
+ATOM 2243 C LYS B 40 4.438 15.511 27.407 1.00 73.08 C
+ATOM 2244 O LYS B 40 3.980 16.237 28.289 1.00 76.24 O
+ATOM 2245 CB LYS B 40 6.898 15.004 27.210 1.00 79.82 C
+ATOM 2246 CG LYS B 40 7.519 16.263 27.791 1.00 79.90 C
+ATOM 2247 CD LYS B 40 8.835 16.514 27.057 1.00 91.47 C
+ATOM 2248 CE LYS B 40 8.650 16.761 25.545 1.00 97.22 C
+ATOM 2249 NZ LYS B 40 9.293 15.742 24.715 1.00 99.33 N
+ATOM 2250 N SER B 41 3.968 15.591 26.168 1.00 69.02 N
+ATOM 2251 CA SER B 41 2.819 16.413 25.859 1.00 70.05 C
+ATOM 2252 C SER B 41 1.571 15.797 26.495 1.00 74.27 C
+ATOM 2253 O SER B 41 0.571 16.489 26.698 1.00 86.86 O
+ATOM 2254 CB SER B 41 2.627 16.523 24.332 1.00 71.22 C
+ATOM 2255 OG SER B 41 2.808 15.317 23.584 1.00 73.63 O
+ATOM 2256 N GLY B 42 1.596 14.512 26.853 1.00 70.13 N
+ATOM 2257 CA GLY B 42 0.438 13.857 27.405 1.00 63.47 C
+ATOM 2258 C GLY B 42 -0.532 13.598 26.266 1.00 59.44 C
+ATOM 2259 O GLY B 42 -1.731 13.779 26.429 1.00 69.31 O
+ATOM 2260 N SER B 43 -0.070 13.240 25.071 1.00 56.71 N
+ATOM 2261 CA SER B 43 -0.939 12.910 23.957 1.00 60.57 C
+ATOM 2262 C SER B 43 -1.754 11.654 24.247 1.00 58.95 C
+ATOM 2263 O SER B 43 -1.260 10.659 24.783 1.00 55.79 O
+ATOM 2264 CB SER B 43 -0.109 12.688 22.705 1.00 67.21 C
+ATOM 2265 OG SER B 43 0.685 13.818 22.337 1.00 76.32 O
+ATOM 2266 N GLU B 44 -3.028 11.687 23.872 1.00 64.11 N
+ATOM 2267 CA GLU B 44 -3.914 10.574 24.145 1.00 66.43 C
+ATOM 2268 C GLU B 44 -3.350 9.314 23.546 1.00 61.02 C
+ATOM 2269 O GLU B 44 -3.311 8.312 24.250 1.00 61.56 O
+ATOM 2270 CB GLU B 44 -5.301 10.879 23.579 1.00 75.35 C
+ATOM 2271 CG GLU B 44 -6.371 9.765 23.612 1.00 82.72 C
+ATOM 2272 CD GLU B 44 -6.927 9.266 24.950 1.00 85.35 C
+ATOM 2273 OE1 GLU B 44 -7.222 10.088 25.819 1.00 89.96 O
+ATOM 2274 OE2 GLU B 44 -7.105 8.050 25.099 1.00 85.12 O
+ATOM 2275 N LEU B 45 -2.848 9.360 22.309 1.00 55.20 N
+ATOM 2276 CA LEU B 45 -2.279 8.167 21.707 1.00 51.44 C
+ATOM 2277 C LEU B 45 -0.802 8.174 22.016 1.00 47.13 C
+ATOM 2278 O LEU B 45 -0.068 8.944 21.391 1.00 53.87 O
+ATOM 2279 CB LEU B 45 -2.454 8.169 20.207 1.00 49.88 C
+ATOM 2280 CG LEU B 45 -1.929 6.973 19.433 1.00 46.27 C
+ATOM 2281 CD1 LEU B 45 -2.779 5.761 19.740 1.00 40.05 C
+ATOM 2282 CD2 LEU B 45 -1.925 7.306 17.946 1.00 41.09 C
+ATOM 2283 N GLY B 46 -0.397 7.440 23.040 1.00 44.11 N
+ATOM 2284 CA GLY B 46 0.994 7.330 23.385 1.00 39.68 C
+ATOM 2285 C GLY B 46 1.269 7.591 24.845 1.00 40.86 C
+ATOM 2286 O GLY B 46 2.190 6.959 25.366 1.00 40.86 O
+ATOM 2287 N LYS B 47 0.516 8.409 25.583 1.00 42.99 N
+ATOM 2288 CA LYS B 47 0.896 8.739 26.955 1.00 51.12 C
+ATOM 2289 C LYS B 47 0.986 7.551 27.909 1.00 55.14 C
+ATOM 2290 O LYS B 47 1.601 7.636 28.977 1.00 60.46 O
+ATOM 2291 CB LYS B 47 -0.083 9.749 27.598 1.00 61.32 C
+ATOM 2292 CG LYS B 47 -1.349 9.152 28.257 1.00 65.74 C
+ATOM 2293 CD LYS B 47 -2.120 10.148 29.094 1.00 62.73 C
+ATOM 2294 CE LYS B 47 -3.090 10.878 28.186 1.00 67.14 C
+ATOM 2295 NZ LYS B 47 -4.131 9.974 27.738 1.00 72.35 N
+ATOM 2296 N GLN B 48 0.329 6.442 27.545 1.00 55.99 N
+ATOM 2297 CA GLN B 48 0.249 5.192 28.309 1.00 52.09 C
+ATOM 2298 C GLN B 48 1.612 4.507 28.445 1.00 50.39 C
+ATOM 2299 O GLN B 48 1.938 3.797 29.409 1.00 50.13 O
+ATOM 2300 CB GLN B 48 -0.726 4.229 27.614 1.00 53.90 C
+ATOM 2301 CG GLN B 48 -2.144 4.711 27.249 1.00 54.06 C
+ATOM 2302 CD GLN B 48 -2.333 5.574 25.995 1.00 56.42 C
+ATOM 2303 OE1 GLN B 48 -1.390 5.994 25.310 1.00 52.39 O
+ATOM 2304 NE2 GLN B 48 -3.569 5.901 25.655 1.00 50.42 N
+ATOM 2305 N ALA B 49 2.453 4.788 27.452 1.00 53.61 N
+ATOM 2306 CA ALA B 49 3.783 4.237 27.335 1.00 52.41 C
+ATOM 2307 C ALA B 49 4.777 4.553 28.453 1.00 48.13 C
+ATOM 2308 O ALA B 49 5.685 3.765 28.719 1.00 54.18 O
+ATOM 2309 CB ALA B 49 4.312 4.711 26.016 1.00 41.39 C
+ATOM 2310 N LYS B 50 4.582 5.631 29.194 1.00 52.36 N
+ATOM 2311 CA LYS B 50 5.489 6.087 30.234 1.00 59.68 C
+ATOM 2312 C LYS B 50 6.086 5.036 31.138 1.00 60.83 C
+ATOM 2313 O LYS B 50 7.301 4.954 31.288 1.00 70.28 O
+ATOM 2314 CB LYS B 50 4.783 7.096 31.108 1.00 66.94 C
+ATOM 2315 CG LYS B 50 5.626 7.789 32.161 1.00 74.82 C
+ATOM 2316 CD LYS B 50 4.632 8.683 32.840 1.00 83.47 C
+ATOM 2317 CE LYS B 50 5.178 9.299 34.103 1.00 92.84 C
+ATOM 2318 NZ LYS B 50 4.081 9.929 34.828 1.00103.03 N
+ATOM 2319 N ASP B 51 5.260 4.164 31.669 1.00 59.52 N
+ATOM 2320 CA ASP B 51 5.736 3.198 32.630 1.00 61.64 C
+ATOM 2321 C ASP B 51 6.553 2.095 32.011 1.00 57.62 C
+ATOM 2322 O ASP B 51 7.607 1.717 32.519 1.00 57.42 O
+ATOM 2323 CB ASP B 51 4.541 2.635 33.335 1.00 74.95 C
+ATOM 2324 CG ASP B 51 3.647 3.750 33.845 1.00 86.22 C
+ATOM 2325 OD1 ASP B 51 4.113 4.530 34.688 1.00 88.32 O
+ATOM 2326 OD2 ASP B 51 2.511 3.838 33.359 1.00 91.88 O
+ATOM 2327 N ILE B 52 6.092 1.683 30.844 1.00 57.61 N
+ATOM 2328 CA ILE B 52 6.692 0.600 30.082 1.00 58.79 C
+ATOM 2329 C ILE B 52 8.089 1.046 29.623 1.00 50.34 C
+ATOM 2330 O ILE B 52 9.080 0.350 29.847 1.00 48.35 O
+ATOM 2331 CB ILE B 52 5.754 0.262 28.869 1.00 58.30 C
+ATOM 2332 CG1 ILE B 52 4.294 -0.025 29.286 1.00 61.62 C
+ATOM 2333 CG2 ILE B 52 6.323 -0.968 28.208 1.00 49.09 C
+ATOM 2334 CD1 ILE B 52 3.223 -0.134 28.157 1.00 61.15 C
+ATOM 2335 N MET B 53 8.216 2.245 29.064 1.00 45.18 N
+ATOM 2336 CA MET B 53 9.509 2.727 28.650 1.00 46.88 C
+ATOM 2337 C MET B 53 10.389 2.778 29.871 1.00 55.17 C
+ATOM 2338 O MET B 53 11.467 2.196 29.842 1.00 63.31 O
+ATOM 2339 CB MET B 53 9.432 4.104 28.065 1.00 40.49 C
+ATOM 2340 CG MET B 53 8.669 4.061 26.775 1.00 44.19 C
+ATOM 2341 SD MET B 53 8.836 5.554 25.762 1.00 59.80 S
+ATOM 2342 CE MET B 53 8.063 6.762 26.802 1.00 57.81 C
+ATOM 2343 N ASP B 54 9.915 3.315 30.994 1.00 61.18 N
+ATOM 2344 CA ASP B 54 10.705 3.391 32.218 1.00 69.24 C
+ATOM 2345 C ASP B 54 11.149 2.033 32.755 1.00 68.36 C
+ATOM 2346 O ASP B 54 12.149 1.951 33.468 1.00 63.31 O
+ATOM 2347 CB ASP B 54 9.923 4.099 33.359 1.00 86.87 C
+ATOM 2348 CG ASP B 54 9.581 5.599 33.232 1.00 99.69 C
+ATOM 2349 OD1 ASP B 54 9.976 6.243 32.249 1.00 98.19 O
+ATOM 2350 OD2 ASP B 54 8.904 6.122 34.135 1.00104.85 O
+ATOM 2351 N ALA B 55 10.424 0.945 32.456 1.00 67.00 N
+ATOM 2352 CA ALA B 55 10.773 -0.390 32.953 1.00 61.13 C
+ATOM 2353 C ALA B 55 11.801 -1.140 32.117 1.00 55.99 C
+ATOM 2354 O ALA B 55 12.313 -2.195 32.516 1.00 45.73 O
+ATOM 2355 CB ALA B 55 9.520 -1.262 33.034 1.00 58.56 C
+ATOM 2356 N GLY B 56 12.033 -0.566 30.923 1.00 53.86 N
+ATOM 2357 CA GLY B 56 12.958 -1.089 29.927 1.00 47.14 C
+ATOM 2358 C GLY B 56 12.318 -2.202 29.137 1.00 39.31 C
+ATOM 2359 O GLY B 56 12.985 -3.089 28.638 1.00 37.04 O
+ATOM 2360 N LYS B 57 11.002 -2.152 29.032 1.00 49.01 N
+ATOM 2361 CA LYS B 57 10.224 -3.170 28.370 1.00 49.99 C
+ATOM 2362 C LYS B 57 9.640 -2.444 27.192 1.00 48.14 C
+ATOM 2363 O LYS B 57 9.420 -1.227 27.247 1.00 46.86 O
+ATOM 2364 CB LYS B 57 9.088 -3.641 29.225 1.00 57.87 C
+ATOM 2365 CG LYS B 57 9.416 -4.276 30.563 1.00 72.30 C
+ATOM 2366 CD LYS B 57 8.061 -4.546 31.235 1.00 90.69 C
+ATOM 2367 CE LYS B 57 8.138 -5.684 32.268 1.00104.95 C
+ATOM 2368 NZ LYS B 57 6.831 -6.094 32.775 1.00109.66 N
+ATOM 2369 N LEU B 58 9.365 -3.223 26.158 1.00 49.74 N
+ATOM 2370 CA LEU B 58 8.770 -2.710 24.929 1.00 47.55 C
+ATOM 2371 C LEU B 58 7.281 -2.432 25.132 1.00 47.77 C
+ATOM 2372 O LEU B 58 6.558 -3.036 25.947 1.00 46.23 O
+ATOM 2373 CB LEU B 58 8.884 -3.712 23.801 1.00 42.98 C
+ATOM 2374 CG LEU B 58 10.140 -4.492 23.547 1.00 40.31 C
+ATOM 2375 CD1 LEU B 58 9.792 -5.698 22.701 1.00 39.11 C
+ATOM 2376 CD2 LEU B 58 11.170 -3.594 22.932 1.00 45.38 C
+ATOM 2377 N VAL B 59 6.813 -1.491 24.345 1.00 41.05 N
+ATOM 2378 CA VAL B 59 5.426 -1.105 24.382 1.00 41.20 C
+ATOM 2379 C VAL B 59 4.610 -2.098 23.555 1.00 46.30 C
+ATOM 2380 O VAL B 59 5.188 -2.787 22.697 1.00 47.85 O
+ATOM 2381 CB VAL B 59 5.419 0.333 23.862 1.00 39.36 C
+ATOM 2382 CG1 VAL B 59 4.086 0.900 23.403 1.00 39.48 C
+ATOM 2383 CG2 VAL B 59 5.898 1.110 25.053 1.00 35.45 C
+ATOM 2384 N THR B 60 3.276 -2.161 23.760 1.00 40.63 N
+ATOM 2385 CA THR B 60 2.428 -3.065 23.022 1.00 41.19 C
+ATOM 2386 C THR B 60 2.498 -2.787 21.527 1.00 40.58 C
+ATOM 2387 O THR B 60 2.586 -1.653 21.042 1.00 48.43 O
+ATOM 2388 CB THR B 60 0.940 -2.955 23.496 1.00 49.53 C
+ATOM 2389 OG1 THR B 60 0.443 -1.640 23.240 1.00 50.99 O
+ATOM 2390 CG2 THR B 60 0.829 -3.289 24.961 1.00 48.56 C
+ATOM 2391 N ASP B 61 2.416 -3.852 20.770 1.00 35.24 N
+ATOM 2392 CA ASP B 61 2.464 -3.706 19.347 1.00 40.31 C
+ATOM 2393 C ASP B 61 1.340 -2.865 18.766 1.00 37.61 C
+ATOM 2394 O ASP B 61 1.680 -1.998 17.962 1.00 37.50 O
+ATOM 2395 CB ASP B 61 2.466 -5.089 18.713 1.00 44.33 C
+ATOM 2396 CG ASP B 61 3.722 -5.934 18.938 1.00 51.23 C
+ATOM 2397 OD1 ASP B 61 4.842 -5.458 18.798 1.00 45.62 O
+ATOM 2398 OD2 ASP B 61 3.571 -7.099 19.262 1.00 55.61 O
+ATOM 2399 N GLU B 62 0.054 -3.007 19.131 1.00 39.71 N
+ATOM 2400 CA GLU B 62 -0.980 -2.262 18.431 1.00 36.29 C
+ATOM 2401 C GLU B 62 -0.812 -0.781 18.674 1.00 40.52 C
+ATOM 2402 O GLU B 62 -0.981 -0.001 17.725 1.00 40.20 O
+ATOM 2403 CB GLU B 62 -2.398 -2.652 18.856 1.00 34.65 C
+ATOM 2404 CG GLU B 62 -2.906 -2.294 20.251 1.00 42.68 C
+ATOM 2405 CD GLU B 62 -4.401 -2.550 20.536 1.00 48.62 C
+ATOM 2406 OE1 GLU B 62 -5.277 -2.371 19.675 1.00 46.42 O
+ATOM 2407 OE2 GLU B 62 -4.698 -2.909 21.669 1.00 43.96 O
+ATOM 2408 N LEU B 63 -0.379 -0.403 19.890 1.00 34.62 N
+ATOM 2409 CA LEU B 63 -0.167 1.001 20.252 1.00 38.93 C
+ATOM 2410 C LEU B 63 0.882 1.632 19.355 1.00 44.33 C
+ATOM 2411 O LEU B 63 0.627 2.675 18.728 1.00 43.64 O
+ATOM 2412 CB LEU B 63 0.252 1.089 21.740 1.00 39.23 C
+ATOM 2413 CG LEU B 63 0.344 2.398 22.544 1.00 44.47 C
+ATOM 2414 CD1 LEU B 63 -0.817 3.360 22.227 1.00 44.57 C
+ATOM 2415 CD2 LEU B 63 0.329 2.022 24.022 1.00 42.25 C
+ATOM 2416 N VAL B 64 2.023 0.949 19.202 1.00 42.68 N
+ATOM 2417 CA VAL B 64 3.083 1.437 18.332 1.00 45.33 C
+ATOM 2418 C VAL B 64 2.649 1.396 16.859 1.00 50.45 C
+ATOM 2419 O VAL B 64 2.973 2.312 16.079 1.00 54.92 O
+ATOM 2420 CB VAL B 64 4.359 0.583 18.528 1.00 47.26 C
+ATOM 2421 CG1 VAL B 64 5.473 1.079 17.666 1.00 45.27 C
+ATOM 2422 CG2 VAL B 64 4.894 0.763 19.910 1.00 44.50 C
+ATOM 2423 N ILE B 65 1.881 0.382 16.430 1.00 47.87 N
+ATOM 2424 CA ILE B 65 1.493 0.261 15.027 1.00 43.32 C
+ATOM 2425 C ILE B 65 0.553 1.381 14.622 1.00 44.40 C
+ATOM 2426 O ILE B 65 0.658 1.929 13.521 1.00 47.81 O
+ATOM 2427 CB ILE B 65 0.871 -1.127 14.814 1.00 35.45 C
+ATOM 2428 CG1 ILE B 65 2.025 -2.107 14.691 1.00 40.80 C
+ATOM 2429 CG2 ILE B 65 0.009 -1.191 13.583 1.00 42.11 C
+ATOM 2430 CD1 ILE B 65 1.611 -3.587 14.634 1.00 36.21 C
+ATOM 2431 N ALA B 66 -0.334 1.772 15.519 1.00 42.96 N
+ATOM 2432 CA ALA B 66 -1.205 2.906 15.276 1.00 43.18 C
+ATOM 2433 C ALA B 66 -0.348 4.153 15.135 1.00 45.50 C
+ATOM 2434 O ALA B 66 -0.538 4.883 14.161 1.00 47.47 O
+ATOM 2435 CB ALA B 66 -2.155 3.117 16.436 1.00 38.56 C
+ATOM 2436 N LEU B 67 0.631 4.370 16.040 1.00 45.88 N
+ATOM 2437 CA LEU B 67 1.480 5.552 16.017 1.00 40.88 C
+ATOM 2438 C LEU B 67 2.198 5.689 14.711 1.00 42.91 C
+ATOM 2439 O LEU B 67 2.193 6.771 14.123 1.00 50.28 O
+ATOM 2440 CB LEU B 67 2.538 5.540 17.131 1.00 47.28 C
+ATOM 2441 CG LEU B 67 2.243 6.252 18.471 1.00 43.39 C
+ATOM 2442 CD1 LEU B 67 3.540 6.387 19.240 1.00 42.26 C
+ATOM 2443 CD2 LEU B 67 1.732 7.674 18.263 1.00 37.14 C
+ATOM 2444 N VAL B 68 2.724 4.565 14.231 1.00 46.93 N
+ATOM 2445 CA VAL B 68 3.397 4.540 12.946 1.00 47.81 C
+ATOM 2446 C VAL B 68 2.403 4.764 11.833 1.00 48.25 C
+ATOM 2447 O VAL B 68 2.696 5.626 11.010 1.00 58.34 O
+ATOM 2448 CB VAL B 68 4.140 3.197 12.725 1.00 43.84 C
+ATOM 2449 CG1 VAL B 68 4.774 3.092 11.339 1.00 38.12 C
+ATOM 2450 CG2 VAL B 68 5.274 3.135 13.726 1.00 41.82 C
+ATOM 2451 N LYS B 69 1.230 4.119 11.778 1.00 52.29 N
+ATOM 2452 CA LYS B 69 0.274 4.312 10.686 1.00 55.24 C
+ATOM 2453 C LYS B 69 -0.219 5.748 10.539 1.00 52.30 C
+ATOM 2454 O LYS B 69 -0.409 6.260 9.427 1.00 59.99 O
+ATOM 2455 CB LYS B 69 -0.915 3.383 10.880 1.00 55.72 C
+ATOM 2456 CG LYS B 69 -0.573 1.977 10.417 1.00 65.34 C
+ATOM 2457 CD LYS B 69 -1.631 0.969 10.859 1.00 67.77 C
+ATOM 2458 CE LYS B 69 -1.179 -0.415 10.424 1.00 69.72 C
+ATOM 2459 NZ LYS B 69 -2.032 -1.424 11.012 1.00 69.22 N
+ATOM 2460 N GLU B 70 -0.361 6.430 11.662 1.00 46.34 N
+ATOM 2461 CA GLU B 70 -0.744 7.814 11.654 1.00 49.90 C
+ATOM 2462 C GLU B 70 0.393 8.510 10.946 1.00 54.20 C
+ATOM 2463 O GLU B 70 0.194 8.940 9.819 1.00 55.85 O
+ATOM 2464 CB GLU B 70 -0.877 8.402 13.071 1.00 60.24 C
+ATOM 2465 CG GLU B 70 -1.886 7.798 14.038 1.00 69.87 C
+ATOM 2466 CD GLU B 70 -3.344 7.828 13.579 1.00 80.64 C
+ATOM 2467 OE1 GLU B 70 -3.979 8.887 13.710 1.00 81.32 O
+ATOM 2468 OE2 GLU B 70 -3.835 6.783 13.116 1.00 84.33 O
+ATOM 2469 N ARG B 71 1.610 8.498 11.506 1.00 59.89 N
+ATOM 2470 CA ARG B 71 2.741 9.226 10.944 1.00 61.90 C
+ATOM 2471 C ARG B 71 2.938 9.030 9.448 1.00 63.69 C
+ATOM 2472 O ARG B 71 3.167 10.007 8.747 1.00 64.67 O
+ATOM 2473 CB ARG B 71 4.030 8.824 11.654 1.00 60.93 C
+ATOM 2474 CG ARG B 71 5.246 9.639 11.205 1.00 64.59 C
+ATOM 2475 CD ARG B 71 5.084 11.108 11.608 1.00 68.28 C
+ATOM 2476 NE ARG B 71 6.132 11.968 11.080 1.00 73.43 N
+ATOM 2477 CZ ARG B 71 6.120 12.405 9.814 1.00 71.37 C
+ATOM 2478 NH1 ARG B 71 5.166 12.031 8.972 1.00 67.91 N
+ATOM 2479 NH2 ARG B 71 7.082 13.218 9.381 1.00 68.81 N
+ATOM 2480 N ILE B 72 2.769 7.813 8.945 1.00 67.64 N
+ATOM 2481 CA ILE B 72 2.974 7.510 7.546 1.00 75.41 C
+ATOM 2482 C ILE B 72 1.957 8.186 6.652 1.00 81.21 C
+ATOM 2483 O ILE B 72 2.263 8.508 5.495 1.00 86.53 O
+ATOM 2484 CB ILE B 72 2.968 5.962 7.404 1.00 78.00 C
+ATOM 2485 CG1 ILE B 72 4.304 5.477 7.952 1.00 81.03 C
+ATOM 2486 CG2 ILE B 72 2.813 5.482 5.964 1.00 83.22 C
+ATOM 2487 CD1 ILE B 72 4.571 3.975 7.791 1.00 84.61 C
+ATOM 2488 N ALA B 73 0.741 8.430 7.128 1.00 86.64 N
+ATOM 2489 CA ALA B 73 -0.224 9.153 6.314 1.00 94.44 C
+ATOM 2490 C ALA B 73 0.275 10.549 5.889 1.00 99.43 C
+ATOM 2491 O ALA B 73 -0.004 10.996 4.761 1.00100.06 O
+ATOM 2492 CB ALA B 73 -1.515 9.314 7.091 1.00 94.36 C
+ATOM 2493 N GLN B 74 1.085 11.194 6.753 1.00100.49 N
+ATOM 2494 CA GLN B 74 1.632 12.531 6.561 1.00 97.33 C
+ATOM 2495 C GLN B 74 2.406 12.700 5.272 1.00 98.96 C
+ATOM 2496 O GLN B 74 3.483 12.122 5.105 1.00 91.79 O
+ATOM 2497 CB GLN B 74 2.573 12.906 7.674 1.00 98.54 C
+ATOM 2498 CG GLN B 74 2.035 13.685 8.854 1.00104.81 C
+ATOM 2499 CD GLN B 74 1.076 12.930 9.751 1.00108.40 C
+ATOM 2500 OE1 GLN B 74 -0.080 12.694 9.407 1.00110.41 O
+ATOM 2501 NE2 GLN B 74 1.513 12.547 10.942 1.00107.95 N
+ATOM 2502 N GLU B 75 1.857 13.593 4.428 1.00103.66 N
+ATOM 2503 CA GLU B 75 2.316 13.888 3.064 1.00102.68 C
+ATOM 2504 C GLU B 75 3.815 13.877 2.779 1.00102.58 C
+ATOM 2505 O GLU B 75 4.265 13.478 1.697 1.00105.22 O
+ATOM 2506 CB GLU B 75 1.796 15.253 2.598 1.00 97.90 C
+ATOM 2507 CG GLU B 75 1.590 15.166 1.080 1.00 92.22 C
+ATOM 2508 CD GLU B 75 1.966 16.317 0.151 1.00 88.06 C
+ATOM 2509 OE1 GLU B 75 1.986 17.495 0.533 1.00 83.87 O
+ATOM 2510 OE2 GLU B 75 2.219 15.994 -1.007 1.00 82.49 O
+ATOM 2511 N ASP B 76 4.619 14.367 3.713 1.00102.35 N
+ATOM 2512 CA ASP B 76 6.069 14.325 3.608 1.00102.20 C
+ATOM 2513 C ASP B 76 6.611 12.948 3.165 1.00105.04 C
+ATOM 2514 O ASP B 76 7.319 12.811 2.148 1.00107.55 O
+ATOM 2515 CB ASP B 76 6.635 14.769 4.995 1.00 98.39 C
+ATOM 2516 CG ASP B 76 6.000 14.159 6.257 1.00 90.97 C
+ATOM 2517 OD1 ASP B 76 6.331 13.036 6.608 1.00 81.22 O
+ATOM 2518 OD2 ASP B 76 5.177 14.804 6.899 1.00 93.21 O
+ATOM 2519 N CYS B 77 6.102 11.912 3.853 1.00103.03 N
+ATOM 2520 CA CYS B 77 6.504 10.515 3.695 1.00 96.29 C
+ATOM 2521 C CYS B 77 6.252 9.939 2.323 1.00 94.12 C
+ATOM 2522 O CYS B 77 6.795 8.873 2.025 1.00 90.44 O
+ATOM 2523 CB CYS B 77 5.769 9.601 4.668 1.00 91.91 C
+ATOM 2524 SG CYS B 77 5.734 10.200 6.370 1.00 99.64 S
+ATOM 2525 N ARG B 78 5.488 10.627 1.453 1.00 95.44 N
+ATOM 2526 CA ARG B 78 5.130 10.084 0.154 1.00 94.64 C
+ATOM 2527 C ARG B 78 6.365 9.702 -0.635 1.00 92.25 C
+ATOM 2528 O ARG B 78 6.292 8.810 -1.477 1.00 96.97 O
+ATOM 2529 CB ARG B 78 4.298 11.085 -0.660 1.00 97.27 C
+ATOM 2530 CG ARG B 78 5.035 12.328 -1.138 1.00102.42 C
+ATOM 2531 CD ARG B 78 4.185 13.041 -2.177 1.00108.33 C
+ATOM 2532 NE ARG B 78 4.955 14.053 -2.895 1.00114.76 N
+ATOM 2533 CZ ARG B 78 4.419 14.868 -3.824 1.00118.63 C
+ATOM 2534 NH1 ARG B 78 3.116 14.827 -4.134 1.00122.84 N
+ATOM 2535 NH2 ARG B 78 5.197 15.760 -4.448 1.00117.49 N
+ATOM 2536 N ASN B 79 7.530 10.285 -0.343 1.00 92.94 N
+ATOM 2537 CA ASN B 79 8.736 9.884 -1.063 1.00 95.50 C
+ATOM 2538 C ASN B 79 9.784 9.053 -0.323 1.00 87.58 C
+ATOM 2539 O ASN B 79 10.985 8.945 -0.651 1.00 79.29 O
+ATOM 2540 CB ASN B 79 9.353 11.143 -1.637 1.00104.04 C
+ATOM 2541 CG ASN B 79 8.667 11.358 -2.977 1.00111.35 C
+ATOM 2542 OD1 ASN B 79 8.837 10.570 -3.905 1.00112.22 O
+ATOM 2543 ND2 ASN B 79 7.827 12.376 -3.147 1.00117.21 N
+ATOM 2544 N GLY B 80 9.251 8.280 0.608 1.00 81.39 N
+ATOM 2545 CA GLY B 80 10.068 7.470 1.453 1.00 68.75 C
+ATOM 2546 C GLY B 80 10.187 8.180 2.776 1.00 66.46 C
+ATOM 2547 O GLY B 80 9.901 9.373 2.958 1.00 61.55 O
+ATOM 2548 N PHE B 81 10.719 7.328 3.636 1.00 61.53 N
+ATOM 2549 CA PHE B 81 10.833 7.550 5.056 1.00 52.83 C
+ATOM 2550 C PHE B 81 11.969 6.653 5.523 1.00 49.29 C
+ATOM 2551 O PHE B 81 12.493 5.775 4.826 1.00 47.07 O
+ATOM 2552 CB PHE B 81 9.539 7.153 5.746 1.00 48.35 C
+ATOM 2553 CG PHE B 81 9.045 5.786 5.292 1.00 56.97 C
+ATOM 2554 CD1 PHE B 81 8.279 5.682 4.145 1.00 59.24 C
+ATOM 2555 CD2 PHE B 81 9.384 4.641 5.984 1.00 59.56 C
+ATOM 2556 CE1 PHE B 81 7.857 4.453 3.685 1.00 63.76 C
+ATOM 2557 CE2 PHE B 81 8.957 3.412 5.518 1.00 62.40 C
+ATOM 2558 CZ PHE B 81 8.199 3.315 4.372 1.00 63.43 C
+ATOM 2559 N LEU B 82 12.312 6.876 6.760 1.00 51.62 N
+ATOM 2560 CA LEU B 82 13.355 6.159 7.442 1.00 50.07 C
+ATOM 2561 C LEU B 82 12.555 5.719 8.633 1.00 46.15 C
+ATOM 2562 O LEU B 82 11.788 6.504 9.200 1.00 48.31 O
+ATOM 2563 CB LEU B 82 14.439 7.148 7.791 1.00 53.03 C
+ATOM 2564 CG LEU B 82 15.647 6.746 8.563 1.00 51.14 C
+ATOM 2565 CD1 LEU B 82 16.451 5.698 7.822 1.00 50.92 C
+ATOM 2566 CD2 LEU B 82 16.485 7.985 8.743 1.00 52.17 C
+ATOM 2567 N LEU B 83 12.681 4.457 8.964 1.00 44.27 N
+ATOM 2568 CA LEU B 83 11.948 3.880 10.053 1.00 45.32 C
+ATOM 2569 C LEU B 83 13.062 3.526 11.000 1.00 44.06 C
+ATOM 2570 O LEU B 83 14.007 2.831 10.612 1.00 46.14 O
+ATOM 2571 CB LEU B 83 11.184 2.659 9.556 1.00 45.72 C
+ATOM 2572 CG LEU B 83 9.743 2.935 9.132 1.00 44.21 C
+ATOM 2573 CD1 LEU B 83 9.077 1.657 8.722 1.00 48.57 C
+ATOM 2574 CD2 LEU B 83 8.918 3.419 10.298 1.00 45.02 C
+ATOM 2575 N ASP B 84 12.970 4.035 12.218 1.00 38.59 N
+ATOM 2576 CA ASP B 84 14.011 3.954 13.209 1.00 39.92 C
+ATOM 2577 C ASP B 84 13.350 3.462 14.465 1.00 46.79 C
+ATOM 2578 O ASP B 84 12.627 4.208 15.132 1.00 44.69 O
+ATOM 2579 CB ASP B 84 14.591 5.354 13.432 1.00 43.74 C
+ATOM 2580 CG ASP B 84 15.772 5.476 14.380 1.00 46.25 C
+ATOM 2581 OD1 ASP B 84 16.560 4.538 14.440 1.00 49.47 O
+ATOM 2582 OD2 ASP B 84 15.905 6.514 15.041 1.00 47.22 O
+ATOM 2583 N GLY B 85 13.579 2.204 14.796 1.00 52.75 N
+ATOM 2584 CA GLY B 85 12.986 1.631 15.992 1.00 53.50 C
+ATOM 2585 C GLY B 85 11.720 0.821 15.721 1.00 50.37 C
+ATOM 2586 O GLY B 85 11.130 0.257 16.651 1.00 56.20 O
+ATOM 2587 N PHE B 86 11.249 0.732 14.486 1.00 37.31 N
+ATOM 2588 CA PHE B 86 10.080 -0.063 14.184 1.00 42.89 C
+ATOM 2589 C PHE B 86 10.480 -0.682 12.861 1.00 41.02 C
+ATOM 2590 O PHE B 86 11.115 0.017 12.061 1.00 41.57 O
+ATOM 2591 CB PHE B 86 8.800 0.806 14.011 1.00 41.29 C
+ATOM 2592 CG PHE B 86 7.480 0.079 13.638 1.00 41.56 C
+ATOM 2593 CD1 PHE B 86 7.161 -0.218 12.328 1.00 40.40 C
+ATOM 2594 CD2 PHE B 86 6.551 -0.266 14.595 1.00 43.57 C
+ATOM 2595 CE1 PHE B 86 5.960 -0.825 12.009 1.00 41.71 C
+ATOM 2596 CE2 PHE B 86 5.351 -0.873 14.264 1.00 41.64 C
+ATOM 2597 CZ PHE B 86 5.049 -1.157 12.965 1.00 38.23 C
+ATOM 2598 N PRO B 87 10.152 -1.940 12.545 1.00 37.40 N
+ATOM 2599 CA PRO B 87 9.584 -2.868 13.486 1.00 38.27 C
+ATOM 2600 C PRO B 87 10.624 -3.366 14.488 1.00 44.11 C
+ATOM 2601 O PRO B 87 11.818 -3.504 14.206 1.00 42.51 O
+ATOM 2602 CB PRO B 87 8.986 -3.921 12.606 1.00 34.37 C
+ATOM 2603 CG PRO B 87 9.854 -3.907 11.376 1.00 38.06 C
+ATOM 2604 CD PRO B 87 10.129 -2.446 11.184 1.00 34.72 C
+ATOM 2605 N ARG B 88 10.094 -3.503 15.698 1.00 38.39 N
+ATOM 2606 CA ARG B 88 10.800 -3.986 16.884 1.00 43.83 C
+ATOM 2607 C ARG B 88 10.410 -5.434 17.227 1.00 47.78 C
+ATOM 2608 O ARG B 88 11.021 -6.026 18.130 1.00 46.59 O
+ATOM 2609 CB ARG B 88 10.441 -3.098 18.067 1.00 43.75 C
+ATOM 2610 CG ARG B 88 11.463 -2.941 19.138 1.00 38.76 C
+ATOM 2611 CD ARG B 88 12.614 -2.060 18.703 1.00 41.21 C
+ATOM 2612 NE ARG B 88 13.239 -1.644 19.945 1.00 47.62 N
+ATOM 2613 CZ ARG B 88 13.296 -0.370 20.370 1.00 49.01 C
+ATOM 2614 NH1 ARG B 88 12.849 0.642 19.630 1.00 43.44 N
+ATOM 2615 NH2 ARG B 88 13.841 -0.111 21.570 1.00 51.64 N
+ATOM 2616 N THR B 89 9.318 -5.984 16.639 1.00 48.49 N
+ATOM 2617 CA THR B 89 8.893 -7.377 16.798 1.00 37.55 C
+ATOM 2618 C THR B 89 8.407 -7.917 15.421 1.00 39.80 C
+ATOM 2619 O THR B 89 8.100 -7.202 14.441 1.00 36.56 O
+ATOM 2620 CB THR B 89 7.738 -7.516 17.885 1.00 36.58 C
+ATOM 2621 OG1 THR B 89 6.574 -6.891 17.319 1.00 36.55 O
+ATOM 2622 CG2 THR B 89 8.067 -6.865 19.259 1.00 28.52 C
+ATOM 2623 N ILE B 90 8.352 -9.248 15.336 1.00 46.49 N
+ATOM 2624 CA ILE B 90 7.803 -10.005 14.204 1.00 45.33 C
+ATOM 2625 C ILE B 90 6.344 -9.527 13.953 1.00 44.83 C
+ATOM 2626 O ILE B 90 6.021 -9.250 12.794 1.00 38.90 O
+ATOM 2627 CB ILE B 90 7.898 -11.567 14.583 1.00 49.03 C
+ATOM 2628 CG1 ILE B 90 9.359 -12.029 14.754 1.00 50.13 C
+ATOM 2629 CG2 ILE B 90 7.179 -12.403 13.523 1.00 48.83 C
+ATOM 2630 CD1 ILE B 90 10.124 -12.434 13.471 1.00 57.73 C
+ATOM 2631 N PRO B 91 5.406 -9.382 14.922 1.00 39.19 N
+ATOM 2632 CA PRO B 91 4.084 -8.813 14.682 1.00 40.59 C
+ATOM 2633 C PRO B 91 4.147 -7.490 13.901 1.00 45.57 C
+ATOM 2634 O PRO B 91 3.482 -7.324 12.869 1.00 39.53 O
+ATOM 2635 CB PRO B 91 3.525 -8.681 16.083 1.00 40.09 C
+ATOM 2636 CG PRO B 91 4.114 -9.839 16.882 1.00 36.32 C
+ATOM 2637 CD PRO B 91 5.512 -9.832 16.325 1.00 35.44 C
+ATOM 2638 N GLN B 92 5.016 -6.575 14.362 1.00 42.20 N
+ATOM 2639 CA GLN B 92 5.130 -5.250 13.791 1.00 38.30 C
+ATOM 2640 C GLN B 92 5.677 -5.292 12.386 1.00 38.16 C
+ATOM 2641 O GLN B 92 5.292 -4.478 11.543 1.00 36.19 O
+ATOM 2642 CB GLN B 92 6.016 -4.388 14.686 1.00 39.89 C
+ATOM 2643 CG GLN B 92 5.447 -3.995 16.061 1.00 34.24 C
+ATOM 2644 CD GLN B 92 6.437 -3.247 16.944 1.00 39.00 C
+ATOM 2645 OE1 GLN B 92 7.404 -2.698 16.430 1.00 40.67 O
+ATOM 2646 NE2 GLN B 92 6.363 -3.131 18.261 1.00 42.39 N
+ATOM 2647 N ALA B 93 6.562 -6.247 12.113 1.00 37.34 N
+ATOM 2648 CA ALA B 93 7.076 -6.402 10.769 1.00 42.76 C
+ATOM 2649 C ALA B 93 5.974 -6.950 9.897 1.00 41.20 C
+ATOM 2650 O ALA B 93 5.808 -6.504 8.773 1.00 47.95 O
+ATOM 2651 CB ALA B 93 8.229 -7.372 10.723 1.00 40.16 C
+ATOM 2652 N ASP B 94 5.168 -7.864 10.421 1.00 44.46 N
+ATOM 2653 CA ASP B 94 4.066 -8.436 9.691 1.00 50.15 C
+ATOM 2654 C ASP B 94 3.023 -7.418 9.348 1.00 52.80 C
+ATOM 2655 O ASP B 94 2.535 -7.409 8.215 1.00 56.26 O
+ATOM 2656 CB ASP B 94 3.400 -9.528 10.487 1.00 57.90 C
+ATOM 2657 CG ASP B 94 4.127 -10.865 10.392 1.00 65.10 C
+ATOM 2658 OD1 ASP B 94 4.729 -11.152 9.351 1.00 59.94 O
+ATOM 2659 OD2 ASP B 94 4.062 -11.630 11.362 1.00 71.87 O
+ATOM 2660 N ALA B 95 2.721 -6.549 10.310 1.00 49.12 N
+ATOM 2661 CA ALA B 95 1.768 -5.465 10.117 1.00 50.67 C
+ATOM 2662 C ALA B 95 2.197 -4.560 8.970 1.00 52.59 C
+ATOM 2663 O ALA B 95 1.348 -4.042 8.239 1.00 64.78 O
+ATOM 2664 CB ALA B 95 1.659 -4.606 11.347 1.00 39.10 C
+ATOM 2665 N MET B 96 3.495 -4.367 8.750 1.00 50.67 N
+ATOM 2666 CA MET B 96 3.926 -3.591 7.615 1.00 54.45 C
+ATOM 2667 C MET B 96 3.616 -4.384 6.362 1.00 57.08 C
+ATOM 2668 O MET B 96 3.193 -3.771 5.386 1.00 52.44 O
+ATOM 2669 CB MET B 96 5.410 -3.331 7.608 1.00 55.67 C
+ATOM 2670 CG MET B 96 5.979 -2.390 8.640 1.00 56.88 C
+ATOM 2671 SD MET B 96 7.776 -2.407 8.402 1.00 60.26 S
+ATOM 2672 CE MET B 96 8.009 -1.756 6.771 1.00 57.70 C
+ATOM 2673 N LYS B 97 3.768 -5.718 6.368 1.00 63.90 N
+ATOM 2674 CA LYS B 97 3.507 -6.545 5.186 1.00 80.27 C
+ATOM 2675 C LYS B 97 2.079 -6.452 4.649 1.00 89.81 C
+ATOM 2676 O LYS B 97 1.875 -6.282 3.438 1.00 93.22 O
+ATOM 2677 CB LYS B 97 3.731 -8.023 5.429 1.00 77.42 C
+ATOM 2678 CG LYS B 97 5.067 -8.366 5.979 1.00 77.92 C
+ATOM 2679 CD LYS B 97 5.414 -9.710 5.426 1.00 78.17 C
+ATOM 2680 CE LYS B 97 5.974 -9.497 4.041 1.00 80.95 C
+ATOM 2681 NZ LYS B 97 6.795 -10.642 3.713 1.00 87.25 N
+ATOM 2682 N GLU B 98 1.074 -6.618 5.524 1.00 92.38 N
+ATOM 2683 CA GLU B 98 -0.293 -6.477 5.069 1.00 91.45 C
+ATOM 2684 C GLU B 98 -0.558 -5.026 4.755 1.00 84.08 C
+ATOM 2685 O GLU B 98 -0.957 -4.785 3.625 1.00 85.55 O
+ATOM 2686 CB GLU B 98 -1.335 -6.936 6.099 1.00100.58 C
+ATOM 2687 CG GLU B 98 -1.102 -6.640 7.569 1.00109.98 C
+ATOM 2688 CD GLU B 98 -0.708 -7.871 8.384 1.00118.05 C
+ATOM 2689 OE1 GLU B 98 0.079 -8.702 7.914 1.00121.67 O
+ATOM 2690 OE2 GLU B 98 -1.195 -7.995 9.508 1.00124.15 O
+ATOM 2691 N ALA B 99 -0.285 -4.030 5.612 1.00 74.32 N
+ATOM 2692 CA ALA B 99 -0.570 -2.637 5.287 1.00 65.79 C
+ATOM 2693 C ALA B 99 0.129 -2.066 4.041 1.00 65.80 C
+ATOM 2694 O ALA B 99 0.049 -0.851 3.841 1.00 72.27 O
+ATOM 2695 CB ALA B 99 -0.222 -1.770 6.503 1.00 58.17 C
+ATOM 2696 N GLY B 100 0.849 -2.863 3.217 1.00 69.76 N
+ATOM 2697 CA GLY B 100 1.413 -2.494 1.905 1.00 75.80 C
+ATOM 2698 C GLY B 100 2.809 -1.860 1.794 1.00 77.82 C
+ATOM 2699 O GLY B 100 3.414 -1.819 0.711 1.00 73.32 O
+ATOM 2700 N ILE B 101 3.336 -1.388 2.930 1.00 78.45 N
+ATOM 2701 CA ILE B 101 4.595 -0.652 3.078 1.00 75.09 C
+ATOM 2702 C ILE B 101 5.810 -1.543 2.802 1.00 69.04 C
+ATOM 2703 O ILE B 101 6.139 -2.414 3.610 1.00 70.36 O
+ATOM 2704 CB ILE B 101 4.635 -0.076 4.536 1.00 77.18 C
+ATOM 2705 CG1 ILE B 101 3.362 0.695 4.915 1.00 73.91 C
+ATOM 2706 CG2 ILE B 101 5.829 0.855 4.621 1.00 79.35 C
+ATOM 2707 CD1 ILE B 101 3.007 0.577 6.411 1.00 72.20 C
+ATOM 2708 N ASN B 102 6.524 -1.412 1.702 1.00 66.44 N
+ATOM 2709 CA ASN B 102 7.652 -2.290 1.495 1.00 72.40 C
+ATOM 2710 C ASN B 102 8.915 -1.437 1.481 1.00 74.03 C
+ATOM 2711 O ASN B 102 8.813 -0.256 1.150 1.00 79.28 O
+ATOM 2712 CB ASN B 102 7.395 -3.057 0.190 1.00 78.17 C
+ATOM 2713 CG ASN B 102 7.033 -4.535 0.424 1.00 86.90 C
+ATOM 2714 OD1 ASN B 102 7.494 -5.414 -0.317 1.00 89.69 O
+ATOM 2715 ND2 ASN B 102 6.248 -4.936 1.429 1.00 83.21 N
+ATOM 2716 N VAL B 103 10.106 -1.918 1.877 1.00 70.60 N
+ATOM 2717 CA VAL B 103 11.319 -1.096 1.926 1.00 61.80 C
+ATOM 2718 C VAL B 103 12.344 -1.510 0.891 1.00 60.21 C
+ATOM 2719 O VAL B 103 12.331 -2.627 0.360 1.00 62.17 O
+ATOM 2720 CB VAL B 103 12.053 -1.133 3.313 1.00 65.17 C
+ATOM 2721 CG1 VAL B 103 11.144 -0.479 4.336 1.00 65.78 C
+ATOM 2722 CG2 VAL B 103 12.417 -2.553 3.751 1.00 60.81 C
+ATOM 2723 N ASP B 104 13.277 -0.603 0.644 1.00 56.76 N
+ATOM 2724 CA ASP B 104 14.312 -0.823 -0.343 1.00 65.01 C
+ATOM 2725 C ASP B 104 15.606 -1.218 0.402 1.00 61.65 C
+ATOM 2726 O ASP B 104 16.433 -2.007 -0.071 1.00 59.10 O
+ATOM 2727 CB ASP B 104 14.404 0.508 -1.196 1.00 74.71 C
+ATOM 2728 CG ASP B 104 13.138 0.894 -2.019 1.00 80.19 C
+ATOM 2729 OD1 ASP B 104 12.965 0.416 -3.144 1.00 77.73 O
+ATOM 2730 OD2 ASP B 104 12.304 1.672 -1.544 1.00 83.94 O
+ATOM 2731 N TYR B 105 15.800 -0.719 1.617 1.00 58.12 N
+ATOM 2732 CA TYR B 105 16.959 -1.061 2.412 1.00 52.14 C
+ATOM 2733 C TYR B 105 16.556 -1.402 3.813 1.00 47.27 C
+ATOM 2734 O TYR B 105 15.613 -0.818 4.374 1.00 45.43 O
+ATOM 2735 CB TYR B 105 17.906 0.056 2.575 1.00 52.57 C
+ATOM 2736 CG TYR B 105 18.581 0.343 1.284 1.00 54.39 C
+ATOM 2737 CD1 TYR B 105 19.722 -0.361 0.957 1.00 54.08 C
+ATOM 2738 CD2 TYR B 105 18.034 1.306 0.469 1.00 58.54 C
+ATOM 2739 CE1 TYR B 105 20.351 -0.090 -0.235 1.00 60.34 C
+ATOM 2740 CE2 TYR B 105 18.662 1.577 -0.727 1.00 65.03 C
+ATOM 2741 CZ TYR B 105 19.813 0.880 -1.070 1.00 65.96 C
+ATOM 2742 OH TYR B 105 20.447 1.201 -2.259 1.00 70.23 O
+ATOM 2743 N VAL B 106 17.291 -2.389 4.299 1.00 36.81 N
+ATOM 2744 CA VAL B 106 17.284 -2.747 5.686 1.00 42.39 C
+ATOM 2745 C VAL B 106 18.760 -2.588 6.110 1.00 42.74 C
+ATOM 2746 O VAL B 106 19.643 -3.228 5.509 1.00 38.45 O
+ATOM 2747 CB VAL B 106 16.816 -4.195 5.893 1.00 44.09 C
+ATOM 2748 CG1 VAL B 106 16.648 -4.367 7.406 1.00 39.96 C
+ATOM 2749 CG2 VAL B 106 15.483 -4.508 5.246 1.00 33.48 C
+ATOM 2750 N LEU B 107 19.099 -1.712 7.079 1.00 45.16 N
+ATOM 2751 CA LEU B 107 20.493 -1.515 7.508 1.00 45.88 C
+ATOM 2752 C LEU B 107 20.603 -1.926 8.990 1.00 42.43 C
+ATOM 2753 O LEU B 107 19.865 -1.405 9.840 1.00 44.70 O
+ATOM 2754 CB LEU B 107 20.885 -0.022 7.259 1.00 37.93 C
+ATOM 2755 CG LEU B 107 20.726 0.431 5.773 1.00 40.47 C
+ATOM 2756 CD1 LEU B 107 20.850 1.917 5.624 1.00 35.44 C
+ATOM 2757 CD2 LEU B 107 21.783 -0.222 4.932 1.00 39.79 C
+ATOM 2758 N GLU B 108 21.483 -2.907 9.264 1.00 34.51 N
+ATOM 2759 CA GLU B 108 21.731 -3.555 10.555 1.00 29.01 C
+ATOM 2760 C GLU B 108 22.957 -2.949 11.187 1.00 30.22 C
+ATOM 2761 O GLU B 108 24.027 -3.103 10.613 1.00 35.65 O
+ATOM 2762 CB GLU B 108 22.032 -5.027 10.389 1.00 31.54 C
+ATOM 2763 CG GLU B 108 21.858 -5.893 11.607 1.00 39.52 C
+ATOM 2764 CD GLU B 108 22.557 -7.238 11.487 1.00 47.20 C
+ATOM 2765 OE1 GLU B 108 22.493 -7.901 10.446 1.00 39.42 O
+ATOM 2766 OE2 GLU B 108 23.200 -7.623 12.461 1.00 44.24 O
+ATOM 2767 N PHE B 109 22.934 -2.279 12.324 1.00 35.28 N
+ATOM 2768 CA PHE B 109 24.139 -1.689 12.885 1.00 35.65 C
+ATOM 2769 C PHE B 109 24.705 -2.732 13.815 1.00 40.32 C
+ATOM 2770 O PHE B 109 24.063 -3.072 14.798 1.00 43.33 O
+ATOM 2771 CB PHE B 109 23.772 -0.415 13.615 1.00 35.16 C
+ATOM 2772 CG PHE B 109 23.404 0.679 12.598 1.00 46.81 C
+ATOM 2773 CD1 PHE B 109 22.303 0.549 11.752 1.00 46.18 C
+ATOM 2774 CD2 PHE B 109 24.206 1.797 12.469 1.00 50.43 C
+ATOM 2775 CE1 PHE B 109 22.019 1.499 10.804 1.00 33.60 C
+ATOM 2776 CE2 PHE B 109 23.911 2.745 11.516 1.00 42.21 C
+ATOM 2777 CZ PHE B 109 22.826 2.594 10.690 1.00 39.24 C
+ATOM 2778 N ASP B 110 25.850 -3.347 13.547 1.00 40.99 N
+ATOM 2779 CA ASP B 110 26.364 -4.400 14.404 1.00 37.31 C
+ATOM 2780 C ASP B 110 27.362 -3.876 15.402 1.00 39.30 C
+ATOM 2781 O ASP B 110 28.427 -3.360 15.052 1.00 40.47 O
+ATOM 2782 CB ASP B 110 27.035 -5.468 13.597 1.00 44.13 C
+ATOM 2783 CG ASP B 110 27.481 -6.621 14.476 1.00 51.16 C
+ATOM 2784 OD1 ASP B 110 26.665 -7.388 14.986 1.00 52.49 O
+ATOM 2785 OD2 ASP B 110 28.677 -6.722 14.676 1.00 61.49 O
+ATOM 2786 N VAL B 111 26.972 -4.007 16.652 1.00 34.65 N
+ATOM 2787 CA VAL B 111 27.765 -3.574 17.767 1.00 37.99 C
+ATOM 2788 C VAL B 111 27.721 -4.752 18.741 1.00 44.36 C
+ATOM 2789 O VAL B 111 26.686 -5.418 18.898 1.00 45.73 O
+ATOM 2790 CB VAL B 111 27.120 -2.322 18.348 1.00 41.44 C
+ATOM 2791 CG1 VAL B 111 27.816 -1.913 19.612 1.00 43.09 C
+ATOM 2792 CG2 VAL B 111 27.302 -1.163 17.416 1.00 43.61 C
+ATOM 2793 N PRO B 112 28.838 -5.062 19.393 1.00 39.17 N
+ATOM 2794 CA PRO B 112 28.904 -5.942 20.550 1.00 39.72 C
+ATOM 2795 C PRO B 112 28.248 -5.465 21.844 1.00 40.17 C
+ATOM 2796 O PRO B 112 28.478 -4.365 22.322 1.00 44.00 O
+ATOM 2797 CB PRO B 112 30.400 -6.196 20.699 1.00 37.13 C
+ATOM 2798 CG PRO B 112 31.031 -4.953 20.133 1.00 38.33 C
+ATOM 2799 CD PRO B 112 30.168 -4.699 18.919 1.00 41.01 C
+ATOM 2800 N ASP B 113 27.502 -6.321 22.522 1.00 44.43 N
+ATOM 2801 CA ASP B 113 26.836 -6.066 23.786 1.00 41.82 C
+ATOM 2802 C ASP B 113 27.585 -5.303 24.851 1.00 39.40 C
+ATOM 2803 O ASP B 113 27.063 -4.437 25.543 1.00 31.96 O
+ATOM 2804 CB ASP B 113 26.428 -7.383 24.401 1.00 50.30 C
+ATOM 2805 CG ASP B 113 25.099 -7.967 23.964 1.00 51.82 C
+ATOM 2806 OD1 ASP B 113 24.582 -7.629 22.898 1.00 49.56 O
+ATOM 2807 OD2 ASP B 113 24.583 -8.762 24.746 1.00 55.49 O
+ATOM 2808 N GLU B 114 28.849 -5.690 24.958 1.00 45.80 N
+ATOM 2809 CA GLU B 114 29.805 -5.138 25.908 1.00 48.55 C
+ATOM 2810 C GLU B 114 29.936 -3.642 25.827 1.00 47.30 C
+ATOM 2811 O GLU B 114 30.258 -3.013 26.837 1.00 47.89 O
+ATOM 2812 CB GLU B 114 31.216 -5.661 25.716 1.00 43.34 C
+ATOM 2813 CG GLU B 114 31.324 -7.141 25.950 1.00 51.65 C
+ATOM 2814 CD GLU B 114 30.922 -8.063 24.809 1.00 53.14 C
+ATOM 2815 OE1 GLU B 114 30.830 -7.654 23.645 1.00 55.58 O
+ATOM 2816 OE2 GLU B 114 30.717 -9.231 25.115 1.00 59.07 O
+ATOM 2817 N LEU B 115 29.722 -3.086 24.632 1.00 44.11 N
+ATOM 2818 CA LEU B 115 29.837 -1.653 24.430 1.00 44.14 C
+ATOM 2819 C LEU B 115 28.589 -0.832 24.760 1.00 43.83 C
+ATOM 2820 O LEU B 115 28.705 0.408 24.842 1.00 36.40 O
+ATOM 2821 CB LEU B 115 30.230 -1.384 22.979 1.00 43.08 C
+ATOM 2822 CG LEU B 115 31.679 -1.341 22.558 1.00 44.40 C
+ATOM 2823 CD1 LEU B 115 32.461 -2.517 23.072 1.00 42.84 C
+ATOM 2824 CD2 LEU B 115 31.685 -1.282 21.059 1.00 40.99 C
+ATOM 2825 N ILE B 116 27.439 -1.517 24.989 1.00 42.25 N
+ATOM 2826 CA ILE B 116 26.136 -0.851 25.127 1.00 41.31 C
+ATOM 2827 C ILE B 116 25.960 -0.014 26.404 1.00 40.76 C
+ATOM 2828 O ILE B 116 25.580 1.155 26.262 1.00 39.57 O
+ATOM 2829 CB ILE B 116 24.963 -1.929 25.001 1.00 38.78 C
+ATOM 2830 CG1 ILE B 116 24.946 -2.722 23.690 1.00 35.40 C
+ATOM 2831 CG2 ILE B 116 23.651 -1.192 25.058 1.00 42.66 C
+ATOM 2832 CD1 ILE B 116 24.965 -2.006 22.348 1.00 37.28 C
+ATOM 2833 N VAL B 117 26.242 -0.477 27.634 1.00 36.96 N
+ATOM 2834 CA VAL B 117 25.998 0.330 28.836 1.00 38.82 C
+ATOM 2835 C VAL B 117 26.735 1.675 28.805 1.00 37.24 C
+ATOM 2836 O VAL B 117 26.097 2.730 28.939 1.00 34.67 O
+ATOM 2837 CB VAL B 117 26.393 -0.501 30.095 1.00 38.72 C
+ATOM 2838 CG1 VAL B 117 26.148 0.214 31.414 1.00 36.94 C
+ATOM 2839 CG2 VAL B 117 25.474 -1.690 30.144 1.00 40.55 C
+ATOM 2840 N ASP B 118 28.046 1.727 28.549 1.00 39.01 N
+ATOM 2841 CA ASP B 118 28.753 2.997 28.479 1.00 41.79 C
+ATOM 2842 C ASP B 118 28.377 3.911 27.317 1.00 42.50 C
+ATOM 2843 O ASP B 118 28.543 5.144 27.382 1.00 42.04 O
+ATOM 2844 CB ASP B 118 30.238 2.724 28.454 1.00 44.34 C
+ATOM 2845 CG ASP B 118 30.729 2.204 29.793 1.00 49.23 C
+ATOM 2846 OD1 ASP B 118 30.114 2.451 30.837 1.00 52.77 O
+ATOM 2847 OD2 ASP B 118 31.752 1.537 29.781 1.00 59.67 O
+ATOM 2848 N ARG B 119 27.834 3.341 26.240 1.00 37.51 N
+ATOM 2849 CA ARG B 119 27.335 4.163 25.177 1.00 32.79 C
+ATOM 2850 C ARG B 119 26.099 4.819 25.696 1.00 35.60 C
+ATOM 2851 O ARG B 119 26.014 6.044 25.686 1.00 40.47 O
+ATOM 2852 CB ARG B 119 26.990 3.363 23.976 1.00 30.74 C
+ATOM 2853 CG ARG B 119 28.238 3.282 23.186 1.00 32.54 C
+ATOM 2854 CD ARG B 119 27.762 2.761 21.860 1.00 30.16 C
+ATOM 2855 NE ARG B 119 28.903 2.525 21.011 1.00 34.70 N
+ATOM 2856 CZ ARG B 119 28.756 2.418 19.687 1.00 35.59 C
+ATOM 2857 NH1 ARG B 119 27.544 2.424 19.126 1.00 37.92 N
+ATOM 2858 NH2 ARG B 119 29.821 2.271 18.900 1.00 28.74 N
+ATOM 2859 N ILE B 120 25.180 4.073 26.266 1.00 42.54 N
+ATOM 2860 CA ILE B 120 23.983 4.699 26.749 1.00 46.01 C
+ATOM 2861 C ILE B 120 24.114 5.525 28.037 1.00 42.56 C
+ATOM 2862 O ILE B 120 23.376 6.512 28.201 1.00 37.32 O
+ATOM 2863 CB ILE B 120 22.961 3.564 26.805 1.00 51.93 C
+ATOM 2864 CG1 ILE B 120 22.588 3.262 25.343 1.00 49.97 C
+ATOM 2865 CG2 ILE B 120 21.735 3.941 27.617 1.00 56.43 C
+ATOM 2866 CD1 ILE B 120 21.428 2.286 25.088 1.00 57.70 C
+ATOM 2867 N VAL B 121 25.052 5.302 28.935 1.00 42.44 N
+ATOM 2868 CA VAL B 121 25.135 6.233 30.063 1.00 52.27 C
+ATOM 2869 C VAL B 121 25.763 7.593 29.702 1.00 46.67 C
+ATOM 2870 O VAL B 121 25.629 8.576 30.434 1.00 52.52 O
+ATOM 2871 CB VAL B 121 25.918 5.582 31.259 1.00 55.87 C
+ATOM 2872 CG1 VAL B 121 25.216 4.263 31.593 1.00 61.21 C
+ATOM 2873 CG2 VAL B 121 27.389 5.348 30.954 1.00 66.37 C
+ATOM 2874 N GLY B 122 26.465 7.746 28.585 1.00 43.23 N
+ATOM 2875 CA GLY B 122 27.035 9.055 28.248 1.00 40.35 C
+ATOM 2876 C GLY B 122 26.214 9.840 27.224 1.00 37.75 C
+ATOM 2877 O GLY B 122 26.672 10.873 26.679 1.00 34.72 O
+ATOM 2878 N ARG B 123 25.030 9.294 26.930 1.00 32.84 N
+ATOM 2879 CA ARG B 123 24.140 9.867 25.935 1.00 35.16 C
+ATOM 2880 C ARG B 123 23.374 11.020 26.529 1.00 38.12 C
+ATOM 2881 O ARG B 123 22.845 10.909 27.650 1.00 38.89 O
+ATOM 2882 CB ARG B 123 23.138 8.817 25.421 1.00 36.62 C
+ATOM 2883 CG ARG B 123 22.053 9.254 24.411 1.00 29.37 C
+ATOM 2884 CD ARG B 123 21.391 8.062 23.694 1.00 34.24 C
+ATOM 2885 NE ARG B 123 20.478 7.240 24.478 1.00 34.98 N
+ATOM 2886 CZ ARG B 123 19.871 6.156 23.971 1.00 36.89 C
+ATOM 2887 NH1 ARG B 123 20.080 5.741 22.722 1.00 33.26 N
+ATOM 2888 NH2 ARG B 123 19.040 5.452 24.747 1.00 40.18 N
+ATOM 2889 N ARG B 124 23.303 12.066 25.701 1.00 32.31 N
+ATOM 2890 CA ARG B 124 22.607 13.305 25.984 1.00 32.45 C
+ATOM 2891 C ARG B 124 21.782 13.602 24.736 1.00 31.11 C
+ATOM 2892 O ARG B 124 22.257 13.394 23.603 1.00 33.70 O
+ATOM 2893 CB ARG B 124 23.605 14.441 26.221 1.00 35.66 C
+ATOM 2894 CG ARG B 124 24.593 14.247 27.367 1.00 36.65 C
+ATOM 2895 CD ARG B 124 23.828 14.216 28.659 1.00 34.70 C
+ATOM 2896 NE ARG B 124 24.734 13.927 29.751 1.00 36.42 N
+ATOM 2897 CZ ARG B 124 25.078 12.686 30.158 1.00 43.40 C
+ATOM 2898 NH1 ARG B 124 24.557 11.551 29.679 1.00 41.83 N
+ATOM 2899 NH2 ARG B 124 25.962 12.562 31.148 1.00 47.44 N
+ATOM 2900 N VAL B 125 20.540 14.065 24.919 1.00 31.78 N
+ATOM 2901 CA VAL B 125 19.590 14.301 23.845 1.00 34.06 C
+ATOM 2902 C VAL B 125 19.139 15.755 23.760 1.00 36.92 C
+ATOM 2903 O VAL B 125 19.062 16.483 24.766 1.00 33.45 O
+ATOM 2904 CB VAL B 125 18.289 13.448 23.977 1.00 36.29 C
+ATOM 2905 CG1 VAL B 125 18.653 11.999 23.812 1.00 47.05 C
+ATOM 2906 CG2 VAL B 125 17.638 13.577 25.336 1.00 39.15 C
+ATOM 2907 N HIS B 126 18.876 16.219 22.526 1.00 35.01 N
+ATOM 2908 CA HIS B 126 18.272 17.509 22.302 1.00 31.55 C
+ATOM 2909 C HIS B 126 16.845 17.001 22.198 1.00 40.68 C
+ATOM 2910 O HIS B 126 16.393 16.660 21.097 1.00 36.55 O
+ATOM 2911 CB HIS B 126 18.685 18.188 20.972 1.00 30.29 C
+ATOM 2912 CG HIS B 126 17.915 19.500 20.737 1.00 34.68 C
+ATOM 2913 ND1 HIS B 126 17.300 19.946 19.649 1.00 32.94 N
+ATOM 2914 CD2 HIS B 126 17.676 20.445 21.702 1.00 35.24 C
+ATOM 2915 CE1 HIS B 126 16.699 21.070 19.893 1.00 30.07 C
+ATOM 2916 NE2 HIS B 126 16.934 21.357 21.130 1.00 32.25 N
+ATOM 2917 N ALA B 127 16.142 16.928 23.335 1.00 41.63 N
+ATOM 2918 CA ALA B 127 14.792 16.394 23.401 1.00 45.59 C
+ATOM 2919 C ALA B 127 13.877 16.966 22.319 1.00 47.98 C
+ATOM 2920 O ALA B 127 13.399 16.134 21.540 1.00 48.09 O
+ATOM 2921 CB ALA B 127 14.196 16.666 24.773 1.00 43.14 C
+ATOM 2922 N PRO B 128 13.721 18.288 22.061 1.00 42.86 N
+ATOM 2923 CA PRO B 128 12.902 18.822 20.986 1.00 40.95 C
+ATOM 2924 C PRO B 128 13.081 18.205 19.595 1.00 47.85 C
+ATOM 2925 O PRO B 128 12.116 18.126 18.824 1.00 55.52 O
+ATOM 2926 CB PRO B 128 13.215 20.282 20.966 1.00 33.02 C
+ATOM 2927 CG PRO B 128 13.567 20.562 22.379 1.00 31.27 C
+ATOM 2928 CD PRO B 128 14.412 19.389 22.716 1.00 39.33 C
+ATOM 2929 N SER B 129 14.296 17.787 19.236 1.00 41.92 N
+ATOM 2930 CA SER B 129 14.521 17.305 17.886 1.00 44.68 C
+ATOM 2931 C SER B 129 14.991 15.838 17.898 1.00 48.54 C
+ATOM 2932 O SER B 129 15.152 15.197 16.845 1.00 47.07 O
+ATOM 2933 CB SER B 129 15.554 18.239 17.225 1.00 38.70 C
+ATOM 2934 OG SER B 129 16.855 18.188 17.836 1.00 39.44 O
+ATOM 2935 N GLY B 130 15.239 15.279 19.083 1.00 39.86 N
+ATOM 2936 CA GLY B 130 15.742 13.931 19.193 1.00 41.24 C
+ATOM 2937 C GLY B 130 17.189 13.834 18.794 1.00 40.68 C
+ATOM 2938 O GLY B 130 17.622 12.707 18.632 1.00 42.99 O
+ATOM 2939 N ARG B 131 17.964 14.927 18.674 1.00 38.18 N
+ATOM 2940 CA ARG B 131 19.364 14.806 18.256 1.00 36.24 C
+ATOM 2941 C ARG B 131 20.167 14.217 19.397 1.00 34.76 C
+ATOM 2942 O ARG B 131 19.945 14.558 20.566 1.00 34.31 O
+ATOM 2943 CB ARG B 131 19.996 16.164 17.868 1.00 41.13 C
+ATOM 2944 CG ARG B 131 19.943 16.482 16.356 1.00 31.92 C
+ATOM 2945 CD ARG B 131 20.590 17.820 15.973 1.00 30.92 C
+ATOM 2946 NE ARG B 131 19.891 18.947 16.591 1.00 33.63 N
+ATOM 2947 CZ ARG B 131 18.871 19.640 16.074 1.00 33.60 C
+ATOM 2948 NH1 ARG B 131 18.421 19.392 14.866 1.00 38.80 N
+ATOM 2949 NH2 ARG B 131 18.260 20.585 16.782 1.00 29.10 N
+ATOM 2950 N VAL B 132 21.112 13.339 19.084 1.00 35.52 N
+ATOM 2951 CA VAL B 132 21.838 12.646 20.118 1.00 29.51 C
+ATOM 2952 C VAL B 132 23.356 12.824 20.074 1.00 32.42 C
+ATOM 2953 O VAL B 132 23.951 13.112 19.043 1.00 28.80 O
+ATOM 2954 CB VAL B 132 21.302 11.219 19.990 1.00 33.75 C
+ATOM 2955 CG1 VAL B 132 21.630 10.620 18.649 1.00 43.53 C
+ATOM 2956 CG2 VAL B 132 21.894 10.390 21.082 1.00 44.88 C
+ATOM 2957 N TYR B 133 23.972 12.853 21.255 1.00 33.86 N
+ATOM 2958 CA TYR B 133 25.388 13.170 21.440 1.00 32.17 C
+ATOM 2959 C TYR B 133 25.885 12.214 22.476 1.00 28.42 C
+ATOM 2960 O TYR B 133 25.074 11.497 23.085 1.00 28.65 O
+ATOM 2961 CB TYR B 133 25.564 14.592 21.977 1.00 25.03 C
+ATOM 2962 CG TYR B 133 24.999 15.668 21.044 1.00 30.28 C
+ATOM 2963 CD1 TYR B 133 23.691 16.096 21.128 1.00 27.62 C
+ATOM 2964 CD2 TYR B 133 25.814 16.230 20.099 1.00 28.36 C
+ATOM 2965 CE1 TYR B 133 23.196 17.078 20.277 1.00 27.70 C
+ATOM 2966 CE2 TYR B 133 25.331 17.203 19.258 1.00 25.41 C
+ATOM 2967 CZ TYR B 133 24.029 17.631 19.339 1.00 25.49 C
+ATOM 2968 OH TYR B 133 23.571 18.597 18.442 1.00 31.77 O
+ATOM 2969 N HIS B 134 27.178 12.177 22.747 1.00 30.17 N
+ATOM 2970 CA HIS B 134 27.706 11.313 23.813 1.00 33.03 C
+ATOM 2971 C HIS B 134 28.769 12.148 24.506 1.00 36.60 C
+ATOM 2972 O HIS B 134 29.676 12.574 23.782 1.00 38.09 O
+ATOM 2973 CB HIS B 134 28.364 10.010 23.238 1.00 30.50 C
+ATOM 2974 CG HIS B 134 28.741 8.968 24.284 1.00 38.26 C
+ATOM 2975 ND1 HIS B 134 29.740 8.911 25.177 1.00 43.35 N
+ATOM 2976 CD2 HIS B 134 27.936 7.896 24.553 1.00 45.97 C
+ATOM 2977 CE1 HIS B 134 29.537 7.883 25.969 1.00 45.39 C
+ATOM 2978 NE2 HIS B 134 28.454 7.281 25.581 1.00 48.15 N
+ATOM 2979 N VAL B 135 28.846 12.384 25.822 1.00 34.09 N
+ATOM 2980 CA VAL B 135 29.908 13.254 26.376 1.00 37.63 C
+ATOM 2981 C VAL B 135 31.381 12.953 26.141 1.00 35.03 C
+ATOM 2982 O VAL B 135 32.258 13.816 26.262 1.00 41.29 O
+ATOM 2983 CB VAL B 135 29.781 13.422 27.902 1.00 34.35 C
+ATOM 2984 CG1 VAL B 135 28.515 14.181 28.186 1.00 35.57 C
+ATOM 2985 CG2 VAL B 135 29.802 12.078 28.593 1.00 34.66 C
+ATOM 2986 N LYS B 136 31.622 11.679 25.876 1.00 39.51 N
+ATOM 2987 CA LYS B 136 32.946 11.172 25.557 1.00 39.39 C
+ATOM 2988 C LYS B 136 33.166 10.760 24.108 1.00 35.32 C
+ATOM 2989 O LYS B 136 34.252 11.018 23.615 1.00 44.61 O
+ATOM 2990 CB LYS B 136 33.267 9.960 26.456 1.00 43.05 C
+ATOM 2991 CG LYS B 136 33.536 10.300 27.921 1.00 52.63 C
+ATOM 2992 CD LYS B 136 32.832 9.334 28.858 1.00 62.42 C
+ATOM 2993 CE LYS B 136 33.353 7.907 28.723 1.00 70.68 C
+ATOM 2994 NZ LYS B 136 32.519 7.004 29.495 1.00 78.33 N
+ATOM 2995 N PHE B 137 32.216 10.164 23.345 1.00 36.72 N
+ATOM 2996 CA PHE B 137 32.538 9.569 22.025 1.00 38.28 C
+ATOM 2997 C PHE B 137 32.005 10.344 20.843 1.00 39.39 C
+ATOM 2998 O PHE B 137 32.415 10.145 19.704 1.00 42.01 O
+ATOM 2999 CB PHE B 137 31.992 8.139 21.864 1.00 43.72 C
+ATOM 3000 CG PHE B 137 32.371 7.151 22.971 1.00 48.21 C
+ATOM 3001 CD1 PHE B 137 33.554 7.288 23.693 1.00 44.68 C
+ATOM 3002 CD2 PHE B 137 31.469 6.153 23.298 1.00 50.95 C
+ATOM 3003 CE1 PHE B 137 33.832 6.450 24.746 1.00 48.49 C
+ATOM 3004 CE2 PHE B 137 31.754 5.308 24.359 1.00 53.15 C
+ATOM 3005 CZ PHE B 137 32.928 5.461 25.079 1.00 56.71 C
+ATOM 3006 N ASN B 138 31.030 11.205 21.093 1.00 40.46 N
+ATOM 3007 CA ASN B 138 30.466 12.065 20.072 1.00 38.14 C
+ATOM 3008 C ASN B 138 29.951 13.366 20.733 1.00 34.75 C
+ATOM 3009 O ASN B 138 28.750 13.588 20.862 1.00 28.61 O
+ATOM 3010 CB ASN B 138 29.335 11.326 19.348 1.00 38.91 C
+ATOM 3011 CG ASN B 138 28.924 12.115 18.108 1.00 46.05 C
+ATOM 3012 OD1 ASN B 138 27.803 12.025 17.614 1.00 47.69 O
+ATOM 3013 ND2 ASN B 138 29.776 12.920 17.473 1.00 50.62 N
+ATOM 3014 N PRO B 139 30.828 14.224 21.266 1.00 34.31 N
+ATOM 3015 CA PRO B 139 30.443 15.390 22.040 1.00 36.64 C
+ATOM 3016 C PRO B 139 29.913 16.537 21.186 1.00 37.60 C
+ATOM 3017 O PRO B 139 30.223 16.700 20.002 1.00 35.56 O
+ATOM 3018 CB PRO B 139 31.686 15.772 22.829 1.00 33.59 C
+ATOM 3019 CG PRO B 139 32.578 14.577 22.627 1.00 38.89 C
+ATOM 3020 CD PRO B 139 32.277 14.112 21.209 1.00 32.43 C
+ATOM 3021 N PRO B 140 29.051 17.359 21.776 1.00 38.12 N
+ATOM 3022 CA PRO B 140 28.602 18.595 21.180 1.00 31.10 C
+ATOM 3023 C PRO B 140 29.760 19.550 21.096 1.00 33.53 C
+ATOM 3024 O PRO B 140 30.818 19.372 21.733 1.00 34.53 O
+ATOM 3025 CB PRO B 140 27.507 19.042 22.087 1.00 34.36 C
+ATOM 3026 CG PRO B 140 27.945 18.520 23.440 1.00 39.15 C
+ATOM 3027 CD PRO B 140 28.454 17.143 23.099 1.00 35.38 C
+ATOM 3028 N LYS B 141 29.464 20.637 20.403 1.00 36.96 N
+ATOM 3029 CA LYS B 141 30.475 21.610 20.043 1.00 45.60 C
+ATOM 3030 C LYS B 141 30.850 22.385 21.278 1.00 42.21 C
+ATOM 3031 O LYS B 141 32.027 22.616 21.522 1.00 46.49 O
+ATOM 3032 CB LYS B 141 29.934 22.563 18.957 1.00 64.40 C
+ATOM 3033 CG LYS B 141 30.883 23.559 18.263 1.00 79.45 C
+ATOM 3034 CD LYS B 141 30.248 24.182 16.995 1.00 92.11 C
+ATOM 3035 CE LYS B 141 29.980 23.128 15.890 1.00 96.98 C
+ATOM 3036 NZ LYS B 141 29.267 23.674 14.747 1.00 98.10 N
+ATOM 3037 N VAL B 142 29.832 22.751 22.041 1.00 40.93 N
+ATOM 3038 CA VAL B 142 29.911 23.495 23.270 1.00 30.77 C
+ATOM 3039 C VAL B 142 29.234 22.499 24.171 1.00 34.12 C
+ATOM 3040 O VAL B 142 28.174 21.971 23.824 1.00 33.67 O
+ATOM 3041 CB VAL B 142 29.118 24.792 23.113 1.00 33.86 C
+ATOM 3042 CG1 VAL B 142 28.884 25.453 24.478 1.00 27.94 C
+ATOM 3043 CG2 VAL B 142 29.883 25.678 22.101 1.00 28.21 C
+ATOM 3044 N GLU B 143 29.874 22.230 25.302 1.00 34.35 N
+ATOM 3045 CA GLU B 143 29.446 21.224 26.254 1.00 35.58 C
+ATOM 3046 C GLU B 143 28.045 21.449 26.699 1.00 26.97 C
+ATOM 3047 O GLU B 143 27.754 22.594 27.000 1.00 37.21 O
+ATOM 3048 CB GLU B 143 30.333 21.240 27.486 1.00 50.15 C
+ATOM 3049 CG GLU B 143 29.889 20.258 28.600 1.00 70.51 C
+ATOM 3050 CD GLU B 143 30.834 20.004 29.787 1.00 82.45 C
+ATOM 3051 OE1 GLU B 143 31.778 20.773 30.004 1.00 89.45 O
+ATOM 3052 OE2 GLU B 143 30.618 19.016 30.502 1.00 89.41 O
+ATOM 3053 N GLY B 144 27.213 20.408 26.690 1.00 30.90 N
+ATOM 3054 CA GLY B 144 25.846 20.427 27.192 1.00 25.54 C
+ATOM 3055 C GLY B 144 24.869 21.255 26.379 1.00 30.82 C
+ATOM 3056 O GLY B 144 23.755 21.498 26.851 1.00 32.61 O
+ATOM 3057 N LYS B 145 25.196 21.720 25.168 1.00 35.88 N
+ATOM 3058 CA LYS B 145 24.281 22.525 24.346 1.00 29.20 C
+ATOM 3059 C LYS B 145 24.153 21.818 23.020 1.00 28.47 C
+ATOM 3060 O LYS B 145 25.057 21.096 22.616 1.00 28.26 O
+ATOM 3061 CB LYS B 145 24.833 23.878 24.089 1.00 25.45 C
+ATOM 3062 CG LYS B 145 25.291 24.655 25.316 1.00 30.24 C
+ATOM 3063 CD LYS B 145 24.107 25.003 26.163 1.00 25.15 C
+ATOM 3064 CE LYS B 145 24.742 25.629 27.384 1.00 31.09 C
+ATOM 3065 NZ LYS B 145 23.677 26.437 27.909 1.00 40.29 N
+ATOM 3066 N ASP B 146 23.048 21.968 22.326 1.00 32.95 N
+ATOM 3067 CA ASP B 146 22.827 21.388 21.006 1.00 29.78 C
+ATOM 3068 C ASP B 146 23.612 22.216 19.961 1.00 30.01 C
+ATOM 3069 O ASP B 146 23.630 23.469 19.938 1.00 27.81 O
+ATOM 3070 CB ASP B 146 21.323 21.429 20.754 1.00 28.61 C
+ATOM 3071 CG ASP B 146 20.879 20.889 19.419 1.00 33.42 C
+ATOM 3072 OD1 ASP B 146 21.223 19.771 19.110 1.00 33.47 O
+ATOM 3073 OD2 ASP B 146 20.197 21.579 18.682 1.00 35.14 O
+ATOM 3074 N ASP B 147 24.208 21.508 19.001 1.00 31.64 N
+ATOM 3075 CA ASP B 147 25.028 22.183 17.990 1.00 38.60 C
+ATOM 3076 C ASP B 147 24.154 23.088 17.114 1.00 32.60 C
+ATOM 3077 O ASP B 147 24.425 24.252 16.843 1.00 37.74 O
+ATOM 3078 CB ASP B 147 25.775 21.140 17.087 1.00 39.26 C
+ATOM 3079 CG ASP B 147 27.007 20.454 17.664 1.00 37.04 C
+ATOM 3080 OD1 ASP B 147 27.418 20.835 18.734 1.00 31.21 O
+ATOM 3081 OD2 ASP B 147 27.571 19.544 17.057 1.00 42.25 O
+ATOM 3082 N VAL B 148 23.003 22.568 16.758 1.00 32.83 N
+ATOM 3083 CA VAL B 148 22.139 23.263 15.847 1.00 31.98 C
+ATOM 3084 C VAL B 148 21.385 24.438 16.457 1.00 31.15 C
+ATOM 3085 O VAL B 148 21.281 25.467 15.796 1.00 27.58 O
+ATOM 3086 CB VAL B 148 21.238 22.125 15.242 1.00 40.57 C
+ATOM 3087 CG1 VAL B 148 20.046 22.730 14.500 1.00 42.08 C
+ATOM 3088 CG2 VAL B 148 22.068 21.257 14.271 1.00 30.00 C
+ATOM 3089 N THR B 149 20.840 24.323 17.680 1.00 32.78 N
+ATOM 3090 CA THR B 149 20.057 25.380 18.293 1.00 27.56 C
+ATOM 3091 C THR B 149 20.768 26.113 19.440 1.00 31.04 C
+ATOM 3092 O THR B 149 20.324 27.172 19.895 1.00 24.71 O
+ATOM 3093 CB THR B 149 18.709 24.816 18.829 1.00 27.00 C
+ATOM 3094 OG1 THR B 149 18.992 23.739 19.702 1.00 28.99 O
+ATOM 3095 CG2 THR B 149 17.832 24.189 17.768 1.00 30.51 C
+ATOM 3096 N GLY B 150 21.860 25.539 19.930 1.00 29.55 N
+ATOM 3097 CA GLY B 150 22.493 26.051 21.123 1.00 35.34 C
+ATOM 3098 C GLY B 150 21.703 25.719 22.405 1.00 32.07 C
+ATOM 3099 O GLY B 150 22.092 26.144 23.493 1.00 29.49 O
+ATOM 3100 N GLU B 151 20.598 24.968 22.318 1.00 29.29 N
+ATOM 3101 CA GLU B 151 19.745 24.695 23.463 1.00 33.55 C
+ATOM 3102 C GLU B 151 20.320 23.634 24.393 1.00 36.80 C
+ATOM 3103 O GLU B 151 21.089 22.760 23.954 1.00 30.85 O
+ATOM 3104 CB GLU B 151 18.391 24.248 22.976 1.00 37.12 C
+ATOM 3105 CG GLU B 151 17.493 25.339 22.380 1.00 46.04 C
+ATOM 3106 CD GLU B 151 16.198 24.780 21.786 1.00 53.15 C
+ATOM 3107 OE1 GLU B 151 15.615 23.895 22.415 1.00 62.90 O
+ATOM 3108 OE2 GLU B 151 15.763 25.210 20.709 1.00 54.09 O
+ATOM 3109 N GLU B 152 19.915 23.692 25.662 1.00 31.95 N
+ATOM 3110 CA GLU B 152 20.404 22.756 26.668 1.00 45.21 C
+ATOM 3111 C GLU B 152 20.117 21.261 26.416 1.00 39.83 C
+ATOM 3112 O GLU B 152 19.004 20.855 26.091 1.00 34.09 O
+ATOM 3113 CB GLU B 152 19.816 23.206 28.015 1.00 65.08 C
+ATOM 3114 CG GLU B 152 20.623 22.930 29.324 1.00 84.28 C
+ATOM 3115 CD GLU B 152 21.785 23.886 29.666 1.00 91.64 C
+ATOM 3116 OE1 GLU B 152 21.514 25.015 30.098 1.00 90.46 O
+ATOM 3117 OE2 GLU B 152 22.956 23.492 29.523 1.00 94.30 O
+ATOM 3118 N LEU B 153 21.077 20.362 26.524 1.00 37.34 N
+ATOM 3119 CA LEU B 153 20.847 18.946 26.292 1.00 38.51 C
+ATOM 3120 C LEU B 153 20.431 18.233 27.574 1.00 44.46 C
+ATOM 3121 O LEU B 153 20.893 18.604 28.659 1.00 51.83 O
+ATOM 3122 CB LEU B 153 22.105 18.300 25.787 1.00 33.60 C
+ATOM 3123 CG LEU B 153 22.803 18.847 24.580 1.00 33.27 C
+ATOM 3124 CD1 LEU B 153 24.156 18.190 24.532 1.00 28.42 C
+ATOM 3125 CD2 LEU B 153 22.005 18.588 23.317 1.00 30.71 C
+ATOM 3126 N THR B 154 19.612 17.181 27.494 1.00 42.04 N
+ATOM 3127 CA THR B 154 19.166 16.487 28.672 1.00 37.52 C
+ATOM 3128 C THR B 154 19.550 15.014 28.642 1.00 41.72 C
+ATOM 3129 O THR B 154 20.181 14.534 27.695 1.00 29.22 O
+ATOM 3130 CB THR B 154 17.653 16.662 28.776 1.00 32.83 C
+ATOM 3131 OG1 THR B 154 16.995 16.186 27.592 1.00 38.82 O
+ATOM 3132 CG2 THR B 154 17.365 18.127 29.040 1.00 34.83 C
+ATOM 3133 N THR B 155 19.185 14.296 29.710 1.00 42.96 N
+ATOM 3134 CA THR B 155 19.397 12.867 29.824 1.00 41.45 C
+ATOM 3135 C THR B 155 18.040 12.186 29.714 1.00 44.17 C
+ATOM 3136 O THR B 155 17.044 12.702 30.243 1.00 49.13 O
+ATOM 3137 CB THR B 155 20.069 12.552 31.184 1.00 43.91 C
+ATOM 3138 OG1 THR B 155 19.251 13.032 32.270 1.00 54.98 O
+ATOM 3139 CG2 THR B 155 21.416 13.246 31.264 1.00 35.97 C
+ATOM 3140 N ARG B 156 17.922 11.068 29.011 1.00 43.58 N
+ATOM 3141 CA ARG B 156 16.674 10.333 28.929 1.00 42.87 C
+ATOM 3142 C ARG B 156 16.485 9.530 30.207 1.00 44.97 C
+ATOM 3143 O ARG B 156 17.411 8.882 30.702 1.00 41.18 O
+ATOM 3144 CB ARG B 156 16.710 9.399 27.735 1.00 39.27 C
+ATOM 3145 CG ARG B 156 16.310 10.053 26.426 1.00 37.84 C
+ATOM 3146 CD ARG B 156 16.517 9.095 25.251 1.00 43.16 C
+ATOM 3147 NE ARG B 156 16.025 7.760 25.551 1.00 42.32 N
+ATOM 3148 CZ ARG B 156 16.214 6.733 24.736 1.00 38.58 C
+ATOM 3149 NH1 ARG B 156 16.626 6.898 23.497 1.00 43.63 N
+ATOM 3150 NH2 ARG B 156 15.885 5.514 25.108 1.00 37.85 N
+ATOM 3151 N LYS B 157 15.259 9.633 30.714 1.00 54.96 N
+ATOM 3152 CA LYS B 157 14.694 8.965 31.896 1.00 62.67 C
+ATOM 3153 C LYS B 157 15.167 7.522 32.015 1.00 60.68 C
+ATOM 3154 O LYS B 157 15.755 7.112 33.017 1.00 58.71 O
+ATOM 3155 CB LYS B 157 13.152 8.873 31.856 1.00 72.40 C
+ATOM 3156 CG LYS B 157 12.188 10.078 31.762 1.00 85.60 C
+ATOM 3157 CD LYS B 157 12.290 11.037 30.548 1.00 91.39 C
+ATOM 3158 CE LYS B 157 12.116 10.478 29.139 1.00 88.15 C
+ATOM 3159 NZ LYS B 157 12.446 11.518 28.179 1.00 88.05 N
+ATOM 3160 N ASP B 158 14.918 6.767 30.949 1.00 51.75 N
+ATOM 3161 CA ASP B 158 15.297 5.383 30.894 1.00 45.75 C
+ATOM 3162 C ASP B 158 16.790 5.104 30.770 1.00 47.61 C
+ATOM 3163 O ASP B 158 17.196 3.942 30.761 1.00 47.08 O
+ATOM 3164 CB ASP B 158 14.512 4.761 29.730 1.00 44.29 C
+ATOM 3165 CG ASP B 158 14.760 5.292 28.320 1.00 42.57 C
+ATOM 3166 OD1 ASP B 158 15.547 6.211 28.136 1.00 45.91 O
+ATOM 3167 OD2 ASP B 158 14.146 4.776 27.390 1.00 42.38 O
+ATOM 3168 N ASP B 159 17.706 6.068 30.699 1.00 52.80 N
+ATOM 3169 CA ASP B 159 19.097 5.725 30.419 1.00 50.22 C
+ATOM 3170 C ASP B 159 19.989 5.377 31.570 1.00 49.07 C
+ATOM 3171 O ASP B 159 20.870 6.157 31.926 1.00 61.90 O
+ATOM 3172 CB ASP B 159 19.760 6.857 29.627 1.00 47.08 C
+ATOM 3173 CG ASP B 159 19.439 6.912 28.148 1.00 37.86 C
+ATOM 3174 OD1 ASP B 159 18.840 5.994 27.583 1.00 46.15 O
+ATOM 3175 OD2 ASP B 159 19.817 7.904 27.552 1.00 42.96 O
+ATOM 3176 N GLN B 160 19.804 4.259 32.239 1.00 55.64 N
+ATOM 3177 CA GLN B 160 20.776 3.883 33.253 1.00 62.07 C
+ATOM 3178 C GLN B 160 21.076 2.402 33.110 1.00 58.32 C
+ATOM 3179 O GLN B 160 20.263 1.698 32.497 1.00 58.76 O
+ATOM 3180 CB GLN B 160 20.257 4.215 34.668 1.00 76.10 C
+ATOM 3181 CG GLN B 160 18.855 3.771 35.123 1.00 90.51 C
+ATOM 3182 CD GLN B 160 17.686 4.680 34.751 1.00 94.79 C
+ATOM 3183 OE1 GLN B 160 16.530 4.251 34.735 1.00 95.56 O
+ATOM 3184 NE2 GLN B 160 17.903 5.958 34.457 1.00 98.96 N
+ATOM 3185 N GLU B 161 22.240 1.959 33.620 1.00 50.75 N
+ATOM 3186 CA GLU B 161 22.768 0.606 33.508 1.00 50.64 C
+ATOM 3187 C GLU B 161 21.725 -0.489 33.583 1.00 50.61 C
+ATOM 3188 O GLU B 161 21.591 -1.266 32.636 1.00 45.78 O
+ATOM 3189 CB GLU B 161 23.803 0.424 34.604 1.00 59.01 C
+ATOM 3190 CG GLU B 161 24.375 -0.969 34.875 1.00 75.32 C
+ATOM 3191 CD GLU B 161 25.309 -1.090 36.094 1.00 85.47 C
+ATOM 3192 OE1 GLU B 161 26.277 -0.334 36.139 1.00 89.92 O
+ATOM 3193 OE2 GLU B 161 25.093 -1.934 36.983 1.00 88.22 O
+ATOM 3194 N GLU B 162 20.920 -0.481 34.655 1.00 52.95 N
+ATOM 3195 CA GLU B 162 19.908 -1.502 34.881 1.00 54.78 C
+ATOM 3196 C GLU B 162 18.739 -1.492 33.908 1.00 46.44 C
+ATOM 3197 O GLU B 162 18.377 -2.571 33.421 1.00 46.02 O
+ATOM 3198 CB GLU B 162 19.392 -1.405 36.350 1.00 63.77 C
+ATOM 3199 CG GLU B 162 20.480 -1.758 37.428 1.00 75.38 C
+ATOM 3200 CD GLU B 162 21.249 -3.110 37.410 1.00 80.75 C
+ATOM 3201 OE1 GLU B 162 20.616 -4.173 37.456 1.00 83.47 O
+ATOM 3202 OE2 GLU B 162 22.488 -3.105 37.383 1.00 77.04 O
+ATOM 3203 N THR B 163 18.165 -0.337 33.564 1.00 42.25 N
+ATOM 3204 CA THR B 163 17.121 -0.240 32.544 1.00 39.90 C
+ATOM 3205 C THR B 163 17.735 -0.685 31.195 1.00 45.40 C
+ATOM 3206 O THR B 163 17.141 -1.495 30.477 1.00 45.06 O
+ATOM 3207 CB THR B 163 16.630 1.209 32.498 1.00 36.70 C
+ATOM 3208 OG1 THR B 163 16.605 1.626 33.852 1.00 46.91 O
+ATOM 3209 CG2 THR B 163 15.248 1.407 31.965 1.00 38.72 C
+ATOM 3210 N VAL B 164 18.978 -0.299 30.841 1.00 47.52 N
+ATOM 3211 CA VAL B 164 19.632 -0.704 29.595 1.00 42.00 C
+ATOM 3212 C VAL B 164 19.774 -2.216 29.565 1.00 44.67 C
+ATOM 3213 O VAL B 164 19.489 -2.848 28.541 1.00 48.44 O
+ATOM 3214 CB VAL B 164 21.019 -0.070 29.476 1.00 44.97 C
+ATOM 3215 CG1 VAL B 164 21.717 -0.396 28.155 1.00 43.33 C
+ATOM 3216 CG2 VAL B 164 20.816 1.411 29.543 1.00 50.80 C
+ATOM 3217 N ARG B 165 20.161 -2.839 30.681 1.00 43.25 N
+ATOM 3218 CA ARG B 165 20.266 -4.286 30.739 1.00 39.09 C
+ATOM 3219 C ARG B 165 18.939 -4.951 30.454 1.00 43.70 C
+ATOM 3220 O ARG B 165 18.881 -5.828 29.582 1.00 42.32 O
+ATOM 3221 CB ARG B 165 20.775 -4.648 32.073 1.00 49.27 C
+ATOM 3222 CG ARG B 165 22.230 -4.255 31.945 1.00 63.64 C
+ATOM 3223 CD ARG B 165 22.947 -4.202 33.268 1.00 76.99 C
+ATOM 3224 NE ARG B 165 24.351 -4.016 32.956 1.00 89.11 N
+ATOM 3225 CZ ARG B 165 25.333 -4.245 33.834 1.00 95.74 C
+ATOM 3226 NH1 ARG B 165 25.101 -4.613 35.108 1.00 97.66 N
+ATOM 3227 NH2 ARG B 165 26.582 -4.060 33.403 1.00 98.02 N
+ATOM 3228 N LYS B 166 17.847 -4.450 31.047 1.00 45.10 N
+ATOM 3229 CA LYS B 166 16.527 -4.992 30.774 1.00 44.51 C
+ATOM 3230 C LYS B 166 16.263 -4.838 29.286 1.00 39.52 C
+ATOM 3231 O LYS B 166 15.883 -5.832 28.651 1.00 41.62 O
+ATOM 3232 CB LYS B 166 15.468 -4.243 31.587 1.00 56.14 C
+ATOM 3233 CG LYS B 166 15.721 -4.374 33.096 1.00 72.40 C
+ATOM 3234 CD LYS B 166 14.807 -3.560 34.043 1.00 82.46 C
+ATOM 3235 CE LYS B 166 15.236 -3.762 35.523 1.00 90.50 C
+ATOM 3236 NZ LYS B 166 14.363 -3.132 36.513 1.00 92.49 N
+ATOM 3237 N ARG B 167 16.614 -3.678 28.697 1.00 34.18 N
+ATOM 3238 CA ARG B 167 16.402 -3.432 27.250 1.00 42.17 C
+ATOM 3239 C ARG B 167 17.162 -4.370 26.330 1.00 41.05 C
+ATOM 3240 O ARG B 167 16.655 -4.736 25.259 1.00 36.15 O
+ATOM 3241 CB ARG B 167 16.824 -2.030 26.767 1.00 37.06 C
+ATOM 3242 CG ARG B 167 15.963 -0.902 27.298 1.00 42.92 C
+ATOM 3243 CD ARG B 167 15.803 0.245 26.305 1.00 41.72 C
+ATOM 3244 NE ARG B 167 16.926 1.143 26.242 1.00 44.97 N
+ATOM 3245 CZ ARG B 167 17.062 2.174 27.084 1.00 50.83 C
+ATOM 3246 NH1 ARG B 167 16.189 2.400 28.060 1.00 58.08 N
+ATOM 3247 NH2 ARG B 167 18.107 2.990 26.955 1.00 49.65 N
+ATOM 3248 N LEU B 168 18.399 -4.730 26.705 1.00 36.25 N
+ATOM 3249 CA LEU B 168 19.127 -5.686 25.920 1.00 32.19 C
+ATOM 3250 C LEU B 168 18.567 -7.085 26.031 1.00 34.90 C
+ATOM 3251 O LEU B 168 18.509 -7.794 25.011 1.00 36.46 O
+ATOM 3252 CB LEU B 168 20.568 -5.699 26.315 1.00 43.47 C
+ATOM 3253 CG LEU B 168 21.512 -4.997 25.333 1.00 51.57 C
+ATOM 3254 CD1 LEU B 168 22.912 -5.091 25.882 1.00 52.48 C
+ATOM 3255 CD2 LEU B 168 21.505 -5.658 23.960 1.00 54.68 C
+ATOM 3256 N VAL B 169 18.066 -7.542 27.177 1.00 36.34 N
+ATOM 3257 CA VAL B 169 17.445 -8.859 27.179 1.00 37.70 C
+ATOM 3258 C VAL B 169 16.229 -8.870 26.253 1.00 40.36 C
+ATOM 3259 O VAL B 169 16.058 -9.815 25.479 1.00 38.39 O
+ATOM 3260 CB VAL B 169 17.045 -9.235 28.617 1.00 40.29 C
+ATOM 3261 CG1 VAL B 169 16.407 -10.621 28.678 1.00 34.16 C
+ATOM 3262 CG2 VAL B 169 18.300 -9.262 29.461 1.00 39.20 C
+ATOM 3263 N GLU B 170 15.375 -7.833 26.261 1.00 47.88 N
+ATOM 3264 CA GLU B 170 14.175 -7.773 25.410 1.00 42.49 C
+ATOM 3265 C GLU B 170 14.595 -7.737 23.968 1.00 43.32 C
+ATOM 3266 O GLU B 170 13.938 -8.334 23.116 1.00 49.06 O
+ATOM 3267 CB GLU B 170 13.325 -6.521 25.607 1.00 46.83 C
+ATOM 3268 CG GLU B 170 12.694 -6.349 26.968 1.00 65.51 C
+ATOM 3269 CD GLU B 170 11.476 -7.230 27.207 1.00 73.41 C
+ATOM 3270 OE1 GLU B 170 10.420 -6.927 26.645 1.00 80.40 O
+ATOM 3271 OE2 GLU B 170 11.583 -8.202 27.960 1.00 74.66 O
+ATOM 3272 N TYR B 171 15.695 -7.067 23.656 1.00 40.50 N
+ATOM 3273 CA TYR B 171 16.181 -7.037 22.299 1.00 35.65 C
+ATOM 3274 C TYR B 171 16.488 -8.460 21.860 1.00 39.53 C
+ATOM 3275 O TYR B 171 16.046 -8.902 20.798 1.00 34.57 O
+ATOM 3276 CB TYR B 171 17.434 -6.179 22.239 1.00 33.25 C
+ATOM 3277 CG TYR B 171 18.030 -6.237 20.851 1.00 32.35 C
+ATOM 3278 CD1 TYR B 171 17.442 -5.542 19.821 1.00 35.62 C
+ATOM 3279 CD2 TYR B 171 19.118 -7.043 20.623 1.00 33.07 C
+ATOM 3280 CE1 TYR B 171 17.931 -5.685 18.542 1.00 35.44 C
+ATOM 3281 CE2 TYR B 171 19.617 -7.191 19.362 1.00 26.79 C
+ATOM 3282 CZ TYR B 171 19.015 -6.507 18.327 1.00 37.06 C
+ATOM 3283 OH TYR B 171 19.480 -6.710 17.035 1.00 38.74 O
+ATOM 3284 N HIS B 172 17.238 -9.183 22.689 1.00 39.64 N
+ATOM 3285 CA HIS B 172 17.653 -10.524 22.354 1.00 42.09 C
+ATOM 3286 C HIS B 172 16.519 -11.497 22.118 1.00 46.79 C
+ATOM 3287 O HIS B 172 16.570 -12.267 21.146 1.00 53.39 O
+ATOM 3288 CB HIS B 172 18.555 -11.049 23.446 1.00 46.86 C
+ATOM 3289 CG HIS B 172 19.918 -10.417 23.251 1.00 55.08 C
+ATOM 3290 ND1 HIS B 172 20.713 -10.500 22.183 1.00 56.84 N
+ATOM 3291 CD2 HIS B 172 20.511 -9.560 24.147 1.00 56.82 C
+ATOM 3292 CE1 HIS B 172 21.747 -9.710 22.401 1.00 59.08 C
+ATOM 3293 NE2 HIS B 172 21.614 -9.151 23.585 1.00 56.29 N
+ATOM 3294 N GLN B 173 15.461 -11.422 22.932 1.00 41.67 N
+ATOM 3295 CA GLN B 173 14.325 -12.339 22.789 1.00 48.59 C
+ATOM 3296 C GLN B 173 13.291 -11.967 21.746 1.00 42.11 C
+ATOM 3297 O GLN B 173 12.684 -12.844 21.134 1.00 37.79 O
+ATOM 3298 CB GLN B 173 13.510 -12.493 24.059 1.00 60.01 C
+ATOM 3299 CG GLN B 173 14.167 -13.057 25.296 1.00 76.38 C
+ATOM 3300 CD GLN B 173 13.243 -12.826 26.474 1.00 82.48 C
+ATOM 3301 OE1 GLN B 173 12.343 -13.616 26.747 1.00 91.60 O
+ATOM 3302 NE2 GLN B 173 13.399 -11.716 27.179 1.00 81.25 N
+ATOM 3303 N MET B 174 13.037 -10.666 21.618 1.00 41.16 N
+ATOM 3304 CA MET B 174 12.005 -10.129 20.759 1.00 44.59 C
+ATOM 3305 C MET B 174 12.443 -9.507 19.433 1.00 43.41 C
+ATOM 3306 O MET B 174 11.829 -9.763 18.390 1.00 42.69 O
+ATOM 3307 CB MET B 174 11.227 -9.085 21.549 1.00 45.47 C
+ATOM 3308 CG MET B 174 10.681 -9.519 22.897 1.00 48.43 C
+ATOM 3309 SD MET B 174 9.632 -10.957 22.656 1.00 61.69 S
+ATOM 3310 CE MET B 174 8.369 -10.191 21.679 1.00 60.46 C
+ATOM 3311 N THR B 175 13.484 -8.680 19.449 1.00 42.94 N
+ATOM 3312 CA THR B 175 13.901 -7.950 18.269 1.00 38.36 C
+ATOM 3313 C THR B 175 14.925 -8.700 17.460 1.00 37.16 C
+ATOM 3314 O THR B 175 14.844 -8.626 16.235 1.00 40.67 O
+ATOM 3315 CB THR B 175 14.461 -6.595 18.693 1.00 34.70 C
+ATOM 3316 OG1 THR B 175 13.698 -6.128 19.797 1.00 34.25 O
+ATOM 3317 CG2 THR B 175 14.397 -5.596 17.562 1.00 37.04 C
+ATOM 3318 N ALA B 176 15.864 -9.451 18.061 1.00 32.51 N
+ATOM 3319 CA ALA B 176 16.843 -10.199 17.307 1.00 31.54 C
+ATOM 3320 C ALA B 176 16.242 -11.067 16.189 1.00 32.00 C
+ATOM 3321 O ALA B 176 16.835 -11.022 15.106 1.00 36.96 O
+ATOM 3322 CB ALA B 176 17.633 -11.078 18.267 1.00 33.81 C
+ATOM 3323 N PRO B 177 15.098 -11.788 16.208 1.00 32.33 N
+ATOM 3324 CA PRO B 177 14.607 -12.567 15.058 1.00 37.50 C
+ATOM 3325 C PRO B 177 14.355 -11.782 13.776 1.00 34.85 C
+ATOM 3326 O PRO B 177 14.255 -12.362 12.693 1.00 42.47 O
+ATOM 3327 CB PRO B 177 13.343 -13.251 15.549 1.00 36.10 C
+ATOM 3328 CG PRO B 177 13.628 -13.393 17.031 1.00 36.27 C
+ATOM 3329 CD PRO B 177 14.222 -12.041 17.348 1.00 30.46 C
+ATOM 3330 N LEU B 178 14.268 -10.462 13.861 1.00 32.26 N
+ATOM 3331 CA LEU B 178 14.019 -9.640 12.710 1.00 33.76 C
+ATOM 3332 C LEU B 178 15.190 -9.639 11.760 1.00 38.81 C
+ATOM 3333 O LEU B 178 14.945 -9.383 10.581 1.00 41.67 O
+ATOM 3334 CB LEU B 178 13.679 -8.202 13.146 1.00 38.52 C
+ATOM 3335 CG LEU B 178 12.275 -7.954 13.699 1.00 35.50 C
+ATOM 3336 CD1 LEU B 178 12.098 -6.486 14.011 1.00 31.03 C
+ATOM 3337 CD2 LEU B 178 11.243 -8.389 12.660 1.00 34.09 C
+ATOM 3338 N ILE B 179 16.429 -9.975 12.170 1.00 39.80 N
+ATOM 3339 CA ILE B 179 17.573 -10.058 11.236 1.00 38.84 C
+ATOM 3340 C ILE B 179 17.335 -11.178 10.198 1.00 43.32 C
+ATOM 3341 O ILE B 179 17.488 -11.020 8.971 1.00 40.13 O
+ATOM 3342 CB ILE B 179 18.854 -10.289 12.098 1.00 31.91 C
+ATOM 3343 CG1 ILE B 179 19.098 -9.010 12.878 1.00 35.72 C
+ATOM 3344 CG2 ILE B 179 20.069 -10.678 11.263 1.00 27.69 C
+ATOM 3345 CD1 ILE B 179 20.025 -9.320 14.055 1.00 36.39 C
+ATOM 3346 N GLY B 180 16.929 -12.340 10.721 1.00 42.11 N
+ATOM 3347 CA GLY B 180 16.545 -13.482 9.909 1.00 42.78 C
+ATOM 3348 C GLY B 180 15.340 -13.184 9.033 1.00 37.36 C
+ATOM 3349 O GLY B 180 15.316 -13.596 7.867 1.00 40.42 O
+ATOM 3350 N TYR B 181 14.385 -12.422 9.564 1.00 30.34 N
+ATOM 3351 CA TYR B 181 13.187 -12.028 8.833 1.00 38.82 C
+ATOM 3352 C TYR B 181 13.573 -11.209 7.599 1.00 47.26 C
+ATOM 3353 O TYR B 181 13.094 -11.535 6.495 1.00 55.98 O
+ATOM 3354 CB TYR B 181 12.325 -11.226 9.765 1.00 38.26 C
+ATOM 3355 CG TYR B 181 10.953 -10.839 9.278 1.00 46.12 C
+ATOM 3356 CD1 TYR B 181 10.811 -9.870 8.305 1.00 49.42 C
+ATOM 3357 CD2 TYR B 181 9.857 -11.478 9.808 1.00 45.31 C
+ATOM 3358 CE1 TYR B 181 9.568 -9.531 7.844 1.00 46.78 C
+ATOM 3359 CE2 TYR B 181 8.602 -11.142 9.354 1.00 47.51 C
+ATOM 3360 CZ TYR B 181 8.482 -10.175 8.377 1.00 46.61 C
+ATOM 3361 OH TYR B 181 7.246 -9.825 7.918 1.00 45.71 O
+ATOM 3362 N TYR B 182 14.426 -10.174 7.690 1.00 44.20 N
+ATOM 3363 CA TYR B 182 14.753 -9.392 6.499 1.00 47.78 C
+ATOM 3364 C TYR B 182 15.852 -9.972 5.611 1.00 49.97 C
+ATOM 3365 O TYR B 182 15.966 -9.659 4.416 1.00 45.63 O
+ATOM 3366 CB TYR B 182 15.069 -7.958 6.953 1.00 42.86 C
+ATOM 3367 CG TYR B 182 13.775 -7.321 7.462 1.00 45.91 C
+ATOM 3368 CD1 TYR B 182 12.767 -7.023 6.568 1.00 43.06 C
+ATOM 3369 CD2 TYR B 182 13.578 -7.087 8.822 1.00 47.20 C
+ATOM 3370 CE1 TYR B 182 11.572 -6.504 7.028 1.00 43.58 C
+ATOM 3371 CE2 TYR B 182 12.386 -6.568 9.292 1.00 43.33 C
+ATOM 3372 CZ TYR B 182 11.385 -6.283 8.379 1.00 49.85 C
+ATOM 3373 OH TYR B 182 10.162 -5.801 8.822 1.00 50.75 O
+ATOM 3374 N SER B 183 16.662 -10.877 6.157 1.00 51.68 N
+ATOM 3375 CA SER B 183 17.601 -11.622 5.333 1.00 48.81 C
+ATOM 3376 C SER B 183 16.747 -12.501 4.427 1.00 43.84 C
+ATOM 3377 O SER B 183 17.052 -12.660 3.255 1.00 43.23 O
+ATOM 3378 CB SER B 183 18.502 -12.499 6.199 1.00 51.07 C
+ATOM 3379 OG SER B 183 19.345 -11.740 7.071 1.00 58.60 O
+ATOM 3380 N LYS B 184 15.635 -13.044 4.927 1.00 43.13 N
+ATOM 3381 CA LYS B 184 14.749 -13.857 4.124 1.00 51.50 C
+ATOM 3382 C LYS B 184 14.102 -13.024 3.010 1.00 52.75 C
+ATOM 3383 O LYS B 184 14.030 -13.471 1.857 1.00 49.50 O
+ATOM 3384 CB LYS B 184 13.717 -14.454 5.044 1.00 51.29 C
+ATOM 3385 CG LYS B 184 13.582 -15.907 4.672 1.00 62.88 C
+ATOM 3386 CD LYS B 184 12.570 -16.571 5.581 1.00 70.91 C
+ATOM 3387 CE LYS B 184 11.906 -17.753 4.883 1.00 77.63 C
+ATOM 3388 NZ LYS B 184 12.859 -18.748 4.423 1.00 84.36 N
+ATOM 3389 N GLU B 185 13.683 -11.791 3.336 1.00 51.88 N
+ATOM 3390 CA GLU B 185 13.140 -10.855 2.362 1.00 46.95 C
+ATOM 3391 C GLU B 185 14.194 -10.465 1.351 1.00 43.00 C
+ATOM 3392 O GLU B 185 13.906 -10.499 0.162 1.00 52.61 O
+ATOM 3393 CB GLU B 185 12.653 -9.562 2.985 1.00 53.16 C
+ATOM 3394 CG GLU B 185 11.594 -9.691 4.074 1.00 61.26 C
+ATOM 3395 CD GLU B 185 10.250 -10.229 3.612 1.00 67.26 C
+ATOM 3396 OE1 GLU B 185 9.681 -9.691 2.651 1.00 66.62 O
+ATOM 3397 OE2 GLU B 185 9.783 -11.186 4.233 1.00 71.90 O
+ATOM 3398 N ALA B 186 15.420 -10.109 1.709 1.00 40.59 N
+ATOM 3399 CA ALA B 186 16.434 -9.751 0.746 1.00 42.91 C
+ATOM 3400 C ALA B 186 16.758 -10.958 -0.128 1.00 56.53 C
+ATOM 3401 O ALA B 186 17.130 -10.784 -1.296 1.00 58.06 O
+ATOM 3402 CB ALA B 186 17.704 -9.293 1.450 1.00 44.61 C
+ATOM 3403 N GLU B 187 16.612 -12.187 0.413 1.00 60.15 N
+ATOM 3404 CA GLU B 187 16.847 -13.418 -0.321 1.00 60.33 C
+ATOM 3405 C GLU B 187 15.784 -13.607 -1.362 1.00 66.23 C
+ATOM 3406 O GLU B 187 16.080 -14.055 -2.473 1.00 68.06 O
+ATOM 3407 CB GLU B 187 16.812 -14.616 0.575 1.00 61.81 C
+ATOM 3408 CG GLU B 187 18.216 -14.898 1.052 1.00 67.86 C
+ATOM 3409 CD GLU B 187 18.290 -15.875 2.214 1.00 73.10 C
+ATOM 3410 OE1 GLU B 187 17.588 -16.903 2.226 1.00 72.53 O
+ATOM 3411 OE2 GLU B 187 19.075 -15.565 3.111 1.00 77.23 O
+ATOM 3412 N ALA B 188 14.542 -13.302 -0.992 1.00 67.26 N
+ATOM 3413 CA ALA B 188 13.470 -13.341 -1.966 1.00 74.45 C
+ATOM 3414 C ALA B 188 13.616 -12.206 -2.999 1.00 76.90 C
+ATOM 3415 O ALA B 188 13.232 -12.374 -4.156 1.00 82.38 O
+ATOM 3416 CB ALA B 188 12.129 -13.217 -1.243 1.00 72.36 C
+ATOM 3417 N GLY B 189 14.202 -11.058 -2.628 1.00 77.17 N
+ATOM 3418 CA GLY B 189 14.364 -9.915 -3.522 1.00 72.41 C
+ATOM 3419 C GLY B 189 13.493 -8.711 -3.145 1.00 69.07 C
+ATOM 3420 O GLY B 189 13.538 -7.675 -3.813 1.00 73.50 O
+ATOM 3421 N ASN B 190 12.734 -8.731 -2.054 1.00 61.51 N
+ATOM 3422 CA ASN B 190 11.857 -7.621 -1.673 1.00 70.48 C
+ATOM 3423 C ASN B 190 12.427 -6.494 -0.779 1.00 74.21 C
+ATOM 3424 O ASN B 190 11.682 -5.679 -0.192 1.00 70.23 O
+ATOM 3425 CB ASN B 190 10.626 -8.230 -1.010 1.00 75.90 C
+ATOM 3426 CG ASN B 190 9.830 -9.076 -1.984 1.00 77.13 C
+ATOM 3427 OD1 ASN B 190 10.391 -9.813 -2.800 1.00 74.64 O
+ATOM 3428 ND2 ASN B 190 8.509 -8.997 -1.943 1.00 80.02 N
+ATOM 3429 N THR B 191 13.768 -6.447 -0.673 1.00 70.29 N
+ATOM 3430 CA THR B 191 14.517 -5.469 0.095 1.00 64.41 C
+ATOM 3431 C THR B 191 16.001 -5.700 -0.165 1.00 66.65 C
+ATOM 3432 O THR B 191 16.378 -6.717 -0.770 1.00 60.96 O
+ATOM 3433 CB THR B 191 14.198 -5.634 1.584 1.00 66.21 C
+ATOM 3434 OG1 THR B 191 14.298 -4.283 1.981 1.00 64.16 O
+ATOM 3435 CG2 THR B 191 15.057 -6.599 2.433 1.00 62.97 C
+ATOM 3436 N LYS B 192 16.855 -4.768 0.252 1.00 70.21 N
+ATOM 3437 CA LYS B 192 18.291 -4.952 0.111 1.00 72.86 C
+ATOM 3438 C LYS B 192 18.764 -4.923 1.548 1.00 67.41 C
+ATOM 3439 O LYS B 192 18.313 -4.056 2.304 1.00 71.61 O
+ATOM 3440 CB LYS B 192 18.900 -3.812 -0.684 1.00 80.64 C
+ATOM 3441 CG LYS B 192 20.250 -4.146 -1.329 1.00 88.95 C
+ATOM 3442 CD LYS B 192 20.300 -3.481 -2.721 1.00 97.79 C
+ATOM 3443 CE LYS B 192 21.563 -3.796 -3.543 1.00 99.49 C
+ATOM 3444 NZ LYS B 192 21.475 -3.263 -4.900 1.00 99.52 N
+ATOM 3445 N TYR B 193 19.605 -5.870 1.956 1.00 59.13 N
+ATOM 3446 CA TYR B 193 20.007 -5.995 3.348 1.00 51.42 C
+ATOM 3447 C TYR B 193 21.475 -5.674 3.399 1.00 50.30 C
+ATOM 3448 O TYR B 193 22.225 -6.113 2.528 1.00 58.56 O
+ATOM 3449 CB TYR B 193 19.789 -7.448 3.901 1.00 51.95 C
+ATOM 3450 CG TYR B 193 19.830 -7.589 5.443 1.00 50.77 C
+ATOM 3451 CD1 TYR B 193 21.034 -7.723 6.129 1.00 42.82 C
+ATOM 3452 CD2 TYR B 193 18.638 -7.507 6.159 1.00 43.90 C
+ATOM 3453 CE1 TYR B 193 21.019 -7.750 7.509 1.00 43.54 C
+ATOM 3454 CE2 TYR B 193 18.622 -7.541 7.537 1.00 40.11 C
+ATOM 3455 CZ TYR B 193 19.816 -7.657 8.200 1.00 42.88 C
+ATOM 3456 OH TYR B 193 19.808 -7.665 9.580 1.00 40.73 O
+ATOM 3457 N ALA B 194 21.911 -4.909 4.387 1.00 46.20 N
+ATOM 3458 CA ALA B 194 23.319 -4.659 4.592 1.00 45.47 C
+ATOM 3459 C ALA B 194 23.613 -4.445 6.074 1.00 50.71 C
+ATOM 3460 O ALA B 194 22.818 -3.873 6.829 1.00 54.61 O
+ATOM 3461 CB ALA B 194 23.763 -3.418 3.867 1.00 48.73 C
+ATOM 3462 N LYS B 195 24.736 -4.965 6.522 1.00 51.89 N
+ATOM 3463 CA LYS B 195 25.150 -4.813 7.904 1.00 61.05 C
+ATOM 3464 C LYS B 195 26.296 -3.810 7.979 1.00 55.55 C
+ATOM 3465 O LYS B 195 27.131 -3.770 7.067 1.00 67.88 O
+ATOM 3466 CB LYS B 195 25.571 -6.185 8.392 1.00 64.89 C
+ATOM 3467 CG LYS B 195 26.011 -6.336 9.829 1.00 67.96 C
+ATOM 3468 CD LYS B 195 26.525 -7.749 9.787 1.00 75.81 C
+ATOM 3469 CE LYS B 195 27.016 -8.210 11.116 1.00 77.92 C
+ATOM 3470 NZ LYS B 195 27.672 -9.479 10.905 1.00 84.89 N
+ATOM 3471 N VAL B 196 26.387 -2.977 9.004 1.00 48.29 N
+ATOM 3472 CA VAL B 196 27.505 -2.054 9.101 1.00 46.39 C
+ATOM 3473 C VAL B 196 28.178 -2.349 10.421 1.00 41.83 C
+ATOM 3474 O VAL B 196 27.534 -2.805 11.368 1.00 40.02 O
+ATOM 3475 CB VAL B 196 27.062 -0.525 9.050 1.00 47.76 C
+ATOM 3476 CG1 VAL B 196 26.316 -0.307 7.727 1.00 38.52 C
+ATOM 3477 CG2 VAL B 196 26.160 -0.104 10.220 1.00 45.69 C
+ATOM 3478 N ASP B 197 29.478 -2.141 10.509 1.00 42.45 N
+ATOM 3479 CA ASP B 197 30.176 -2.289 11.771 1.00 47.11 C
+ATOM 3480 C ASP B 197 29.876 -1.025 12.567 1.00 44.78 C
+ATOM 3481 O ASP B 197 30.469 0.031 12.315 1.00 45.82 O
+ATOM 3482 CB ASP B 197 31.681 -2.416 11.515 1.00 47.13 C
+ATOM 3483 CG ASP B 197 32.619 -2.512 12.723 1.00 47.42 C
+ATOM 3484 OD1 ASP B 197 32.148 -2.531 13.857 1.00 42.49 O
+ATOM 3485 OD2 ASP B 197 33.829 -2.595 12.509 1.00 50.76 O
+ATOM 3486 N GLY B 198 28.996 -1.106 13.556 1.00 38.00 N
+ATOM 3487 CA GLY B 198 28.672 0.058 14.330 1.00 36.33 C
+ATOM 3488 C GLY B 198 29.810 0.469 15.275 1.00 44.24 C
+ATOM 3489 O GLY B 198 29.575 1.415 16.029 1.00 48.83 O
+ATOM 3490 N THR B 199 31.017 -0.141 15.336 1.00 44.16 N
+ATOM 3491 CA THR B 199 32.052 0.254 16.304 1.00 48.27 C
+ATOM 3492 C THR B 199 33.026 1.340 15.822 1.00 48.50 C
+ATOM 3493 O THR B 199 33.764 1.943 16.638 1.00 46.73 O
+ATOM 3494 CB THR B 199 32.878 -1.002 16.777 1.00 47.18 C
+ATOM 3495 OG1 THR B 199 33.614 -1.522 15.674 1.00 45.37 O
+ATOM 3496 CG2 THR B 199 31.962 -2.090 17.337 1.00 49.24 C
+ATOM 3497 N LYS B 200 32.955 1.525 14.479 1.00 45.04 N
+ATOM 3498 CA LYS B 200 33.734 2.494 13.729 1.00 37.02 C
+ATOM 3499 C LYS B 200 33.315 3.880 14.144 1.00 41.61 C
+ATOM 3500 O LYS B 200 32.166 4.094 14.548 1.00 44.98 O
+ATOM 3501 CB LYS B 200 33.494 2.447 12.262 1.00 38.35 C
+ATOM 3502 CG LYS B 200 34.150 1.348 11.551 1.00 41.43 C
+ATOM 3503 CD LYS B 200 33.829 1.627 10.119 1.00 46.23 C
+ATOM 3504 CE LYS B 200 34.381 0.466 9.329 1.00 48.49 C
+ATOM 3505 NZ LYS B 200 34.303 0.796 7.931 1.00 52.79 N
+ATOM 3506 N PRO B 201 34.211 4.859 14.019 1.00 43.75 N
+ATOM 3507 CA PRO B 201 33.901 6.270 14.226 1.00 43.54 C
+ATOM 3508 C PRO B 201 32.650 6.691 13.485 1.00 37.46 C
+ATOM 3509 O PRO B 201 32.403 6.261 12.351 1.00 35.82 O
+ATOM 3510 CB PRO B 201 35.150 6.983 13.766 1.00 46.15 C
+ATOM 3511 CG PRO B 201 36.205 6.004 14.203 1.00 44.17 C
+ATOM 3512 CD PRO B 201 35.631 4.672 13.750 1.00 38.45 C
+ATOM 3513 N VAL B 202 31.894 7.575 14.131 1.00 39.22 N
+ATOM 3514 CA VAL B 202 30.613 8.034 13.612 1.00 40.34 C
+ATOM 3515 C VAL B 202 30.708 8.446 12.143 1.00 42.18 C
+ATOM 3516 O VAL B 202 29.909 8.016 11.304 1.00 48.53 O
+ATOM 3517 CB VAL B 202 30.136 9.183 14.530 1.00 37.09 C
+ATOM 3518 CG1 VAL B 202 28.956 9.914 13.900 1.00 38.08 C
+ATOM 3519 CG2 VAL B 202 29.672 8.607 15.867 1.00 32.16 C
+ATOM 3520 N ALA B 203 31.778 9.168 11.776 1.00 46.01 N
+ATOM 3521 CA ALA B 203 31.964 9.635 10.406 1.00 33.87 C
+ATOM 3522 C ALA B 203 32.311 8.511 9.476 1.00 36.96 C
+ATOM 3523 O ALA B 203 31.962 8.594 8.306 1.00 47.24 O
+ATOM 3524 CB ALA B 203 33.077 10.643 10.321 1.00 40.62 C
+ATOM 3525 N GLU B 204 32.954 7.454 9.967 1.00 33.26 N
+ATOM 3526 CA GLU B 204 33.291 6.328 9.158 1.00 39.10 C
+ATOM 3527 C GLU B 204 32.050 5.508 8.898 1.00 45.64 C
+ATOM 3528 O GLU B 204 31.827 5.081 7.758 1.00 51.75 O
+ATOM 3529 CB GLU B 204 34.346 5.500 9.856 1.00 53.18 C
+ATOM 3530 CG GLU B 204 35.763 5.912 9.440 1.00 66.23 C
+ATOM 3531 CD GLU B 204 36.888 5.111 10.100 1.00 76.78 C
+ATOM 3532 OE1 GLU B 204 36.927 3.869 10.030 1.00 77.38 O
+ATOM 3533 OE2 GLU B 204 37.745 5.765 10.698 1.00 86.08 O
+ATOM 3534 N VAL B 205 31.197 5.318 9.908 1.00 44.14 N
+ATOM 3535 CA VAL B 205 29.926 4.622 9.719 1.00 40.70 C
+ATOM 3536 C VAL B 205 29.133 5.491 8.736 1.00 36.73 C
+ATOM 3537 O VAL B 205 28.571 4.951 7.790 1.00 37.11 O
+ATOM 3538 CB VAL B 205 29.144 4.474 11.066 1.00 37.34 C
+ATOM 3539 CG1 VAL B 205 27.871 3.668 10.822 1.00 37.31 C
+ATOM 3540 CG2 VAL B 205 29.968 3.717 12.112 1.00 33.15 C
+ATOM 3541 N ARG B 206 29.131 6.822 8.839 1.00 33.63 N
+ATOM 3542 CA ARG B 206 28.437 7.674 7.897 1.00 43.93 C
+ATOM 3543 C ARG B 206 28.896 7.366 6.452 1.00 45.24 C
+ATOM 3544 O ARG B 206 28.087 7.178 5.536 1.00 42.62 O
+ATOM 3545 CB ARG B 206 28.711 9.146 8.304 1.00 50.94 C
+ATOM 3546 CG ARG B 206 28.074 10.180 7.350 1.00 69.00 C
+ATOM 3547 CD ARG B 206 28.509 11.672 7.368 1.00 82.22 C
+ATOM 3548 NE ARG B 206 27.921 12.365 6.204 1.00 99.36 N
+ATOM 3549 CZ ARG B 206 27.967 13.692 5.942 1.00104.25 C
+ATOM 3550 NH1 ARG B 206 28.593 14.554 6.748 1.00107.32 N
+ATOM 3551 NH2 ARG B 206 27.366 14.169 4.839 1.00104.42 N
+ATOM 3552 N ALA B 207 30.205 7.188 6.278 1.00 43.83 N
+ATOM 3553 CA ALA B 207 30.781 6.879 4.985 1.00 46.95 C
+ATOM 3554 C ALA B 207 30.343 5.539 4.444 1.00 45.84 C
+ATOM 3555 O ALA B 207 30.001 5.461 3.274 1.00 46.56 O
+ATOM 3556 CB ALA B 207 32.279 6.830 5.047 1.00 47.27 C
+ATOM 3557 N ASP B 208 30.344 4.480 5.252 1.00 46.78 N
+ATOM 3558 CA ASP B 208 29.902 3.156 4.816 1.00 50.67 C
+ATOM 3559 C ASP B 208 28.443 3.200 4.412 1.00 51.20 C
+ATOM 3560 O ASP B 208 27.995 2.522 3.488 1.00 53.49 O
+ATOM 3561 CB ASP B 208 29.959 2.082 5.899 1.00 53.42 C
+ATOM 3562 CG ASP B 208 31.260 1.885 6.654 1.00 60.20 C
+ATOM 3563 OD1 ASP B 208 32.312 1.857 6.020 1.00 63.21 O
+ATOM 3564 OD2 ASP B 208 31.217 1.748 7.880 1.00 69.30 O
+ATOM 3565 N LEU B 209 27.694 3.992 5.161 1.00 47.37 N
+ATOM 3566 CA LEU B 209 26.288 4.114 4.933 1.00 47.53 C
+ATOM 3567 C LEU B 209 26.049 4.822 3.657 1.00 47.99 C
+ATOM 3568 O LEU B 209 25.261 4.318 2.867 1.00 52.26 O
+ATOM 3569 CB LEU B 209 25.613 4.894 6.012 1.00 49.50 C
+ATOM 3570 CG LEU B 209 25.268 4.068 7.202 1.00 46.22 C
+ATOM 3571 CD1 LEU B 209 24.648 4.994 8.221 1.00 48.83 C
+ATOM 3572 CD2 LEU B 209 24.327 2.937 6.815 1.00 43.54 C
+ATOM 3573 N GLU B 210 26.761 5.929 3.463 1.00 51.95 N
+ATOM 3574 CA GLU B 210 26.684 6.680 2.232 1.00 58.59 C
+ATOM 3575 C GLU B 210 27.003 5.725 1.076 1.00 66.91 C
+ATOM 3576 O GLU B 210 26.240 5.674 0.106 1.00 69.90 O
+ATOM 3577 CB GLU B 210 27.670 7.820 2.326 1.00 62.46 C
+ATOM 3578 CG GLU B 210 26.938 9.124 2.095 1.00 68.16 C
+ATOM 3579 CD GLU B 210 27.760 10.383 2.306 1.00 72.92 C
+ATOM 3580 OE1 GLU B 210 28.160 10.690 3.426 1.00 75.42 O
+ATOM 3581 OE2 GLU B 210 27.993 11.077 1.327 1.00 82.20 O
+ATOM 3582 N LYS B 211 28.035 4.863 1.200 1.00 70.99 N
+ATOM 3583 CA LYS B 211 28.363 3.832 0.200 1.00 72.23 C
+ATOM 3584 C LYS B 211 27.245 2.866 -0.160 1.00 65.61 C
+ATOM 3585 O LYS B 211 27.123 2.452 -1.311 1.00 63.49 O
+ATOM 3586 CB LYS B 211 29.542 2.949 0.631 1.00 78.16 C
+ATOM 3587 CG LYS B 211 30.865 3.601 0.328 1.00 89.99 C
+ATOM 3588 CD LYS B 211 31.986 2.898 1.057 1.00100.42 C
+ATOM 3589 CE LYS B 211 33.189 3.836 1.020 1.00110.36 C
+ATOM 3590 NZ LYS B 211 34.131 3.549 2.092 1.00119.63 N
+ATOM 3591 N ILE B 212 26.432 2.465 0.807 1.00 61.38 N
+ATOM 3592 CA ILE B 212 25.357 1.553 0.525 1.00 55.20 C
+ATOM 3593 C ILE B 212 24.174 2.273 -0.092 1.00 54.42 C
+ATOM 3594 O ILE B 212 23.385 1.622 -0.779 1.00 61.03 O
+ATOM 3595 CB ILE B 212 25.037 0.858 1.846 1.00 51.74 C
+ATOM 3596 CG1 ILE B 212 26.216 -0.034 2.178 1.00 54.21 C
+ATOM 3597 CG2 ILE B 212 23.793 0.014 1.764 1.00 48.78 C
+ATOM 3598 CD1 ILE B 212 26.365 -0.365 3.677 1.00 61.40 C
+ATOM 3599 N LEU B 213 23.973 3.574 0.049 1.00 51.82 N
+ATOM 3600 CA LEU B 213 22.748 4.118 -0.514 1.00 63.92 C
+ATOM 3601 C LEU B 213 22.827 4.814 -1.894 1.00 73.67 C
+ATOM 3602 O LEU B 213 22.087 4.433 -2.815 1.00 74.46 O
+ATOM 3603 CB LEU B 213 22.166 5.010 0.596 1.00 59.88 C
+ATOM 3604 CG LEU B 213 21.938 4.358 1.991 1.00 52.75 C
+ATOM 3605 CD1 LEU B 213 21.434 5.431 2.933 1.00 54.79 C
+ATOM 3606 CD2 LEU B 213 20.923 3.223 1.949 1.00 44.34 C
+ATOM 3607 N GLY B 214 23.691 5.789 -2.152 1.00 80.17 N
+ATOM 3608 CA GLY B 214 23.754 6.450 -3.450 1.00 88.01 C
+ATOM 3609 C GLY B 214 24.173 7.911 -3.276 1.00 94.23 C
+ATOM 3610 O GLY B 214 24.730 8.496 -4.208 1.00 94.94 O
+ATOM 3611 OXT GLY B 214 23.962 8.474 -2.196 1.00 95.71 O
+TER 3612 GLY B 214
+HETATM 3613 PA AP5 B 215 22.201 6.089 19.452 1.00 37.30 P
+HETATM 3614 O1A AP5 B 215 22.416 6.745 18.144 1.00 32.10 O
+HETATM 3615 O2A AP5 B 215 21.476 6.864 20.478 1.00 33.29 O
+HETATM 3616 O3A AP5 B 215 21.770 4.549 19.290 1.00 30.65 O
+HETATM 3617 PB AP5 B 215 20.344 3.896 18.917 1.00 31.29 P
+HETATM 3618 O1B AP5 B 215 20.857 2.643 18.377 1.00 33.55 O
+HETATM 3619 O2B AP5 B 215 19.561 4.700 17.951 1.00 44.91 O
+HETATM 3620 O3B AP5 B 215 19.580 3.556 20.304 1.00 43.60 O
+HETATM 3621 PG AP5 B 215 17.985 3.557 20.606 1.00 45.69 P
+HETATM 3622 O1G AP5 B 215 17.476 4.926 20.866 1.00 43.69 O
+HETATM 3623 O2G AP5 B 215 17.289 2.760 19.558 1.00 55.55 O
+HETATM 3624 O3G AP5 B 215 18.082 2.680 21.967 1.00 58.11 O
+HETATM 3625 PD AP5 B 215 16.945 2.326 23.101 1.00 63.48 P
+HETATM 3626 O1D AP5 B 215 16.975 0.838 23.248 1.00 48.98 O
+HETATM 3627 O2D AP5 B 215 17.317 3.050 24.336 1.00 60.31 O
+HETATM 3628 O3D AP5 B 215 15.397 2.495 22.602 1.00 62.90 O
+HETATM 3629 PE AP5 B 215 14.541 3.700 21.938 1.00 54.65 P
+HETATM 3630 O1E AP5 B 215 14.837 5.089 22.338 1.00 72.00 O
+HETATM 3631 O2E AP5 B 215 14.021 3.514 20.557 1.00 43.23 O
+HETATM 3632 O5F AP5 B 215 23.694 5.984 20.010 1.00 31.76 O
+HETATM 3633 C5F AP5 B 215 23.863 5.533 21.343 1.00 30.61 C
+HETATM 3634 C4F AP5 B 215 24.868 6.417 22.062 1.00 35.15 C
+HETATM 3635 O4F AP5 B 215 26.197 6.203 21.583 1.00 39.02 O
+HETATM 3636 C3F AP5 B 215 24.677 7.945 21.924 1.00 31.89 C
+HETATM 3637 O3F AP5 B 215 25.346 8.532 23.016 1.00 31.03 O
+HETATM 3638 C2F AP5 B 215 25.443 8.295 20.628 1.00 36.27 C
+HETATM 3639 O2F AP5 B 215 26.145 9.548 20.716 1.00 33.15 O
+HETATM 3640 C1F AP5 B 215 26.421 7.150 20.562 1.00 38.30 C
+HETATM 3641 N9A AP5 B 215 27.112 6.824 19.345 1.00 34.90 N
+HETATM 3642 C8A AP5 B 215 26.489 6.695 18.135 1.00 29.88 C
+HETATM 3643 N7A AP5 B 215 27.295 6.275 17.223 1.00 29.22 N
+HETATM 3644 C5A AP5 B 215 28.529 6.124 17.797 1.00 35.00 C
+HETATM 3645 C6A AP5 B 215 29.735 5.649 17.285 1.00 40.51 C
+HETATM 3646 N6A AP5 B 215 29.771 5.190 16.024 1.00 36.93 N
+HETATM 3647 N1A AP5 B 215 30.793 5.669 18.130 1.00 42.32 N
+HETATM 3648 C2A AP5 B 215 30.595 6.010 19.414 1.00 34.63 C
+HETATM 3649 N3A AP5 B 215 29.508 6.464 20.023 1.00 36.24 N
+HETATM 3650 C4A AP5 B 215 28.440 6.487 19.168 1.00 33.97 C
+HETATM 3651 O5J AP5 B 215 13.178 3.399 22.744 1.00 56.44 O
+HETATM 3652 C5J AP5 B 215 13.096 3.370 24.177 1.00 45.38 C
+HETATM 3653 C4J AP5 B 215 11.797 2.648 24.646 1.00 39.49 C
+HETATM 3654 O4J AP5 B 215 10.642 3.052 23.872 1.00 38.58 O
+HETATM 3655 C3J AP5 B 215 11.850 1.118 24.442 1.00 38.37 C
+HETATM 3656 O3J AP5 B 215 12.535 0.450 25.490 1.00 35.76 O
+HETATM 3657 C2J AP5 B 215 10.402 0.698 24.318 1.00 34.32 C
+HETATM 3658 O2J AP5 B 215 9.706 0.889 25.519 1.00 36.76 O
+HETATM 3659 C1J AP5 B 215 10.066 1.830 23.414 1.00 35.78 C
+HETATM 3660 N9B AP5 B 215 9.747 1.616 22.023 1.00 36.11 N
+HETATM 3661 C8B AP5 B 215 10.182 2.374 20.967 1.00 34.84 C
+HETATM 3662 N7B AP5 B 215 9.821 1.888 19.815 1.00 38.30 N
+HETATM 3663 C5B AP5 B 215 9.099 0.730 20.087 1.00 37.03 C
+HETATM 3664 C6B AP5 B 215 8.487 -0.225 19.272 1.00 36.27 C
+HETATM 3665 N6B AP5 B 215 8.669 -0.222 17.956 1.00 35.20 N
+HETATM 3666 N1B AP5 B 215 7.799 -1.199 19.879 1.00 41.59 N
+HETATM 3667 C2B AP5 B 215 7.763 -1.199 21.208 1.00 40.84 C
+HETATM 3668 N3B AP5 B 215 8.373 -0.426 22.108 1.00 36.71 N
+HETATM 3669 C4B AP5 B 215 9.034 0.571 21.499 1.00 30.89 C
+HETATM 3670 O HOH B 532 27.600 25.972 30.626 1.00 79.23 O
+HETATM 3671 O HOH B 533 17.974 30.572 30.201 1.00 91.93 O
+HETATM 3672 O HOH B 601 14.262 -4.102 21.572 1.00 29.20 O
+HETATM 3673 O HOH B 602 14.508 -3.401 24.138 1.00 44.68 O
+HETATM 3674 O HOH B 603 12.809 2.042 27.522 1.00 48.81 O
+HETATM 3675 O HOH B 604 25.424 10.836 18.328 1.00 26.42 O
+HETATM 3676 O HOH B 605 27.080 5.928 14.673 1.00 29.83 O
+HETATM 3677 O HOH B 606 27.155 3.168 14.978 1.00 33.75 O
+HETATM 3678 O HOH B 607 13.146 4.311 18.331 1.00 61.95 O
+HETATM 3679 O HOH B 608 9.283 -10.922 17.996 1.00 40.47 O
+HETATM 3680 O HOH B 609 23.684 -6.770 15.000 1.00 52.05 O
+HETATM 3681 O HOH B 610 27.294 22.690 20.713 1.00 22.54 O
+HETATM 3682 O HOH B 611 14.038 -1.934 14.863 1.00 36.23 O
+HETATM 3683 O HOH B 612 30.865 -1.257 8.032 1.00 42.48 O
+HETATM 3684 O HOH B 613 23.300 -4.486 16.874 1.00 50.62 O
+HETATM 3685 O HOH B 614 36.194 -0.357 15.183 1.00 40.67 O
+HETATM 3686 O HOH B 615 8.078 -6.158 6.927 1.00 41.50 O
+HETATM 3687 O HOH B 616 14.938 7.129 18.969 1.00 43.71 O
+HETATM 3688 O HOH B 617 12.624 7.473 28.626 1.00 53.66 O
+HETATM 3689 O HOH B 618 5.822 -5.075 21.277 1.00 40.77 O
+HETATM 3690 O HOH B 619 5.656 -8.926 20.631 1.00 40.57 O
+HETATM 3691 O HOH B 620 18.812 7.475 20.270 1.00 43.71 O
+HETATM 3692 O HOH B 621 27.161 -3.197 28.023 1.00 43.36 O
+HETATM 3693 O HOH B 622 16.306 -2.364 18.273 1.00 56.48 O
+HETATM 3694 O HOH B 623 26.262 -6.933 4.576 1.00 62.51 O
+HETATM 3695 O HOH B 624 27.732 17.512 27.265 1.00 39.28 O
+HETATM 3696 O HOH B 625 16.075 -3.508 15.805 1.00 53.75 O
+HETATM 3697 O HOH B 626 24.777 14.775 17.003 1.00 65.65 O
+HETATM 3698 O HOH B 627 11.433 13.919 26.646 1.00 52.58 O
+HETATM 3699 O HOH B 628 21.935 -8.276 16.655 1.00 64.77 O
+HETATM 3700 O HOH B 629 12.653 -2.910 25.978 1.00 41.70 O
+HETATM 3701 O HOH B 630 10.547 13.281 22.576 1.00 47.66 O
+HETATM 3702 O HOH B 631 29.546 -0.764 28.431 1.00 49.67 O
+HETATM 3703 O HOH B 632 10.057 10.512 14.629 1.00 68.20 O
+HETATM 3704 O HOH B 633 31.004 -6.079 12.407 1.00 63.45 O
+HETATM 3705 O HOH B 634 32.468 23.483 25.572 1.00 61.99 O
+HETATM 3706 O HOH B 635 16.481 11.283 21.359 1.00 44.47 O
+HETATM 3707 O HOH B 636 9.027 11.838 28.200 1.00 48.83 O
+HETATM 3708 O HOH B 637 30.543 16.996 26.794 1.00 50.07 O
+HETATM 3709 O HOH B 638 -2.574 -3.060 14.718 1.00 62.64 O
+HETATM 3710 O HOH B 639 14.859 14.032 27.367 1.00 54.32 O
+HETATM 3711 O HOH B 640 13.655 0.649 12.731 1.00 68.16 O
+HETATM 3712 O HOH B 641 18.067 9.039 22.417 1.00 44.96 O
+HETATM 3713 O HOH B 642 26.493 15.961 31.982 1.00 57.56 O
+HETATM 3714 O HOH B 643 3.860 11.813 19.839 1.00 53.65 O
+HETATM 3715 O HOH B 644 1.192 0.670 31.965 1.00 61.41 O
+HETATM 3716 O HOH B 645 13.301 12.513 22.066 1.00 38.82 O
+HETATM 3717 O HOH B 646 7.241 0.734 35.037 1.00 68.91 O
+HETATM 3718 O HOH B 647 -3.144 -0.652 16.183 1.00 35.82 O
+HETATM 3719 O HOH B 648 14.823 21.679 17.608 1.00 59.60 O
+HETATM 3720 O HOH B 649 26.485 -8.797 21.103 1.00 79.23 O
+HETATM 3721 O HOH B 650 5.979 16.827 22.814 1.00 56.88 O
+HETATM 3722 O HOH B 651 26.273 12.843 15.518 1.00 50.62 O
+HETATM 3723 O HOH B 652 28.605 17.145 9.953 1.00 70.21 O
+HETATM 3724 O HOH B 653 16.783 -6.342 14.912 1.00 70.08 O
+HETATM 3725 O HOH B 654 -0.379 13.042 1.442 1.00 60.69 O
+HETATM 3726 O HOH B 655 16.741 0.350 19.669 1.00 42.77 O
+HETATM 3727 O HOH B 656 24.251 -9.881 9.498 1.00 41.98 O
+HETATM 3728 O HOH B 657 11.420 13.205 17.112 1.00 54.84 O
+HETATM 3729 O HOH B 658 0.156 1.470 29.588 1.00 34.07 O
+HETATM 3730 O HOH B 659 0.068 -8.426 19.940 1.00 52.11 O
+HETATM 3731 O HOH B 660 -5.777 4.897 27.627 1.00 36.48 O
+HETATM 3732 O HOH B 661 18.421 26.044 26.361 1.00 45.14 O
+HETATM 3733 O HOH B 662 1.451 14.197 19.730 1.00 62.26 O
+HETATM 3734 O HOH B 663 33.486 19.697 22.158 1.00 54.81 O
+HETATM 3735 O HOH B 664 16.604 18.860 25.124 1.00 41.75 O
+HETATM 3736 O HOH B 665 23.409 27.189 31.356 1.00 49.04 O
+HETATM 3737 O HOH B 666 33.433 5.012 19.162 1.00 64.69 O
+HETATM 3738 O HOH B 667 24.702 -10.861 22.043 1.00 52.32 O
+HETATM 3739 O HOH B 668 18.202 29.291 18.618 1.00 42.27 O
+HETATM 3740 O HOH B 669 24.806 26.086 14.054 1.00 53.35 O
+HETATM 3741 O HOH B 670 3.413 2.498 37.269 1.00 81.37 O
+HETATM 3742 O HOH B 671 -3.637 0.822 13.866 1.00 40.98 O
+HETATM 3743 O HOH B 672 34.054 9.850 13.628 1.00 62.62 O
+HETATM 3744 O HOH B 673 0.636 19.313 27.366 1.00 95.62 O
+HETATM 3745 O HOH B 674 2.008 10.222 2.938 1.00 48.67 O
+HETATM 3746 O HOH B 675 24.219 -7.060 20.238 1.00 45.06 O
+HETATM 3747 O HOH B 676 22.044 28.201 29.205 1.00 47.66 O
+HETATM 3748 O HOH B 677 20.948 -7.852 -0.325 1.00 48.16 O
+HETATM 3749 O HOH B 678 5.720 16.059 0.775 1.00 79.93 O
+HETATM 3750 O HOH B 679 -7.668 9.530 28.979 1.00 57.70 O
+HETATM 3751 O HOH B 680 15.305 -1.481 -5.343 1.00 63.31 O
+HETATM 3752 O HOH B 681 6.179 -12.703 0.598 1.00 62.32 O
+HETATM 3753 O HOH B 682 14.527 13.865 29.996 1.00 63.43 O
+HETATM 3754 O HOH B 683 30.980 1.856 25.286 1.00 42.16 O
+HETATM 3755 O HOH B 684 20.040 10.695 27.163 1.00 42.75 O
+HETATM 3756 O HOH B 685 16.245 -2.027 21.032 1.00 53.14 O
+HETATM 3757 O HOH B 686 6.857 12.812 34.962 1.00 66.68 O
+HETATM 3758 O HOH B 687 0.721 -8.017 12.167 1.00 64.25 O
+HETATM 3759 O HOH B 688 23.427 -6.208 38.643 1.00 83.39 O
+HETATM 3760 O HOH B 689 33.202 9.472 16.354 1.00 49.00 O
+HETATM 3761 O HOH B 690 14.673 -17.530 0.817 1.00 58.58 O
+HETATM 3762 O HOH B 691 -3.896 -1.428 8.614 1.00 98.40 O
+HETATM 3763 O HOH B 692 29.993 13.720 9.810 1.00 73.33 O
+HETATM 3764 O HOH B 693 19.071 15.842 32.800 1.00 78.67 O
+HETATM 3765 O HOH B 694 32.008 19.405 24.569 1.00 63.58 O
+HETATM 3766 O HOH B 695 5.560 -13.800 16.544 1.00 93.11 O
+HETATM 3767 O HOH B 696 -1.792 -5.424 11.954 1.00 59.42 O
+HETATM 3768 O HOH B 697 10.148 7.509 29.811 1.00 66.17 O
+HETATM 3769 O HOH B 698 14.310 12.573 24.883 1.00 56.18 O
+HETATM 3770 O HOH B 699 6.123 -0.872 33.139 1.00 55.86 O
+HETATM 3771 O HOH B 700 28.749 24.817 28.172 1.00 53.60 O
+HETATM 3772 O HOH B 701 18.400 9.388 33.137 1.00 47.18 O
+HETATM 3773 O HOH B 702 35.070 7.944 19.914 1.00 56.91 O
+HETATM 3774 O HOH B 703 24.752 11.075 -3.179 1.00 67.32 O
+HETATM 3775 O HOH B 704 9.949 -9.523 -5.593 1.00 89.09 O
+HETATM 3776 O HOH B 705 9.942 19.330 23.088 1.00 64.17 O
+HETATM 3777 O HOH B 706 13.726 19.246 26.405 1.00 49.09 O
+HETATM 3778 O HOH B 707 31.961 13.776 7.446 1.00 73.55 O
+HETATM 3779 O HOH B 708 -0.822 10.816 18.021 1.00 95.39 O
+HETATM 3780 O HOH B 709 13.000 -3.184 -4.148 1.00 76.83 O
+HETATM 3781 O HOH B 710 14.202 16.495 4.958 1.00 76.08 O
+HETATM 3782 O HOH B 711 -1.174 -5.432 20.724 1.00 67.54 O
+HETATM 3783 O HOH B 712 3.128 11.513 32.191 1.00 70.79 O
+HETATM 3784 O HOH B 713 16.282 22.447 26.712 1.00 76.08 O
+HETATM 3785 O HOH B 714 18.971 28.066 29.665 1.00 89.64 O
+HETATM 3786 O HOH B 715 26.365 2.181 34.042 1.00 51.61 O
+HETATM 3787 O HOH B 716 23.727 3.680 35.684 1.00 70.58 O
+HETATM 3788 O HOH B 717 23.151 -12.467 24.419 1.00 79.25 O
+HETATM 3789 O HOH B 718 20.135 -10.789 -1.732 1.00 56.50 O
+HETATM 3790 O HOH B 719 6.636 6.283 -0.077 1.00 48.04 O
+HETATM 3791 O HOH B 720 32.218 10.973 5.537 1.00 62.14 O
+HETATM 3792 O HOH B 721 22.443 27.117 12.621 1.00 80.07 O
+HETATM 3793 O HOH B 722 26.616 18.010 15.049 1.00 85.62 O
+HETATM 3794 O HOH B 723 23.710 17.075 16.032 1.00 77.45 O
+HETATM 3795 O HOH B 724 11.615 23.280 22.798 1.00 67.20 O
+HETATM 3796 O HOH B 725 34.939 14.336 27.553 1.00 51.15 O
+HETATM 3797 O HOH B 726 11.124 -3.299 -2.129 1.00 72.53 O
+HETATM 3798 O HOH B 727 20.985 -10.100 27.399 1.00 57.72 O
+HETATM 3799 O HOH B 728 8.250 10.481 35.969 1.00 76.62 O
+HETATM 3800 O HOH B 729 14.948 -4.898 -3.489 1.00 58.26 O
+HETATM 3801 O HOH B 730 34.776 4.217 5.146 1.00 62.26 O
+HETATM 3802 O HOH B 731 16.727 -16.699 -3.703 1.00 61.27 O
+HETATM 3803 O HOH B 732 1.429 8.800 0.402 1.00 77.69 O
+HETATM 3804 O HOH B 733 24.241 12.734 13.411 1.00 67.64 O
+HETATM 3805 O HOH B 734 24.591 -9.996 12.367 1.00 68.65 O
+HETATM 3806 O HOH B 735 34.364 -6.362 12.342 1.00 70.58 O
+CONECT 1658 1659 1660 1661 1677
+CONECT 1659 1658
+CONECT 1660 1658
+CONECT 1661 1658 1662
+CONECT 1662 1661 1663 1664 1665
+CONECT 1663 1662
+CONECT 1664 1662
+CONECT 1665 1662 1666
+CONECT 1666 1665 1667 1668 1669
+CONECT 1667 1666
+CONECT 1668 1666
+CONECT 1669 1666 1670
+CONECT 1670 1669 1671 1672 1673
+CONECT 1671 1670
+CONECT 1672 1670
+CONECT 1673 1670 1674
+CONECT 1674 1673 1675 1676 1696
+CONECT 1675 1674
+CONECT 1676 1674
+CONECT 1677 1658 1678
+CONECT 1678 1677 1679
+CONECT 1679 1678 1680 1681
+CONECT 1680 1679 1685
+CONECT 1681 1679 1682 1683
+CONECT 1682 1681
+CONECT 1683 1681 1684 1685
+CONECT 1684 1683
+CONECT 1685 1680 1683 1686
+CONECT 1686 1685 1687 1695
+CONECT 1687 1686 1688
+CONECT 1688 1687 1689
+CONECT 1689 1688 1690 1695
+CONECT 1690 1689 1691 1692
+CONECT 1691 1690
+CONECT 1692 1690 1693
+CONECT 1693 1692 1694
+CONECT 1694 1693 1695
+CONECT 1695 1686 1689 1694
+CONECT 1696 1674 1697
+CONECT 1697 1696 1698
+CONECT 1698 1697 1699 1700
+CONECT 1699 1698 1704
+CONECT 1700 1698 1701 1702
+CONECT 1701 1700
+CONECT 1702 1700 1703 1704
+CONECT 1703 1702
+CONECT 1704 1699 1702 1705
+CONECT 1705 1704 1706 1714
+CONECT 1706 1705 1707
+CONECT 1707 1706 1708
+CONECT 1708 1707 1709 1714
+CONECT 1709 1708 1710 1711
+CONECT 1710 1709
+CONECT 1711 1709 1712
+CONECT 1712 1711 1713
+CONECT 1713 1712 1714
+CONECT 1714 1705 1708 1713
+CONECT 3613 3614 3615 3616 3632
+CONECT 3614 3613
+CONECT 3615 3613
+CONECT 3616 3613 3617
+CONECT 3617 3616 3618 3619 3620
+CONECT 3618 3617
+CONECT 3619 3617
+CONECT 3620 3617 3621
+CONECT 3621 3620 3622 3623 3624
+CONECT 3622 3621
+CONECT 3623 3621
+CONECT 3624 3621 3625
+CONECT 3625 3624 3626 3627 3628
+CONECT 3626 3625
+CONECT 3627 3625
+CONECT 3628 3625 3629
+CONECT 3629 3628 3630 3631 3651
+CONECT 3630 3629
+CONECT 3631 3629
+CONECT 3632 3613 3633
+CONECT 3633 3632 3634
+CONECT 3634 3633 3635 3636
+CONECT 3635 3634 3640
+CONECT 3636 3634 3637 3638
+CONECT 3637 3636
+CONECT 3638 3636 3639 3640
+CONECT 3639 3638
+CONECT 3640 3635 3638 3641
+CONECT 3641 3640 3642 3650
+CONECT 3642 3641 3643
+CONECT 3643 3642 3644
+CONECT 3644 3643 3645 3650
+CONECT 3645 3644 3646 3647
+CONECT 3646 3645
+CONECT 3647 3645 3648
+CONECT 3648 3647 3649
+CONECT 3649 3648 3650
+CONECT 3650 3641 3644 3649
+CONECT 3651 3629 3652
+CONECT 3652 3651 3653
+CONECT 3653 3652 3654 3655
+CONECT 3654 3653 3659
+CONECT 3655 3653 3656 3657
+CONECT 3656 3655
+CONECT 3657 3655 3658 3659
+CONECT 3658 3657
+CONECT 3659 3654 3657 3660
+CONECT 3660 3659 3661 3669
+CONECT 3661 3660 3662
+CONECT 3662 3661 3663
+CONECT 3663 3662 3664 3669
+CONECT 3664 3663 3665 3666
+CONECT 3665 3664
+CONECT 3666 3664 3667
+CONECT 3667 3666 3668
+CONECT 3668 3667 3669
+CONECT 3669 3660 3663 3668
+END
diff --git a/doc/tests/data/1E2Q.pdb b/doc/tests/data/1E2Q.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..a752e0719ed88711f2038846194f1e06cc1cdc4b
--- /dev/null
+++ b/doc/tests/data/1E2Q.pdb
@@ -0,0 +1,1998 @@
+ATOM 1 N ARG A 4 -8.627 65.141 3.488 1.00 38.55 N
+ATOM 2 CA ARG A 4 -8.922 65.673 4.855 1.00 35.09 C
+ATOM 3 C ARG A 4 -7.591 65.897 5.589 1.00 30.55 C
+ATOM 4 O ARG A 4 -6.916 64.915 5.878 1.00 30.50 O
+ATOM 5 CB ARG A 4 -9.786 64.699 5.627 1.00 38.16 C
+ATOM 6 CG ARG A 4 -11.076 64.312 4.915 1.00 45.58 C
+ATOM 7 CD ARG A 4 -11.760 63.157 5.636 1.00 50.56 C
+ATOM 8 NE ARG A 4 -11.968 63.397 7.056 1.00 52.66 N
+ATOM 9 CZ ARG A 4 -12.991 64.058 7.589 1.00 56.94 C
+ATOM 10 NH1 ARG A 4 -13.945 64.562 6.813 1.00 56.97 N
+ATOM 11 NH2 ARG A 4 -13.068 64.210 8.908 1.00 56.38 N
+ATOM 12 N ARG A 5 -7.249 67.164 5.794 1.00 22.68 N
+ATOM 13 CA ARG A 5 -5.921 67.404 6.383 1.00 21.84 C
+ATOM 14 C ARG A 5 -5.876 67.038 7.872 1.00 21.09 C
+ATOM 15 O ARG A 5 -6.895 67.037 8.548 1.00 20.69 O
+ATOM 16 CB ARG A 5 -5.570 68.882 6.179 1.00 20.84 C
+ATOM 17 CG ARG A 5 -6.354 69.821 7.087 1.00 23.07 C
+ATOM 18 CD ARG A 5 -5.799 71.223 6.936 1.00 26.17 C
+ATOM 19 NE ARG A 5 -6.412 72.295 7.694 1.00 21.82 N
+ATOM 20 CZ ARG A 5 -6.105 72.620 8.946 1.00 21.65 C
+ATOM 21 NH1 ARG A 5 -5.172 71.890 9.570 1.00 19.29 N
+ATOM 22 NH2 ARG A 5 -6.716 73.639 9.535 1.00 17.85 N
+ATOM 23 N GLY A 6 -4.635 66.842 8.332 1.00 21.40 N
+ATOM 24 CA GLY A 6 -4.454 66.561 9.770 1.00 19.33 C
+ATOM 25 C GLY A 6 -4.487 67.899 10.515 1.00 19.64 C
+ATOM 26 O GLY A 6 -4.463 68.972 9.869 1.00 19.42 O
+ATOM 27 N ALA A 7 -4.636 67.841 11.842 1.00 18.04 N
+ATOM 28 CA ALA A 7 -4.565 69.041 12.665 1.00 16.15 C
+ATOM 29 C ALA A 7 -3.124 69.313 13.141 1.00 17.35 C
+ATOM 30 O ALA A 7 -2.384 68.375 13.387 1.00 18.00 O
+ATOM 31 CB ALA A 7 -5.414 68.887 13.920 1.00 16.68 C
+ATOM 32 N LEU A 8 -2.884 70.603 13.421 1.00 16.95 N
+ATOM 33 CA LEU A 8 -1.570 71.003 13.958 1.00 15.48 C
+ATOM 34 C LEU A 8 -1.825 71.373 15.401 1.00 15.91 C
+ATOM 35 O LEU A 8 -2.438 72.406 15.664 1.00 16.59 O
+ATOM 36 CB LEU A 8 -0.993 72.181 13.159 1.00 14.46 C
+ATOM 37 CG LEU A 8 0.383 72.656 13.682 1.00 18.19 C
+ATOM 38 CD1 LEU A 8 1.433 71.568 13.643 1.00 18.35 C
+ATOM 39 CD2 LEU A 8 0.814 73.867 12.822 1.00 18.84 C
+ATOM 40 N ILE A 9 -1.423 70.525 16.340 1.00 14.94 N
+ATOM 41 CA ILE A 9 -1.667 70.744 17.773 1.00 14.18 C
+ATOM 42 C ILE A 9 -0.348 71.025 18.485 1.00 16.12 C
+ATOM 43 O ILE A 9 0.594 70.236 18.377 1.00 17.08 O
+ATOM 44 CB ILE A 9 -2.276 69.447 18.348 1.00 15.82 C
+ATOM 45 CG1 ILE A 9 -3.639 69.192 17.664 1.00 15.90 C
+ATOM 46 CG2 ILE A 9 -2.499 69.597 19.858 1.00 16.54 C
+ATOM 47 CD1 ILE A 9 -4.234 67.839 18.075 1.00 16.64 C
+ATOM 48 N VAL A 10 -0.338 72.181 19.161 1.00 15.66 N
+ATOM 49 CA VAL A 10 0.862 72.539 19.911 1.00 14.92 C
+ATOM 50 C VAL A 10 0.659 72.457 21.406 1.00 14.30 C
+ATOM 51 O VAL A 10 -0.397 72.914 21.899 1.00 15.54 O
+ATOM 52 CB VAL A 10 1.282 73.975 19.518 1.00 15.17 C
+ATOM 53 CG1 VAL A 10 2.330 74.565 20.459 1.00 17.46 C
+ATOM 54 CG2 VAL A 10 1.787 73.982 18.073 1.00 14.02 C
+ATOM 55 N LEU A 11 1.655 71.926 22.126 1.00 14.55 N
+ATOM 56 CA LEU A 11 1.640 71.980 23.589 1.00 15.29 C
+ATOM 57 C LEU A 11 2.704 72.988 24.070 1.00 17.70 C
+ATOM 58 O LEU A 11 3.863 72.917 23.657 1.00 16.70 O
+ATOM 59 CB LEU A 11 1.959 70.652 24.307 1.00 16.07 C
+ATOM 60 CG LEU A 11 0.790 69.641 24.292 1.00 16.95 C
+ATOM 61 CD1 LEU A 11 0.655 69.007 22.913 1.00 20.23 C
+ATOM 62 CD2 LEU A 11 1.079 68.535 25.336 1.00 15.12 C
+ATOM 63 N GLU A 12 2.243 73.910 24.913 1.00 15.87 N
+ATOM 64 CA GLU A 12 3.144 74.936 25.463 1.00 18.99 C
+ATOM 65 C GLU A 12 2.999 74.940 26.979 1.00 20.97 C
+ATOM 66 O GLU A 12 2.076 74.350 27.567 1.00 19.95 O
+ATOM 67 CB GLU A 12 2.779 76.319 24.905 1.00 17.48 C
+ATOM 68 CG GLU A 12 3.293 76.635 23.511 1.00 16.71 C
+ATOM 69 CD GLU A 12 4.815 76.769 23.421 1.00 16.74 C
+ATOM 70 OE1 GLU A 12 5.522 76.536 24.403 1.00 17.64 O
+ATOM 71 OE2 GLU A 12 5.242 77.042 22.276 1.00 18.51 O
+ATOM 72 N GLY A 13 3.927 75.633 27.638 1.00 22.95 N
+ATOM 73 CA GLY A 13 3.964 75.690 29.082 1.00 23.58 C
+ATOM 74 C GLY A 13 5.424 75.987 29.484 1.00 26.19 C
+ATOM 75 O GLY A 13 6.338 75.884 28.636 1.00 27.61 O
+ATOM 76 N VAL A 14 5.591 76.374 30.730 1.00 28.14 N
+ATOM 77 CA VAL A 14 6.948 76.634 31.226 1.00 33.49 C
+ATOM 78 C VAL A 14 7.714 75.330 31.342 1.00 35.77 C
+ATOM 79 O VAL A 14 7.142 74.252 31.135 1.00 33.54 O
+ATOM 80 CB VAL A 14 6.862 77.289 32.628 1.00 36.39 C
+ATOM 81 CG1 VAL A 14 6.119 78.607 32.526 1.00 35.35 C
+ATOM 82 CG2 VAL A 14 6.204 76.323 33.603 1.00 39.17 C
+ATOM 83 N ASP A 15 8.997 75.423 31.714 1.00 35.31 N
+ATOM 84 CA ASP A 15 9.758 74.179 31.938 1.00 36.70 C
+ATOM 85 C ASP A 15 9.080 73.369 33.038 1.00 34.83 C
+ATOM 86 O ASP A 15 8.481 73.837 34.002 1.00 35.03 O
+ATOM 87 CB ASP A 15 11.217 74.581 32.223 1.00 38.98 C
+ATOM 88 CG ASP A 15 11.891 75.204 31.016 1.00 42.01 C
+ATOM 89 OD1 ASP A 15 11.469 74.828 29.895 1.00 43.58 O
+ATOM 90 OD2 ASP A 15 12.835 76.026 31.013 1.00 37.09 O
+ATOM 91 N ARG A 16 9.001 72.052 32.887 1.00 33.83 N
+ATOM 92 CA ARG A 16 8.435 71.065 33.775 1.00 35.49 C
+ATOM 93 C ARG A 16 6.938 70.961 33.922 1.00 31.13 C
+ATOM 94 O ARG A 16 6.398 70.324 34.831 1.00 26.38 O
+ATOM 95 CB ARG A 16 9.025 71.143 35.205 1.00 41.69 C
+ATOM 96 CG ARG A 16 10.063 70.055 35.379 1.00 49.93 C
+ATOM 97 CD ARG A 16 11.244 70.442 36.226 1.00 52.84 C
+ATOM 98 NE ARG A 16 10.905 71.273 37.378 1.00 57.00 N
+ATOM 99 CZ ARG A 16 11.876 71.723 38.175 1.00 59.99 C
+ATOM 100 NH1 ARG A 16 13.142 71.407 37.916 1.00 61.49 N
+ATOM 101 NH2 ARG A 16 11.588 72.480 39.219 1.00 62.44 N
+ATOM 102 N ALA A 17 6.205 71.585 33.002 1.00 30.30 N
+ATOM 103 CA ALA A 17 4.765 71.572 33.023 1.00 28.03 C
+ATOM 104 C ALA A 17 4.157 70.232 32.595 1.00 26.20 C
+ATOM 105 O ALA A 17 2.980 70.009 32.814 1.00 27.05 O
+ATOM 106 CB ALA A 17 4.252 72.657 32.081 1.00 25.44 C
+ATOM 107 N GLY A 18 4.970 69.378 31.993 1.00 20.72 N
+ATOM 108 CA GLY A 18 4.479 68.092 31.499 1.00 18.16 C
+ATOM 109 C GLY A 18 4.317 68.073 29.971 1.00 17.89 C
+ATOM 110 O GLY A 18 3.694 67.165 29.424 1.00 16.37 O
+ATOM 111 N LYS A 19 4.837 69.041 29.222 1.00 18.46 N
+ATOM 112 CA LYS A 19 4.687 69.088 27.786 1.00 17.39 C
+ATOM 113 C LYS A 19 5.163 67.841 27.051 1.00 16.37 C
+ATOM 114 O LYS A 19 4.494 67.304 26.179 1.00 16.53 O
+ATOM 115 CB LYS A 19 5.482 70.288 27.173 1.00 19.72 C
+ATOM 116 CG LYS A 19 5.033 71.590 27.872 1.00 22.70 C
+ATOM 117 CD LYS A 19 5.690 72.787 27.186 1.00 25.17 C
+ATOM 118 CE LYS A 19 7.211 72.739 27.352 1.00 26.22 C
+ATOM 119 NZ LYS A 19 7.584 72.803 28.792 1.00 29.15 N
+ATOM 120 N SER A 20 6.353 67.345 27.363 1.00 15.85 N
+ATOM 121 CA SER A 20 6.903 66.200 26.662 1.00 13.99 C
+ATOM 122 C SER A 20 6.126 64.918 27.019 1.00 14.44 C
+ATOM 123 O SER A 20 5.841 64.091 26.149 1.00 15.73 O
+ATOM 124 CB SER A 20 8.376 66.008 26.995 1.00 16.19 C
+ATOM 125 OG SER A 20 9.072 67.160 26.478 1.00 18.88 O
+ATOM 126 N THR A 21 5.804 64.792 28.304 1.00 14.69 N
+ATOM 127 CA THR A 21 5.061 63.588 28.726 1.00 14.89 C
+ATOM 128 C THR A 21 3.697 63.556 28.048 1.00 17.59 C
+ATOM 129 O THR A 21 3.267 62.530 27.493 1.00 14.55 O
+ATOM 130 CB THR A 21 4.880 63.619 30.254 1.00 15.96 C
+ATOM 131 OG1 THR A 21 6.124 63.480 30.915 1.00 17.90 O
+ATOM 132 CG2 THR A 21 3.996 62.427 30.674 1.00 14.14 C
+ATOM 133 N GLN A 22 3.034 64.729 28.047 1.00 15.52 N
+ATOM 134 CA GLN A 22 1.690 64.761 27.441 1.00 14.62 C
+ATOM 135 C GLN A 22 1.754 64.665 25.930 1.00 16.23 C
+ATOM 136 O GLN A 22 0.849 64.094 25.315 1.00 15.60 O
+ATOM 137 CB GLN A 22 0.935 66.013 27.929 1.00 14.49 C
+ATOM 138 CG GLN A 22 0.604 66.020 29.425 1.00 13.95 C
+ATOM 139 CD GLN A 22 -0.204 64.821 29.887 1.00 16.15 C
+ATOM 140 OE1 GLN A 22 -0.975 64.245 29.121 1.00 19.04 O
+ATOM 141 NE2 GLN A 22 -0.045 64.392 31.128 1.00 16.05 N
+ATOM 142 N SER A 23 2.808 65.211 25.278 1.00 14.38 N
+ATOM 143 CA SER A 23 2.856 65.090 23.814 1.00 14.84 C
+ATOM 144 C SER A 23 3.062 63.619 23.424 1.00 15.60 C
+ATOM 145 O SER A 23 2.357 63.164 22.517 1.00 15.61 O
+ATOM 146 CB SER A 23 3.985 65.901 23.173 1.00 14.89 C
+ATOM 147 OG ASER A 23 5.202 65.724 23.847 0.50 18.77 O
+ATOM 147 OG BSER A 23 3.879 67.268 23.480 0.50 10.23 O
+ATOM 148 N ARG A 24 3.944 62.911 24.143 1.00 14.75 N
+ATOM 149 CA ARG A 24 4.116 61.482 23.838 1.00 13.88 C
+ATOM 150 C ARG A 24 2.833 60.664 24.055 1.00 14.41 C
+ATOM 151 O ARG A 24 2.456 59.844 23.191 1.00 16.63 O
+ATOM 152 CB ARG A 24 5.191 60.823 24.749 1.00 16.69 C
+ATOM 153 CG ARG A 24 6.588 61.405 24.467 1.00 13.72 C
+ATOM 154 CD ARG A 24 7.590 60.548 25.287 1.00 17.36 C
+ATOM 155 NE ARG A 24 7.399 60.652 26.712 1.00 16.43 N
+ATOM 156 CZ ARG A 24 7.970 61.543 27.526 1.00 16.12 C
+ATOM 157 NH1 ARG A 24 8.843 62.458 27.090 1.00 17.38 N
+ATOM 158 NH2 ARG A 24 7.696 61.433 28.815 1.00 19.63 N
+ATOM 159 N LYS A 25 2.191 60.905 25.184 1.00 12.91 N
+ATOM 160 CA LYS A 25 0.933 60.177 25.472 1.00 13.14 C
+ATOM 161 C LYS A 25 -0.162 60.543 24.482 1.00 14.43 C
+ATOM 162 O LYS A 25 -0.994 59.656 24.209 1.00 17.63 O
+ATOM 163 CB LYS A 25 0.443 60.405 26.897 1.00 15.52 C
+ATOM 164 CG LYS A 25 1.366 59.744 27.959 1.00 14.59 C
+ATOM 165 CD LYS A 25 0.832 59.936 29.367 1.00 16.28 C
+ATOM 166 CE LYS A 25 -0.467 59.238 29.701 1.00 16.50 C
+ATOM 167 NZ LYS A 25 -0.257 57.733 29.633 1.00 19.72 N
+ATOM 168 N LEU A 26 -0.192 61.809 24.058 1.00 14.26 N
+ATOM 169 CA LEU A 26 -1.260 62.164 23.106 1.00 12.79 C
+ATOM 170 C LEU A 26 -1.078 61.411 21.788 1.00 14.97 C
+ATOM 171 O LEU A 26 -2.034 60.847 21.247 1.00 14.67 O
+ATOM 172 CB LEU A 26 -1.301 63.670 22.867 1.00 13.27 C
+ATOM 173 CG LEU A 26 -2.319 64.166 21.836 1.00 13.44 C
+ATOM 174 CD1 LEU A 26 -3.719 63.710 22.253 1.00 14.89 C
+ATOM 175 CD2 LEU A 26 -2.162 65.691 21.751 1.00 14.81 C
+ATOM 176 N VAL A 27 0.126 61.422 21.218 1.00 14.66 N
+ATOM 177 CA VAL A 27 0.313 60.699 19.951 1.00 16.52 C
+ATOM 178 C VAL A 27 -0.054 59.226 20.111 1.00 17.21 C
+ATOM 179 O VAL A 27 -0.719 58.657 19.236 1.00 16.09 O
+ATOM 180 CB VAL A 27 1.767 60.871 19.489 1.00 17.09 C
+ATOM 181 CG1 VAL A 27 2.035 59.999 18.263 1.00 14.67 C
+ATOM 182 CG2 VAL A 27 1.925 62.367 19.185 1.00 16.71 C
+ATOM 183 N GLU A 28 0.377 58.655 21.253 1.00 15.78 N
+ATOM 184 CA GLU A 28 0.084 57.236 21.482 1.00 17.18 C
+ATOM 185 C GLU A 28 -1.418 56.973 21.475 1.00 16.38 C
+ATOM 186 O GLU A 28 -1.898 56.003 20.838 1.00 16.09 O
+ATOM 187 CB GLU A 28 0.709 56.847 22.844 1.00 18.41 C
+ATOM 188 CG GLU A 28 0.425 55.381 23.233 1.00 21.64 C
+ATOM 189 CD GLU A 28 0.994 55.130 24.628 1.00 26.63 C
+ATOM 190 OE1 GLU A 28 1.052 56.012 25.507 1.00 26.50 O
+ATOM 191 OE2 GLU A 28 1.426 53.980 24.845 1.00 33.24 O
+ATOM 192 N ALA A 29 -2.143 57.817 22.224 1.00 16.33 N
+ATOM 193 CA ALA A 29 -3.595 57.618 22.324 1.00 15.26 C
+ATOM 194 C ALA A 29 -4.294 57.846 21.005 1.00 14.58 C
+ATOM 195 O ALA A 29 -5.261 57.105 20.685 1.00 16.56 O
+ATOM 196 CB ALA A 29 -4.158 58.509 23.426 1.00 15.26 C
+ATOM 197 N LEU A 30 -3.872 58.864 20.275 1.00 14.68 N
+ATOM 198 CA LEU A 30 -4.544 59.133 18.980 1.00 15.88 C
+ATOM 199 C LEU A 30 -4.328 57.971 18.014 1.00 14.95 C
+ATOM 200 O LEU A 30 -5.259 57.512 17.355 1.00 17.50 O
+ATOM 201 CB LEU A 30 -3.989 60.448 18.413 1.00 17.83 C
+ATOM 202 CG LEU A 30 -4.323 61.714 19.189 1.00 14.57 C
+ATOM 203 CD1 LEU A 30 -3.652 62.983 18.585 1.00 15.28 C
+ATOM 204 CD2 LEU A 30 -5.840 62.007 19.171 1.00 17.09 C
+ATOM 205 N CYS A 31 -3.095 57.461 17.950 1.00 16.11 N
+ATOM 206 CA CYS A 31 -2.792 56.335 17.054 1.00 15.11 C
+ATOM 207 C CYS A 31 -3.566 55.091 17.451 1.00 17.35 C
+ATOM 208 O CYS A 31 -4.068 54.371 16.565 1.00 17.27 O
+ATOM 209 CB CYS A 31 -1.274 56.065 17.068 1.00 16.21 C
+ATOM 210 SG CYS A 31 -0.376 57.348 16.161 1.00 16.78 S
+ATOM 211 N ALA A 32 -3.745 54.910 18.765 1.00 14.46 N
+ATOM 212 CA ALA A 32 -4.472 53.733 19.231 1.00 17.02 C
+ATOM 213 C ALA A 32 -5.948 53.869 18.869 1.00 19.06 C
+ATOM 214 O ALA A 32 -6.647 52.870 18.793 1.00 19.68 O
+ATOM 215 CB ALA A 32 -4.265 53.437 20.704 1.00 19.75 C
+ATOM 216 N ALA A 33 -6.462 55.082 18.700 1.00 15.46 N
+ATOM 217 CA ALA A 33 -7.838 55.347 18.323 1.00 18.00 C
+ATOM 218 C ALA A 33 -7.983 55.500 16.819 1.00 16.33 C
+ATOM 219 O ALA A 33 -9.006 56.035 16.346 1.00 18.03 O
+ATOM 220 CB ALA A 33 -8.356 56.598 19.041 1.00 17.75 C
+ATOM 221 N GLY A 34 -7.020 55.021 16.035 1.00 17.61 N
+ATOM 222 CA GLY A 34 -7.120 54.992 14.581 1.00 15.75 C
+ATOM 223 C GLY A 34 -6.647 56.240 13.848 1.00 17.34 C
+ATOM 224 O GLY A 34 -6.793 56.269 12.617 1.00 17.52 O
+ATOM 225 N HIS A 35 -6.228 57.281 14.590 1.00 16.32 N
+ATOM 226 CA HIS A 35 -5.763 58.452 13.843 1.00 15.41 C
+ATOM 227 C HIS A 35 -4.345 58.222 13.367 1.00 16.24 C
+ATOM 228 O HIS A 35 -3.569 57.429 13.937 1.00 17.86 O
+ATOM 229 CB HIS A 35 -5.682 59.662 14.800 1.00 14.62 C
+ATOM 230 CG HIS A 35 -6.975 60.108 15.386 1.00 17.99 C
+ATOM 231 ND1 HIS A 35 -7.858 60.889 14.672 1.00 20.35 N
+ATOM 232 CD2 HIS A 35 -7.582 59.844 16.579 1.00 17.72 C
+ATOM 233 CE1 HIS A 35 -8.906 61.193 15.420 1.00 19.08 C
+ATOM 234 NE2 HIS A 35 -8.743 60.579 16.573 1.00 18.37 N
+ATOM 235 N ARG A 36 -3.978 58.911 12.273 1.00 17.29 N
+ATOM 236 CA ARG A 36 -2.576 58.968 11.867 1.00 19.01 C
+ATOM 237 C ARG A 36 -2.019 60.234 12.568 1.00 19.56 C
+ATOM 238 O ARG A 36 -2.523 61.320 12.292 1.00 22.22 O
+ATOM 239 CB ARG A 36 -2.446 59.103 10.346 1.00 25.77 C
+ATOM 240 CG ARG A 36 -2.932 57.832 9.620 1.00 30.68 C
+ATOM 241 CD ARG A 36 -3.200 58.216 8.157 1.00 37.15 C
+ATOM 242 NE ARG A 36 -1.928 58.434 7.465 1.00 43.56 N
+ATOM 243 CZ ARG A 36 -1.855 59.257 6.411 1.00 47.52 C
+ATOM 244 NH1 ARG A 36 -2.957 59.892 6.019 1.00 47.47 N
+ATOM 245 NH2 ARG A 36 -0.687 59.422 5.803 1.00 47.49 N
+ATOM 246 N ALA A 37 -1.149 60.061 13.542 1.00 19.06 N
+ATOM 247 CA ALA A 37 -0.619 61.220 14.270 1.00 17.22 C
+ATOM 248 C ALA A 37 0.865 60.981 14.505 1.00 18.19 C
+ATOM 249 O ALA A 37 1.260 59.837 14.729 1.00 19.85 O
+ATOM 250 CB ALA A 37 -1.338 61.355 15.607 1.00 18.14 C
+ATOM 251 N GLU A 38 1.666 62.047 14.493 1.00 16.94 N
+ATOM 252 CA GLU A 38 3.083 61.948 14.724 1.00 17.35 C
+ATOM 253 C GLU A 38 3.550 63.103 15.639 1.00 17.70 C
+ATOM 254 O GLU A 38 2.928 64.145 15.680 1.00 18.07 O
+ATOM 255 CB GLU A 38 3.894 62.015 13.413 1.00 22.34 C
+ATOM 256 CG GLU A 38 3.581 60.784 12.551 1.00 22.33 C
+ATOM 257 CD GLU A 38 4.383 60.825 11.251 1.00 28.94 C
+ATOM 258 OE1 GLU A 38 5.522 61.319 11.321 1.00 33.58 O
+ATOM 259 OE2 GLU A 38 3.877 60.393 10.198 1.00 32.17 O
+ATOM 260 N LEU A 39 4.628 62.808 16.361 1.00 17.08 N
+ATOM 261 CA LEU A 39 5.176 63.791 17.304 1.00 16.09 C
+ATOM 262 C LEU A 39 6.323 64.610 16.710 1.00 17.89 C
+ATOM 263 O LEU A 39 7.223 64.056 16.065 1.00 19.36 O
+ATOM 264 CB LEU A 39 5.730 62.929 18.453 1.00 18.98 C
+ATOM 265 CG LEU A 39 6.461 63.668 19.569 1.00 21.21 C
+ATOM 266 CD1 LEU A 39 5.447 64.537 20.303 1.00 19.72 C
+ATOM 267 CD2 LEU A 39 7.103 62.670 20.541 1.00 21.88 C
+ATOM 268 N LEU A 40 6.340 65.914 16.942 1.00 16.34 N
+ATOM 269 CA LEU A 40 7.436 66.808 16.563 1.00 16.64 C
+ATOM 270 C LEU A 40 7.814 67.593 17.816 1.00 17.65 C
+ATOM 271 O LEU A 40 7.053 67.627 18.806 1.00 19.96 O
+ATOM 272 CB LEU A 40 7.010 67.852 15.536 1.00 20.60 C
+ATOM 273 CG LEU A 40 6.781 67.332 14.117 1.00 23.28 C
+ATOM 274 CD1 LEU A 40 6.395 68.539 13.253 1.00 26.30 C
+ATOM 275 CD2 LEU A 40 8.056 66.678 13.627 1.00 30.17 C
+ATOM 276 N ARG A 41 9.055 68.119 17.865 1.00 17.52 N
+ATOM 277 CA ARG A 41 9.377 68.935 19.025 1.00 16.70 C
+ATOM 278 C ARG A 41 10.340 70.078 18.614 1.00 17.35 C
+ATOM 279 O ARG A 41 11.049 69.922 17.624 1.00 19.17 O
+ATOM 280 CB ARG A 41 10.065 68.209 20.178 1.00 21.07 C
+ATOM 281 CG ARG A 41 11.550 67.989 19.982 1.00 30.00 C
+ATOM 282 CD ARG A 41 11.801 67.242 18.687 1.00 29.01 C
+ATOM 283 NE ARG A 41 11.075 65.970 18.711 1.00 38.12 N
+ATOM 284 CZ ARG A 41 10.751 65.306 17.594 1.00 42.43 C
+ATOM 285 NH1 ARG A 41 11.061 65.782 16.390 1.00 40.56 N
+ATOM 286 NH2 ARG A 41 10.089 64.161 17.726 1.00 40.87 N
+ATOM 287 N PHE A 42 10.235 71.176 19.342 1.00 16.67 N
+ATOM 288 CA PHE A 42 11.211 72.258 19.108 1.00 15.65 C
+ATOM 289 C PHE A 42 11.850 72.578 20.437 1.00 16.44 C
+ATOM 290 O PHE A 42 11.235 72.647 21.502 1.00 18.28 O
+ATOM 291 CB PHE A 42 10.501 73.447 18.450 1.00 14.26 C
+ATOM 292 CG PHE A 42 10.058 73.114 17.062 1.00 17.39 C
+ATOM 293 CD1 PHE A 42 11.030 73.056 16.051 1.00 12.40 C
+ATOM 294 CD2 PHE A 42 8.743 72.833 16.762 1.00 15.53 C
+ATOM 295 CE1 PHE A 42 10.651 72.698 14.764 1.00 14.98 C
+ATOM 296 CE2 PHE A 42 8.377 72.479 15.461 1.00 17.69 C
+ATOM 297 CZ PHE A 42 9.333 72.429 14.454 1.00 17.26 C
+ATOM 298 N PRO A 43 13.175 72.891 20.438 1.00 17.20 N
+ATOM 299 CA PRO A 43 13.967 72.771 19.235 1.00 17.53 C
+ATOM 300 C PRO A 43 14.164 71.347 18.751 1.00 19.06 C
+ATOM 301 O PRO A 43 14.098 70.364 19.555 1.00 19.43 O
+ATOM 302 CB PRO A 43 15.367 73.266 19.703 1.00 16.79 C
+ATOM 303 CG PRO A 43 15.367 73.005 21.165 1.00 17.01 C
+ATOM 304 CD PRO A 43 13.936 73.223 21.647 1.00 18.01 C
+ATOM 305 N GLU A 44 14.356 71.186 17.464 1.00 20.65 N
+ATOM 306 CA GLU A 44 14.613 69.894 16.827 1.00 18.71 C
+ATOM 307 C GLU A 44 16.149 69.856 16.797 1.00 25.09 C
+ATOM 308 O GLU A 44 16.737 70.493 15.926 1.00 25.45 O
+ATOM 309 CB GLU A 44 13.997 69.803 15.449 1.00 22.64 C
+ATOM 310 CG GLU A 44 14.476 68.584 14.665 1.00 28.01 C
+ATOM 311 CD GLU A 44 14.367 67.301 15.466 1.00 33.54 C
+ATOM 312 OE1 GLU A 44 13.245 66.964 15.928 1.00 31.99 O
+ATOM 313 OE2 GLU A 44 15.401 66.646 15.674 1.00 32.12 O
+ATOM 314 N ARG A 45 16.701 69.183 17.793 1.00 24.08 N
+ATOM 315 CA ARG A 45 18.158 69.240 17.961 1.00 28.33 C
+ATOM 316 C ARG A 45 18.947 68.405 16.998 1.00 30.19 C
+ATOM 317 O ARG A 45 20.193 68.418 17.122 1.00 35.44 O
+ATOM 318 CB ARG A 45 18.456 68.842 19.412 1.00 31.72 C
+ATOM 319 CG ARG A 45 17.763 69.689 20.466 1.00 30.53 C
+ATOM 320 CD ARG A 45 18.177 69.230 21.855 1.00 37.79 C
+ATOM 321 NE ARG A 45 17.476 69.908 22.926 1.00 39.74 N
+ATOM 322 CZ ARG A 45 18.056 70.301 24.062 1.00 41.06 C
+ATOM 323 NH1 ARG A 45 19.344 70.122 24.335 1.00 42.01 N
+ATOM 324 NH2 ARG A 45 17.269 70.907 24.945 1.00 36.24 N
+ATOM 325 N SER A 46 18.335 67.705 16.061 1.00 29.85 N
+ATOM 326 CA SER A 46 19.089 66.838 15.163 1.00 32.75 C
+ATOM 327 C SER A 46 19.727 67.551 13.976 1.00 34.19 C
+ATOM 328 O SER A 46 20.666 67.007 13.365 1.00 29.89 O
+ATOM 329 CB SER A 46 18.210 65.675 14.688 1.00 32.57 C
+ATOM 330 OG SER A 46 17.109 66.110 13.905 1.00 39.39 O
+ATOM 331 N THR A 47 19.215 68.725 13.614 1.00 25.92 N
+ATOM 332 CA THR A 47 19.772 69.455 12.467 1.00 23.81 C
+ATOM 333 C THR A 47 21.005 70.228 12.883 1.00 21.20 C
+ATOM 334 O THR A 47 21.310 70.412 14.066 1.00 23.58 O
+ATOM 335 CB THR A 47 18.742 70.470 11.906 1.00 27.51 C
+ATOM 336 OG1 THR A 47 18.526 71.494 12.910 1.00 24.59 O
+ATOM 337 CG2 THR A 47 17.463 69.787 11.469 1.00 24.33 C
+ATOM 338 N GLU A 48 21.724 70.795 11.905 1.00 25.22 N
+ATOM 339 CA GLU A 48 22.892 71.627 12.154 1.00 25.23 C
+ATOM 340 C GLU A 48 22.556 72.774 13.095 1.00 23.82 C
+ATOM 341 O GLU A 48 23.300 73.025 14.042 1.00 20.77 O
+ATOM 342 CB GLU A 48 23.482 72.158 10.828 1.00 26.34 C
+ATOM 343 CG GLU A 48 23.831 71.013 9.878 1.00 33.08 C
+ATOM 344 CD GLU A 48 24.105 71.421 8.442 1.00 33.97 C
+ATOM 345 OE1 GLU A 48 23.155 71.545 7.641 1.00 35.60 O
+ATOM 346 OE2 GLU A 48 25.290 71.602 8.070 1.00 37.49 O
+ATOM 347 N ILE A 49 21.444 73.440 12.808 1.00 26.81 N
+ATOM 348 CA ILE A 49 20.967 74.517 13.682 1.00 20.32 C
+ATOM 349 C ILE A 49 20.605 73.960 15.042 1.00 19.16 C
+ATOM 350 O ILE A 49 20.968 74.504 16.095 1.00 22.06 O
+ATOM 351 CB ILE A 49 19.799 75.281 13.032 1.00 24.27 C
+ATOM 352 CG1 ILE A 49 20.358 76.051 11.803 1.00 23.68 C
+ATOM 353 CG2 ILE A 49 19.142 76.231 14.013 1.00 24.19 C
+ATOM 354 CD1 ILE A 49 19.246 76.660 10.962 1.00 25.51 C
+ATOM 355 N GLY A 50 19.856 72.850 15.039 1.00 25.28 N
+ATOM 356 CA GLY A 50 19.489 72.235 16.321 1.00 24.33 C
+ATOM 357 C GLY A 50 20.724 71.897 17.145 1.00 24.36 C
+ATOM 358 O GLY A 50 20.659 71.965 18.399 1.00 24.40 O
+ATOM 359 N LYS A 51 21.841 71.505 16.548 1.00 26.34 N
+ATOM 360 CA LYS A 51 23.019 71.182 17.370 1.00 26.81 C
+ATOM 361 C LYS A 51 23.608 72.416 18.039 1.00 28.35 C
+ATOM 362 O LYS A 51 24.135 72.385 19.147 1.00 27.71 O
+ATOM 363 CB LYS A 51 24.116 70.503 16.537 1.00 28.45 C
+ATOM 364 CG LYS A 51 23.839 69.059 16.184 1.00 34.64 C
+ATOM 365 CD LYS A 51 24.843 68.571 15.153 1.00 37.93 C
+ATOM 366 CE LYS A 51 24.601 67.114 14.799 1.00 45.38 C
+ATOM 367 NZ LYS A 51 25.753 66.587 14.000 1.00 49.77 N
+ATOM 368 N LEU A 52 23.568 73.556 17.327 1.00 26.04 N
+ATOM 369 CA LEU A 52 24.077 74.795 17.920 1.00 24.41 C
+ATOM 370 C LEU A 52 23.187 75.181 19.095 1.00 19.97 C
+ATOM 371 O LEU A 52 23.611 75.630 20.139 1.00 26.12 O
+ATOM 372 CB LEU A 52 24.105 75.911 16.868 1.00 26.82 C
+ATOM 373 CG LEU A 52 24.888 75.674 15.596 1.00 30.76 C
+ATOM 374 CD1 LEU A 52 24.685 76.873 14.649 1.00 31.77 C
+ATOM 375 CD2 LEU A 52 26.375 75.442 15.856 1.00 34.17 C
+ATOM 376 N LEU A 53 21.876 75.000 18.897 1.00 21.32 N
+ATOM 377 CA LEU A 53 20.914 75.284 19.953 1.00 21.33 C
+ATOM 378 C LEU A 53 21.111 74.411 21.187 1.00 22.65 C
+ATOM 379 O LEU A 53 20.990 74.886 22.329 1.00 23.39 O
+ATOM 380 CB LEU A 53 19.479 75.134 19.402 1.00 19.97 C
+ATOM 381 CG LEU A 53 19.109 76.237 18.377 1.00 22.53 C
+ATOM 382 CD1 LEU A 53 17.728 75.912 17.827 1.00 22.67 C
+ATOM 383 CD2 LEU A 53 19.151 77.607 19.020 1.00 23.99 C
+ATOM 384 N SER A 54 21.392 73.120 20.959 1.00 26.77 N
+ATOM 385 CA SER A 54 21.593 72.197 22.069 1.00 25.84 C
+ATOM 386 C SER A 54 22.861 72.562 22.846 1.00 27.18 C
+ATOM 387 O SER A 54 22.820 72.592 24.062 1.00 27.95 O
+ATOM 388 CB SER A 54 21.709 70.763 21.537 1.00 28.77 C
+ATOM 389 OG SER A 54 21.747 69.837 22.616 1.00 31.17 O
+ATOM 390 N SER A 55 23.933 72.891 22.137 1.00 30.63 N
+ATOM 391 CA SER A 55 25.168 73.275 22.835 1.00 30.72 C
+ATOM 392 C SER A 55 24.900 74.514 23.665 1.00 33.05 C
+ATOM 393 O SER A 55 25.279 74.571 24.840 1.00 32.51 O
+ATOM 394 CB SER A 55 26.277 73.457 21.796 1.00 32.70 C
+ATOM 395 OG SER A 55 27.419 74.046 22.374 1.00 35.40 O
+ATOM 396 N TYR A 56 24.135 75.477 23.121 1.00 27.79 N
+ATOM 397 CA TYR A 56 23.797 76.685 23.844 1.00 26.70 C
+ATOM 398 C TYR A 56 23.000 76.404 25.123 1.00 28.30 C
+ATOM 399 O TYR A 56 23.317 76.935 26.200 1.00 32.31 O
+ATOM 400 CB TYR A 56 22.956 77.631 22.964 1.00 26.45 C
+ATOM 401 CG TYR A 56 22.398 78.835 23.674 1.00 25.57 C
+ATOM 402 CD1 TYR A 56 23.193 79.926 24.015 1.00 22.26 C
+ATOM 403 CD2 TYR A 56 21.045 78.919 24.042 1.00 26.37 C
+ATOM 404 CE1 TYR A 56 22.696 81.035 24.666 1.00 24.71 C
+ATOM 405 CE2 TYR A 56 20.545 80.004 24.713 1.00 25.91 C
+ATOM 406 CZ TYR A 56 21.367 81.068 25.023 1.00 26.22 C
+ATOM 407 OH TYR A 56 20.861 82.177 25.677 1.00 27.37 O
+ATOM 408 N LEU A 57 21.943 75.606 24.984 1.00 28.48 N
+ATOM 409 CA LEU A 57 21.093 75.289 26.130 1.00 27.84 C
+ATOM 410 C LEU A 57 21.846 74.551 27.229 1.00 31.08 C
+ATOM 411 O LEU A 57 21.502 74.684 28.401 1.00 32.21 O
+ATOM 412 CB LEU A 57 19.881 74.465 25.622 1.00 25.56 C
+ATOM 413 CG LEU A 57 18.834 75.344 24.919 1.00 27.23 C
+ATOM 414 CD1 LEU A 57 17.757 74.459 24.278 1.00 27.09 C
+ATOM 415 CD2 LEU A 57 18.273 76.409 25.847 1.00 25.08 C
+ATOM 416 N GLN A 58 22.863 73.787 26.863 1.00 32.27 N
+ATOM 417 CA GLN A 58 23.667 73.031 27.814 1.00 37.66 C
+ATOM 418 C GLN A 58 24.830 73.835 28.386 1.00 38.02 C
+ATOM 419 O GLN A 58 25.639 73.321 29.173 1.00 38.10 O
+ATOM 420 CB GLN A 58 24.240 71.779 27.150 1.00 40.04 C
+ATOM 421 CG GLN A 58 23.198 70.792 26.636 1.00 43.44 C
+ATOM 422 CD GLN A 58 23.895 69.745 25.777 1.00 48.14 C
+ATOM 423 OE1 GLN A 58 24.711 68.988 26.304 1.00 50.94 O
+ATOM 424 NE2 GLN A 58 23.608 69.717 24.485 1.00 48.40 N
+ATOM 425 N LYS A 59 24.945 75.084 27.968 1.00 33.51 N
+ATOM 426 CA LYS A 59 25.990 75.993 28.417 1.00 38.26 C
+ATOM 427 C LYS A 59 27.364 75.552 27.939 1.00 38.67 C
+ATOM 428 O LYS A 59 28.388 75.944 28.502 1.00 39.64 O
+ATOM 429 CB LYS A 59 25.984 76.220 29.926 1.00 39.54 C
+ATOM 430 CG LYS A 59 24.636 76.647 30.485 1.00 44.42 C
+ATOM 431 CD LYS A 59 24.774 77.047 31.952 1.00 48.69 C
+ATOM 432 CE LYS A 59 23.578 77.871 32.401 1.00 52.59 C
+ATOM 433 NZ LYS A 59 23.948 78.878 33.437 1.00 53.83 N
+ATOM 434 N LYS A 60 27.385 74.740 26.892 1.00 36.55 N
+ATOM 435 CA LYS A 60 28.667 74.313 26.320 1.00 36.52 C
+ATOM 436 C LYS A 60 29.143 75.419 25.385 1.00 34.17 C
+ATOM 437 O LYS A 60 30.298 75.567 25.004 1.00 33.02 O
+ATOM 438 CB LYS A 60 28.535 72.965 25.631 1.00 38.64 C
+ATOM 439 CG LYS A 60 28.095 71.850 26.584 1.00 41.42 C
+ATOM 440 CD LYS A 60 28.122 70.505 25.876 1.00 45.87 C
+ATOM 441 CE LYS A 60 28.445 69.366 26.821 1.00 51.63 C
+ATOM 442 NZ LYS A 60 27.309 68.896 27.655 1.00 54.12 N
+ATOM 443 N SER A 61 28.191 76.288 25.007 1.00 34.88 N
+ATOM 444 CA SER A 61 28.543 77.409 24.148 1.00 33.34 C
+ATOM 445 C SER A 61 27.696 78.620 24.528 1.00 35.18 C
+ATOM 446 O SER A 61 26.625 78.521 25.129 1.00 32.23 O
+ATOM 447 CB SER A 61 28.387 77.048 22.678 1.00 36.26 C
+ATOM 448 OG SER A 61 27.008 76.974 22.341 1.00 40.61 O
+ATOM 449 N ASP A 62 28.233 79.784 24.190 1.00 32.29 N
+ATOM 450 CA ASP A 62 27.563 81.049 24.436 1.00 34.82 C
+ATOM 451 C ASP A 62 27.188 81.631 23.073 1.00 33.33 C
+ATOM 452 O ASP A 62 27.975 81.501 22.129 1.00 35.65 O
+ATOM 453 CB ASP A 62 28.457 82.021 25.209 1.00 41.96 C
+ATOM 454 CG ASP A 62 27.904 82.197 26.619 1.00 50.75 C
+ATOM 455 OD1 ASP A 62 27.826 81.215 27.388 1.00 50.80 O
+ATOM 456 OD2 ASP A 62 27.525 83.360 26.894 1.00 56.37 O
+ATOM 457 N VAL A 63 26.011 82.223 22.998 1.00 27.73 N
+ATOM 458 CA VAL A 63 25.535 82.757 21.727 1.00 25.09 C
+ATOM 459 C VAL A 63 24.855 84.082 22.027 1.00 28.41 C
+ATOM 460 O VAL A 63 24.120 84.205 23.021 1.00 25.01 O
+ATOM 461 CB VAL A 63 24.522 81.798 21.045 1.00 23.86 C
+ATOM 462 CG1 VAL A 63 24.140 82.298 19.647 1.00 23.14 C
+ATOM 463 CG2 VAL A 63 25.115 80.404 20.913 1.00 23.96 C
+ATOM 464 N GLU A 64 25.099 85.066 21.177 1.00 21.86 N
+ATOM 465 CA GLU A 64 24.503 86.386 21.319 1.00 19.78 C
+ATOM 466 C GLU A 64 22.968 86.254 21.321 1.00 20.80 C
+ATOM 467 O GLU A 64 22.513 85.434 20.542 1.00 19.41 O
+ATOM 468 CB GLU A 64 25.024 87.209 20.135 1.00 21.29 C
+ATOM 469 CG GLU A 64 24.812 88.701 20.307 1.00 20.08 C
+ATOM 470 CD GLU A 64 23.411 89.178 20.018 1.00 19.71 C
+ATOM 471 OE1 GLU A 64 22.724 88.483 19.232 1.00 20.77 O
+ATOM 472 OE2 GLU A 64 22.982 90.212 20.562 1.00 22.79 O
+ATOM 473 N ASP A 65 22.295 86.968 22.218 1.00 20.50 N
+ATOM 474 CA ASP A 65 20.849 86.743 22.402 1.00 24.31 C
+ATOM 475 C ASP A 65 19.985 86.866 21.170 1.00 21.98 C
+ATOM 476 O ASP A 65 18.949 86.147 21.029 1.00 19.98 O
+ATOM 477 CB ASP A 65 20.302 87.633 23.525 1.00 22.30 C
+ATOM 478 CG ASP A 65 20.783 87.302 24.925 1.00 29.01 C
+ATOM 479 OD1 ASP A 65 20.973 86.122 25.281 1.00 26.77 O
+ATOM 480 OD2 ASP A 65 20.970 88.244 25.743 1.00 30.83 O
+ATOM 481 N HIS A 66 20.240 87.843 20.311 1.00 19.92 N
+ATOM 482 CA HIS A 66 19.419 88.010 19.107 1.00 18.42 C
+ATOM 483 C HIS A 66 19.713 86.864 18.157 1.00 16.47 C
+ATOM 484 O HIS A 66 18.822 86.337 17.495 1.00 16.73 O
+ATOM 485 CB HIS A 66 19.703 89.359 18.406 1.00 16.74 C
+ATOM 486 CG HIS A 66 19.494 90.564 19.282 1.00 21.18 C
+ATOM 487 ND1 HIS A 66 20.432 90.984 20.228 1.00 20.30 N
+ATOM 488 CD2 HIS A 66 18.448 91.400 19.359 1.00 22.99 C
+ATOM 489 CE1 HIS A 66 19.924 92.048 20.824 1.00 21.50 C
+ATOM 490 NE2 HIS A 66 18.729 92.349 20.313 1.00 24.69 N
+ATOM 491 N SER A 67 20.996 86.504 18.011 1.00 17.16 N
+ATOM 492 CA SER A 67 21.362 85.404 17.144 1.00 18.59 C
+ATOM 493 C SER A 67 20.657 84.101 17.568 1.00 18.83 C
+ATOM 494 O SER A 67 20.118 83.398 16.715 1.00 18.30 O
+ATOM 495 CB SER A 67 22.891 85.189 17.200 1.00 21.51 C
+ATOM 496 OG SER A 67 23.262 84.139 16.358 1.00 27.40 O
+ATOM 497 N VAL A 68 20.698 83.824 18.872 1.00 18.95 N
+ATOM 498 CA VAL A 68 20.076 82.529 19.288 1.00 17.66 C
+ATOM 499 C VAL A 68 18.570 82.582 19.025 1.00 19.18 C
+ATOM 500 O VAL A 68 18.032 81.544 18.631 1.00 18.48 O
+ATOM 501 CB VAL A 68 20.452 82.188 20.720 1.00 22.26 C
+ATOM 502 CG1 VAL A 68 19.636 82.973 21.727 1.00 23.57 C
+ATOM 503 CG2 VAL A 68 20.277 80.665 20.884 1.00 27.26 C
+ATOM 504 N HIS A 69 17.935 83.711 19.286 1.00 17.35 N
+ATOM 505 CA HIS A 69 16.492 83.841 18.977 1.00 15.15 C
+ATOM 506 C HIS A 69 16.198 83.513 17.516 1.00 17.81 C
+ATOM 507 O HIS A 69 15.305 82.731 17.186 1.00 16.77 O
+ATOM 508 CB HIS A 69 16.070 85.279 19.311 1.00 17.33 C
+ATOM 509 CG HIS A 69 14.575 85.396 19.096 1.00 17.65 C
+ATOM 510 ND1 HIS A 69 13.706 84.842 20.036 1.00 21.77 N
+ATOM 511 CD2 HIS A 69 13.848 85.947 18.112 1.00 20.59 C
+ATOM 512 CE1 HIS A 69 12.471 85.084 19.598 1.00 19.29 C
+ATOM 513 NE2 HIS A 69 12.536 85.727 18.450 1.00 21.40 N
+ATOM 514 N LEU A 70 17.040 84.044 16.600 1.00 15.93 N
+ATOM 515 CA LEU A 70 16.835 83.772 15.179 1.00 16.69 C
+ATOM 516 C LEU A 70 17.148 82.345 14.805 1.00 15.47 C
+ATOM 517 O LEU A 70 16.468 81.768 13.956 1.00 18.00 O
+ATOM 518 CB LEU A 70 17.678 84.795 14.362 1.00 15.27 C
+ATOM 519 CG LEU A 70 17.290 86.254 14.625 1.00 16.07 C
+ATOM 520 CD1 LEU A 70 18.317 87.184 13.949 1.00 17.13 C
+ATOM 521 CD2 LEU A 70 15.893 86.617 14.097 1.00 17.92 C
+ATOM 522 N LEU A 71 18.114 81.691 15.472 1.00 17.00 N
+ATOM 523 CA LEU A 71 18.378 80.276 15.199 1.00 17.79 C
+ATOM 524 C LEU A 71 17.184 79.413 15.663 1.00 15.73 C
+ATOM 525 O LEU A 71 16.836 78.469 14.917 1.00 16.87 O
+ATOM 526 CB LEU A 71 19.638 79.806 15.957 1.00 17.33 C
+ATOM 527 CG LEU A 71 20.973 80.356 15.436 1.00 23.50 C
+ATOM 528 CD1 LEU A 71 22.103 79.821 16.321 1.00 21.00 C
+ATOM 529 CD2 LEU A 71 21.217 79.910 14.004 1.00 25.83 C
+ATOM 530 N PHE A 72 16.592 79.742 16.795 1.00 17.33 N
+ATOM 531 CA PHE A 72 15.395 78.953 17.231 1.00 17.26 C
+ATOM 532 C PHE A 72 14.287 79.030 16.191 1.00 15.42 C
+ATOM 533 O PHE A 72 13.612 78.067 15.860 1.00 18.42 O
+ATOM 534 CB PHE A 72 14.890 79.484 18.580 1.00 16.86 C
+ATOM 535 CG PHE A 72 15.512 78.854 19.799 1.00 18.15 C
+ATOM 536 CD1 PHE A 72 15.279 77.500 20.091 1.00 19.13 C
+ATOM 537 CD2 PHE A 72 16.319 79.596 20.640 1.00 19.39 C
+ATOM 538 CE1 PHE A 72 15.849 76.940 21.213 1.00 15.22 C
+ATOM 539 CE2 PHE A 72 16.876 79.026 21.769 1.00 21.79 C
+ATOM 540 CZ PHE A 72 16.642 77.696 22.081 1.00 19.03 C
+ATOM 541 N SER A 73 14.061 80.232 15.626 1.00 16.83 N
+ATOM 542 CA SER A 73 13.020 80.391 14.610 1.00 15.13 C
+ATOM 543 C SER A 73 13.407 79.709 13.314 1.00 16.09 C
+ATOM 544 O SER A 73 12.581 79.045 12.651 1.00 15.90 O
+ATOM 545 CB SER A 73 12.756 81.897 14.394 1.00 14.98 C
+ATOM 546 OG SER A 73 11.813 82.030 13.356 1.00 15.96 O
+ATOM 547 N ALA A 74 14.702 79.790 12.920 1.00 15.58 N
+ATOM 548 CA ALA A 74 15.120 79.131 11.704 1.00 14.82 C
+ATOM 549 C ALA A 74 14.939 77.618 11.816 1.00 18.97 C
+ATOM 550 O ALA A 74 14.629 76.996 10.801 1.00 16.38 O
+ATOM 551 CB ALA A 74 16.595 79.469 11.427 1.00 15.55 C
+ATOM 552 N ASN A 75 15.106 77.130 13.038 1.00 17.32 N
+ATOM 553 CA ASN A 75 14.917 75.685 13.310 1.00 15.55 C
+ATOM 554 C ASN A 75 13.449 75.282 13.102 1.00 16.88 C
+ATOM 555 O ASN A 75 13.178 74.118 12.772 1.00 16.74 O
+ATOM 556 CB ASN A 75 15.355 75.474 14.752 1.00 17.52 C
+ATOM 557 CG ASN A 75 15.335 74.022 15.187 1.00 21.31 C
+ATOM 558 OD1 ASN A 75 14.704 73.767 16.208 1.00 19.31 O
+ATOM 559 ND2 ASN A 75 16.018 73.153 14.439 1.00 21.30 N
+ATOM 560 N ARG A 76 12.514 76.192 13.322 1.00 16.84 N
+ATOM 561 CA ARG A 76 11.114 75.872 12.988 1.00 16.67 C
+ATOM 562 C ARG A 76 10.933 75.936 11.490 1.00 17.00 C
+ATOM 563 O ARG A 76 10.364 75.028 10.879 1.00 15.11 O
+ATOM 564 CB ARG A 76 10.111 76.791 13.710 1.00 16.07 C
+ATOM 565 CG ARG A 76 10.001 76.408 15.194 1.00 15.45 C
+ATOM 566 CD ARG A 76 9.129 77.436 15.878 1.00 16.69 C
+ATOM 567 NE ARG A 76 9.694 78.740 16.176 1.00 15.06 N
+ATOM 568 CZ ARG A 76 10.495 78.984 17.210 1.00 16.00 C
+ATOM 569 NH1 ARG A 76 10.930 77.998 18.036 1.00 15.77 N
+ATOM 570 NH2 ARG A 76 10.885 80.217 17.484 1.00 16.45 N
+ATOM 571 N TRP A 77 11.362 77.025 10.810 1.00 14.49 N
+ATOM 572 CA TRP A 77 11.188 77.135 9.372 1.00 15.71 C
+ATOM 573 C TRP A 77 11.759 75.960 8.564 1.00 17.95 C
+ATOM 574 O TRP A 77 11.158 75.566 7.560 1.00 18.37 O
+ATOM 575 CB TRP A 77 11.839 78.469 8.888 1.00 15.18 C
+ATOM 576 CG TRP A 77 10.940 79.652 9.154 1.00 18.46 C
+ATOM 577 CD1 TRP A 77 11.109 80.627 10.104 1.00 18.21 C
+ATOM 578 CD2 TRP A 77 9.730 79.979 8.462 1.00 13.92 C
+ATOM 579 NE1 TRP A 77 10.080 81.526 10.055 1.00 19.21 N
+ATOM 580 CE2 TRP A 77 9.215 81.148 9.045 1.00 15.19 C
+ATOM 581 CE3 TRP A 77 9.023 79.399 7.400 1.00 15.03 C
+ATOM 582 CZ2 TRP A 77 8.052 81.769 8.612 1.00 17.00 C
+ATOM 583 CZ3 TRP A 77 7.859 80.005 6.972 1.00 16.54 C
+ATOM 584 CH2 TRP A 77 7.374 81.164 7.582 1.00 19.34 C
+ATOM 585 N GLU A 78 12.879 75.401 8.997 1.00 19.40 N
+ATOM 586 CA GLU A 78 13.489 74.284 8.281 1.00 21.07 C
+ATOM 587 C GLU A 78 12.562 73.068 8.297 1.00 23.55 C
+ATOM 588 O GLU A 78 12.676 72.231 7.384 1.00 22.69 O
+ATOM 589 CB GLU A 78 14.913 73.992 8.754 1.00 24.49 C
+ATOM 590 CG GLU A 78 15.056 73.380 10.139 1.00 26.04 C
+ATOM 591 CD GLU A 78 16.512 73.170 10.538 1.00 24.09 C
+ATOM 592 OE1 GLU A 78 17.423 73.078 9.661 1.00 26.81 O
+ATOM 593 OE2 GLU A 78 16.798 73.140 11.735 1.00 24.53 O
+ATOM 594 N GLN A 79 11.623 73.018 9.245 1.00 18.52 N
+ATOM 595 CA GLN A 79 10.673 71.892 9.288 1.00 20.39 C
+ATOM 596 C GLN A 79 9.365 72.209 8.607 1.00 19.77 C
+ATOM 597 O GLN A 79 8.434 71.374 8.522 1.00 20.10 O
+ATOM 598 CB GLN A 79 10.433 71.533 10.762 1.00 21.18 C
+ATOM 599 CG GLN A 79 11.654 71.040 11.527 1.00 23.59 C
+ATOM 600 CD GLN A 79 12.218 69.765 10.913 1.00 30.83 C
+ATOM 601 OE1 GLN A 79 11.458 68.933 10.428 1.00 33.29 O
+ATOM 602 NE2 GLN A 79 13.531 69.628 10.925 1.00 35.05 N
+ATOM 603 N VAL A 80 9.195 73.434 8.080 1.00 17.20 N
+ATOM 604 CA VAL A 80 7.880 73.791 7.481 1.00 17.59 C
+ATOM 605 C VAL A 80 7.501 72.963 6.291 1.00 19.84 C
+ATOM 606 O VAL A 80 6.368 72.485 6.211 1.00 17.30 O
+ATOM 607 CB VAL A 80 7.786 75.311 7.268 1.00 18.77 C
+ATOM 608 CG1 VAL A 80 6.636 75.750 6.393 1.00 16.83 C
+ATOM 609 CG2 VAL A 80 7.704 76.030 8.615 1.00 16.62 C
+ATOM 610 N PRO A 81 8.356 72.677 5.324 1.00 20.00 N
+ATOM 611 CA PRO A 81 7.965 71.808 4.200 1.00 21.98 C
+ATOM 612 C PRO A 81 7.460 70.443 4.708 1.00 20.59 C
+ATOM 613 O PRO A 81 6.368 70.038 4.284 1.00 20.56 O
+ATOM 614 CB PRO A 81 9.219 71.746 3.362 1.00 23.33 C
+ATOM 615 CG PRO A 81 9.914 73.029 3.690 1.00 23.66 C
+ATOM 616 CD PRO A 81 9.718 73.240 5.197 1.00 21.70 C
+ATOM 617 N LEU A 82 8.091 69.852 5.694 1.00 18.71 N
+ATOM 618 CA LEU A 82 7.671 68.578 6.288 1.00 20.77 C
+ATOM 619 C LEU A 82 6.310 68.706 6.976 1.00 21.04 C
+ATOM 620 O LEU A 82 5.446 67.827 6.816 1.00 21.65 O
+ATOM 621 CB LEU A 82 8.707 68.065 7.300 1.00 22.20 C
+ATOM 622 CG LEU A 82 8.224 66.866 8.132 1.00 29.10 C
+ATOM 623 CD1 LEU A 82 8.194 65.627 7.254 1.00 32.78 C
+ATOM 624 CD2 LEU A 82 9.099 66.637 9.356 1.00 35.33 C
+ATOM 625 N ILE A 83 6.139 69.755 7.771 1.00 18.87 N
+ATOM 626 CA ILE A 83 4.874 69.982 8.446 1.00 20.58 C
+ATOM 627 C ILE A 83 3.729 70.106 7.467 1.00 22.06 C
+ATOM 628 O ILE A 83 2.640 69.545 7.642 1.00 18.87 O
+ATOM 629 CB ILE A 83 4.957 71.285 9.307 1.00 17.90 C
+ATOM 630 CG1 ILE A 83 5.865 70.992 10.505 1.00 17.32 C
+ATOM 631 CG2 ILE A 83 3.585 71.765 9.716 1.00 19.06 C
+ATOM 632 CD1 ILE A 83 6.181 72.294 11.257 1.00 21.12 C
+ATOM 633 N LYS A 84 3.923 70.878 6.382 1.00 19.51 N
+ATOM 634 CA LYS A 84 2.848 71.065 5.413 1.00 22.30 C
+ATOM 635 C LYS A 84 2.584 69.768 4.658 1.00 21.39 C
+ATOM 636 O LYS A 84 1.405 69.427 4.419 1.00 22.26 O
+ATOM 637 CB LYS A 84 3.216 72.201 4.430 1.00 21.19 C
+ATOM 638 CG LYS A 84 3.177 73.584 5.087 1.00 22.46 C
+ATOM 639 CD LYS A 84 3.563 74.616 4.000 1.00 27.31 C
+ATOM 640 CE LYS A 84 3.411 76.013 4.575 1.00 33.71 C
+ATOM 641 NZ LYS A 84 3.423 77.043 3.497 1.00 38.57 N
+ATOM 642 N GLU A 85 3.646 69.029 4.368 1.00 20.54 N
+ATOM 643 CA GLU A 85 3.444 67.758 3.653 1.00 21.75 C
+ATOM 644 C GLU A 85 2.620 66.806 4.530 1.00 23.46 C
+ATOM 645 O GLU A 85 1.555 66.329 4.101 1.00 23.61 O
+ATOM 646 CB GLU A 85 4.778 67.164 3.264 1.00 27.33 C
+ATOM 647 CG GLU A 85 4.679 65.919 2.375 1.00 35.37 C
+ATOM 648 CD GLU A 85 6.084 65.447 2.016 1.00 42.21 C
+ATOM 649 OE1 GLU A 85 6.665 64.664 2.787 1.00 44.95 O
+ATOM 650 OE2 GLU A 85 6.609 65.891 0.970 1.00 48.53 O
+ATOM 651 N LYS A 86 3.086 66.609 5.768 1.00 17.17 N
+ATOM 652 CA LYS A 86 2.317 65.702 6.635 1.00 20.46 C
+ATOM 653 C LYS A 86 0.864 66.090 6.830 1.00 21.62 C
+ATOM 654 O LYS A 86 -0.046 65.240 6.731 1.00 23.07 O
+ATOM 655 CB LYS A 86 3.032 65.631 8.003 1.00 19.31 C
+ATOM 656 CG LYS A 86 4.366 64.911 7.874 1.00 21.81 C
+ATOM 657 CD LYS A 86 4.209 63.407 7.871 1.00 31.26 C
+ATOM 658 CE LYS A 86 5.600 62.758 7.916 1.00 30.90 C
+ATOM 659 NZ LYS A 86 5.416 61.282 8.063 1.00 32.55 N
+ATOM 660 N LEU A 87 0.611 67.359 7.159 1.00 18.54 N
+ATOM 661 CA LEU A 87 -0.770 67.779 7.379 1.00 17.63 C
+ATOM 662 C LEU A 87 -1.579 67.540 6.093 1.00 22.70 C
+ATOM 663 O LEU A 87 -2.720 67.075 6.171 1.00 20.43 O
+ATOM 664 CB LEU A 87 -0.879 69.255 7.793 1.00 18.97 C
+ATOM 665 CG LEU A 87 -0.198 69.659 9.098 1.00 20.41 C
+ATOM 666 CD1 LEU A 87 -0.181 71.202 9.161 1.00 19.57 C
+ATOM 667 CD2 LEU A 87 -0.878 69.070 10.337 1.00 20.99 C
+ATOM 668 N SER A 88 -0.962 67.783 4.942 1.00 24.29 N
+ATOM 669 CA SER A 88 -1.731 67.640 3.689 1.00 24.25 C
+ATOM 670 C SER A 88 -2.098 66.189 3.441 1.00 24.82 C
+ATOM 671 O SER A 88 -3.099 65.943 2.763 1.00 28.24 O
+ATOM 672 CB SER A 88 -0.935 68.206 2.504 1.00 24.39 C
+ATOM 673 OG SER A 88 0.083 67.302 2.094 1.00 27.16 O
+ATOM 674 N GLN A 89 -1.315 65.283 3.991 1.00 21.67 N
+ATOM 675 CA GLN A 89 -1.535 63.853 3.811 1.00 26.48 C
+ATOM 676 C GLN A 89 -2.540 63.295 4.820 1.00 26.66 C
+ATOM 677 O GLN A 89 -2.739 62.063 4.831 1.00 29.76 O
+ATOM 678 CB GLN A 89 -0.227 63.095 3.962 1.00 23.68 C
+ATOM 679 CG GLN A 89 0.716 63.263 2.780 1.00 30.62 C
+ATOM 680 CD GLN A 89 2.130 62.830 3.042 1.00 35.48 C
+ATOM 681 OE1 GLN A 89 2.550 62.599 4.184 1.00 41.43 O
+ATOM 682 NE2 GLN A 89 2.911 62.743 1.968 1.00 39.32 N
+ATOM 683 N GLY A 90 -3.009 64.137 5.706 1.00 20.26 N
+ATOM 684 CA GLY A 90 -3.982 63.717 6.719 1.00 20.32 C
+ATOM 685 C GLY A 90 -3.379 63.346 8.067 1.00 22.61 C
+ATOM 686 O GLY A 90 -4.055 62.724 8.922 1.00 23.56 O
+ATOM 687 N VAL A 91 -2.089 63.629 8.227 1.00 20.07 N
+ATOM 688 CA VAL A 91 -1.412 63.257 9.468 1.00 19.89 C
+ATOM 689 C VAL A 91 -1.513 64.392 10.467 1.00 22.44 C
+ATOM 690 O VAL A 91 -1.113 65.507 10.104 1.00 20.11 O
+ATOM 691 CB VAL A 91 0.080 62.992 9.229 1.00 19.24 C
+ATOM 692 CG1 VAL A 91 0.764 62.645 10.554 1.00 19.79 C
+ATOM 693 CG2 VAL A 91 0.267 61.896 8.186 1.00 19.91 C
+ATOM 694 N THR A 92 -2.068 64.162 11.633 1.00 17.41 N
+ATOM 695 CA THR A 92 -2.152 65.179 12.684 1.00 14.97 C
+ATOM 696 C THR A 92 -0.789 65.266 13.359 1.00 16.79 C
+ATOM 697 O THR A 92 -0.126 64.247 13.613 1.00 19.16 O
+ATOM 698 CB THR A 92 -3.228 64.780 13.717 1.00 15.95 C
+ATOM 699 OG1 THR A 92 -4.477 65.140 13.089 1.00 20.22 O
+ATOM 700 CG2 THR A 92 -3.085 65.535 15.032 1.00 17.14 C
+ATOM 701 N LEU A 93 -0.298 66.487 13.595 1.00 13.14 N
+ATOM 702 CA LEU A 93 1.032 66.616 14.194 1.00 13.33 C
+ATOM 703 C LEU A 93 0.850 67.216 15.595 1.00 15.37 C
+ATOM 704 O LEU A 93 0.153 68.216 15.774 1.00 18.12 O
+ATOM 705 CB LEU A 93 1.925 67.566 13.381 1.00 18.32 C
+ATOM 706 CG LEU A 93 2.216 67.114 11.958 1.00 17.62 C
+ATOM 707 CD1 LEU A 93 2.957 68.241 11.225 1.00 17.05 C
+ATOM 708 CD2 LEU A 93 3.069 65.849 11.959 1.00 18.38 C
+ATOM 709 N VAL A 94 1.470 66.541 16.539 1.00 15.36 N
+ATOM 710 CA VAL A 94 1.507 66.971 17.939 1.00 15.75 C
+ATOM 711 C VAL A 94 2.889 67.552 18.209 1.00 16.16 C
+ATOM 712 O VAL A 94 3.837 66.789 18.058 1.00 16.25 O
+ATOM 713 CB VAL A 94 1.257 65.757 18.857 1.00 16.68 C
+ATOM 714 CG1 VAL A 94 1.390 66.217 20.329 1.00 16.89 C
+ATOM 715 CG2 VAL A 94 -0.165 65.263 18.622 1.00 17.08 C
+ATOM 716 N VAL A 95 2.945 68.833 18.493 1.00 14.52 N
+ATOM 717 CA VAL A 95 4.227 69.569 18.606 1.00 16.22 C
+ATOM 718 C VAL A 95 4.504 70.004 20.024 1.00 14.90 C
+ATOM 719 O VAL A 95 3.763 70.809 20.621 1.00 16.35 O
+ATOM 720 CB VAL A 95 4.098 70.788 17.660 1.00 13.99 C
+ATOM 721 CG1 VAL A 95 5.480 71.447 17.530 1.00 17.29 C
+ATOM 722 CG2 VAL A 95 3.590 70.305 16.303 1.00 19.22 C
+ATOM 723 N ASP A 96 5.659 69.582 20.546 1.00 14.68 N
+ATOM 724 CA ASP A 96 6.126 69.893 21.887 1.00 16.55 C
+ATOM 725 C ASP A 96 6.990 71.150 21.845 1.00 17.10 C
+ATOM 726 O ASP A 96 8.159 71.015 21.462 1.00 16.69 O
+ATOM 727 CB ASP A 96 6.909 68.652 22.329 1.00 17.21 C
+ATOM 728 CG ASP A 96 7.482 68.707 23.724 1.00 15.79 C
+ATOM 729 OD1 ASP A 96 7.322 69.709 24.477 1.00 19.59 O
+ATOM 730 OD2 ASP A 96 8.223 67.722 24.040 1.00 21.30 O
+ATOM 731 N ARG A 97 6.375 72.267 22.131 1.00 17.07 N
+ATOM 732 CA ARG A 97 6.878 73.627 22.058 1.00 18.08 C
+ATOM 733 C ARG A 97 6.888 74.123 20.596 1.00 16.09 C
+ATOM 734 O ARG A 97 7.080 73.335 19.649 1.00 17.14 O
+ATOM 735 CB ARG A 97 8.279 73.863 22.649 1.00 16.60 C
+ATOM 736 CG ARG A 97 8.364 73.547 24.160 1.00 18.77 C
+ATOM 737 CD ARG A 97 9.774 74.011 24.592 1.00 20.26 C
+ATOM 738 NE ARG A 97 10.030 73.968 26.003 1.00 25.45 N
+ATOM 739 CZ ARG A 97 9.694 74.760 27.010 1.00 24.88 C
+ATOM 740 NH1 ARG A 97 8.936 75.862 26.917 1.00 19.67 N
+ATOM 741 NH2 ARG A 97 10.169 74.281 28.175 1.00 23.25 N
+ATOM 742 N TYR A 98 6.610 75.428 20.429 1.00 16.14 N
+ATOM 743 CA TYR A 98 6.615 75.991 19.076 1.00 16.68 C
+ATOM 744 C TYR A 98 7.042 77.453 19.171 1.00 17.87 C
+ATOM 745 O TYR A 98 7.825 77.823 20.052 1.00 16.92 O
+ATOM 746 CB TYR A 98 5.223 75.855 18.479 1.00 17.17 C
+ATOM 747 CG TYR A 98 4.999 76.008 16.996 1.00 16.50 C
+ATOM 748 CD1 TYR A 98 5.766 75.276 16.083 1.00 16.11 C
+ATOM 749 CD2 TYR A 98 4.014 76.855 16.503 1.00 17.09 C
+ATOM 750 CE1 TYR A 98 5.513 75.388 14.727 1.00 19.90 C
+ATOM 751 CE2 TYR A 98 3.748 76.961 15.133 1.00 18.10 C
+ATOM 752 CZ TYR A 98 4.515 76.234 14.262 1.00 16.75 C
+ATOM 753 OH TYR A 98 4.294 76.297 12.897 1.00 18.48 O
+ATOM 754 N ALA A 99 6.458 78.316 18.334 1.00 15.70 N
+ATOM 755 CA ALA A 99 6.922 79.712 18.338 1.00 15.98 C
+ATOM 756 C ALA A 99 6.666 80.436 19.635 1.00 17.09 C
+ATOM 757 O ALA A 99 7.287 81.475 19.962 1.00 16.79 O
+ATOM 758 CB ALA A 99 6.121 80.411 17.213 1.00 16.39 C
+ATOM 759 N PHE A 100 5.657 80.007 20.403 1.00 14.83 N
+ATOM 760 CA PHE A 100 5.283 80.707 21.633 1.00 16.96 C
+ATOM 761 C PHE A 100 6.414 80.618 22.634 1.00 15.49 C
+ATOM 762 O PHE A 100 6.758 81.609 23.280 1.00 17.35 O
+ATOM 763 CB PHE A 100 3.958 80.108 22.168 1.00 15.87 C
+ATOM 764 CG PHE A 100 2.933 79.993 21.064 1.00 15.22 C
+ATOM 765 CD1 PHE A 100 2.290 81.116 20.564 1.00 17.50 C
+ATOM 766 CD2 PHE A 100 2.660 78.757 20.492 1.00 16.36 C
+ATOM 767 CE1 PHE A 100 1.399 80.989 19.506 1.00 18.96 C
+ATOM 768 CE2 PHE A 100 1.778 78.637 19.424 1.00 19.16 C
+ATOM 769 CZ PHE A 100 1.152 79.776 18.924 1.00 18.79 C
+ATOM 770 N SER A 101 7.014 79.426 22.776 1.00 16.42 N
+ATOM 771 CA SER A 101 8.168 79.271 23.671 1.00 17.26 C
+ATOM 772 C SER A 101 9.276 80.225 23.158 1.00 19.23 C
+ATOM 773 O SER A 101 9.986 80.856 23.921 1.00 19.73 O
+ATOM 774 CB SER A 101 8.722 77.851 23.683 1.00 19.96 C
+ATOM 775 OG SER A 101 7.997 77.002 24.601 1.00 19.33 O
+ATOM 776 N GLY A 102 9.424 80.271 21.847 1.00 17.39 N
+ATOM 777 CA GLY A 102 10.514 81.127 21.263 1.00 17.67 C
+ATOM 778 C GLY A 102 10.349 82.558 21.777 1.00 16.94 C
+ATOM 779 O GLY A 102 11.331 83.229 22.153 1.00 18.89 O
+ATOM 780 N VAL A 103 9.157 83.107 21.599 1.00 14.32 N
+ATOM 781 CA VAL A 103 8.898 84.485 22.023 1.00 18.66 C
+ATOM 782 C VAL A 103 8.966 84.617 23.529 1.00 21.38 C
+ATOM 783 O VAL A 103 9.510 85.609 24.015 1.00 20.14 O
+ATOM 784 CB VAL A 103 7.524 84.944 21.488 1.00 17.26 C
+ATOM 785 CG1 VAL A 103 7.149 86.329 21.987 1.00 21.80 C
+ATOM 786 CG2 VAL A 103 7.527 84.886 19.958 1.00 19.17 C
+ATOM 787 N ALA A 104 8.360 83.691 24.292 1.00 17.18 N
+ATOM 788 CA ALA A 104 8.370 83.861 25.741 1.00 17.73 C
+ATOM 789 C ALA A 104 9.729 83.788 26.400 1.00 20.89 C
+ATOM 790 O ALA A 104 10.006 84.565 27.330 1.00 20.98 O
+ATOM 791 CB ALA A 104 7.447 82.812 26.415 1.00 18.33 C
+ATOM 792 N PHE A 105 10.637 82.943 25.944 1.00 19.97 N
+ATOM 793 CA PHE A 105 11.950 82.821 26.523 1.00 19.63 C
+ATOM 794 C PHE A 105 12.835 84.002 26.124 1.00 24.21 C
+ATOM 795 O PHE A 105 13.463 84.566 27.028 1.00 21.74 O
+ATOM 796 CB PHE A 105 12.542 81.438 26.196 1.00 20.12 C
+ATOM 797 CG PHE A 105 11.889 80.485 27.189 1.00 24.57 C
+ATOM 798 CD1 PHE A 105 10.632 79.961 26.955 1.00 25.17 C
+ATOM 799 CD2 PHE A 105 12.551 80.159 28.363 1.00 25.64 C
+ATOM 800 CE1 PHE A 105 10.044 79.099 27.872 1.00 26.78 C
+ATOM 801 CE2 PHE A 105 11.964 79.307 29.280 1.00 29.43 C
+ATOM 802 CZ PHE A 105 10.705 78.792 29.043 1.00 27.91 C
+ATOM 803 N THR A 106 12.858 84.395 24.847 1.00 20.52 N
+ATOM 804 CA THR A 106 13.676 85.572 24.519 1.00 19.99 C
+ATOM 805 C THR A 106 13.047 86.830 25.095 1.00 21.17 C
+ATOM 806 O THR A 106 13.752 87.721 25.592 1.00 22.46 O
+ATOM 807 CB THR A 106 13.825 85.723 22.982 1.00 22.02 C
+ATOM 808 OG1 THR A 106 14.536 84.574 22.501 1.00 19.61 O
+ATOM 809 CG2 THR A 106 14.576 86.973 22.559 1.00 21.14 C
+ATOM 810 N GLY A 107 11.697 86.877 25.087 1.00 19.12 N
+ATOM 811 CA GLY A 107 11.012 88.077 25.571 1.00 24.91 C
+ATOM 812 C GLY A 107 11.215 88.248 27.076 1.00 24.08 C
+ATOM 813 O GLY A 107 10.907 89.327 27.587 1.00 26.21 O
+ATOM 814 N ALA A 108 11.703 87.218 27.740 1.00 24.88 N
+ATOM 815 CA ALA A 108 11.951 87.324 29.178 1.00 26.51 C
+ATOM 816 C ALA A 108 13.286 88.018 29.465 1.00 28.63 C
+ATOM 817 O ALA A 108 13.641 88.218 30.621 1.00 27.32 O
+ATOM 818 CB ALA A 108 12.003 85.936 29.789 1.00 26.91 C
+ATOM 819 N LYS A 109 14.075 88.245 28.426 1.00 24.68 N
+ATOM 820 CA LYS A 109 15.378 88.895 28.591 1.00 25.57 C
+ATOM 821 C LYS A 109 15.201 90.391 28.540 1.00 26.79 C
+ATOM 822 O LYS A 109 14.209 90.910 28.007 1.00 29.34 O
+ATOM 823 CB LYS A 109 16.360 88.415 27.519 1.00 26.46 C
+ATOM 824 CG LYS A 109 16.624 86.922 27.573 1.00 26.63 C
+ATOM 825 CD LYS A 109 17.401 86.459 26.341 1.00 30.01 C
+ATOM 826 CE LYS A 109 17.828 85.021 26.520 1.00 28.06 C
+ATOM 827 NZ LYS A 109 18.705 84.502 25.438 1.00 29.59 N
+ATOM 828 N GLU A 110 16.189 91.138 29.105 1.00 28.04 N
+ATOM 829 CA GLU A 110 16.040 92.586 29.088 1.00 34.52 C
+ATOM 830 C GLU A 110 16.159 93.153 27.680 1.00 26.44 C
+ATOM 831 O GLU A 110 16.941 92.667 26.879 1.00 30.02 O
+ATOM 832 CB GLU A 110 17.100 93.270 29.975 1.00 38.36 C
+ATOM 833 CG GLU A 110 16.479 94.371 30.835 1.00 46.34 C
+ATOM 834 CD GLU A 110 15.477 93.826 31.842 1.00 49.17 C
+ATOM 835 OE1 GLU A 110 15.805 92.879 32.582 1.00 48.76 O
+ATOM 836 OE2 GLU A 110 14.341 94.356 31.887 1.00 53.43 O
+ATOM 837 N ASN A 111 15.378 94.187 27.415 1.00 29.57 N
+ATOM 838 CA ASN A 111 15.448 94.887 26.143 1.00 32.35 C
+ATOM 839 C ASN A 111 15.106 94.031 24.932 1.00 28.58 C
+ATOM 840 O ASN A 111 15.646 94.217 23.843 1.00 27.36 O
+ATOM 841 CB ASN A 111 16.823 95.565 25.992 1.00 41.19 C
+ATOM 842 CG ASN A 111 17.029 96.657 27.028 1.00 46.34 C
+ATOM 843 OD1 ASN A 111 16.196 97.551 27.216 1.00 52.60 O
+ATOM 844 ND2 ASN A 111 18.142 96.632 27.745 1.00 49.08 N
+ATOM 845 N PHE A 112 14.123 93.141 25.086 1.00 27.40 N
+ATOM 846 CA PHE A 112 13.576 92.401 23.958 1.00 22.28 C
+ATOM 847 C PHE A 112 12.064 92.620 23.918 1.00 27.86 C
+ATOM 848 O PHE A 112 11.353 92.191 24.839 1.00 29.87 O
+ATOM 849 CB PHE A 112 13.869 90.909 24.028 1.00 23.69 C
+ATOM 850 CG PHE A 112 15.243 90.529 23.557 1.00 23.36 C
+ATOM 851 CD1 PHE A 112 16.334 90.582 24.402 1.00 22.46 C
+ATOM 852 CD2 PHE A 112 15.406 90.125 22.229 1.00 25.46 C
+ATOM 853 CE1 PHE A 112 17.601 90.230 23.949 1.00 26.31 C
+ATOM 854 CE2 PHE A 112 16.678 89.768 21.793 1.00 26.02 C
+ATOM 855 CZ PHE A 112 17.754 89.832 22.640 1.00 28.59 C
+ATOM 856 N SER A 113 11.583 93.334 22.912 1.00 23.51 N
+ATOM 857 CA SER A 113 10.145 93.606 22.842 1.00 24.65 C
+ATOM 858 C SER A 113 9.409 92.372 22.321 1.00 23.11 C
+ATOM 859 O SER A 113 9.980 91.582 21.563 1.00 21.88 O
+ATOM 860 CB SER A 113 9.829 94.782 21.943 1.00 27.58 C
+ATOM 861 OG SER A 113 10.103 94.511 20.567 1.00 25.67 O
+ATOM 862 N LEU A 114 8.173 92.197 22.776 1.00 21.77 N
+ATOM 863 CA LEU A 114 7.406 91.061 22.236 1.00 24.45 C
+ATOM 864 C LEU A 114 7.314 91.175 20.717 1.00 22.90 C
+ATOM 865 O LEU A 114 7.359 90.162 19.997 1.00 20.99 O
+ATOM 866 CB LEU A 114 6.019 91.003 22.876 1.00 26.84 C
+ATOM 867 CG LEU A 114 5.364 89.635 22.993 1.00 36.39 C
+ATOM 868 CD1 LEU A 114 6.037 88.783 24.062 1.00 36.15 C
+ATOM 869 CD2 LEU A 114 3.871 89.793 23.261 1.00 40.62 C
+ATOM 870 N ASP A 115 7.100 92.369 20.194 1.00 21.04 N
+ATOM 871 CA ASP A 115 6.985 92.558 18.750 1.00 22.43 C
+ATOM 872 C ASP A 115 8.235 92.057 18.022 1.00 18.71 C
+ATOM 873 O ASP A 115 8.051 91.267 17.085 1.00 18.01 O
+ATOM 874 CB ASP A 115 6.752 94.038 18.394 1.00 22.80 C
+ATOM 875 CG ASP A 115 6.548 94.191 16.898 1.00 24.46 C
+ATOM 876 OD1 ASP A 115 5.457 93.877 16.383 1.00 25.76 O
+ATOM 877 OD2 ASP A 115 7.454 94.576 16.125 1.00 25.79 O
+ATOM 878 N TRP A 116 9.429 92.472 18.428 1.00 19.52 N
+ATOM 879 CA TRP A 116 10.650 92.024 17.741 1.00 19.72 C
+ATOM 880 C TRP A 116 10.753 90.490 17.832 1.00 19.69 C
+ATOM 881 O TRP A 116 11.092 89.835 16.848 1.00 17.58 O
+ATOM 882 CB TRP A 116 11.886 92.655 18.411 1.00 21.66 C
+ATOM 883 CG TRP A 116 13.122 92.357 17.589 1.00 21.21 C
+ATOM 884 CD1 TRP A 116 13.613 93.112 16.572 1.00 20.77 C
+ATOM 885 CD2 TRP A 116 13.964 91.226 17.718 1.00 18.10 C
+ATOM 886 NE1 TRP A 116 14.741 92.499 16.052 1.00 18.36 N
+ATOM 887 CE2 TRP A 116 14.975 91.324 16.720 1.00 19.43 C
+ATOM 888 CE3 TRP A 116 13.969 90.108 18.566 1.00 18.61 C
+ATOM 889 CZ2 TRP A 116 15.957 90.367 16.577 1.00 17.06 C
+ATOM 890 CZ3 TRP A 116 14.966 89.166 18.408 1.00 18.65 C
+ATOM 891 CH2 TRP A 116 15.957 89.271 17.414 1.00 19.25 C
+ATOM 892 N CYS A 117 10.422 89.941 19.013 1.00 16.79 N
+ATOM 893 CA CYS A 117 10.514 88.499 19.167 1.00 17.29 C
+ATOM 894 C CYS A 117 9.541 87.720 18.276 1.00 15.71 C
+ATOM 895 O CYS A 117 9.918 86.630 17.811 1.00 17.21 O
+ATOM 896 CB CYS A 117 10.275 88.168 20.651 1.00 17.65 C
+ATOM 897 SG CYS A 117 11.629 88.691 21.712 1.00 18.22 S
+ATOM 898 N LYS A 118 8.348 88.279 18.040 1.00 17.04 N
+ATOM 899 CA LYS A 118 7.410 87.554 17.170 1.00 18.36 C
+ATOM 900 C LYS A 118 7.764 87.508 15.697 1.00 17.96 C
+ATOM 901 O LYS A 118 7.469 86.514 15.015 1.00 17.24 O
+ATOM 902 CB LYS A 118 5.992 88.141 17.314 1.00 18.42 C
+ATOM 903 CG LYS A 118 5.379 87.846 18.682 1.00 18.94 C
+ATOM 904 CD LYS A 118 4.170 88.762 18.911 1.00 25.47 C
+ATOM 905 CE LYS A 118 3.157 88.734 17.785 1.00 27.39 C
+ATOM 906 NZ LYS A 118 1.842 89.316 18.236 1.00 30.21 N
+ATOM 907 N GLN A 119 8.430 88.552 15.159 1.00 17.38 N
+ATOM 908 CA GLN A 119 8.553 88.699 13.723 1.00 16.15 C
+ATOM 909 C GLN A 119 9.105 87.516 12.975 1.00 16.46 C
+ATOM 910 O GLN A 119 8.589 87.184 11.896 1.00 16.57 O
+ATOM 911 CB GLN A 119 9.299 90.008 13.340 1.00 16.99 C
+ATOM 912 CG GLN A 119 8.582 91.260 13.900 1.00 17.00 C
+ATOM 913 CD GLN A 119 7.110 91.306 13.569 1.00 18.21 C
+ATOM 914 OE1 GLN A 119 6.699 91.260 12.422 1.00 18.70 O
+ATOM 915 NE2 GLN A 119 6.240 91.358 14.575 1.00 21.10 N
+ATOM 916 N PRO A 120 10.200 86.905 13.393 1.00 17.81 N
+ATOM 917 CA PRO A 120 10.797 85.824 12.640 1.00 15.05 C
+ATOM 918 C PRO A 120 9.831 84.661 12.421 1.00 18.04 C
+ATOM 919 O PRO A 120 9.867 84.093 11.321 1.00 15.99 O
+ATOM 920 CB PRO A 120 11.989 85.378 13.464 1.00 18.10 C
+ATOM 921 CG PRO A 120 12.313 86.608 14.279 1.00 23.52 C
+ATOM 922 CD PRO A 120 10.999 87.295 14.601 1.00 17.84 C
+ATOM 923 N ASP A 121 8.949 84.438 13.388 1.00 18.25 N
+ATOM 924 CA ASP A 121 7.979 83.335 13.249 1.00 16.68 C
+ATOM 925 C ASP A 121 6.688 83.747 12.555 1.00 15.40 C
+ATOM 926 O ASP A 121 5.852 82.857 12.303 1.00 15.75 O
+ATOM 927 CB ASP A 121 7.647 82.796 14.643 1.00 14.73 C
+ATOM 928 CG ASP A 121 8.778 81.940 15.209 1.00 17.32 C
+ATOM 929 OD1 ASP A 121 9.445 81.201 14.482 1.00 16.75 O
+ATOM 930 OD2 ASP A 121 8.953 82.046 16.457 1.00 16.75 O
+ATOM 931 N VAL A 122 6.587 85.018 12.172 1.00 16.46 N
+ATOM 932 CA VAL A 122 5.364 85.393 11.423 1.00 17.32 C
+ATOM 933 C VAL A 122 5.285 84.612 10.140 1.00 17.50 C
+ATOM 934 O VAL A 122 6.248 84.576 9.382 1.00 16.81 O
+ATOM 935 CB VAL A 122 5.374 86.911 11.153 1.00 15.26 C
+ATOM 936 CG1 VAL A 122 4.333 87.280 10.112 1.00 19.15 C
+ATOM 937 CG2 VAL A 122 5.095 87.623 12.482 1.00 17.96 C
+ATOM 938 N GLY A 123 4.103 84.016 9.864 1.00 15.46 N
+ATOM 939 CA GLY A 123 3.934 83.217 8.673 1.00 16.86 C
+ATOM 940 C GLY A 123 4.152 81.712 8.831 1.00 17.74 C
+ATOM 941 O GLY A 123 3.861 80.993 7.864 1.00 17.76 O
+ATOM 942 N LEU A 124 4.577 81.241 9.993 1.00 14.33 N
+ATOM 943 CA LEU A 124 4.707 79.770 10.146 1.00 15.18 C
+ATOM 944 C LEU A 124 3.312 79.144 10.076 1.00 16.29 C
+ATOM 945 O LEU A 124 2.273 79.799 10.275 1.00 17.30 O
+ATOM 946 CB LEU A 124 5.226 79.502 11.570 1.00 13.74 C
+ATOM 947 CG LEU A 124 6.741 79.601 11.822 1.00 14.40 C
+ATOM 948 CD1 LEU A 124 7.003 79.309 13.307 1.00 17.20 C
+ATOM 949 CD2 LEU A 124 7.552 78.659 10.968 1.00 15.75 C
+ATOM 950 N PRO A 125 3.263 77.836 9.825 1.00 16.03 N
+ATOM 951 CA PRO A 125 1.971 77.129 9.900 1.00 19.50 C
+ATOM 952 C PRO A 125 1.302 77.493 11.218 1.00 18.14 C
+ATOM 953 O PRO A 125 1.856 77.429 12.330 1.00 15.89 O
+ATOM 954 CB PRO A 125 2.351 75.655 9.815 1.00 16.58 C
+ATOM 955 CG PRO A 125 3.620 75.701 8.970 1.00 18.93 C
+ATOM 956 CD PRO A 125 4.359 76.939 9.474 1.00 15.13 C
+ATOM 957 N LYS A 126 0.024 77.894 11.172 1.00 17.55 N
+ATOM 958 CA LYS A 126 -0.719 78.287 12.353 1.00 14.77 C
+ATOM 959 C LYS A 126 -1.355 77.079 13.056 1.00 15.72 C
+ATOM 960 O LYS A 126 -2.058 76.302 12.412 1.00 17.49 O
+ATOM 961 CB LYS A 126 -1.858 79.245 11.953 1.00 17.26 C
+ATOM 962 CG LYS A 126 -2.577 79.806 13.165 1.00 16.72 C
+ATOM 963 CD LYS A 126 -3.786 80.630 12.657 1.00 24.13 C
+ATOM 964 CE LYS A 126 -4.509 81.398 13.738 1.00 24.90 C
+ATOM 965 NZ LYS A 126 -5.501 82.349 13.060 1.00 28.55 N
+ATOM 966 N PRO A 127 -1.059 76.857 14.314 1.00 14.97 N
+ATOM 967 CA PRO A 127 -1.664 75.717 15.012 1.00 15.98 C
+ATOM 968 C PRO A 127 -3.197 75.824 15.022 1.00 17.08 C
+ATOM 969 O PRO A 127 -3.725 76.930 15.094 1.00 17.79 O
+ATOM 970 CB PRO A 127 -1.192 75.871 16.453 1.00 18.19 C
+ATOM 971 CG PRO A 127 0.131 76.590 16.280 1.00 20.62 C
+ATOM 972 CD PRO A 127 -0.195 77.629 15.214 1.00 16.05 C
+ATOM 973 N ASP A 128 -3.805 74.642 14.873 1.00 14.41 N
+ATOM 974 CA ASP A 128 -5.273 74.618 15.015 1.00 15.62 C
+ATOM 975 C ASP A 128 -5.726 74.626 16.463 1.00 18.12 C
+ATOM 976 O ASP A 128 -6.905 74.937 16.755 1.00 19.00 O
+ATOM 977 CB ASP A 128 -5.767 73.283 14.405 1.00 18.02 C
+ATOM 978 CG ASP A 128 -5.496 73.353 12.909 1.00 18.87 C
+ATOM 979 OD1 ASP A 128 -5.987 74.327 12.278 1.00 20.34 O
+ATOM 980 OD2 ASP A 128 -4.768 72.522 12.397 1.00 21.20 O
+ATOM 981 N LEU A 129 -4.848 74.292 17.381 1.00 17.10 N
+ATOM 982 CA LEU A 129 -5.073 74.178 18.802 1.00 17.80 C
+ATOM 983 C LEU A 129 -3.752 74.409 19.552 1.00 18.20 C
+ATOM 984 O LEU A 129 -2.743 73.803 19.196 1.00 16.82 O
+ATOM 985 CB LEU A 129 -5.570 72.751 19.149 1.00 16.49 C
+ATOM 986 CG LEU A 129 -5.684 72.386 20.623 1.00 16.53 C
+ATOM 987 CD1 LEU A 129 -6.687 73.259 21.380 1.00 19.86 C
+ATOM 988 CD2 LEU A 129 -6.125 70.913 20.757 1.00 19.61 C
+ATOM 989 N VAL A 130 -3.766 75.303 20.512 1.00 15.80 N
+ATOM 990 CA VAL A 130 -2.599 75.534 21.354 1.00 18.39 C
+ATOM 991 C VAL A 130 -2.978 75.236 22.809 1.00 18.22 C
+ATOM 992 O VAL A 130 -3.754 75.984 23.389 1.00 19.23 O
+ATOM 993 CB VAL A 130 -2.079 76.978 21.295 1.00 18.38 C
+ATOM 994 CG1 VAL A 130 -0.745 77.044 22.038 1.00 20.39 C
+ATOM 995 CG2 VAL A 130 -1.913 77.426 19.857 1.00 17.59 C
+ATOM 996 N LEU A 131 -2.426 74.138 23.322 1.00 16.25 N
+ATOM 997 CA LEU A 131 -2.728 73.783 24.713 1.00 15.40 C
+ATOM 998 C LEU A 131 -1.716 74.399 25.646 1.00 17.21 C
+ATOM 999 O LEU A 131 -0.500 74.227 25.420 1.00 19.15 O
+ATOM 1000 CB LEU A 131 -2.649 72.245 24.848 1.00 16.40 C
+ATOM 1001 CG LEU A 131 -3.649 71.478 23.986 1.00 18.86 C
+ATOM 1002 CD1 LEU A 131 -3.132 70.130 23.525 1.00 18.38 C
+ATOM 1003 CD2 LEU A 131 -4.954 71.311 24.766 1.00 21.76 C
+ATOM 1004 N PHE A 132 -2.194 75.079 26.679 1.00 15.11 N
+ATOM 1005 CA PHE A 132 -1.214 75.692 27.618 1.00 17.47 C
+ATOM 1006 C PHE A 132 -1.320 74.976 28.951 1.00 17.97 C
+ATOM 1007 O PHE A 132 -2.388 75.047 29.580 1.00 20.57 O
+ATOM 1008 CB PHE A 132 -1.416 77.207 27.783 1.00 20.15 C
+ATOM 1009 CG PHE A 132 -0.307 77.814 28.611 1.00 22.36 C
+ATOM 1010 CD1 PHE A 132 0.914 78.137 28.020 1.00 19.99 C
+ATOM 1011 CD2 PHE A 132 -0.456 78.066 29.958 1.00 22.70 C
+ATOM 1012 CE1 PHE A 132 1.913 78.685 28.791 1.00 21.61 C
+ATOM 1013 CE2 PHE A 132 0.542 78.616 30.727 1.00 24.61 C
+ATOM 1014 CZ PHE A 132 1.762 78.913 30.147 1.00 22.32 C
+ATOM 1015 N LEU A 133 -0.261 74.246 29.281 1.00 17.39 N
+ATOM 1016 CA LEU A 133 -0.271 73.436 30.514 1.00 15.58 C
+ATOM 1017 C LEU A 133 0.085 74.305 31.712 1.00 17.18 C
+ATOM 1018 O LEU A 133 1.248 74.613 31.982 1.00 18.61 O
+ATOM 1019 CB LEU A 133 0.724 72.296 30.305 1.00 17.77 C
+ATOM 1020 CG LEU A 133 0.135 71.063 29.586 1.00 17.17 C
+ATOM 1021 CD1 LEU A 133 -0.330 71.384 28.177 1.00 18.56 C
+ATOM 1022 CD2 LEU A 133 1.248 70.004 29.558 1.00 18.34 C
+ATOM 1023 N GLN A 134 -0.999 74.725 32.398 1.00 20.64 N
+ATOM 1024 CA GLN A 134 -0.850 75.652 33.541 1.00 21.87 C
+ATOM 1025 C GLN A 134 -0.542 74.905 34.816 1.00 25.61 C
+ATOM 1026 O GLN A 134 -1.188 73.927 35.206 1.00 23.03 O
+ATOM 1027 CB GLN A 134 -2.142 76.431 33.543 1.00 26.80 C
+ATOM 1028 CG GLN A 134 -2.587 77.430 34.565 1.00 36.58 C
+ATOM 1029 CD GLN A 134 -3.619 78.346 33.885 1.00 36.44 C
+ATOM 1030 OE1 GLN A 134 -4.618 77.852 33.342 1.00 33.24 O
+ATOM 1031 NE2 GLN A 134 -3.322 79.631 33.918 1.00 36.92 N
+ATOM 1032 N LEU A 135 0.424 75.427 35.563 1.00 26.75 N
+ATOM 1033 CA LEU A 135 0.865 74.833 36.820 1.00 30.84 C
+ATOM 1034 C LEU A 135 1.576 75.961 37.593 1.00 34.23 C
+ATOM 1035 O LEU A 135 2.229 76.791 36.936 1.00 36.32 O
+ATOM 1036 CB LEU A 135 1.878 73.738 36.502 1.00 35.41 C
+ATOM 1037 CG LEU A 135 2.499 72.869 37.583 1.00 38.08 C
+ATOM 1038 CD1 LEU A 135 1.475 71.979 38.286 1.00 38.92 C
+ATOM 1039 CD2 LEU A 135 3.567 71.968 36.945 1.00 37.58 C
+ATOM 1040 N GLN A 136 1.444 75.974 38.911 1.00 36.00 N
+ATOM 1041 CA GLN A 136 2.193 77.022 39.636 1.00 39.75 C
+ATOM 1042 C GLN A 136 3.687 76.779 39.447 1.00 35.65 C
+ATOM 1043 O GLN A 136 4.166 75.642 39.489 1.00 35.09 O
+ATOM 1044 CB GLN A 136 1.829 77.007 41.114 1.00 42.76 C
+ATOM 1045 CG GLN A 136 0.339 77.029 41.403 1.00 49.01 C
+ATOM 1046 CD GLN A 136 -0.325 78.322 40.976 1.00 54.13 C
+ATOM 1047 OE1 GLN A 136 -0.496 79.232 41.788 1.00 57.31 O
+ATOM 1048 NE2 GLN A 136 -0.704 78.421 39.705 1.00 56.66 N
+ATOM 1049 N LEU A 137 4.485 77.856 39.331 1.00 33.74 N
+ATOM 1050 CA LEU A 137 5.923 77.662 39.181 1.00 35.74 C
+ATOM 1051 C LEU A 137 6.488 76.862 40.340 1.00 35.35 C
+ATOM 1052 O LEU A 137 7.407 76.057 40.140 1.00 37.11 O
+ATOM 1053 CB LEU A 137 6.637 79.015 39.030 1.00 33.75 C
+ATOM 1054 CG LEU A 137 6.428 79.565 37.596 1.00 36.62 C
+ATOM 1055 CD1 LEU A 137 6.867 81.020 37.494 1.00 36.09 C
+ATOM 1056 CD2 LEU A 137 7.186 78.662 36.616 1.00 38.65 C
+ATOM 1057 N ALA A 138 5.937 77.069 41.536 1.00 39.22 N
+ATOM 1058 CA ALA A 138 6.473 76.339 42.689 1.00 45.68 C
+ATOM 1059 C ALA A 138 6.325 74.837 42.476 1.00 48.23 C
+ATOM 1060 O ALA A 138 7.301 74.095 42.587 1.00 50.64 O
+ATOM 1061 CB ALA A 138 5.828 76.803 43.978 1.00 44.39 C
+ATOM 1062 N ASP A 139 5.107 74.402 42.165 1.00 53.25 N
+ATOM 1063 CA ASP A 139 4.862 72.970 41.964 1.00 54.95 C
+ATOM 1064 C ASP A 139 5.684 72.445 40.806 1.00 54.80 C
+ATOM 1065 O ASP A 139 6.168 71.316 40.842 1.00 58.94 O
+ATOM 1066 CB ASP A 139 3.380 72.682 41.735 1.00 58.93 C
+ATOM 1067 CG ASP A 139 2.600 73.079 42.982 1.00 60.40 C
+ATOM 1068 OD1 ASP A 139 3.252 73.045 44.048 1.00 63.85 O
+ATOM 1069 OD2 ASP A 139 1.409 73.409 42.835 1.00 61.24 O
+ATOM 1070 N ALA A 140 5.881 73.288 39.793 1.00 52.75 N
+ATOM 1071 CA ALA A 140 6.692 72.875 38.653 1.00 50.90 C
+ATOM 1072 C ALA A 140 8.130 72.630 39.105 1.00 53.38 C
+ATOM 1073 O ALA A 140 8.839 71.779 38.561 1.00 48.83 O
+ATOM 1074 CB ALA A 140 6.663 73.891 37.529 1.00 49.80 C
+ATOM 1075 N ALA A 141 8.558 73.417 40.094 1.00 55.75 N
+ATOM 1076 CA ALA A 141 9.922 73.297 40.605 1.00 57.77 C
+ATOM 1077 C ALA A 141 10.043 72.045 41.469 1.00 59.89 C
+ATOM 1078 O ALA A 141 11.075 71.383 41.484 1.00 61.73 O
+ATOM 1079 CB ALA A 141 10.326 74.543 41.366 1.00 59.03 C
+ATOM 1080 N LYS A 142 8.953 71.717 42.156 1.00 61.29 N
+ATOM 1081 CA LYS A 142 8.887 70.540 43.008 1.00 59.77 C
+ATOM 1082 C LYS A 142 8.751 69.262 42.179 1.00 59.63 C
+ATOM 1083 O LYS A 142 8.538 68.185 42.743 1.00 60.66 O
+ATOM 1084 CB LYS A 142 7.725 70.618 43.982 1.00 61.39 C
+ATOM 1085 N ARG A 143 8.792 69.413 40.854 1.00 55.80 N
+ATOM 1086 CA ARG A 143 8.786 68.217 40.007 1.00 51.20 C
+ATOM 1087 C ARG A 143 10.283 67.887 39.928 1.00 50.21 C
+ATOM 1088 O ARG A 143 10.948 68.064 38.928 1.00 47.38 O
+ATOM 1089 CB ARG A 143 8.140 68.329 38.642 1.00 43.40 C
+ATOM 1090 CG ARG A 143 6.661 68.011 38.795 1.00 40.10 C
+ATOM 1091 CD ARG A 143 5.830 68.587 37.650 1.00 30.71 C
+ATOM 1092 NE ARG A 143 4.432 68.487 38.057 1.00 34.54 N
+ATOM 1093 CZ ARG A 143 3.451 68.571 37.147 1.00 33.21 C
+ATOM 1094 NH1 ARG A 143 3.811 68.750 35.883 1.00 33.71 N
+ATOM 1095 NH2 ARG A 143 2.206 68.483 37.539 1.00 34.78 N
+ATOM 1096 N GLY A 144 10.718 67.513 41.138 1.00 51.72 N
+ATOM 1097 CA GLY A 144 12.143 67.208 41.328 1.00 54.77 C
+ATOM 1098 C GLY A 144 12.831 68.571 41.512 1.00 57.48 C
+ATOM 1099 O GLY A 144 12.255 69.496 42.091 1.00 55.48 O
+ATOM 1100 N ALA A 145 14.032 68.686 40.961 1.00 59.40 N
+ATOM 1101 CA ALA A 145 14.751 69.945 41.079 1.00 61.72 C
+ATOM 1102 C ALA A 145 15.262 70.445 39.731 1.00 63.76 C
+ATOM 1103 O ALA A 145 15.279 69.744 38.724 1.00 62.66 O
+ATOM 1104 CB ALA A 145 15.899 69.800 42.064 1.00 62.28 C
+ATOM 1105 N PHE A 146 15.666 71.717 39.769 1.00 65.40 N
+ATOM 1106 CA PHE A 146 16.209 72.353 38.586 1.00 68.32 C
+ATOM 1107 C PHE A 146 17.391 71.531 38.066 1.00 70.98 C
+ATOM 1108 O PHE A 146 18.131 70.887 38.803 1.00 72.17 O
+ATOM 1109 CB PHE A 146 16.698 73.776 38.852 1.00 67.55 C
+ATOM 1110 CG PHE A 146 15.591 74.790 38.807 1.00 66.89 C
+ATOM 1111 CD1 PHE A 146 14.919 75.027 37.617 1.00 66.60 C
+ATOM 1112 CD2 PHE A 146 15.215 75.487 39.938 1.00 66.00 C
+ATOM 1113 CE1 PHE A 146 13.898 75.956 37.560 1.00 65.75 C
+ATOM 1114 CE2 PHE A 146 14.193 76.419 39.886 1.00 65.80 C
+ATOM 1115 CZ PHE A 146 13.534 76.655 38.695 1.00 65.56 C
+ATOM 1116 N GLY A 147 17.525 71.614 36.749 1.00 72.86 N
+ATOM 1117 CA GLY A 147 18.627 70.949 36.057 1.00 72.23 C
+ATOM 1118 C GLY A 147 19.708 72.020 35.848 1.00 72.00 C
+ATOM 1119 O GLY A 147 19.565 73.158 36.298 1.00 71.69 O
+ATOM 1120 N HIS A 148 20.756 71.610 35.145 1.00 70.10 N
+ATOM 1121 CA HIS A 148 21.865 72.510 34.863 1.00 68.26 C
+ATOM 1122 C HIS A 148 21.750 73.174 33.496 1.00 65.60 C
+ATOM 1123 O HIS A 148 22.752 73.728 33.027 1.00 65.38 O
+ATOM 1124 CB HIS A 148 23.175 71.735 34.984 1.00 68.01 C
+ATOM 1125 N GLU A 149 20.585 73.146 32.852 1.00 61.38 N
+ATOM 1126 CA GLU A 149 20.456 73.776 31.539 1.00 58.23 C
+ATOM 1127 C GLU A 149 20.104 75.258 31.686 1.00 53.64 C
+ATOM 1128 O GLU A 149 19.565 75.761 32.671 1.00 50.39 O
+ATOM 1129 CB GLU A 149 19.473 73.073 30.598 1.00 61.57 C
+ATOM 1130 CG GLU A 149 20.002 71.933 29.748 1.00 63.34 C
+ATOM 1131 CD GLU A 149 19.268 71.655 28.453 1.00 66.48 C
+ATOM 1132 OE1 GLU A 149 18.122 72.124 28.237 1.00 67.31 O
+ATOM 1133 OE2 GLU A 149 19.831 70.941 27.584 1.00 66.26 O
+ATOM 1134 N ARG A 150 20.433 76.025 30.653 1.00 46.29 N
+ATOM 1135 CA ARG A 150 20.129 77.449 30.579 1.00 43.66 C
+ATOM 1136 C ARG A 150 18.665 77.733 30.898 1.00 39.05 C
+ATOM 1137 O ARG A 150 17.805 76.923 30.553 1.00 40.44 O
+ATOM 1138 CB ARG A 150 20.415 77.836 29.124 1.00 44.86 C
+ATOM 1139 CG ARG A 150 20.203 79.270 28.726 1.00 47.30 C
+ATOM 1140 CD ARG A 150 21.493 80.061 28.668 1.00 45.59 C
+ATOM 1141 NE ARG A 150 22.519 79.466 27.808 1.00 39.99 N
+ATOM 1142 CZ ARG A 150 23.786 79.881 27.890 1.00 43.16 C
+ATOM 1143 NH1 ARG A 150 24.103 80.829 28.772 1.00 45.30 N
+ATOM 1144 NH2 ARG A 150 24.758 79.395 27.143 1.00 42.16 N
+ATOM 1145 N TYR A 151 18.352 78.841 31.546 1.00 33.69 N
+ATOM 1146 CA TYR A 151 17.008 79.290 31.865 1.00 35.97 C
+ATOM 1147 C TYR A 151 16.380 78.536 33.040 1.00 34.82 C
+ATOM 1148 O TYR A 151 15.271 78.868 33.455 1.00 35.43 O
+ATOM 1149 CB TYR A 151 16.039 79.223 30.680 1.00 30.77 C
+ATOM 1150 CG TYR A 151 16.481 79.919 29.411 1.00 27.71 C
+ATOM 1151 CD1 TYR A 151 17.265 81.076 29.466 1.00 29.97 C
+ATOM 1152 CD2 TYR A 151 16.121 79.435 28.163 1.00 31.06 C
+ATOM 1153 CE1 TYR A 151 17.675 81.701 28.301 1.00 30.49 C
+ATOM 1154 CE2 TYR A 151 16.511 80.069 27.002 1.00 29.47 C
+ATOM 1155 CZ TYR A 151 17.307 81.205 27.077 1.00 32.24 C
+ATOM 1156 OH TYR A 151 17.688 81.799 25.900 1.00 30.93 O
+ATOM 1157 N GLU A 152 17.086 77.535 33.545 1.00 40.14 N
+ATOM 1158 CA GLU A 152 16.586 76.719 34.648 1.00 46.25 C
+ATOM 1159 C GLU A 152 16.605 77.415 36.004 1.00 44.20 C
+ATOM 1160 O GLU A 152 17.224 76.865 36.923 1.00 46.58 O
+ATOM 1161 CB GLU A 152 17.420 75.429 34.746 1.00 48.75 C
+ATOM 1162 CG GLU A 152 17.349 74.516 33.539 1.00 54.59 C
+ATOM 1163 CD GLU A 152 16.479 73.291 33.746 1.00 58.91 C
+ATOM 1164 OE1 GLU A 152 16.272 72.922 34.931 1.00 60.09 O
+ATOM 1165 OE2 GLU A 152 16.009 72.689 32.753 1.00 56.39 O
+ATOM 1166 N ASN A 153 15.983 78.574 36.156 1.00 41.65 N
+ATOM 1167 CA ASN A 153 15.913 79.273 37.426 1.00 39.28 C
+ATOM 1168 C ASN A 153 14.558 79.967 37.575 1.00 37.27 C
+ATOM 1169 O ASN A 153 13.927 80.318 36.578 1.00 35.89 O
+ATOM 1170 CB ASN A 153 17.007 80.309 37.664 1.00 40.11 C
+ATOM 1171 CG ASN A 153 16.941 81.505 36.745 1.00 40.37 C
+ATOM 1172 OD1 ASN A 153 16.246 82.496 36.980 1.00 39.00 O
+ATOM 1173 ND2 ASN A 153 17.718 81.398 35.659 1.00 43.48 N
+ATOM 1174 N GLY A 154 14.119 80.184 38.818 1.00 31.26 N
+ATOM 1175 CA GLY A 154 12.840 80.806 39.067 1.00 29.78 C
+ATOM 1176 C GLY A 154 12.555 82.185 38.555 1.00 27.44 C
+ATOM 1177 O GLY A 154 11.430 82.502 38.153 1.00 28.39 O
+ATOM 1178 N ALA A 155 13.520 83.136 38.592 1.00 23.40 N
+ATOM 1179 CA ALA A 155 13.187 84.475 38.160 1.00 22.30 C
+ATOM 1180 C ALA A 155 12.980 84.504 36.620 1.00 18.05 C
+ATOM 1181 O ALA A 155 12.123 85.273 36.187 1.00 24.85 O
+ATOM 1182 CB ALA A 155 14.287 85.442 38.587 1.00 29.96 C
+ATOM 1183 N PHE A 156 13.812 83.693 35.978 1.00 25.01 N
+ATOM 1184 CA PHE A 156 13.655 83.696 34.501 1.00 24.23 C
+ATOM 1185 C PHE A 156 12.345 82.995 34.121 1.00 22.60 C
+ATOM 1186 O PHE A 156 11.578 83.546 33.342 1.00 22.97 O
+ATOM 1187 CB PHE A 156 14.849 82.978 33.868 1.00 24.44 C
+ATOM 1188 CG PHE A 156 14.815 83.254 32.379 1.00 23.12 C
+ATOM 1189 CD1 PHE A 156 15.421 84.381 31.874 1.00 29.97 C
+ATOM 1190 CD2 PHE A 156 14.147 82.374 31.539 1.00 29.82 C
+ATOM 1191 CE1 PHE A 156 15.384 84.642 30.514 1.00 32.95 C
+ATOM 1192 CE2 PHE A 156 14.107 82.643 30.176 1.00 32.62 C
+ATOM 1193 CZ PHE A 156 14.724 83.766 29.678 1.00 32.47 C
+ATOM 1194 N GLN A 157 12.055 81.877 34.797 1.00 24.46 N
+ATOM 1195 CA GLN A 157 10.786 81.198 34.473 1.00 26.31 C
+ATOM 1196 C GLN A 157 9.602 82.122 34.671 1.00 27.02 C
+ATOM 1197 O GLN A 157 8.636 82.140 33.881 1.00 23.17 O
+ATOM 1198 CB GLN A 157 10.623 79.901 35.282 1.00 25.23 C
+ATOM 1199 CG GLN A 157 11.666 78.836 34.970 1.00 23.52 C
+ATOM 1200 CD GLN A 157 11.489 78.246 33.584 1.00 28.38 C
+ATOM 1201 OE1 GLN A 157 10.376 77.925 33.181 1.00 28.82 O
+ATOM 1202 NE2 GLN A 157 12.560 78.071 32.824 1.00 25.56 N
+ATOM 1203 N GLU A 158 9.595 82.921 35.751 1.00 26.56 N
+ATOM 1204 CA GLU A 158 8.495 83.841 35.993 1.00 29.20 C
+ATOM 1205 C GLU A 158 8.376 84.883 34.901 1.00 25.16 C
+ATOM 1206 O GLU A 158 7.263 85.237 34.510 1.00 25.46 O
+ATOM 1207 CB GLU A 158 8.621 84.454 37.400 1.00 33.70 C
+ATOM 1208 CG GLU A 158 8.175 85.874 37.563 1.00 43.08 C
+ATOM 1209 CD GLU A 158 6.731 86.272 37.547 1.00 50.76 C
+ATOM 1210 OE1 GLU A 158 5.828 85.430 37.728 1.00 54.78 O
+ATOM 1211 OE2 GLU A 158 6.445 87.489 37.354 1.00 52.88 O
+ATOM 1212 N ARG A 159 9.479 85.419 34.337 1.00 23.20 N
+ATOM 1213 CA ARG A 159 9.319 86.401 33.267 1.00 25.45 C
+ATOM 1214 C ARG A 159 8.782 85.755 31.973 1.00 22.91 C
+ATOM 1215 O ARG A 159 7.975 86.375 31.279 1.00 26.09 O
+ATOM 1216 CB ARG A 159 10.653 87.104 32.955 1.00 26.61 C
+ATOM 1217 CG ARG A 159 11.146 87.880 34.172 1.00 36.09 C
+ATOM 1218 CD ARG A 159 12.430 88.635 33.910 1.00 40.30 C
+ATOM 1219 NE ARG A 159 12.362 89.486 32.729 1.00 40.48 N
+ATOM 1220 CZ ARG A 159 12.957 90.686 32.733 1.00 46.29 C
+ATOM 1221 NH1 ARG A 159 13.575 91.054 33.850 1.00 43.20 N
+ATOM 1222 NH2 ARG A 159 12.916 91.460 31.662 1.00 43.30 N
+ATOM 1223 N ALA A 160 9.239 84.534 31.741 1.00 21.25 N
+ATOM 1224 CA ALA A 160 8.773 83.792 30.561 1.00 21.61 C
+ATOM 1225 C ALA A 160 7.262 83.569 30.679 1.00 20.94 C
+ATOM 1226 O ALA A 160 6.501 83.701 29.731 1.00 21.08 O
+ATOM 1227 CB ALA A 160 9.459 82.450 30.425 1.00 22.00 C
+ATOM 1228 N LEU A 161 6.833 83.168 31.882 1.00 23.25 N
+ATOM 1229 CA LEU A 161 5.402 82.947 32.089 1.00 24.47 C
+ATOM 1230 C LEU A 161 4.586 84.202 31.801 1.00 24.47 C
+ATOM 1231 O LEU A 161 3.524 84.199 31.194 1.00 23.38 O
+ATOM 1232 CB LEU A 161 5.114 82.475 33.516 1.00 23.97 C
+ATOM 1233 CG LEU A 161 3.625 82.196 33.794 1.00 23.93 C
+ATOM 1234 CD1 LEU A 161 3.078 81.153 32.834 1.00 24.01 C
+ATOM 1235 CD2 LEU A 161 3.468 81.780 35.250 1.00 30.00 C
+ATOM 1236 N ARG A 162 5.080 85.376 32.221 1.00 27.60 N
+ATOM 1237 CA ARG A 162 4.382 86.624 31.958 1.00 27.84 C
+ATOM 1238 C ARG A 162 4.224 86.855 30.467 1.00 28.66 C
+ATOM 1239 O ARG A 162 3.213 87.384 30.018 1.00 23.92 O
+ATOM 1240 CB ARG A 162 5.126 87.791 32.608 1.00 33.26 C
+ATOM 1241 CG ARG A 162 5.181 87.724 34.131 1.00 38.93 C
+ATOM 1242 CD ARG A 162 3.807 88.077 34.701 1.00 44.53 C
+ATOM 1243 NE ARG A 162 2.985 86.889 34.764 1.00 49.82 N
+ATOM 1244 CZ ARG A 162 1.707 86.668 34.529 1.00 52.49 C
+ATOM 1245 NH1 ARG A 162 0.870 87.621 34.134 1.00 50.52 N
+ATOM 1246 NH2 ARG A 162 1.271 85.417 34.700 1.00 53.43 N
+ATOM 1247 N CYS A 163 5.275 86.517 29.705 1.00 24.15 N
+ATOM 1248 CA CYS A 163 5.224 86.672 28.257 1.00 22.10 C
+ATOM 1249 C CYS A 163 4.167 85.725 27.683 1.00 22.08 C
+ATOM 1250 O CYS A 163 3.435 86.128 26.796 1.00 25.20 O
+ATOM 1251 CB CYS A 163 6.577 86.376 27.613 1.00 22.71 C
+ATOM 1252 SG CYS A 163 7.849 87.618 28.036 1.00 24.02 S
+ATOM 1253 N PHE A 164 4.142 84.490 28.203 1.00 20.37 N
+ATOM 1254 CA PHE A 164 3.098 83.580 27.690 1.00 18.90 C
+ATOM 1255 C PHE A 164 1.698 84.192 27.850 1.00 19.65 C
+ATOM 1256 O PHE A 164 0.888 84.085 26.943 1.00 22.64 O
+ATOM 1257 CB PHE A 164 3.114 82.205 28.335 1.00 23.02 C
+ATOM 1258 CG PHE A 164 4.104 81.216 27.787 1.00 19.95 C
+ATOM 1259 CD1 PHE A 164 3.966 80.724 26.490 1.00 22.83 C
+ATOM 1260 CD2 PHE A 164 5.151 80.787 28.571 1.00 19.41 C
+ATOM 1261 CE1 PHE A 164 4.854 79.770 26.031 1.00 19.39 C
+ATOM 1262 CE2 PHE A 164 6.059 79.848 28.080 1.00 21.55 C
+ATOM 1263 CZ PHE A 164 5.911 79.327 26.809 1.00 22.42 C
+ATOM 1264 N HIS A 165 1.431 84.799 28.985 1.00 25.78 N
+ATOM 1265 CA HIS A 165 0.107 85.401 29.220 1.00 28.13 C
+ATOM 1266 C HIS A 165 -0.157 86.541 28.249 1.00 25.84 C
+ATOM 1267 O HIS A 165 -1.278 86.637 27.726 1.00 26.18 O
+ATOM 1268 CB HIS A 165 -0.034 85.754 30.703 1.00 32.20 C
+ATOM 1269 CG HIS A 165 -0.265 84.518 31.533 1.00 36.76 C
+ATOM 1270 ND1 HIS A 165 -1.487 83.878 31.580 1.00 39.04 N
+ATOM 1271 CD2 HIS A 165 0.546 83.805 32.348 1.00 39.10 C
+ATOM 1272 CE1 HIS A 165 -1.401 82.827 32.378 1.00 38.97 C
+ATOM 1273 NE2 HIS A 165 -0.164 82.764 32.865 1.00 38.58 N
+ATOM 1274 N GLN A 166 0.884 87.295 27.867 1.00 27.72 N
+ATOM 1275 CA GLN A 166 0.651 88.317 26.834 1.00 28.68 C
+ATOM 1276 C GLN A 166 0.243 87.679 25.505 1.00 27.01 C
+ATOM 1277 O GLN A 166 -0.614 88.164 24.766 1.00 27.97 O
+ATOM 1278 CB GLN A 166 1.894 89.175 26.591 1.00 33.00 C
+ATOM 1279 CG GLN A 166 2.017 90.342 27.553 1.00 40.81 C
+ATOM 1280 CD GLN A 166 0.779 91.228 27.500 1.00 46.68 C
+ATOM 1281 OE1 GLN A 166 0.185 91.532 26.463 1.00 51.39 O
+ATOM 1282 NE2 GLN A 166 0.373 91.661 28.691 1.00 51.70 N
+ATOM 1283 N LEU A 167 0.879 86.559 25.154 1.00 22.60 N
+ATOM 1284 CA LEU A 167 0.584 85.901 23.890 1.00 22.03 C
+ATOM 1285 C LEU A 167 -0.825 85.319 23.863 1.00 24.75 C
+ATOM 1286 O LEU A 167 -1.430 85.097 22.813 1.00 25.74 O
+ATOM 1287 CB LEU A 167 1.621 84.772 23.653 1.00 23.90 C
+ATOM 1288 CG LEU A 167 3.029 85.336 23.434 1.00 24.68 C
+ATOM 1289 CD1 LEU A 167 4.062 84.206 23.335 1.00 26.07 C
+ATOM 1290 CD2 LEU A 167 3.099 86.193 22.181 1.00 21.42 C
+ATOM 1291 N MET A 168 -1.327 85.006 25.038 1.00 26.74 N
+ATOM 1292 CA MET A 168 -2.655 84.395 25.120 1.00 30.64 C
+ATOM 1293 C MET A 168 -3.773 85.392 24.905 1.00 34.11 C
+ATOM 1294 O MET A 168 -4.935 84.982 24.771 1.00 34.55 O
+ATOM 1295 CB MET A 168 -2.796 83.747 26.484 1.00 32.35 C
+ATOM 1296 CG MET A 168 -2.037 82.440 26.594 1.00 35.22 C
+ATOM 1297 SD MET A 168 -2.238 81.892 28.301 1.00 43.06 S
+ATOM 1298 CE MET A 168 -0.615 81.312 28.720 1.00 36.23 C
+ATOM 1299 N LYS A 169 -3.431 86.672 24.821 1.00 36.27 N
+ATOM 1300 CA LYS A 169 -4.447 87.689 24.553 1.00 37.83 C
+ATOM 1301 C LYS A 169 -4.829 87.614 23.080 1.00 39.26 C
+ATOM 1302 O LYS A 169 -5.889 88.067 22.666 1.00 41.15 O
+ATOM 1303 CB LYS A 169 -3.943 89.091 24.855 1.00 38.87 C
+ATOM 1304 CG LYS A 169 -3.587 89.409 26.299 1.00 40.17 C
+ATOM 1305 CD LYS A 169 -3.402 90.923 26.371 1.00 49.40 C
+ATOM 1306 CE LYS A 169 -2.468 91.366 27.476 1.00 52.61 C
+ATOM 1307 NZ LYS A 169 -2.019 92.771 27.222 1.00 56.80 N
+ATOM 1308 N ASP A 170 -3.939 87.017 22.286 1.00 37.49 N
+ATOM 1309 CA ASP A 170 -4.135 86.905 20.857 1.00 35.29 C
+ATOM 1310 C ASP A 170 -5.310 85.995 20.522 1.00 37.16 C
+ATOM 1311 O ASP A 170 -5.161 84.774 20.528 1.00 37.30 O
+ATOM 1312 CB ASP A 170 -2.857 86.368 20.207 1.00 37.07 C
+ATOM 1313 CG ASP A 170 -2.843 86.680 18.720 1.00 37.89 C
+ATOM 1314 OD1 ASP A 170 -3.923 86.605 18.101 1.00 37.60 O
+ATOM 1315 OD2 ASP A 170 -1.712 86.973 18.261 1.00 39.55 O
+ATOM 1316 N THR A 171 -6.454 86.615 20.208 1.00 36.56 N
+ATOM 1317 CA THR A 171 -7.657 85.852 19.924 1.00 36.72 C
+ATOM 1318 C THR A 171 -7.624 85.207 18.554 1.00 38.36 C
+ATOM 1319 O THR A 171 -8.513 84.387 18.283 1.00 41.74 O
+ATOM 1320 CB THR A 171 -8.927 86.725 20.081 1.00 43.23 C
+ATOM 1321 OG1 THR A 171 -8.891 87.803 19.137 1.00 44.22 O
+ATOM 1322 CG2 THR A 171 -8.976 87.294 21.489 1.00 45.22 C
+ATOM 1323 N THR A 172 -6.601 85.484 17.738 1.00 33.04 N
+ATOM 1324 CA THR A 172 -6.576 84.795 16.443 1.00 33.54 C
+ATOM 1325 C THR A 172 -6.226 83.309 16.671 1.00 30.29 C
+ATOM 1326 O THR A 172 -6.368 82.549 15.706 1.00 34.79 O
+ATOM 1327 CB THR A 172 -5.579 85.374 15.439 1.00 34.99 C
+ATOM 1328 OG1 THR A 172 -4.235 85.280 15.951 1.00 35.55 O
+ATOM 1329 CG2 THR A 172 -5.847 86.850 15.166 1.00 39.40 C
+ATOM 1330 N LEU A 173 -5.851 82.933 17.885 1.00 23.77 N
+ATOM 1331 CA LEU A 173 -5.405 81.551 18.103 1.00 23.77 C
+ATOM 1332 C LEU A 173 -6.321 80.809 19.065 1.00 24.46 C
+ATOM 1333 O LEU A 173 -6.850 81.412 20.005 1.00 25.67 O
+ATOM 1334 CB LEU A 173 -3.975 81.519 18.659 1.00 22.55 C
+ATOM 1335 CG LEU A 173 -2.892 81.959 17.669 1.00 24.99 C
+ATOM 1336 CD1 LEU A 173 -1.723 82.611 18.372 1.00 26.15 C
+ATOM 1337 CD2 LEU A 173 -2.441 80.720 16.891 1.00 21.53 C
+ATOM 1338 N ASN A 174 -6.461 79.524 18.796 1.00 20.29 N
+ATOM 1339 CA ASN A 174 -7.317 78.623 19.589 1.00 18.82 C
+ATOM 1340 C ASN A 174 -6.561 78.093 20.790 1.00 20.70 C
+ATOM 1341 O ASN A 174 -6.089 76.955 20.870 1.00 21.51 O
+ATOM 1342 CB ASN A 174 -7.801 77.481 18.684 1.00 18.71 C
+ATOM 1343 CG ASN A 174 -8.779 76.533 19.380 1.00 20.20 C
+ATOM 1344 OD1 ASN A 174 -9.468 76.986 20.325 1.00 24.57 O
+ATOM 1345 ND2 ASN A 174 -8.846 75.306 18.895 1.00 23.66 N
+ATOM 1346 N TRP A 175 -6.433 78.961 21.805 1.00 20.52 N
+ATOM 1347 CA TRP A 175 -5.800 78.619 23.043 1.00 20.38 C
+ATOM 1348 C TRP A 175 -6.747 77.850 23.970 1.00 23.16 C
+ATOM 1349 O TRP A 175 -7.884 78.277 24.216 1.00 23.60 O
+ATOM 1350 CB TRP A 175 -5.367 79.866 23.805 1.00 20.04 C
+ATOM 1351 CG TRP A 175 -4.197 80.631 23.266 1.00 22.09 C
+ATOM 1352 CD1 TRP A 175 -4.281 81.714 22.424 1.00 25.94 C
+ATOM 1353 CD2 TRP A 175 -2.808 80.407 23.519 1.00 22.61 C
+ATOM 1354 NE1 TRP A 175 -3.017 82.163 22.155 1.00 27.25 N
+ATOM 1355 CE2 TRP A 175 -2.096 81.393 22.801 1.00 27.97 C
+ATOM 1356 CE3 TRP A 175 -2.090 79.500 24.285 1.00 26.04 C
+ATOM 1357 CZ2 TRP A 175 -0.707 81.478 22.830 1.00 24.64 C
+ATOM 1358 CZ3 TRP A 175 -0.710 79.571 24.310 1.00 30.69 C
+ATOM 1359 CH2 TRP A 175 -0.028 80.572 23.586 1.00 27.98 C
+ATOM 1360 N LYS A 176 -6.251 76.787 24.591 1.00 18.66 N
+ATOM 1361 CA LYS A 176 -7.009 76.055 25.598 1.00 20.85 C
+ATOM 1362 C LYS A 176 -6.098 75.854 26.814 1.00 23.86 C
+ATOM 1363 O LYS A 176 -4.975 75.312 26.759 1.00 21.31 O
+ATOM 1364 CB LYS A 176 -7.540 74.693 25.167 1.00 21.71 C
+ATOM 1365 CG LYS A 176 -8.475 74.686 23.983 1.00 24.66 C
+ATOM 1366 CD LYS A 176 -9.852 75.226 24.366 1.00 27.23 C
+ATOM 1367 CE LYS A 176 -10.803 75.073 23.186 1.00 29.98 C
+ATOM 1368 NZ LYS A 176 -12.196 75.467 23.567 1.00 30.57 N
+ATOM 1369 N MET A 177 -6.600 76.303 27.959 1.00 21.80 N
+ATOM 1370 CA MET A 177 -5.858 76.138 29.212 1.00 24.33 C
+ATOM 1371 C MET A 177 -6.084 74.713 29.745 1.00 22.08 C
+ATOM 1372 O MET A 177 -7.187 74.161 29.799 1.00 23.86 O
+ATOM 1373 CB MET A 177 -6.323 77.093 30.302 1.00 24.64 C
+ATOM 1374 CG MET A 177 -6.226 78.569 29.985 1.00 26.84 C
+ATOM 1375 SD MET A 177 -4.536 79.087 29.595 1.00 25.75 S
+ATOM 1376 CE MET A 177 -4.597 79.065 27.807 1.00 28.16 C
+ATOM 1377 N VAL A 178 -5.048 74.101 30.238 1.00 19.20 N
+ATOM 1378 CA VAL A 178 -5.094 72.760 30.799 1.00 17.97 C
+ATOM 1379 C VAL A 178 -4.565 72.817 32.231 1.00 19.18 C
+ATOM 1380 O VAL A 178 -3.521 73.376 32.499 1.00 18.77 O
+ATOM 1381 CB VAL A 178 -4.202 71.810 29.955 1.00 19.84 C
+ATOM 1382 CG1 VAL A 178 -4.130 70.428 30.577 1.00 19.83 C
+ATOM 1383 CG2 VAL A 178 -4.744 71.758 28.526 1.00 19.22 C
+ATOM 1384 N ASP A 179 -5.291 72.191 33.165 1.00 19.48 N
+ATOM 1385 CA ASP A 179 -4.809 72.187 34.550 1.00 21.09 C
+ATOM 1386 C ASP A 179 -3.785 71.067 34.689 1.00 22.10 C
+ATOM 1387 O ASP A 179 -4.187 69.901 34.786 1.00 22.81 O
+ATOM 1388 CB ASP A 179 -5.990 71.970 35.490 1.00 24.97 C
+ATOM 1389 CG ASP A 179 -5.522 71.819 36.920 1.00 26.92 C
+ATOM 1390 OD1 ASP A 179 -4.331 71.958 37.191 1.00 24.42 O
+ATOM 1391 OD2 ASP A 179 -6.415 71.608 37.786 1.00 29.91 O
+ATOM 1392 N ALA A 180 -2.518 71.443 34.515 1.00 24.09 N
+ATOM 1393 CA ALA A 180 -1.431 70.475 34.516 1.00 25.48 C
+ATOM 1394 C ALA A 180 -0.959 70.047 35.896 1.00 25.61 C
+ATOM 1395 O ALA A 180 0.032 69.339 35.996 1.00 24.79 O
+ATOM 1396 CB ALA A 180 -0.265 71.071 33.726 1.00 23.83 C
+ATOM 1397 N SER A 181 -1.677 70.489 36.936 1.00 27.81 N
+ATOM 1398 CA SER A 181 -1.335 70.075 38.299 1.00 26.81 C
+ATOM 1399 C SER A 181 -1.930 68.729 38.640 1.00 29.02 C
+ATOM 1400 O SER A 181 -1.547 68.123 39.665 1.00 31.07 O
+ATOM 1401 CB SER A 181 -1.841 71.129 39.309 1.00 27.86 C
+ATOM 1402 OG SER A 181 -3.253 71.038 39.454 1.00 30.40 O
+ATOM 1403 N LYS A 182 -2.850 68.230 37.806 1.00 25.01 N
+ATOM 1404 CA LYS A 182 -3.446 66.919 38.096 1.00 23.89 C
+ATOM 1405 C LYS A 182 -2.519 65.755 37.764 1.00 24.26 C
+ATOM 1406 O LYS A 182 -1.385 66.022 37.387 1.00 25.46 O
+ATOM 1407 CB LYS A 182 -4.783 66.800 37.360 1.00 24.92 C
+ATOM 1408 CG LYS A 182 -5.664 68.006 37.725 1.00 30.05 C
+ATOM 1409 CD LYS A 182 -7.079 67.812 37.223 1.00 34.82 C
+ATOM 1410 CE LYS A 182 -7.208 67.853 35.716 1.00 32.28 C
+ATOM 1411 NZ LYS A 182 -8.643 67.956 35.305 1.00 29.86 N
+ATOM 1412 N SER A 183 -3.002 64.522 37.899 1.00 23.46 N
+ATOM 1413 CA SER A 183 -2.141 63.367 37.646 1.00 22.67 C
+ATOM 1414 C SER A 183 -1.758 63.279 36.161 1.00 21.07 C
+ATOM 1415 O SER A 183 -2.497 63.857 35.369 1.00 19.87 O
+ATOM 1416 CB SER A 183 -2.863 62.088 38.024 1.00 22.09 C
+ATOM 1417 OG SER A 183 -3.944 61.740 37.165 1.00 22.30 O
+ATOM 1418 N ILE A 184 -0.753 62.476 35.830 1.00 20.52 N
+ATOM 1419 CA ILE A 184 -0.429 62.339 34.397 1.00 20.43 C
+ATOM 1420 C ILE A 184 -1.619 61.834 33.614 1.00 19.42 C
+ATOM 1421 O ILE A 184 -1.911 62.343 32.514 1.00 17.49 O
+ATOM 1422 CB ILE A 184 0.808 61.421 34.252 1.00 18.11 C
+ATOM 1423 CG1 ILE A 184 2.032 62.186 34.763 1.00 22.08 C
+ATOM 1424 CG2 ILE A 184 0.990 60.943 32.817 1.00 18.26 C
+ATOM 1425 CD1 ILE A 184 3.269 61.306 34.682 1.00 22.16 C
+ATOM 1426 N GLU A 185 -2.324 60.800 34.122 1.00 18.58 N
+ATOM 1427 CA GLU A 185 -3.484 60.305 33.387 1.00 20.22 C
+ATOM 1428 C GLU A 185 -4.632 61.298 33.360 1.00 19.20 C
+ATOM 1429 O GLU A 185 -5.312 61.342 32.311 1.00 17.32 O
+ATOM 1430 CB GLU A 185 -3.953 58.989 34.039 1.00 23.88 C
+ATOM 1431 CG GLU A 185 -3.024 57.813 33.807 1.00 31.89 C
+ATOM 1432 CD GLU A 185 -2.811 57.527 32.322 1.00 38.55 C
+ATOM 1433 OE1 GLU A 185 -3.748 57.683 31.501 1.00 35.91 O
+ATOM 1434 OE2 GLU A 185 -1.656 57.170 31.997 1.00 36.85 O
+ATOM 1435 N ALA A 186 -4.859 62.094 34.423 1.00 17.52 N
+ATOM 1436 CA ALA A 186 -6.004 63.018 34.324 1.00 19.98 C
+ATOM 1437 C ALA A 186 -5.761 64.146 33.331 1.00 19.27 C
+ATOM 1438 O ALA A 186 -6.661 64.561 32.605 1.00 18.40 O
+ATOM 1439 CB ALA A 186 -6.331 63.641 35.679 1.00 20.50 C
+ATOM 1440 N VAL A 187 -4.501 64.642 33.388 1.00 19.00 N
+ATOM 1441 CA VAL A 187 -4.139 65.708 32.422 1.00 17.90 C
+ATOM 1442 C VAL A 187 -4.272 65.151 31.011 1.00 18.67 C
+ATOM 1443 O VAL A 187 -4.727 65.826 30.086 1.00 15.66 O
+ATOM 1444 CB VAL A 187 -2.708 66.149 32.738 1.00 15.95 C
+ATOM 1445 CG1 VAL A 187 -2.213 67.220 31.752 1.00 15.65 C
+ATOM 1446 CG2 VAL A 187 -2.695 66.764 34.148 1.00 15.76 C
+ATOM 1447 N HIS A 188 -3.774 63.929 30.819 1.00 17.24 N
+ATOM 1448 CA HIS A 188 -3.845 63.326 29.473 1.00 15.77 C
+ATOM 1449 C HIS A 188 -5.266 63.246 28.970 1.00 17.85 C
+ATOM 1450 O HIS A 188 -5.534 63.545 27.807 1.00 17.65 O
+ATOM 1451 CB HIS A 188 -3.175 61.951 29.477 1.00 16.63 C
+ATOM 1452 CG HIS A 188 -3.527 61.106 28.292 1.00 13.33 C
+ATOM 1453 ND1 HIS A 188 -3.109 61.467 27.015 1.00 15.14 N
+ATOM 1454 CD2 HIS A 188 -4.228 59.954 28.147 1.00 16.84 C
+ATOM 1455 CE1 HIS A 188 -3.530 60.582 26.138 1.00 15.74 C
+ATOM 1456 NE2 HIS A 188 -4.217 59.623 26.817 1.00 17.47 N
+ATOM 1457 N GLU A 189 -6.207 62.806 29.801 1.00 17.85 N
+ATOM 1458 CA GLU A 189 -7.577 62.672 29.301 1.00 20.42 C
+ATOM 1459 C GLU A 189 -8.110 64.033 28.898 1.00 18.55 C
+ATOM 1460 O GLU A 189 -8.778 64.158 27.866 1.00 18.48 O
+ATOM 1461 CB GLU A 189 -8.442 61.911 30.305 1.00 21.24 C
+ATOM 1462 CG GLU A 189 -9.897 61.841 29.789 1.00 24.58 C
+ATOM 1463 CD GLU A 189 -10.008 60.806 28.670 1.00 29.59 C
+ATOM 1464 OE1 GLU A 189 -9.016 60.103 28.351 1.00 32.21 O
+ATOM 1465 OE2 GLU A 189 -11.111 60.744 28.110 1.00 33.66 O
+ATOM 1466 N ASP A 190 -7.819 65.080 29.668 1.00 18.49 N
+ATOM 1467 CA ASP A 190 -8.272 66.417 29.292 1.00 17.62 C
+ATOM 1468 C ASP A 190 -7.743 66.856 27.919 1.00 16.01 C
+ATOM 1469 O ASP A 190 -8.470 67.371 27.052 1.00 17.75 O
+ATOM 1470 CB ASP A 190 -7.817 67.459 30.323 1.00 18.97 C
+ATOM 1471 CG ASP A 190 -8.636 67.412 31.602 1.00 28.16 C
+ATOM 1472 OD1 ASP A 190 -9.664 66.712 31.644 1.00 26.16 O
+ATOM 1473 OD2 ASP A 190 -8.243 68.104 32.573 1.00 27.30 O
+ATOM 1474 N ILE A 191 -6.429 66.588 27.751 1.00 16.19 N
+ATOM 1475 CA ILE A 191 -5.788 66.953 26.484 1.00 16.20 C
+ATOM 1476 C ILE A 191 -6.318 66.124 25.338 1.00 16.71 C
+ATOM 1477 O ILE A 191 -6.477 66.641 24.244 1.00 16.51 O
+ATOM 1478 CB ILE A 191 -4.255 66.798 26.639 1.00 14.68 C
+ATOM 1479 CG1 ILE A 191 -3.782 67.989 27.490 1.00 13.17 C
+ATOM 1480 CG2 ILE A 191 -3.567 66.730 25.283 1.00 15.47 C
+ATOM 1481 CD1 ILE A 191 -2.349 67.704 27.987 1.00 15.56 C
+ATOM 1482 N ARG A 192 -6.573 64.839 25.571 1.00 14.60 N
+ATOM 1483 CA ARG A 192 -7.013 63.934 24.498 1.00 15.41 C
+ATOM 1484 C ARG A 192 -8.371 64.343 23.961 1.00 16.31 C
+ATOM 1485 O ARG A 192 -8.586 64.362 22.734 1.00 17.76 O
+ATOM 1486 CB ARG A 192 -6.996 62.486 25.005 1.00 18.58 C
+ATOM 1487 CG ARG A 192 -7.189 61.432 23.932 1.00 17.81 C
+ATOM 1488 CD ARG A 192 -7.437 60.057 24.582 1.00 16.66 C
+ATOM 1489 NE ARG A 192 -8.709 60.076 25.320 1.00 20.25 N
+ATOM 1490 CZ ARG A 192 -9.874 60.081 24.684 1.00 21.63 C
+ATOM 1491 NH1 ARG A 192 -9.917 60.067 23.362 1.00 21.94 N
+ATOM 1492 NH2 ARG A 192 -11.014 60.113 25.380 1.00 25.01 N
+ATOM 1493 N VAL A 193 -9.259 64.678 24.916 1.00 16.64 N
+ATOM 1494 CA VAL A 193 -10.618 65.084 24.463 1.00 17.65 C
+ATOM 1495 C VAL A 193 -10.579 66.378 23.692 1.00 17.19 C
+ATOM 1496 O VAL A 193 -11.163 66.490 22.623 1.00 17.15 O
+ATOM 1497 CB VAL A 193 -11.479 65.152 25.743 1.00 20.27 C
+ATOM 1498 CG1 VAL A 193 -12.802 65.857 25.443 1.00 23.65 C
+ATOM 1499 CG2 VAL A 193 -11.744 63.714 26.190 1.00 19.99 C
+ATOM 1500 N LEU A 194 -9.767 67.350 24.130 1.00 17.18 N
+ATOM 1501 CA LEU A 194 -9.658 68.613 23.377 1.00 17.19 C
+ATOM 1502 C LEU A 194 -9.064 68.373 21.993 1.00 16.47 C
+ATOM 1503 O LEU A 194 -9.474 68.983 20.980 1.00 18.14 O
+ATOM 1504 CB LEU A 194 -8.828 69.610 24.159 1.00 16.85 C
+ATOM 1505 CG LEU A 194 -9.384 70.186 25.472 1.00 18.32 C
+ATOM 1506 CD1 LEU A 194 -8.262 70.879 26.200 1.00 18.75 C
+ATOM 1507 CD2 LEU A 194 -10.505 71.185 25.195 1.00 22.53 C
+ATOM 1508 N SER A 195 -8.067 67.468 21.941 1.00 16.40 N
+ATOM 1509 CA SER A 195 -7.444 67.180 20.650 1.00 15.61 C
+ATOM 1510 C SER A 195 -8.381 66.474 19.671 1.00 17.33 C
+ATOM 1511 O SER A 195 -8.373 66.784 18.463 1.00 18.70 O
+ATOM 1512 CB SER A 195 -6.162 66.322 20.864 1.00 15.98 C
+ATOM 1513 OG SER A 195 -5.245 67.072 21.669 1.00 16.01 O
+ATOM 1514 N GLU A 196 -9.156 65.498 20.136 1.00 17.63 N
+ATOM 1515 CA GLU A 196 -10.135 64.816 19.285 1.00 17.53 C
+ATOM 1516 C GLU A 196 -11.089 65.850 18.668 1.00 20.42 C
+ATOM 1517 O GLU A 196 -11.387 65.789 17.477 1.00 19.66 O
+ATOM 1518 CB GLU A 196 -10.959 63.820 20.139 1.00 18.44 C
+ATOM 1519 CG GLU A 196 -10.123 62.548 20.377 1.00 21.29 C
+ATOM 1520 CD GLU A 196 -10.325 61.484 19.335 1.00 27.24 C
+ATOM 1521 OE1 GLU A 196 -11.083 61.678 18.349 1.00 30.97 O
+ATOM 1522 OE2 GLU A 196 -9.725 60.394 19.470 1.00 20.40 O
+ATOM 1523 N ASP A 197 -11.502 66.805 19.502 1.00 20.15 N
+ATOM 1524 CA ASP A 197 -12.439 67.839 18.983 1.00 23.22 C
+ATOM 1525 C ASP A 197 -11.790 68.696 17.917 1.00 22.69 C
+ATOM 1526 O ASP A 197 -12.354 68.922 16.830 1.00 23.95 O
+ATOM 1527 CB ASP A 197 -12.948 68.676 20.150 1.00 26.97 C
+ATOM 1528 CG ASP A 197 -14.091 69.588 19.745 1.00 37.77 C
+ATOM 1529 OD1 ASP A 197 -15.116 69.056 19.265 1.00 36.52 O
+ATOM 1530 OD2 ASP A 197 -13.968 70.818 19.913 1.00 40.08 O
+ATOM 1531 N ALA A 198 -10.529 69.087 18.133 1.00 19.86 N
+ATOM 1532 CA ALA A 198 -9.809 69.872 17.121 1.00 21.52 C
+ATOM 1533 C ALA A 198 -9.581 69.103 15.832 1.00 21.85 C
+ATOM 1534 O ALA A 198 -9.686 69.625 14.706 1.00 24.22 O
+ATOM 1535 CB ALA A 198 -8.452 70.312 17.685 1.00 19.80 C
+ATOM 1536 N ILE A 199 -9.263 67.810 15.919 1.00 18.75 N
+ATOM 1537 CA ILE A 199 -9.010 67.008 14.734 1.00 19.07 C
+ATOM 1538 C ILE A 199 -10.294 66.909 13.893 1.00 24.67 C
+ATOM 1539 O ILE A 199 -10.239 67.030 12.668 1.00 27.77 O
+ATOM 1540 CB ILE A 199 -8.545 65.593 15.083 1.00 19.61 C
+ATOM 1541 CG1 ILE A 199 -7.152 65.716 15.731 1.00 20.78 C
+ATOM 1542 CG2 ILE A 199 -8.521 64.724 13.843 1.00 21.24 C
+ATOM 1543 CD1 ILE A 199 -6.728 64.395 16.392 1.00 20.06 C
+ATOM 1544 N ALA A 200 -11.394 66.745 14.585 1.00 23.40 N
+ATOM 1545 CA ALA A 200 -12.707 66.612 13.955 1.00 29.40 C
+ATOM 1546 C ALA A 200 -13.312 67.920 13.447 1.00 34.16 C
+ATOM 1547 O ALA A 200 -14.124 67.836 12.511 1.00 34.43 O
+ATOM 1548 CB ALA A 200 -13.728 66.102 14.965 1.00 29.27 C
+ATOM 1549 N THR A 201 -13.025 69.041 14.092 1.00 28.88 N
+ATOM 1550 CA THR A 201 -13.772 70.245 13.683 1.00 38.17 C
+ATOM 1551 C THR A 201 -12.922 71.415 13.255 1.00 36.97 C
+ATOM 1552 O THR A 201 -13.375 72.256 12.455 1.00 36.87 O
+ATOM 1553 CB THR A 201 -14.711 70.709 14.823 1.00 38.83 C
+ATOM 1554 OG1 THR A 201 -13.904 71.342 15.815 1.00 45.72 O
+ATOM 1555 CG2 THR A 201 -15.462 69.554 15.462 1.00 41.61 C
+ATOM 1556 N ALA A 202 -11.741 71.534 13.820 1.00 36.45 N
+ATOM 1557 CA ALA A 202 -10.815 72.621 13.514 1.00 36.32 C
+ATOM 1558 C ALA A 202 -10.192 72.466 12.138 1.00 38.83 C
+ATOM 1559 O ALA A 202 -9.701 73.448 11.575 1.00 39.64 O
+ATOM 1560 CB ALA A 202 -9.722 72.666 14.600 1.00 32.59 C
+ATOM 1561 N THR A 203 -10.220 71.262 11.553 1.00 34.55 N
+ATOM 1562 CA THR A 203 -9.594 71.051 10.251 1.00 33.64 C
+ATOM 1563 C THR A 203 -10.441 71.362 9.028 1.00 39.40 C
+ATOM 1564 O THR A 203 -9.924 71.193 7.918 1.00 42.25 O
+ATOM 1565 CB THR A 203 -9.166 69.576 10.137 1.00 37.74 C
+ATOM 1566 OG1 THR A 203 -10.328 68.775 10.398 1.00 36.25 O
+ATOM 1567 CG2 THR A 203 -8.088 69.289 11.185 1.00 38.68 C
+ATOM 1568 N GLU A 204 -11.697 71.733 9.162 1.00 36.85 N
+ATOM 1569 CA GLU A 204 -12.568 72.048 8.033 1.00 37.74 C
+ATOM 1570 C GLU A 204 -12.032 73.230 7.224 1.00 39.50 C
+ATOM 1571 O GLU A 204 -12.340 73.403 6.046 1.00 41.71 O
+ATOM 1572 CB GLU A 204 -13.984 72.412 8.530 1.00 35.48 C
+ATOM 1573 CG GLU A 204 -14.798 71.211 8.971 1.00 38.50 C
+ATOM 1574 CD GLU A 204 -16.106 71.509 9.673 1.00 42.43 C
+ATOM 1575 OE1 GLU A 204 -16.816 72.476 9.308 1.00 37.98 O
+ATOM 1576 OE2 GLU A 204 -16.455 70.771 10.628 1.00 43.02 O
+ATOM 1577 N LYS A 205 -11.260 74.089 7.874 1.00 39.21 N
+ATOM 1578 CA LYS A 205 -10.712 75.286 7.212 1.00 33.94 C
+ATOM 1579 C LYS A 205 -9.260 75.027 6.859 1.00 33.08 C
+ATOM 1580 O LYS A 205 -8.631 74.161 7.462 1.00 28.48 O
+ATOM 1581 CB LYS A 205 -10.968 76.465 8.114 1.00 39.81 C
+ATOM 1582 CG LYS A 205 -10.163 76.783 9.321 1.00 39.09 C
+ATOM 1583 CD LYS A 205 -9.867 75.699 10.337 1.00 42.08 C
+ATOM 1584 CE LYS A 205 -9.403 76.364 11.639 1.00 44.67 C
+ATOM 1585 NZ LYS A 205 -8.483 75.539 12.470 1.00 37.61 N
+ATOM 1586 N PRO A 206 -8.705 75.688 5.860 1.00 32.58 N
+ATOM 1587 CA PRO A 206 -7.333 75.503 5.454 1.00 27.09 C
+ATOM 1588 C PRO A 206 -6.370 75.867 6.600 1.00 23.95 C
+ATOM 1589 O PRO A 206 -6.768 76.643 7.454 1.00 25.26 O
+ATOM 1590 CB PRO A 206 -7.112 76.505 4.317 1.00 31.84 C
+ATOM 1591 CG PRO A 206 -8.479 76.910 3.877 1.00 34.13 C
+ATOM 1592 CD PRO A 206 -9.407 76.730 5.054 1.00 35.92 C
+ATOM 1593 N LEU A 207 -5.179 75.314 6.496 1.00 25.77 N
+ATOM 1594 CA LEU A 207 -4.107 75.649 7.442 1.00 22.51 C
+ATOM 1595 C LEU A 207 -3.867 77.155 7.365 1.00 22.97 C
+ATOM 1596 O LEU A 207 -3.720 77.674 6.236 1.00 24.44 O
+ATOM 1597 CB LEU A 207 -2.865 74.876 7.031 1.00 24.77 C
+ATOM 1598 CG LEU A 207 -1.557 75.049 7.795 1.00 22.76 C
+ATOM 1599 CD1 LEU A 207 -1.713 74.601 9.237 1.00 25.50 C
+ATOM 1600 CD2 LEU A 207 -0.437 74.273 7.109 1.00 21.80 C
+ATOM 1601 N GLY A 208 -3.815 77.810 8.508 1.00 19.37 N
+ATOM 1602 CA GLY A 208 -3.601 79.253 8.569 1.00 18.27 C
+ATOM 1603 C GLY A 208 -2.089 79.583 8.657 1.00 20.66 C
+ATOM 1604 O GLY A 208 -1.199 78.729 8.645 1.00 19.44 O
+ATOM 1605 N GLU A 209 -1.870 80.895 8.767 1.00 19.21 N
+ATOM 1606 CA GLU A 209 -0.496 81.416 8.889 1.00 18.73 C
+ATOM 1607 C GLU A 209 -0.419 82.134 10.216 1.00 18.04 C
+ATOM 1608 O GLU A 209 -1.294 82.945 10.591 1.00 20.96 O
+ATOM 1609 CB GLU A 209 -0.186 82.419 7.755 1.00 22.15 C
+ATOM 1610 CG GLU A 209 -0.071 81.751 6.379 1.00 31.53 C
+ATOM 1611 CD GLU A 209 0.080 82.864 5.330 1.00 34.15 C
+ATOM 1612 OE1 GLU A 209 -0.933 83.522 5.032 1.00 40.50 O
+ATOM 1613 OE2 GLU A 209 1.204 83.072 4.869 1.00 40.52 O
+ATOM 1614 N LEU A 210 0.640 81.847 10.995 1.00 18.08 N
+ATOM 1615 CA LEU A 210 0.783 82.434 12.311 1.00 16.09 C
+ATOM 1616 C LEU A 210 1.045 83.954 12.301 1.00 19.01 C
+ATOM 1617 O LEU A 210 1.975 84.422 11.650 1.00 16.95 O
+ATOM 1618 CB LEU A 210 1.943 81.706 13.031 1.00 17.66 C
+ATOM 1619 CG LEU A 210 2.236 82.167 14.460 1.00 15.41 C
+ATOM 1620 CD1 LEU A 210 1.025 81.900 15.371 1.00 19.64 C
+ATOM 1621 CD2 LEU A 210 3.501 81.488 14.951 1.00 16.46 C
+ATOM 1622 N TRP A 211 0.282 84.676 13.118 1.00 20.02 N
+ATOM 1623 CA TRP A 211 0.567 86.103 13.347 1.00 21.73 C
+ATOM 1624 C TRP A 211 0.516 86.951 12.092 1.00 26.46 C
+ATOM 1625 O TRP A 211 1.181 88.002 11.945 1.00 23.73 O
+ATOM 1626 CB TRP A 211 1.903 86.246 14.126 1.00 18.54 C
+ATOM 1627 CG TRP A 211 1.822 85.711 15.534 1.00 19.41 C
+ATOM 1628 CD1 TRP A 211 0.702 85.655 16.328 1.00 23.84 C
+ATOM 1629 CD2 TRP A 211 2.868 85.177 16.332 1.00 21.27 C
+ATOM 1630 NE1 TRP A 211 1.019 85.118 17.549 1.00 22.05 N
+ATOM 1631 CE2 TRP A 211 2.342 84.786 17.575 1.00 19.47 C
+ATOM 1632 CE3 TRP A 211 4.244 84.974 16.091 1.00 19.01 C
+ATOM 1633 CZ2 TRP A 211 3.127 84.221 18.578 1.00 20.79 C
+ATOM 1634 CZ3 TRP A 211 5.011 84.402 17.079 1.00 19.10 C
+ATOM 1635 CH2 TRP A 211 4.458 84.019 18.307 1.00 21.38 C
+ATOM 1636 N LYS A 212 -0.283 86.478 11.134 1.00 23.22 N
+ATOM 1637 CA LYS A 212 -0.553 87.299 9.948 1.00 32.48 C
+ATOM 1638 C LYS A 212 -1.945 86.959 9.416 1.00 36.83 C
+ATOM 1639 O LYS A 212 -2.509 85.889 9.744 1.00 37.02 O
+ATOM 1640 CB LYS A 212 0.488 87.219 8.852 1.00 33.78 C
+ATOM 1641 CG LYS A 212 0.612 85.892 8.146 1.00 35.82 C
+ATOM 1642 CD LYS A 212 1.758 85.909 7.147 1.00 37.15 C
+ATOM 1643 CE LYS A 212 1.371 86.617 5.858 1.00 39.65 C
+ATOM 1644 NZ LYS A 212 2.384 86.336 4.796 1.00 40.08 N
+ATOM 1645 OXT LYS A 212 -2.467 87.806 8.668 1.00 40.05 O
+TER 1646 LYS A 212
+HETATM 1647 P TMP A 301 12.610 71.926 26.526 1.00 39.30 P
+HETATM 1648 O1P TMP A 301 12.225 72.268 27.953 1.00 42.81 O
+HETATM 1649 O2P TMP A 301 11.542 71.678 25.556 1.00 35.74 O
+HETATM 1650 O3P TMP A 301 13.762 70.816 26.639 1.00 36.59 O
+HETATM 1651 O5' TMP A 301 13.399 73.189 25.942 1.00 34.53 O
+HETATM 1652 C5' TMP A 301 14.761 73.577 26.272 1.00 31.79 C
+HETATM 1653 C4' TMP A 301 14.671 75.126 26.263 1.00 24.30 C
+HETATM 1654 O4' TMP A 301 14.572 75.881 25.066 1.00 20.31 O
+HETATM 1655 C3' TMP A 301 13.560 75.560 27.204 1.00 23.69 C
+HETATM 1656 O3' TMP A 301 14.096 76.298 28.298 1.00 23.86 O
+HETATM 1657 C2' TMP A 301 12.706 76.498 26.333 1.00 20.65 C
+HETATM 1658 C1' TMP A 301 13.709 76.967 25.260 1.00 20.42 C
+HETATM 1659 N1 TMP A 301 13.285 77.478 23.970 1.00 18.39 N
+HETATM 1660 C2 TMP A 301 13.710 78.779 23.590 1.00 18.82 C
+HETATM 1661 O2 TMP A 301 14.363 79.545 24.311 1.00 18.79 O
+HETATM 1662 N3 TMP A 301 13.264 79.143 22.361 1.00 17.49 N
+HETATM 1663 C4 TMP A 301 12.526 78.311 21.528 1.00 16.92 C
+HETATM 1664 O4 TMP A 301 12.153 78.772 20.296 1.00 17.58 O
+HETATM 1665 C5 TMP A 301 12.148 76.952 21.973 1.00 16.89 C
+HETATM 1666 C5M TMP A 301 11.340 76.081 21.052 1.00 17.75 C
+HETATM 1667 C6 TMP A 301 12.587 76.615 23.218 1.00 17.74 C
+HETATM 1668 PG ATP A 302 10.856 70.720 29.877 1.00 41.25 P
+HETATM 1669 O1G ATP A 302 12.121 70.634 30.686 1.00 44.18 O
+HETATM 1670 O2G ATP A 302 10.243 72.053 29.963 1.00 42.17 O
+HETATM 1671 O3G ATP A 302 11.156 70.056 28.572 1.00 33.67 O
+HETATM 1672 PB ATP A 302 8.287 69.347 30.229 1.00 21.78 P
+HETATM 1673 O1B ATP A 302 8.570 68.708 28.936 1.00 20.55 O
+HETATM 1674 O2B ATP A 302 7.222 70.364 30.269 1.00 22.79 O
+HETATM 1675 O3B ATP A 302 9.739 69.910 30.729 1.00 27.91 O
+HETATM 1676 PA ATP A 302 8.085 66.652 31.361 1.00 22.42 P
+HETATM 1677 O1A ATP A 302 6.953 66.067 30.602 1.00 20.66 O
+HETATM 1678 O2A ATP A 302 9.439 66.202 30.960 1.00 22.33 O
+HETATM 1679 O3A ATP A 302 7.949 68.247 31.323 1.00 23.96 O
+HETATM 1680 O5' ATP A 302 7.884 66.353 32.866 1.00 20.25 O
+HETATM 1681 C5' ATP A 302 8.889 66.801 33.860 1.00 22.47 C
+HETATM 1682 C4' ATP A 302 8.846 65.944 34.998 1.00 24.84 C
+HETATM 1683 O4' ATP A 302 7.625 65.967 35.721 1.00 23.52 O
+HETATM 1684 C3' ATP A 302 9.075 64.485 34.585 1.00 26.34 C
+HETATM 1685 O3' ATP A 302 9.831 63.762 35.587 1.00 28.34 O
+HETATM 1686 C2' ATP A 302 7.675 63.883 34.597 1.00 22.80 C
+HETATM 1687 O2' ATP A 302 7.486 62.500 34.845 1.00 23.30 O
+HETATM 1688 C1' ATP A 302 7.016 64.654 35.782 1.00 22.92 C
+HETATM 1689 N9 ATP A 302 5.598 64.937 35.440 1.00 20.77 N
+HETATM 1690 C8 ATP A 302 5.030 65.160 34.178 1.00 19.82 C
+HETATM 1691 N7 ATP A 302 3.738 65.337 34.370 1.00 18.46 N
+HETATM 1692 C5 ATP A 302 3.442 65.218 35.700 1.00 22.18 C
+HETATM 1693 C6 ATP A 302 2.251 65.297 36.435 1.00 24.15 C
+HETATM 1694 N6 ATP A 302 1.070 65.509 35.849 1.00 20.76 N
+HETATM 1695 N1 ATP A 302 2.463 65.124 37.732 1.00 26.90 N
+HETATM 1696 C2 ATP A 302 3.639 64.919 38.364 1.00 25.78 C
+HETATM 1697 N3 ATP A 302 4.792 64.839 37.695 1.00 25.63 N
+HETATM 1698 C4 ATP A 302 4.596 64.989 36.434 1.00 23.66 C
+HETATM 1699 MG MG A 401 10.133 68.590 27.602 1.00 24.88 MG
+HETATM 1700 MG MG A 402 5.749 95.364 12.274 0.50 25.10 MG
+HETATM 1701 O HOH A2001 -7.930 62.914 7.809 1.00 37.75 O
+HETATM 1702 O HOH A2002 -15.568 63.668 11.282 1.00 53.21 O
+HETATM 1703 O HOH A2003 -10.160 62.737 11.068 1.00 35.24 O
+HETATM 1704 O HOH A2004 -7.779 64.250 10.049 1.00 32.48 O
+HETATM 1705 O HOH A2005 -9.031 69.271 4.793 1.00 32.08 O
+HETATM 1706 O HOH A2006 6.332 56.674 19.538 1.00 48.17 O
+HETATM 1707 O HOH A2007 5.810 59.227 19.102 1.00 39.35 O
+HETATM 1708 O HOH A2008 10.124 61.674 22.153 1.00 40.84 O
+HETATM 1709 O HOH A2009 11.999 64.642 25.157 1.00 38.96 O
+HETATM 1710 O HOH A2010 1.945 54.372 18.986 1.00 57.73 O
+HETATM 1711 O HOH A2011 3.190 56.284 16.922 1.00 41.53 O
+HETATM 1712 O HOH A2012 3.322 76.350 32.062 1.00 28.26 O
+HETATM 1713 O HOH A2013 -4.472 54.738 24.161 1.00 44.26 O
+HETATM 1714 O HOH A2014 -9.330 59.524 9.549 1.00 45.60 O
+HETATM 1715 O HOH A2015 1.698 68.370 33.767 1.00 35.90 O
+HETATM 1716 O HOH A2016 14.391 67.275 22.397 1.00 41.04 O
+HETATM 1717 O HOH A2017 11.728 68.256 26.299 1.00 27.40 O
+HETATM 1718 O HOH A2018 26.649 70.189 12.227 1.00 41.53 O
+HETATM 1719 O HOH A2019 27.592 71.644 15.776 1.00 35.68 O
+HETATM 1720 O HOH A2020 -1.646 63.837 26.593 1.00 15.41 O
+HETATM 1721 O HOH A2021 1.440 66.017 32.857 1.00 22.91 O
+HETATM 1722 O HOH A2022 9.673 63.335 24.438 1.00 20.36 O
+HETATM 1723 O HOH A2023 4.076 58.659 21.345 1.00 28.91 O
+HETATM 1724 O HOH A2024 11.797 64.261 27.185 1.00 40.36 O
+HETATM 1725 O HOH A2025 28.461 87.484 21.938 1.00 37.06 O
+HETATM 1726 O HOH A2026 26.039 94.077 22.199 1.00 34.29 O
+HETATM 1727 O HOH A2027 21.821 92.374 23.637 1.00 53.74 O
+HETATM 1728 O HOH A2028 25.537 91.426 24.018 1.00 50.87 O
+HETATM 1729 O HOH A2029 27.191 89.155 23.837 1.00 56.55 O
+HETATM 1730 O HOH A2030 -4.102 56.929 40.658 1.00 65.11 O
+HETATM 1731 O HOH A2031 2.634 55.918 40.708 1.00 68.55 O
+HETATM 1732 O HOH A2032 24.882 88.569 30.412 1.00 62.11 O
+HETATM 1733 O HOH A2033 -7.864 59.796 35.001 1.00 61.13 O
+HETATM 1734 O HOH A2034 -14.994 63.918 32.137 1.00 57.89 O
+HETATM 1735 O HOH A2035 -0.452 53.798 19.953 1.00 22.17 O
+HETATM 1736 O HOH A2036 1.432 55.852 28.154 1.00 25.89 O
+HETATM 1737 O HOH A2037 3.044 53.061 26.622 1.00 34.46 O
+HETATM 1738 O HOH A2038 2.944 56.664 19.686 1.00 42.35 O
+HETATM 1739 O HOH A2039 -1.120 57.420 26.179 1.00 25.63 O
+HETATM 1740 O HOH A2040 -6.750 55.504 22.259 1.00 27.32 O
+HETATM 1741 O HOH A2041 20.675 75.059 8.155 1.00 33.18 O
+HETATM 1742 O HOH A2042 6.612 73.424 1.042 1.00 53.59 O
+HETATM 1743 O HOH A2043 -7.553 52.872 21.838 1.00 41.56 O
+HETATM 1744 O HOH A2044 -3.194 71.053 4.405 1.00 34.03 O
+HETATM 1745 O HOH A2045 -0.135 73.819 3.117 1.00 45.01 O
+HETATM 1746 O HOH A2046 -7.348 57.149 10.322 1.00 40.57 O
+HETATM 1747 O HOH A2047 -4.386 70.009 2.230 1.00 45.40 O
+HETATM 1748 O HOH A2048 -7.704 61.585 11.873 1.00 29.63 O
+HETATM 1749 O HOH A2049 -6.488 59.562 10.407 1.00 33.86 O
+HETATM 1750 O HOH A2050 0.708 58.162 7.836 1.00 50.03 O
+HETATM 1751 O HOH A2051 3.426 58.271 15.480 1.00 23.49 O
+HETATM 1752 O HOH A2052 0.722 57.719 12.638 1.00 30.62 O
+HETATM 1753 O HOH A2053 1.525 58.932 10.136 1.00 43.80 O
+HETATM 1754 O HOH A2054 6.856 60.152 13.766 1.00 48.51 O
+HETATM 1755 O HOH A2055 7.692 63.614 11.104 1.00 46.83 O
+HETATM 1756 O HOH A2056 5.546 60.011 16.307 1.00 21.47 O
+HETATM 1757 O HOH A2057 7.966 62.573 13.858 1.00 52.03 O
+HETATM 1758 O HOH A2058 10.524 69.051 14.727 1.00 27.73 O
+HETATM 1759 O HOH A2059 10.401 63.833 20.741 1.00 44.54 O
+HETATM 1760 O HOH A2060 9.247 60.199 17.979 1.00 53.55 O
+HETATM 1761 O HOH A2061 13.371 69.766 22.050 1.00 27.10 O
+HETATM 1762 O HOH A2062 3.648 94.329 20.979 1.00 46.52 O
+HETATM 1763 O HOH A2063 5.500 97.152 13.360 1.00 31.28 O
+HETATM 1764 O HOH A2064 9.775 97.435 14.495 1.00 37.75 O
+HETATM 1765 O HOH A2065 15.443 67.329 19.460 1.00 38.12 O
+HETATM 1766 O HOH A2066 14.258 65.785 11.979 1.00 57.73 O
+HETATM 1767 O HOH A2067 -7.429 78.876 14.528 1.00 40.64 O
+HETATM 1768 O HOH A2068 -11.433 76.059 16.036 1.00 42.11 O
+HETATM 1769 O HOH A2069 20.913 70.698 9.116 1.00 32.45 O
+HETATM 1770 O HOH A2070 25.939 72.412 13.933 1.00 32.28 O
+HETATM 1771 O HOH A2071 26.092 72.845 5.542 1.00 32.33 O
+HETATM 1772 O HOH A2072 22.561 70.339 5.495 1.00 54.83 O
+HETATM 1773 O HOH A2073 22.277 73.786 6.379 1.00 32.93 O
+HETATM 1774 O HOH A2074 6.470 81.203 42.865 1.00 44.76 O
+HETATM 1775 O HOH A2075 25.481 70.032 20.093 1.00 38.19 O
+HETATM 1776 O HOH A2076 12.401 67.494 34.784 1.00 44.34 O
+HETATM 1777 O HOH A2077 23.076 83.132 33.322 1.00 65.40 O
+HETATM 1778 O HOH A2078 3.580 91.075 31.814 1.00 55.46 O
+HETATM 1779 O HOH A2079 26.225 76.969 19.884 1.00 31.75 O
+HETATM 1780 O HOH A2080 28.722 84.100 21.750 1.00 62.52 O
+HETATM 1781 O HOH A2081 25.391 83.139 26.022 1.00 39.55 O
+HETATM 1782 O HOH A2082 28.963 80.634 19.684 1.00 55.12 O
+HETATM 1783 O HOH A2083 24.157 92.613 20.835 1.00 41.91 O
+HETATM 1784 O HOH A2084 27.173 84.548 19.262 1.00 33.75 O
+HETATM 1785 O HOH A2085 -10.632 70.641 29.412 1.00 34.54 O
+HETATM 1786 O HOH A2086 -9.520 71.962 33.933 1.00 51.00 O
+HETATM 1787 O HOH A2087 23.770 88.526 24.038 1.00 29.55 O
+HETATM 1788 O HOH A2088 22.905 84.239 25.650 1.00 46.09 O
+HETATM 1789 O HOH A2089 20.969 86.993 28.268 1.00 47.48 O
+HETATM 1790 O HOH A2090 20.923 90.912 25.601 1.00 44.40 O
+HETATM 1791 O HOH A2091 -8.114 66.081 40.651 1.00 63.29 O
+HETATM 1792 O HOH A2092 -3.426 57.360 37.333 1.00 58.81 O
+HETATM 1793 O HOH A2093 2.987 58.408 38.337 1.00 49.35 O
+HETATM 1794 O HOH A2094 3.535 61.415 38.367 1.00 35.18 O
+HETATM 1795 O HOH A2095 15.661 93.040 20.039 1.00 30.00 O
+HETATM 1796 O HOH A2096 0.310 57.464 35.107 1.00 38.17 O
+HETATM 1797 O HOH A2097 -8.349 58.397 32.646 1.00 51.28 O
+HETATM 1798 O HOH A2098 25.788 83.200 16.673 1.00 29.37 O
+HETATM 1799 O HOH A2099 -13.472 64.109 29.670 1.00 49.32 O
+HETATM 1800 O HOH A2100 -13.206 69.272 26.819 1.00 31.03 O
+HETATM 1801 O HOH A2101 13.125 75.811 17.474 1.00 19.23 O
+HETATM 1802 O HOH A2102 -14.517 68.957 7.014 1.00 39.98 O
+HETATM 1803 O HOH A2103 14.685 71.798 12.861 1.00 30.15 O
+HETATM 1804 O HOH A2104 -0.242 92.073 12.026 1.00 44.58 O
+HETATM 1805 O HOH A2105 12.793 82.042 18.682 1.00 18.70 O
+HETATM 1806 O HOH A2106 11.106 70.268 6.228 1.00 24.49 O
+HETATM 1807 O HOH A2107 14.239 72.231 5.179 1.00 30.43 O
+HETATM 1808 O HOH A2108 20.101 72.959 10.237 1.00 23.85 O
+HETATM 1809 O HOH A2109 12.679 68.138 7.881 1.00 37.56 O
+HETATM 1810 O HOH A2110 5.673 70.796 1.823 1.00 31.87 O
+HETATM 1811 O HOH A2111 -0.455 71.596 4.537 1.00 29.95 O
+HETATM 1812 O HOH A2112 -5.148 67.455 1.992 1.00 49.26 O
+HETATM 1813 O HOH A2113 3.216 60.885 5.635 1.00 60.07 O
+HETATM 1814 O HOH A2114 -6.035 60.960 8.217 1.00 27.69 O
+HETATM 1815 O HOH A2115 -5.425 63.335 11.242 1.00 24.25 O
+HETATM 1816 O HOH A2116 10.509 70.208 23.082 1.00 30.07 O
+HETATM 1817 O HOH A2117 9.279 70.056 26.214 1.00 22.45 O
+HETATM 1818 O HOH A2118 11.141 67.743 23.693 1.00 29.14 O
+HETATM 1819 O HOH A2119 8.019 65.311 23.174 1.00 35.25 O
+HETATM 1820 O HOH A2120 10.166 90.380 30.225 1.00 38.05 O
+HETATM 1821 O HOH A2121 15.694 88.492 32.234 1.00 37.29 O
+HETATM 1822 O HOH A2122 13.744 67.230 29.190 1.00 40.59 O
+HETATM 1823 O HOH A2123 17.369 84.834 23.016 1.00 24.39 O
+HETATM 1824 O HOH A2124 12.250 92.423 27.374 1.00 36.52 O
+HETATM 1825 O HOH A2125 19.400 89.595 29.667 1.00 58.83 O
+HETATM 1826 O HOH A2126 17.519 94.385 21.838 1.00 37.12 O
+HETATM 1827 O HOH A2127 9.290 91.110 25.962 1.00 35.16 O
+HETATM 1828 O HOH A2128 10.359 96.673 19.439 1.00 50.75 O
+HETATM 1829 O HOH A2129 13.664 94.420 21.171 1.00 29.84 O
+HETATM 1830 O HOH A2130 7.143 94.248 24.529 1.00 34.21 O
+HETATM 1831 O HOH A2131 6.143 94.744 21.694 1.00 28.94 O
+HETATM 1832 O HOH A2132 4.562 94.333 13.836 1.00 28.25 O
+HETATM 1833 O HOH A2133 10.187 95.254 16.310 1.00 26.92 O
+HETATM 1834 O HOH A2134 3.480 92.419 17.487 1.00 36.39 O
+HETATM 1835 O HOH A2135 7.455 94.893 13.487 1.00 28.98 O
+HETATM 1836 O HOH A2136 12.280 90.834 14.593 1.00 23.75 O
+HETATM 1837 O HOH A2137 0.456 87.980 19.913 1.00 37.61 O
+HETATM 1838 O HOH A2138 0.131 89.784 16.056 1.00 42.14 O
+HETATM 1839 O HOH A2139 3.315 91.237 14.375 1.00 36.85 O
+HETATM 1840 O HOH A2140 7.410 89.870 10.133 1.00 20.13 O
+HETATM 1841 O HOH A2141 10.260 83.634 18.211 1.00 23.89 O
+HETATM 1842 O HOH A2142 6.168 85.129 6.531 1.00 24.87 O
+HETATM 1843 O HOH A2143 3.607 78.450 6.569 1.00 26.57 O
+HETATM 1844 O HOH A2144 -6.917 80.709 11.166 1.00 47.39 O
+HETATM 1845 O HOH A2145 -4.454 76.506 11.162 1.00 23.03 O
+HETATM 1846 O HOH A2146 -5.644 78.581 16.279 1.00 21.56 O
+HETATM 1847 O HOH A2147 -8.598 76.373 15.117 1.00 29.21 O
+HETATM 1848 O HOH A2148 -7.074 79.137 33.911 1.00 42.45 O
+HETATM 1849 O HOH A2149 -5.816 75.471 34.465 1.00 38.19 O
+HETATM 1850 O HOH A2150 1.871 77.953 34.247 1.00 29.74 O
+HETATM 1851 O HOH A2151 -1.053 78.370 37.372 1.00 48.07 O
+HETATM 1852 O HOH A2152 -0.665 74.340 40.060 1.00 41.71 O
+HETATM 1853 O HOH A2153 9.544 76.239 38.346 1.00 59.93 O
+HETATM 1854 O HOH A2154 3.111 80.801 39.147 1.00 37.80 O
+HETATM 1855 O HOH A2155 4.282 79.521 42.176 1.00 39.07 O
+HETATM 1856 O HOH A2156 11.595 66.377 37.870 1.00 41.57 O
+HETATM 1857 O HOH A2157 14.514 66.956 38.032 1.00 57.98 O
+HETATM 1858 O HOH A2158 22.634 69.690 32.158 1.00 68.57 O
+HETATM 1859 O HOH A2159 20.588 75.639 35.174 1.00 63.35 O
+HETATM 1860 O HOH A2160 22.115 82.071 30.536 1.00 53.35 O
+HETATM 1861 O HOH A2161 16.336 75.250 29.332 1.00 42.49 O
+HETATM 1862 O HOH A2162 20.411 81.354 32.735 1.00 50.60 O
+HETATM 1863 O HOH A2163 14.099 71.868 35.229 1.00 59.79 O
+HETATM 1864 O HOH A2164 15.440 79.470 41.112 1.00 43.76 O
+HETATM 1865 O HOH A2165 14.202 82.769 42.107 1.00 43.36 O
+HETATM 1866 O HOH A2166 10.967 87.141 37.503 1.00 38.98 O
+HETATM 1867 O HOH A2167 16.130 82.498 40.430 1.00 53.84 O
+HETATM 1868 O HOH A2168 8.004 89.054 31.337 1.00 36.28 O
+HETATM 1869 O HOH A2169 1.743 89.025 31.400 1.00 34.92 O
+HETATM 1870 O HOH A2170 -4.075 84.956 30.097 1.00 56.05 O
+HETATM 1871 O HOH A2171 -0.361 80.187 34.418 1.00 24.94 O
+HETATM 1872 O HOH A2172 0.210 85.044 20.390 1.00 33.11 O
+HETATM 1873 O HOH A2173 -7.123 83.370 24.492 1.00 59.22 O
+HETATM 1874 O HOH A2174 -1.918 88.351 15.712 1.00 42.10 O
+HETATM 1875 O HOH A2175 -4.736 89.619 17.237 1.00 59.65 O
+HETATM 1876 O HOH A2176 -5.800 89.762 19.627 1.00 48.73 O
+HETATM 1877 O HOH A2177 -2.220 83.957 14.366 1.00 22.66 O
+HETATM 1878 O HOH A2178 -10.904 73.353 19.610 1.00 27.48 O
+HETATM 1879 O HOH A2179 -9.960 78.919 22.463 1.00 41.51 O
+HETATM 1880 O HOH A2180 -12.031 78.259 23.900 1.00 44.61 O
+HETATM 1881 O HOH A2181 -13.176 73.900 25.513 1.00 45.91 O
+HETATM 1882 O HOH A2182 -13.011 74.885 20.437 1.00 39.47 O
+HETATM 1883 O HOH A2183 -8.083 75.098 33.210 1.00 53.35 O
+HETATM 1884 O HOH A2184 -8.270 71.353 29.798 1.00 36.26 O
+HETATM 1885 O HOH A2185 -9.656 74.199 28.404 1.00 47.12 O
+HETATM 1886 O HOH A2186 -9.406 77.421 28.125 1.00 27.47 O
+HETATM 1887 O HOH A2187 -6.860 70.651 40.004 1.00 43.99 O
+HETATM 1888 O HOH A2188 -3.050 74.302 37.228 1.00 39.47 O
+HETATM 1889 O HOH A2189 1.167 69.039 40.784 1.00 52.43 O
+HETATM 1890 O HOH A2190 -9.900 65.297 35.874 1.00 31.09 O
+HETATM 1891 O HOH A2191 -9.356 70.634 36.566 1.00 45.78 O
+HETATM 1892 O HOH A2192 -5.440 59.737 37.867 1.00 42.78 O
+HETATM 1893 O HOH A2193 -5.688 64.050 39.381 1.00 28.57 O
+HETATM 1894 O HOH A2194 0.870 61.358 37.968 1.00 27.12 O
+HETATM 1895 O HOH A2195 -2.928 56.278 29.313 1.00 42.24 O
+HETATM 1896 O HOH A2196 -0.511 54.324 31.630 1.00 41.46 O
+HETATM 1897 O HOH A2197 -5.977 58.870 31.081 1.00 37.05 O
+HETATM 1898 O HOH A2198 -1.248 59.142 36.436 1.00 23.27 O
+HETATM 1899 O HOH A2199 -9.363 64.164 33.250 1.00 30.19 O
+HETATM 1900 O HOH A2200 -5.816 57.322 26.538 1.00 26.63 O
+HETATM 1901 O HOH A2201 -13.520 61.619 28.733 1.00 35.38 O
+HETATM 1902 O HOH A2202 -7.451 58.258 28.952 1.00 32.09 O
+HETATM 1903 O HOH A2203 -11.118 57.782 27.562 1.00 35.94 O
+HETATM 1904 O HOH A2204 -11.956 66.542 29.867 1.00 37.64 O
+HETATM 1905 O HOH A2205 -10.992 68.341 27.970 1.00 27.01 O
+HETATM 1906 O HOH A2206 -7.671 70.823 32.390 1.00 26.05 O
+HETATM 1907 O HOH A2207 -7.844 56.755 24.461 1.00 31.47 O
+HETATM 1908 O HOH A2208 -14.243 60.086 26.589 1.00 31.91 O
+HETATM 1909 O HOH A2209 -13.684 65.356 22.187 1.00 23.90 O
+HETATM 1910 O HOH A2210 -10.540 71.508 21.483 1.00 24.84 O
+HETATM 1911 O HOH A2211 -14.458 64.600 18.595 1.00 40.43 O
+HETATM 1912 O HOH A2212 -12.961 59.990 17.651 1.00 23.22 O
+HETATM 1913 O HOH A2213 -11.541 63.325 16.088 1.00 24.08 O
+HETATM 1914 O HOH A2214 -7.974 59.465 21.283 1.00 22.45 O
+HETATM 1915 O HOH A2215 -13.116 71.279 22.423 1.00 31.15 O
+HETATM 1916 O HOH A2216 -15.655 68.025 10.888 1.00 46.62 O
+HETATM 1917 O HOH A2217 -16.329 65.971 12.268 1.00 39.35 O
+HETATM 1918 O HOH A2218 -12.495 74.435 10.761 1.00 40.82 O
+HETATM 1919 O HOH A2219 -8.888 71.674 5.541 1.00 38.34 O
+HETATM 1920 O HOH A2220 -12.658 67.860 8.783 1.00 43.23 O
+HETATM 1921 O HOH A2221 -17.209 73.060 6.987 1.00 39.49 O
+HETATM 1922 O HOH A2222 -6.437 78.252 11.289 1.00 41.73 O
+HETATM 1923 O HOH A2223 -7.467 79.228 6.821 1.00 40.02 O
+HETATM 1924 O HOH A2224 -3.217 77.044 3.705 1.00 44.67 O
+HETATM 1925 O HOH A2225 -4.652 73.580 4.183 1.00 29.64 O
+HETATM 1926 O HOH A2226 0.706 77.756 6.517 1.00 27.89 O
+HETATM 1927 O HOH A2227 -4.115 82.698 8.411 1.00 31.42 O
+HETATM 1928 O HOH A2228 -3.514 84.220 11.948 1.00 31.23 O
+HETATM 1929 O HOH A2229 3.340 81.901 5.307 1.00 27.61 O
+HETATM 1930 O HOH A2230 1.890 90.375 10.985 1.00 35.42 O
+HETATM 1931 O HOH A2231 4.883 83.855 4.551 1.00 32.21 O
+HETATM 1932 O HOH A2232 -2.687 87.711 13.470 1.00 50.43 O
+HETATM 1933 O HOH A2233 4.936 87.491 5.882 1.00 34.57 O
+HETATM 1934 O HOH A2234 14.841 67.654 26.435 1.00 53.63 O
+HETATM 1935 O HOH A2235 15.657 81.897 24.003 1.00 27.16 O
+HETATM 1936 O HOH A2236 13.785 81.765 21.341 1.00 18.95 O
+HETATM 1937 O HOH A2237 7.040 64.447 39.485 1.00 28.62 O
+HETATM 1938 O HOH A2238 12.221 64.389 34.816 1.00 39.98 O
+HETATM 1939 O HOH A2239 6.266 61.281 37.175 1.00 25.98 O
+HETATM 1940 O HOH A2240 11.781 65.202 31.953 1.00 36.55 O
+HETATM 1941 O HOH A2241 12.062 68.816 31.903 1.00 51.29 O
+HETATM 1942 O HOH A2242 0.393 65.751 39.730 1.00 32.74 O
+HETATM 1943 O HOH A2243 7.396 61.652 32.467 1.00 21.56 O
+HETATM 1944 O HOH A2244 10.906 67.071 28.822 1.00 22.41 O
+CONECT 1647 1648 1649 1650 1651
+CONECT 1648 1647
+CONECT 1649 1647
+CONECT 1650 1647
+CONECT 1651 1647 1652
+CONECT 1652 1651 1653
+CONECT 1653 1652 1654 1655
+CONECT 1654 1653 1658
+CONECT 1655 1653 1656 1657
+CONECT 1656 1655
+CONECT 1657 1655 1658
+CONECT 1658 1654 1657 1659
+CONECT 1659 1658 1660 1667
+CONECT 1660 1659 1661 1662
+CONECT 1661 1660
+CONECT 1662 1660 1663
+CONECT 1663 1662 1664 1665
+CONECT 1664 1663
+CONECT 1665 1663 1666 1667
+CONECT 1666 1665
+CONECT 1667 1659 1665
+CONECT 1668 1669 1670 1671 1675
+CONECT 1669 1668
+CONECT 1670 1668
+CONECT 1671 1668
+CONECT 1672 1673 1674 1675 1679
+CONECT 1673 1672
+CONECT 1674 1672
+CONECT 1675 1668 1672
+CONECT 1676 1677 1678 1679 1680
+CONECT 1677 1676
+CONECT 1678 1676
+CONECT 1679 1672 1676
+CONECT 1680 1676 1681
+CONECT 1681 1680 1682
+CONECT 1682 1681 1683 1684
+CONECT 1683 1682 1688
+CONECT 1684 1682 1685 1686
+CONECT 1685 1684
+CONECT 1686 1684 1687 1688
+CONECT 1687 1686
+CONECT 1688 1683 1686 1689
+CONECT 1689 1688 1690 1698
+CONECT 1690 1689 1691
+CONECT 1691 1690 1692
+CONECT 1692 1691 1693 1698
+CONECT 1693 1692 1694 1695
+CONECT 1694 1693
+CONECT 1695 1693 1696
+CONECT 1696 1695 1697
+CONECT 1697 1696 1698
+CONECT 1698 1689 1692 1697
+END
diff --git a/doc/tests/data/1KO5.pdb b/doc/tests/data/1KO5.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..e3f86bbdbcb6692daac2e1f7704547defd11fcaa
--- /dev/null
+++ b/doc/tests/data/1KO5.pdb
@@ -0,0 +1,2925 @@
+ATOM 1 N THR A 3 9.456 13.668 31.384 1.00 32.61 N
+ATOM 2 CA THR A 3 10.000 12.753 30.317 1.00 33.76 C
+ATOM 3 C THR A 3 9.089 11.564 30.149 1.00 32.96 C
+ATOM 4 O THR A 3 8.637 11.267 29.046 1.00 32.45 O
+ATOM 5 CB THR A 3 11.376 12.253 30.654 1.00 34.01 C
+ATOM 6 OG1 THR A 3 12.258 13.373 30.839 1.00 38.44 O
+ATOM 7 CG2 THR A 3 11.947 11.542 29.455 1.00 33.21 C
+ATOM 8 N THR A 4 8.873 10.844 31.240 1.00 32.14 N
+ATOM 9 CA THR A 4 7.773 9.917 31.245 1.00 31.46 C
+ATOM 10 C THR A 4 6.536 10.839 31.371 1.00 30.61 C
+ATOM 11 O THR A 4 6.514 11.737 32.202 1.00 30.89 O
+ATOM 12 CB THR A 4 7.874 8.933 32.436 1.00 31.49 C
+ATOM 13 OG1 THR A 4 8.742 7.836 32.089 1.00 32.61 O
+ATOM 14 CG2 THR A 4 6.539 8.233 32.648 1.00 30.92 C
+ATOM 15 N ASN A 5 5.536 10.654 30.521 1.00 29.51 N
+ATOM 16 CA ASN A 5 4.309 11.431 30.607 1.00 28.50 C
+ATOM 17 C ASN A 5 3.238 10.599 31.304 1.00 28.13 C
+ATOM 18 O ASN A 5 2.575 9.758 30.698 1.00 27.00 O
+ATOM 19 CB ASN A 5 3.863 11.907 29.219 1.00 28.53 C
+ATOM 20 CG ASN A 5 2.709 12.888 29.276 1.00 28.16 C
+ATOM 21 OD1 ASN A 5 1.877 12.819 30.168 1.00 27.31 O
+ATOM 22 ND2 ASN A 5 2.649 13.799 28.308 1.00 28.41 N
+ATOM 23 N HIS A 6 3.060 10.861 32.592 1.00 27.90 N
+ATOM 24 CA HIS A 6 2.212 10.007 33.410 1.00 28.29 C
+ATOM 25 C HIS A 6 0.749 10.041 33.049 1.00 28.65 C
+ATOM 26 O HIS A 6 -0.018 9.235 33.552 1.00 28.46 O
+ATOM 27 CB HIS A 6 2.448 10.242 34.901 1.00 27.84 C
+ATOM 28 CG HIS A 6 3.859 9.982 35.330 1.00 27.97 C
+ATOM 29 ND1 HIS A 6 4.805 10.984 35.436 1.00 28.88 N
+ATOM 30 CD2 HIS A 6 4.491 8.832 35.676 1.00 26.24 C
+ATOM 31 CE1 HIS A 6 5.957 10.464 35.833 1.00 26.21 C
+ATOM 32 NE2 HIS A 6 5.793 9.160 35.988 1.00 26.11 N
+ATOM 33 N ASP A 7 0.353 10.968 32.179 1.00 29.02 N
+ATOM 34 CA ASP A 7 -1.031 10.978 31.714 1.00 29.20 C
+ATOM 35 C ASP A 7 -1.185 10.196 30.421 1.00 27.98 C
+ATOM 36 O ASP A 7 -2.280 10.076 29.881 1.00 28.18 O
+ATOM 37 CB ASP A 7 -1.552 12.404 31.547 1.00 30.25 C
+ATOM 38 CG ASP A 7 -1.949 13.013 32.861 1.00 33.81 C
+ATOM 39 OD1 ASP A 7 -2.983 12.582 33.440 1.00 36.93 O
+ATOM 40 OD2 ASP A 7 -1.257 13.888 33.418 1.00 37.28 O
+ATOM 41 N HIS A 8 -0.080 9.687 29.903 1.00 26.59 N
+ATOM 42 CA HIS A 8 -0.156 8.830 28.719 1.00 26.21 C
+ATOM 43 C HIS A 8 0.060 7.417 29.193 1.00 24.80 C
+ATOM 44 O HIS A 8 0.783 7.199 30.134 1.00 25.46 O
+ATOM 45 CB HIS A 8 0.894 9.222 27.680 1.00 25.82 C
+ATOM 46 CG HIS A 8 0.643 10.559 27.058 1.00 27.39 C
+ATOM 47 ND1 HIS A 8 1.485 11.118 26.118 1.00 29.14 N
+ATOM 48 CD2 HIS A 8 -0.360 11.450 27.244 1.00 27.44 C
+ATOM 49 CE1 HIS A 8 1.001 12.290 25.744 1.00 29.63 C
+ATOM 50 NE2 HIS A 8 -0.113 12.517 26.417 1.00 29.67 N
+ATOM 51 N HIS A 9 -0.572 6.449 28.565 1.00 24.28 N
+ATOM 52 CA HIS A 9 -0.409 5.076 29.024 1.00 23.44 C
+ATOM 53 C HIS A 9 -0.053 4.144 27.864 1.00 22.44 C
+ATOM 54 O HIS A 9 -0.375 4.435 26.706 1.00 22.45 O
+ATOM 55 CB HIS A 9 -1.684 4.617 29.712 1.00 23.34 C
+ATOM 56 CG HIS A 9 -1.447 3.623 30.797 1.00 24.86 C
+ATOM 57 ND1 HIS A 9 -1.028 3.989 32.059 1.00 26.31 N
+ATOM 58 CD2 HIS A 9 -1.536 2.272 30.802 1.00 23.13 C
+ATOM 59 CE1 HIS A 9 -0.889 2.907 32.801 1.00 25.78 C
+ATOM 60 NE2 HIS A 9 -1.201 1.854 32.064 1.00 26.66 N
+ATOM 61 N ILE A 10 0.632 3.050 28.182 1.00 20.91 N
+ATOM 62 CA ILE A 10 1.006 2.011 27.212 1.00 19.98 C
+ATOM 63 C ILE A 10 0.351 0.679 27.627 1.00 19.32 C
+ATOM 64 O ILE A 10 0.382 0.320 28.802 1.00 18.91 O
+ATOM 65 CB ILE A 10 2.533 1.830 27.206 1.00 19.84 C
+ATOM 66 CG1 ILE A 10 3.205 3.167 26.941 1.00 20.42 C
+ATOM 67 CG2 ILE A 10 2.988 0.755 26.194 1.00 18.60 C
+ATOM 68 CD1 ILE A 10 4.466 3.309 27.684 1.00 21.97 C
+ATOM 69 N TYR A 11 -0.249 -0.033 26.678 1.00 18.35 N
+ATOM 70 CA TYR A 11 -0.854 -1.329 26.958 1.00 18.19 C
+ATOM 71 C TYR A 11 -0.235 -2.364 26.054 1.00 18.62 C
+ATOM 72 O TYR A 11 -0.331 -2.259 24.820 1.00 18.06 O
+ATOM 73 CB TYR A 11 -2.348 -1.321 26.705 1.00 18.18 C
+ATOM 74 CG TYR A 11 -3.074 -0.326 27.548 1.00 20.90 C
+ATOM 75 CD1 TYR A 11 -3.362 0.935 27.049 1.00 22.58 C
+ATOM 76 CD2 TYR A 11 -3.471 -0.635 28.836 1.00 22.24 C
+ATOM 77 CE1 TYR A 11 -4.018 1.860 27.801 1.00 24.10 C
+ATOM 78 CE2 TYR A 11 -4.133 0.308 29.620 1.00 25.31 C
+ATOM 79 CZ TYR A 11 -4.401 1.558 29.080 1.00 24.13 C
+ATOM 80 OH TYR A 11 -5.057 2.509 29.794 1.00 23.35 O
+ATOM 81 N VAL A 12 0.420 -3.343 26.671 1.00 18.33 N
+ATOM 82 CA VAL A 12 1.037 -4.419 25.953 1.00 17.66 C
+ATOM 83 C VAL A 12 0.016 -5.540 25.839 1.00 18.19 C
+ATOM 84 O VAL A 12 -0.333 -6.148 26.841 1.00 18.34 O
+ATOM 85 CB VAL A 12 2.260 -4.946 26.697 1.00 17.18 C
+ATOM 86 CG1 VAL A 12 2.807 -6.169 25.986 1.00 16.82 C
+ATOM 87 CG2 VAL A 12 3.319 -3.877 26.785 1.00 16.26 C
+ATOM 88 N LEU A 13 -0.499 -5.788 24.638 1.00 17.94 N
+ATOM 89 CA LEU A 13 -1.417 -6.927 24.455 1.00 19.11 C
+ATOM 90 C LEU A 13 -0.644 -8.243 24.516 1.00 17.63 C
+ATOM 91 O LEU A 13 0.203 -8.502 23.663 1.00 17.09 O
+ATOM 92 CB LEU A 13 -2.179 -6.887 23.131 1.00 18.90 C
+ATOM 93 CG LEU A 13 -3.376 -5.933 23.076 1.00 22.74 C
+ATOM 94 CD1 LEU A 13 -4.593 -6.534 23.763 1.00 24.42 C
+ATOM 95 CD2 LEU A 13 -3.034 -4.577 23.681 1.00 23.53 C
+ATOM 96 N MET A 14 -0.947 -9.081 25.491 1.00 16.85 N
+ATOM 97 CA MET A 14 -0.173 -10.310 25.650 1.00 17.41 C
+ATOM 98 C MET A 14 -1.031 -11.584 25.651 1.00 17.59 C
+ATOM 99 O MET A 14 -2.274 -11.538 25.750 1.00 17.02 O
+ATOM 100 CB MET A 14 0.656 -10.258 26.945 1.00 17.19 C
+ATOM 101 CG MET A 14 -0.203 -10.279 28.215 1.00 18.19 C
+ATOM 102 SD MET A 14 0.748 -10.530 29.752 1.00 19.48 S
+ATOM 103 CE MET A 14 0.931 -12.312 29.670 1.00 20.01 C
+ATOM 104 N GLY A 15 -0.352 -12.720 25.569 1.00 17.09 N
+ATOM 105 CA GLY A 15 -1.039 -13.999 25.561 1.00 17.46 C
+ATOM 106 C GLY A 15 -0.387 -14.954 24.587 1.00 17.32 C
+ATOM 107 O GLY A 15 0.457 -14.560 23.785 1.00 16.16 O
+ATOM 108 N VAL A 16 -0.773 -16.210 24.625 1.00 17.67 N
+ATOM 109 CA VAL A 16 -0.116 -17.137 23.726 1.00 18.42 C
+ATOM 110 C VAL A 16 -0.472 -16.920 22.252 1.00 19.38 C
+ATOM 111 O VAL A 16 -1.407 -16.216 21.924 1.00 19.08 O
+ATOM 112 CB VAL A 16 -0.424 -18.570 24.135 1.00 17.84 C
+ATOM 113 CG1 VAL A 16 -0.182 -18.719 25.601 1.00 17.09 C
+ATOM 114 CG2 VAL A 16 -1.862 -18.904 23.803 1.00 19.53 C
+ATOM 115 N SER A 17 0.290 -17.546 21.369 1.00 20.54 N
+ATOM 116 CA SER A 17 0.008 -17.521 19.952 1.00 22.06 C
+ATOM 117 C SER A 17 -1.421 -17.991 19.690 1.00 22.69 C
+ATOM 118 O SER A 17 -1.853 -19.012 20.230 1.00 23.05 O
+ATOM 119 CB SER A 17 0.974 -18.456 19.231 1.00 22.55 C
+ATOM 120 OG SER A 17 1.081 -18.122 17.852 1.00 25.15 O
+ATOM 121 N GLY A 18 -2.161 -17.248 18.867 1.00 22.77 N
+ATOM 122 CA GLY A 18 -3.537 -17.603 18.571 1.00 21.96 C
+ATOM 123 C GLY A 18 -4.553 -17.070 19.570 1.00 22.43 C
+ATOM 124 O GLY A 18 -5.744 -17.422 19.532 1.00 23.50 O
+ATOM 125 N SER A 19 -4.119 -16.200 20.461 1.00 21.35 N
+ATOM 126 CA SER A 19 -5.026 -15.736 21.493 1.00 21.16 C
+ATOM 127 C SER A 19 -5.750 -14.475 21.084 1.00 20.65 C
+ATOM 128 O SER A 19 -6.615 -14.022 21.800 1.00 21.08 O
+ATOM 129 CB SER A 19 -4.294 -15.520 22.820 1.00 20.54 C
+ATOM 130 OG SER A 19 -3.288 -14.534 22.698 1.00 19.91 O
+ATOM 131 N GLY A 20 -5.361 -13.901 19.956 1.00 20.40 N
+ATOM 132 CA GLY A 20 -6.041 -12.736 19.408 1.00 20.32 C
+ATOM 133 C GLY A 20 -5.285 -11.415 19.457 1.00 20.57 C
+ATOM 134 O GLY A 20 -5.852 -10.362 19.132 1.00 20.79 O
+ATOM 135 N LYS A 21 -4.019 -11.457 19.869 1.00 19.71 N
+ATOM 136 CA LYS A 21 -3.260 -10.230 20.063 1.00 19.27 C
+ATOM 137 C LYS A 21 -3.332 -9.309 18.864 1.00 19.05 C
+ATOM 138 O LYS A 21 -3.708 -8.152 19.004 1.00 18.12 O
+ATOM 139 CB LYS A 21 -1.785 -10.508 20.449 1.00 18.96 C
+ATOM 140 CG LYS A 21 -1.623 -11.322 21.725 1.00 17.78 C
+ATOM 141 CD LYS A 21 -0.153 -11.475 22.081 1.00 16.81 C
+ATOM 142 CE LYS A 21 0.589 -12.124 20.937 1.00 14.74 C
+ATOM 143 NZ LYS A 21 0.119 -13.536 20.776 1.00 13.98 N
+ATOM 144 N SER A 22 -2.966 -9.807 17.683 1.00 19.42 N
+ATOM 145 CA SER A 22 -3.014 -8.944 16.494 1.00 20.34 C
+ATOM 146 C SER A 22 -4.438 -8.467 16.121 1.00 20.86 C
+ATOM 147 O SER A 22 -4.632 -7.292 15.783 1.00 20.95 O
+ATOM 148 CB SER A 22 -2.346 -9.609 15.297 1.00 19.15 C
+ATOM 149 OG SER A 22 -1.053 -10.051 15.676 1.00 22.34 O
+ATOM 150 N ALA A 23 -5.416 -9.368 16.167 1.00 21.11 N
+ATOM 151 CA ALA A 23 -6.774 -8.993 15.763 1.00 21.95 C
+ATOM 152 C ALA A 23 -7.294 -7.962 16.737 1.00 21.93 C
+ATOM 153 O ALA A 23 -7.684 -6.876 16.342 1.00 21.77 O
+ATOM 154 CB ALA A 23 -7.704 -10.203 15.743 1.00 22.01 C
+ATOM 155 N VAL A 24 -7.276 -8.288 18.023 1.00 21.94 N
+ATOM 156 CA VAL A 24 -7.768 -7.337 18.999 1.00 21.88 C
+ATOM 157 C VAL A 24 -7.051 -5.987 18.908 1.00 22.61 C
+ATOM 158 O VAL A 24 -7.693 -4.934 18.778 1.00 22.29 O
+ATOM 159 CB VAL A 24 -7.630 -7.884 20.401 1.00 22.04 C
+ATOM 160 CG1 VAL A 24 -7.970 -6.792 21.445 1.00 20.62 C
+ATOM 161 CG2 VAL A 24 -8.514 -9.125 20.547 1.00 21.19 C
+ATOM 162 N ALA A 25 -5.724 -6.020 18.970 1.00 23.06 N
+ATOM 163 CA ALA A 25 -4.933 -4.795 18.923 1.00 24.00 C
+ATOM 164 C ALA A 25 -5.191 -3.974 17.657 1.00 24.62 C
+ATOM 165 O ALA A 25 -5.250 -2.747 17.726 1.00 22.95 O
+ATOM 166 CB ALA A 25 -3.453 -5.084 19.065 1.00 23.17 C
+ATOM 167 N SER A 26 -5.320 -4.654 16.516 1.00 26.20 N
+ATOM 168 CA SER A 26 -5.659 -3.977 15.256 1.00 28.95 C
+ATOM 169 C SER A 26 -6.973 -3.190 15.371 1.00 29.00 C
+ATOM 170 O SER A 26 -7.064 -2.043 14.954 1.00 29.59 O
+ATOM 171 CB SER A 26 -5.836 -4.992 14.123 1.00 28.73 C
+ATOM 172 OG SER A 26 -4.604 -5.603 13.803 1.00 33.34 O
+ATOM 173 N GLU A 27 -7.988 -3.825 15.929 1.00 29.46 N
+ATOM 174 CA GLU A 27 -9.305 -3.200 16.006 1.00 29.87 C
+ATOM 175 C GLU A 27 -9.331 -2.135 17.071 1.00 29.16 C
+ATOM 176 O GLU A 27 -9.899 -1.052 16.865 1.00 29.35 O
+ATOM 177 CB GLU A 27 -10.383 -4.237 16.307 1.00 29.57 C
+ATOM 178 CG GLU A 27 -11.103 -4.788 15.090 1.00 33.34 C
+ATOM 179 CD GLU A 27 -11.747 -3.712 14.213 1.00 34.40 C
+ATOM 180 OE1 GLU A 27 -11.459 -3.718 13.003 1.00 35.13 O
+ATOM 181 OE2 GLU A 27 -12.527 -2.871 14.720 1.00 34.32 O
+ATOM 182 N VAL A 28 -8.733 -2.438 18.218 1.00 28.43 N
+ATOM 183 CA VAL A 28 -8.750 -1.478 19.298 1.00 27.97 C
+ATOM 184 C VAL A 28 -8.049 -0.184 18.925 1.00 28.83 C
+ATOM 185 O VAL A 28 -8.485 0.871 19.358 1.00 29.17 O
+ATOM 186 CB VAL A 28 -8.189 -2.037 20.619 1.00 27.89 C
+ATOM 187 CG1 VAL A 28 -8.090 -0.918 21.663 1.00 26.88 C
+ATOM 188 CG2 VAL A 28 -9.077 -3.141 21.131 1.00 26.01 C
+ATOM 189 N ALA A 29 -7.001 -0.239 18.102 1.00 29.03 N
+ATOM 190 CA ALA A 29 -6.290 0.986 17.756 1.00 30.02 C
+ATOM 191 C ALA A 29 -7.058 1.792 16.726 1.00 31.10 C
+ATOM 192 O ALA A 29 -6.996 3.028 16.703 1.00 30.52 O
+ATOM 193 CB ALA A 29 -4.880 0.689 17.249 1.00 29.81 C
+ATOM 194 N HIS A 30 -7.746 1.072 15.850 1.00 32.14 N
+ATOM 195 CA HIS A 30 -8.585 1.693 14.849 1.00 33.70 C
+ATOM 196 C HIS A 30 -9.690 2.495 15.528 1.00 33.76 C
+ATOM 197 O HIS A 30 -9.789 3.701 15.336 1.00 34.24 O
+ATOM 198 CB HIS A 30 -9.216 0.627 13.970 1.00 34.20 C
+ATOM 199 CG HIS A 30 -10.073 1.185 12.879 1.00 37.52 C
+ATOM 200 ND1 HIS A 30 -11.407 0.858 12.738 1.00 39.83 N
+ATOM 201 CD2 HIS A 30 -9.782 2.038 11.867 1.00 40.52 C
+ATOM 202 CE1 HIS A 30 -11.900 1.488 11.685 1.00 42.14 C
+ATOM 203 NE2 HIS A 30 -10.936 2.216 11.142 1.00 42.19 N
+ATOM 204 N GLN A 31 -10.495 1.823 16.347 1.00 33.53 N
+ATOM 205 CA GLN A 31 -11.620 2.462 17.032 1.00 32.98 C
+ATOM 206 C GLN A 31 -11.221 3.561 18.016 1.00 33.00 C
+ATOM 207 O GLN A 31 -12.029 4.457 18.308 1.00 33.13 O
+ATOM 208 CB GLN A 31 -12.486 1.422 17.764 1.00 32.31 C
+ATOM 209 CG GLN A 31 -13.181 0.397 16.848 1.00 32.83 C
+ATOM 210 CD GLN A 31 -14.084 -0.579 17.622 1.00 32.93 C
+ATOM 211 OE1 GLN A 31 -14.438 -0.317 18.771 1.00 35.06 O
+ATOM 212 NE2 GLN A 31 -14.447 -1.690 16.996 1.00 31.83 N
+ATOM 213 N LEU A 32 -10.000 3.502 18.548 1.00 32.05 N
+ATOM 214 CA LEU A 32 -9.597 4.471 19.565 1.00 31.37 C
+ATOM 215 C LEU A 32 -8.691 5.562 19.043 1.00 30.65 C
+ATOM 216 O LEU A 32 -8.344 6.471 19.780 1.00 29.89 O
+ATOM 217 CB LEU A 32 -8.834 3.784 20.701 1.00 32.00 C
+ATOM 218 CG LEU A 32 -9.423 2.756 21.678 1.00 33.96 C
+ATOM 219 CD1 LEU A 32 -8.394 2.544 22.763 1.00 34.39 C
+ATOM 220 CD2 LEU A 32 -10.723 3.254 22.298 1.00 35.83 C
+ATOM 221 N HIS A 33 -8.275 5.448 17.789 1.00 30.30 N
+ATOM 222 CA HIS A 33 -7.275 6.354 17.223 1.00 30.65 C
+ATOM 223 C HIS A 33 -6.003 6.337 18.073 1.00 29.47 C
+ATOM 224 O HIS A 33 -5.398 7.371 18.359 1.00 29.55 O
+ATOM 225 CB HIS A 33 -7.847 7.753 17.057 1.00 31.29 C
+ATOM 226 CG HIS A 33 -9.117 7.764 16.269 1.00 34.58 C
+ATOM 227 ND1 HIS A 33 -10.359 7.806 16.864 1.00 35.86 N
+ATOM 228 CD2 HIS A 33 -9.337 7.696 14.931 1.00 36.43 C
+ATOM 229 CE1 HIS A 33 -11.291 7.780 15.926 1.00 38.51 C
+ATOM 230 NE2 HIS A 33 -10.697 7.716 14.745 1.00 38.42 N
+ATOM 231 N ALA A 34 -5.594 5.134 18.454 1.00 28.00 N
+ATOM 232 CA ALA A 34 -4.420 4.965 19.285 1.00 26.85 C
+ATOM 233 C ALA A 34 -3.213 4.518 18.476 1.00 25.43 C
+ATOM 234 O ALA A 34 -3.332 3.957 17.396 1.00 25.71 O
+ATOM 235 CB ALA A 34 -4.706 3.965 20.414 1.00 26.74 C
+ATOM 236 N ALA A 35 -2.043 4.788 19.017 1.00 24.11 N
+ATOM 237 CA ALA A 35 -0.810 4.327 18.419 1.00 23.08 C
+ATOM 238 C ALA A 35 -0.733 2.815 18.594 1.00 22.67 C
+ATOM 239 O ALA A 35 -1.215 2.260 19.576 1.00 22.36 O
+ATOM 240 CB ALA A 35 0.351 4.997 19.055 1.00 22.70 C
+ATOM 241 N PHE A 36 -0.101 2.158 17.641 1.00 22.21 N
+ATOM 242 CA PHE A 36 -0.070 0.724 17.628 1.00 22.86 C
+ATOM 243 C PHE A 36 1.243 0.225 17.059 1.00 22.18 C
+ATOM 244 O PHE A 36 1.594 0.556 15.945 1.00 22.84 O
+ATOM 245 CB PHE A 36 -1.223 0.235 16.753 1.00 23.25 C
+ATOM 246 CG PHE A 36 -1.085 -1.186 16.299 1.00 25.96 C
+ATOM 247 CD1 PHE A 36 -1.716 -2.202 16.979 1.00 28.22 C
+ATOM 248 CD2 PHE A 36 -0.338 -1.499 15.185 1.00 29.95 C
+ATOM 249 CE1 PHE A 36 -1.595 -3.496 16.579 1.00 30.66 C
+ATOM 250 CE2 PHE A 36 -0.218 -2.810 14.764 1.00 31.95 C
+ATOM 251 CZ PHE A 36 -0.850 -3.808 15.467 1.00 32.08 C
+ATOM 252 N LEU A 37 1.955 -0.596 17.814 1.00 21.80 N
+ATOM 253 CA LEU A 37 3.210 -1.175 17.372 1.00 20.37 C
+ATOM 254 C LEU A 37 3.172 -2.696 17.531 1.00 20.11 C
+ATOM 255 O LEU A 37 2.868 -3.204 18.619 1.00 20.32 O
+ATOM 256 CB LEU A 37 4.338 -0.577 18.198 1.00 20.80 C
+ATOM 257 CG LEU A 37 5.798 -1.062 18.065 1.00 23.34 C
+ATOM 258 CD1 LEU A 37 6.435 -0.521 16.806 1.00 24.38 C
+ATOM 259 CD2 LEU A 37 6.609 -0.601 19.240 1.00 21.16 C
+ATOM 260 N ASP A 38 3.439 -3.428 16.453 1.00 19.49 N
+ATOM 261 CA ASP A 38 3.598 -4.879 16.526 1.00 19.87 C
+ATOM 262 C ASP A 38 5.043 -5.140 16.967 1.00 19.90 C
+ATOM 263 O ASP A 38 5.986 -4.818 16.236 1.00 19.18 O
+ATOM 264 CB ASP A 38 3.339 -5.529 15.159 1.00 20.44 C
+ATOM 265 CG ASP A 38 3.375 -7.067 15.197 1.00 20.98 C
+ATOM 266 OD1 ASP A 38 4.052 -7.681 16.059 1.00 23.66 O
+ATOM 267 OD2 ASP A 38 2.751 -7.759 14.374 1.00 22.63 O
+ATOM 268 N GLY A 39 5.213 -5.718 18.153 1.00 20.02 N
+ATOM 269 CA GLY A 39 6.533 -5.992 18.707 1.00 20.65 C
+ATOM 270 C GLY A 39 7.479 -6.834 17.859 1.00 21.56 C
+ATOM 271 O GLY A 39 8.688 -6.680 17.973 1.00 22.07 O
+ATOM 272 N ASP A 40 6.971 -7.696 16.989 1.00 21.89 N
+ATOM 273 CA ASP A 40 7.882 -8.485 16.153 1.00 23.49 C
+ATOM 274 C ASP A 40 8.781 -7.601 15.276 1.00 23.81 C
+ATOM 275 O ASP A 40 9.822 -8.054 14.818 1.00 24.40 O
+ATOM 276 CB ASP A 40 7.156 -9.480 15.213 1.00 23.43 C
+ATOM 277 CG ASP A 40 6.278 -10.497 15.947 1.00 25.20 C
+ATOM 278 OD1 ASP A 40 6.278 -10.565 17.206 1.00 24.78 O
+ATOM 279 OD2 ASP A 40 5.533 -11.289 15.314 1.00 27.80 O
+ATOM 280 N PHE A 41 8.388 -6.361 15.014 1.00 23.65 N
+ATOM 281 CA PHE A 41 9.166 -5.552 14.092 1.00 23.69 C
+ATOM 282 C PHE A 41 10.374 -4.931 14.773 1.00 24.07 C
+ATOM 283 O PHE A 41 11.149 -4.236 14.147 1.00 23.82 O
+ATOM 284 CB PHE A 41 8.305 -4.476 13.444 1.00 23.56 C
+ATOM 285 CG PHE A 41 7.027 -5.002 12.847 1.00 23.85 C
+ATOM 286 CD1 PHE A 41 5.944 -4.163 12.642 1.00 21.58 C
+ATOM 287 CD2 PHE A 41 6.921 -6.334 12.472 1.00 23.33 C
+ATOM 288 CE1 PHE A 41 4.770 -4.646 12.109 1.00 21.75 C
+ATOM 289 CE2 PHE A 41 5.740 -6.821 11.937 1.00 24.73 C
+ATOM 290 CZ PHE A 41 4.660 -5.973 11.760 1.00 22.35 C
+ATOM 291 N LEU A 42 10.527 -5.173 16.066 1.00 24.24 N
+ATOM 292 CA LEU A 42 11.652 -4.599 16.773 1.00 24.36 C
+ATOM 293 C LEU A 42 12.808 -5.586 16.897 1.00 24.22 C
+ATOM 294 O LEU A 42 13.844 -5.241 17.421 1.00 24.63 O
+ATOM 295 CB LEU A 42 11.231 -4.082 18.140 1.00 24.09 C
+ATOM 296 CG LEU A 42 10.700 -2.655 18.205 1.00 25.71 C
+ATOM 297 CD1 LEU A 42 11.852 -1.675 18.324 1.00 27.31 C
+ATOM 298 CD2 LEU A 42 9.789 -2.307 17.015 1.00 25.22 C
+ATOM 299 N HIS A 43 12.642 -6.814 16.435 1.00 23.90 N
+ATOM 300 CA HIS A 43 13.769 -7.746 16.482 1.00 24.15 C
+ATOM 301 C HIS A 43 14.946 -7.195 15.692 1.00 24.50 C
+ATOM 302 O HIS A 43 14.770 -6.673 14.609 1.00 23.74 O
+ATOM 303 CB HIS A 43 13.395 -9.102 15.889 1.00 23.60 C
+ATOM 304 CG HIS A 43 12.650 -9.981 16.836 1.00 23.77 C
+ATOM 305 ND1 HIS A 43 13.253 -10.584 17.919 1.00 23.68 N
+ATOM 306 CD2 HIS A 43 11.346 -10.337 16.881 1.00 22.36 C
+ATOM 307 CE1 HIS A 43 12.356 -11.283 18.585 1.00 24.15 C
+ATOM 308 NE2 HIS A 43 11.190 -11.149 17.976 1.00 25.04 N
+ATOM 309 N PRO A 44 16.135 -7.260 16.268 1.00 26.04 N
+ATOM 310 CA PRO A 44 17.376 -6.936 15.544 1.00 27.61 C
+ATOM 311 C PRO A 44 17.570 -7.838 14.297 1.00 28.75 C
+ATOM 312 O PRO A 44 16.989 -8.922 14.211 1.00 28.57 O
+ATOM 313 CB PRO A 44 18.478 -7.275 16.542 1.00 27.30 C
+ATOM 314 CG PRO A 44 17.823 -7.391 17.870 1.00 28.68 C
+ATOM 315 CD PRO A 44 16.357 -7.605 17.677 1.00 25.95 C
+ATOM 316 N ARG A 45 18.376 -7.370 13.347 1.00 30.17 N
+ATOM 317 CA ARG A 45 18.692 -8.114 12.128 1.00 31.68 C
+ATOM 318 C ARG A 45 19.109 -9.545 12.509 1.00 32.34 C
+ATOM 319 O ARG A 45 18.631 -10.528 11.929 1.00 32.00 O
+ATOM 320 CB ARG A 45 19.821 -7.387 11.389 1.00 32.05 C
+ATOM 321 CG ARG A 45 19.984 -7.709 9.914 1.00 34.13 C
+ATOM 322 CD ARG A 45 20.744 -6.624 9.120 1.00 36.18 C
+ATOM 323 NE ARG A 45 19.924 -5.441 8.875 1.00 37.72 N
+ATOM 324 CZ ARG A 45 19.104 -5.282 7.834 1.00 37.08 C
+ATOM 325 NH1 ARG A 45 18.983 -6.231 6.910 1.00 36.91 N
+ATOM 326 NH2 ARG A 45 18.391 -4.169 7.726 1.00 34.53 N
+ATOM 327 N ARG A 46 20.005 -9.628 13.494 1.00 32.64 N
+ATOM 328 CA ARG A 46 20.456 -10.880 14.085 1.00 33.74 C
+ATOM 329 C ARG A 46 19.347 -11.904 14.248 1.00 33.60 C
+ATOM 330 O ARG A 46 19.519 -13.078 13.937 1.00 33.57 O
+ATOM 331 CB ARG A 46 20.910 -10.625 15.529 1.00 34.20 C
+ATOM 332 CG ARG A 46 22.166 -9.846 15.766 1.00 35.23 C
+ATOM 333 CD ARG A 46 22.631 -9.943 17.238 1.00 37.68 C
+ATOM 334 NE ARG A 46 22.203 -8.838 18.109 1.00 40.45 N
+ATOM 335 CZ ARG A 46 21.975 -7.581 17.706 1.00 41.36 C
+ATOM 336 NH1 ARG A 46 22.097 -7.246 16.421 1.00 41.46 N
+ATOM 337 NH2 ARG A 46 21.603 -6.658 18.587 1.00 40.08 N
+ATOM 338 N ASN A 47 18.233 -11.471 14.828 1.00 33.69 N
+ATOM 339 CA ASN A 47 17.167 -12.405 15.162 1.00 33.98 C
+ATOM 340 C ASN A 47 16.369 -12.829 13.963 1.00 34.00 C
+ATOM 341 O ASN A 47 15.920 -13.963 13.882 1.00 33.70 O
+ATOM 342 CB ASN A 47 16.257 -11.849 16.262 1.00 33.79 C
+ATOM 343 CG ASN A 47 17.006 -11.591 17.551 1.00 33.30 C
+ATOM 344 OD1 ASN A 47 18.181 -11.914 17.662 1.00 31.75 O
+ATOM 345 ND2 ASN A 47 16.324 -11.010 18.534 1.00 33.15 N
+ATOM 346 N ILE A 48 16.200 -11.909 13.034 1.00 34.65 N
+ATOM 347 CA ILE A 48 15.456 -12.198 11.827 1.00 36.03 C
+ATOM 348 C ILE A 48 16.197 -13.257 11.011 1.00 37.13 C
+ATOM 349 O ILE A 48 15.580 -14.099 10.374 1.00 37.09 O
+ATOM 350 CB ILE A 48 15.251 -10.912 11.000 1.00 35.84 C
+ATOM 351 CG1 ILE A 48 14.487 -9.868 11.818 1.00 35.75 C
+ATOM 352 CG2 ILE A 48 14.513 -11.219 9.705 1.00 34.86 C
+ATOM 353 CD1 ILE A 48 13.131 -10.371 12.304 1.00 35.75 C
+ATOM 354 N GLU A 49 17.523 -13.212 11.048 1.00 38.27 N
+ATOM 355 CA GLU A 49 18.316 -14.158 10.281 1.00 39.55 C
+ATOM 356 C GLU A 49 18.359 -15.488 11.011 1.00 39.83 C
+ATOM 357 O GLU A 49 18.190 -16.528 10.387 1.00 39.57 O
+ATOM 358 CB GLU A 49 19.728 -13.620 9.994 1.00 39.42 C
+ATOM 359 CG GLU A 49 19.754 -12.319 9.199 1.00 40.68 C
+ATOM 360 CD GLU A 49 19.695 -12.480 7.677 1.00 42.00 C
+ATOM 361 OE1 GLU A 49 19.594 -13.614 7.155 1.00 42.37 O
+ATOM 362 OE2 GLU A 49 19.746 -11.440 6.984 1.00 42.38 O
+ATOM 363 N LYS A 50 18.601 -15.462 12.322 1.00 40.35 N
+ATOM 364 CA LYS A 50 18.543 -16.703 13.078 1.00 40.84 C
+ATOM 365 C LYS A 50 17.225 -17.336 12.653 1.00 41.33 C
+ATOM 366 O LYS A 50 17.209 -18.373 12.015 1.00 41.61 O
+ATOM 367 CB LYS A 50 18.577 -16.446 14.590 1.00 40.83 C
+ATOM 368 CG LYS A 50 19.017 -17.626 15.486 1.00 40.05 C
+ATOM 369 CD LYS A 50 19.431 -17.117 16.866 1.00 40.08 C
+ATOM 370 CE LYS A 50 20.097 -18.172 17.761 1.00 40.64 C
+ATOM 371 NZ LYS A 50 21.173 -17.544 18.618 1.00 41.99 N
+ATOM 372 N MET A 51 16.119 -16.664 12.938 1.00 41.88 N
+ATOM 373 CA MET A 51 14.800 -17.201 12.594 1.00 42.64 C
+ATOM 374 C MET A 51 14.622 -17.716 11.158 1.00 43.61 C
+ATOM 375 O MET A 51 14.022 -18.773 10.964 1.00 43.79 O
+ATOM 376 CB MET A 51 13.677 -16.233 12.986 1.00 41.82 C
+ATOM 377 CG MET A 51 13.391 -16.247 14.494 1.00 41.28 C
+ATOM 378 SD MET A 51 11.995 -15.205 14.993 1.00 38.55 S
+ATOM 379 CE MET A 51 12.695 -13.565 14.767 1.00 37.02 C
+ATOM 380 N ALA A 52 15.114 -16.982 10.158 1.00 44.42 N
+ATOM 381 CA ALA A 52 14.974 -17.433 8.779 1.00 45.46 C
+ATOM 382 C ALA A 52 15.628 -18.804 8.638 1.00 46.43 C
+ATOM 383 O ALA A 52 15.094 -19.702 7.981 1.00 46.50 O
+ATOM 384 CB ALA A 52 15.600 -16.459 7.831 1.00 45.27 C
+ATOM 385 N SER A 53 16.773 -18.952 9.297 1.00 47.08 N
+ATOM 386 CA SER A 53 17.544 -20.176 9.262 1.00 47.98 C
+ATOM 387 C SER A 53 16.958 -21.252 10.178 1.00 48.91 C
+ATOM 388 O SER A 53 17.636 -22.217 10.528 1.00 48.87 O
+ATOM 389 CB SER A 53 18.993 -19.891 9.655 1.00 48.00 C
+ATOM 390 OG SER A 53 19.140 -19.875 11.061 1.00 47.24 O
+ATOM 391 N GLY A 54 15.707 -21.075 10.581 1.00 49.66 N
+ATOM 392 CA GLY A 54 15.017 -22.087 11.364 1.00 50.97 C
+ATOM 393 C GLY A 54 15.455 -22.390 12.792 1.00 51.46 C
+ATOM 394 O GLY A 54 14.833 -23.229 13.446 1.00 51.58 O
+ATOM 395 N GLU A 55 16.513 -21.740 13.275 1.00 51.90 N
+ATOM 396 CA GLU A 55 16.933 -21.900 14.667 1.00 52.67 C
+ATOM 397 C GLU A 55 15.940 -21.108 15.519 1.00 52.36 C
+ATOM 398 O GLU A 55 15.487 -20.057 15.086 1.00 52.68 O
+ATOM 399 CB GLU A 55 18.335 -21.320 14.879 1.00 53.12 C
+ATOM 400 CG GLU A 55 19.460 -22.011 14.127 1.00 55.64 C
+ATOM 401 CD GLU A 55 20.279 -22.929 15.018 1.00 59.99 C
+ATOM 402 OE1 GLU A 55 19.811 -23.236 16.141 1.00 60.28 O
+ATOM 403 OE2 GLU A 55 21.391 -23.342 14.594 1.00 61.65 O
+ATOM 404 N PRO A 56 15.594 -21.596 16.712 1.00 51.97 N
+ATOM 405 CA PRO A 56 14.650 -20.895 17.584 1.00 51.19 C
+ATOM 406 C PRO A 56 15.356 -19.969 18.570 1.00 50.34 C
+ATOM 407 O PRO A 56 16.282 -20.392 19.265 1.00 50.52 O
+ATOM 408 CB PRO A 56 14.006 -22.032 18.377 1.00 51.39 C
+ATOM 409 CG PRO A 56 14.838 -23.249 18.109 1.00 51.82 C
+ATOM 410 CD PRO A 56 16.062 -22.845 17.333 1.00 52.13 C
+ATOM 411 N LEU A 57 14.897 -18.727 18.657 1.00 48.80 N
+ATOM 412 CA LEU A 57 15.483 -17.761 19.575 1.00 47.26 C
+ATOM 413 C LEU A 57 15.632 -18.288 21.001 1.00 46.56 C
+ATOM 414 O LEU A 57 14.923 -19.203 21.414 1.00 46.21 O
+ATOM 415 CB LEU A 57 14.624 -16.504 19.602 1.00 46.66 C
+ATOM 416 CG LEU A 57 14.581 -15.741 18.289 1.00 46.75 C
+ATOM 417 CD1 LEU A 57 13.993 -14.368 18.515 1.00 47.47 C
+ATOM 418 CD2 LEU A 57 15.966 -15.627 17.701 1.00 45.81 C
+ATOM 419 N ASN A 58 16.557 -17.692 21.743 1.00 45.47 N
+ATOM 420 CA ASN A 58 16.727 -17.981 23.165 1.00 45.14 C
+ATOM 421 C ASN A 58 16.529 -16.689 23.982 1.00 44.42 C
+ATOM 422 O ASN A 58 16.511 -15.585 23.429 1.00 43.84 O
+ATOM 423 CB ASN A 58 18.111 -18.570 23.436 1.00 45.28 C
+ATOM 424 CG ASN A 58 19.235 -17.642 22.997 1.00 45.90 C
+ATOM 425 OD1 ASN A 58 19.295 -16.468 23.396 1.00 46.55 O
+ATOM 426 ND2 ASN A 58 20.126 -18.158 22.159 1.00 45.01 N
+ATOM 427 N ASP A 59 16.381 -16.841 25.295 1.00 43.97 N
+ATOM 428 CA ASP A 59 16.196 -15.696 26.179 1.00 43.62 C
+ATOM 429 C ASP A 59 17.313 -14.676 26.027 1.00 43.61 C
+ATOM 430 O ASP A 59 17.092 -13.484 26.219 1.00 43.79 O
+ATOM 431 CB ASP A 59 16.014 -16.129 27.634 1.00 43.42 C
+ATOM 432 CG ASP A 59 14.658 -16.737 27.877 1.00 43.24 C
+ATOM 433 OD1 ASP A 59 13.858 -16.717 26.925 1.00 44.81 O
+ATOM 434 OD2 ASP A 59 14.296 -17.264 28.956 1.00 42.82 O
+ATOM 435 N ASP A 60 18.506 -15.128 25.655 1.00 43.64 N
+ATOM 436 CA ASP A 60 19.597 -14.188 25.392 1.00 43.16 C
+ATOM 437 C ASP A 60 19.342 -13.402 24.100 1.00 42.41 C
+ATOM 438 O ASP A 60 19.748 -12.230 23.991 1.00 42.38 O
+ATOM 439 CB ASP A 60 20.967 -14.885 25.374 1.00 43.80 C
+ATOM 440 CG ASP A 60 21.322 -15.516 26.719 1.00 44.96 C
+ATOM 441 OD1 ASP A 60 21.506 -14.767 27.700 1.00 45.05 O
+ATOM 442 OD2 ASP A 60 21.417 -16.753 26.894 1.00 47.05 O
+ATOM 443 N ASP A 61 18.662 -14.017 23.127 1.00 41.46 N
+ATOM 444 CA ASP A 61 18.316 -13.301 21.886 1.00 40.39 C
+ATOM 445 C ASP A 61 17.133 -12.331 22.089 1.00 39.24 C
+ATOM 446 O ASP A 61 17.040 -11.285 21.442 1.00 38.75 O
+ATOM 447 CB ASP A 61 17.947 -14.271 20.757 1.00 40.65 C
+ATOM 448 CG ASP A 61 19.003 -15.345 20.523 1.00 41.89 C
+ATOM 449 OD1 ASP A 61 20.194 -15.091 20.785 1.00 44.55 O
+ATOM 450 OD2 ASP A 61 18.728 -16.474 20.076 1.00 41.00 O
+ATOM 451 N ARG A 62 16.226 -12.713 22.982 1.00 38.02 N
+ATOM 452 CA ARG A 62 15.007 -11.969 23.257 1.00 37.73 C
+ATOM 453 C ARG A 62 15.330 -10.684 23.990 1.00 37.52 C
+ATOM 454 O ARG A 62 14.639 -9.673 23.843 1.00 37.94 O
+ATOM 455 CB ARG A 62 14.058 -12.821 24.107 1.00 37.68 C
+ATOM 456 CG ARG A 62 13.448 -14.000 23.381 1.00 37.05 C
+ATOM 457 CD ARG A 62 12.267 -14.612 24.105 1.00 37.70 C
+ATOM 458 NE ARG A 62 11.581 -15.581 23.262 1.00 40.57 N
+ATOM 459 CZ ARG A 62 12.024 -16.818 23.040 1.00 43.72 C
+ATOM 460 NH1 ARG A 62 13.148 -17.243 23.610 1.00 43.61 N
+ATOM 461 NH2 ARG A 62 11.341 -17.662 22.266 1.00 44.47 N
+ATOM 462 N LYS A 63 16.404 -10.727 24.767 1.00 36.98 N
+ATOM 463 CA LYS A 63 16.840 -9.599 25.576 1.00 36.64 C
+ATOM 464 C LYS A 63 17.038 -8.253 24.826 1.00 35.46 C
+ATOM 465 O LYS A 63 16.498 -7.244 25.255 1.00 35.16 O
+ATOM 466 CB LYS A 63 18.049 -10.016 26.424 1.00 37.01 C
+ATOM 467 CG LYS A 63 18.928 -8.891 26.887 1.00 39.65 C
+ATOM 468 CD LYS A 63 19.489 -9.183 28.265 1.00 43.28 C
+ATOM 469 CE LYS A 63 18.671 -8.503 29.352 1.00 44.59 C
+ATOM 470 NZ LYS A 63 19.129 -7.091 29.534 1.00 45.02 N
+ATOM 471 N PRO A 64 17.817 -8.237 23.743 1.00 34.46 N
+ATOM 472 CA PRO A 64 17.977 -7.054 22.886 1.00 32.92 C
+ATOM 473 C PRO A 64 16.675 -6.635 22.208 1.00 31.75 C
+ATOM 474 O PRO A 64 16.430 -5.453 21.972 1.00 31.46 O
+ATOM 475 CB PRO A 64 18.953 -7.544 21.817 1.00 32.75 C
+ATOM 476 CG PRO A 64 19.701 -8.605 22.485 1.00 34.17 C
+ATOM 477 CD PRO A 64 18.663 -9.357 23.286 1.00 34.69 C
+ATOM 478 N TRP A 65 15.853 -7.615 21.860 1.00 30.00 N
+ATOM 479 CA TRP A 65 14.573 -7.314 21.245 1.00 28.67 C
+ATOM 480 C TRP A 65 13.687 -6.598 22.252 1.00 27.86 C
+ATOM 481 O TRP A 65 13.109 -5.568 21.949 1.00 27.47 O
+ATOM 482 CB TRP A 65 13.923 -8.605 20.769 1.00 27.91 C
+ATOM 483 CG TRP A 65 12.420 -8.608 20.587 1.00 27.83 C
+ATOM 484 CD1 TRP A 65 11.659 -7.782 19.790 1.00 26.92 C
+ATOM 485 CD2 TRP A 65 11.515 -9.538 21.167 1.00 26.73 C
+ATOM 486 NE1 TRP A 65 10.337 -8.153 19.857 1.00 28.01 N
+ATOM 487 CE2 TRP A 65 10.228 -9.233 20.698 1.00 28.15 C
+ATOM 488 CE3 TRP A 65 11.665 -10.611 22.044 1.00 28.44 C
+ATOM 489 CZ2 TRP A 65 9.112 -9.945 21.097 1.00 28.06 C
+ATOM 490 CZ3 TRP A 65 10.563 -11.319 22.429 1.00 27.30 C
+ATOM 491 CH2 TRP A 65 9.303 -10.983 21.965 1.00 26.77 C
+ATOM 492 N LEU A 66 13.607 -7.155 23.457 1.00 27.21 N
+ATOM 493 CA LEU A 66 12.764 -6.608 24.515 1.00 27.81 C
+ATOM 494 C LEU A 66 13.161 -5.177 24.948 1.00 27.81 C
+ATOM 495 O LEU A 66 12.285 -4.361 25.227 1.00 26.87 O
+ATOM 496 CB LEU A 66 12.705 -7.553 25.717 1.00 27.57 C
+ATOM 497 CG LEU A 66 11.962 -8.864 25.448 1.00 28.47 C
+ATOM 498 CD1 LEU A 66 12.330 -9.930 26.464 1.00 30.22 C
+ATOM 499 CD2 LEU A 66 10.486 -8.645 25.431 1.00 27.93 C
+ATOM 500 N GLN A 67 14.464 -4.892 24.996 1.00 27.45 N
+ATOM 501 CA GLN A 67 14.988 -3.567 25.362 1.00 28.49 C
+ATOM 502 C GLN A 67 14.589 -2.540 24.316 1.00 27.72 C
+ATOM 503 O GLN A 67 14.327 -1.352 24.615 1.00 28.03 O
+ATOM 504 CB GLN A 67 16.518 -3.625 25.479 1.00 29.27 C
+ATOM 505 CG GLN A 67 17.242 -2.281 25.735 1.00 32.94 C
+ATOM 506 CD GLN A 67 16.708 -1.559 26.949 1.00 37.22 C
+ATOM 507 OE1 GLN A 67 16.596 -2.148 28.028 1.00 41.73 O
+ATOM 508 NE2 GLN A 67 16.352 -0.290 26.776 1.00 37.65 N
+ATOM 509 N ALA A 68 14.551 -2.997 23.072 1.00 26.83 N
+ATOM 510 CA ALA A 68 14.148 -2.135 21.978 1.00 26.21 C
+ATOM 511 C ALA A 68 12.640 -1.928 22.076 1.00 25.49 C
+ATOM 512 O ALA A 68 12.115 -0.826 21.801 1.00 25.40 O
+ATOM 513 CB ALA A 68 14.533 -2.772 20.643 1.00 27.31 C
+ATOM 514 N LEU A 69 11.935 -2.985 22.485 1.00 23.61 N
+ATOM 515 CA LEU A 69 10.513 -2.836 22.746 1.00 22.20 C
+ATOM 516 C LEU A 69 10.316 -1.780 23.830 1.00 21.04 C
+ATOM 517 O LEU A 69 9.473 -0.900 23.698 1.00 20.12 O
+ATOM 518 CB LEU A 69 9.884 -4.150 23.194 1.00 22.16 C
+ATOM 519 CG LEU A 69 8.818 -4.722 22.267 1.00 22.74 C
+ATOM 520 CD1 LEU A 69 7.737 -5.365 23.103 1.00 25.19 C
+ATOM 521 CD2 LEU A 69 8.203 -3.639 21.400 1.00 23.60 C
+ATOM 522 N ASN A 70 11.087 -1.911 24.905 1.00 18.88 N
+ATOM 523 CA ASN A 70 11.031 -0.983 26.022 1.00 19.44 C
+ATOM 524 C ASN A 70 11.188 0.439 25.510 1.00 18.80 C
+ATOM 525 O ASN A 70 10.361 1.303 25.750 1.00 18.25 O
+ATOM 526 CB ASN A 70 12.149 -1.301 27.023 1.00 19.32 C
+ATOM 527 CG ASN A 70 12.111 -0.409 28.219 1.00 19.37 C
+ATOM 528 OD1 ASN A 70 11.775 -0.841 29.335 1.00 21.73 O
+ATOM 529 ND2 ASN A 70 12.461 0.835 28.017 1.00 15.28 N
+ATOM 530 N ASP A 71 12.242 0.632 24.737 1.00 19.08 N
+ATOM 531 CA ASP A 71 12.558 1.953 24.203 1.00 19.45 C
+ATOM 532 C ASP A 71 11.495 2.494 23.262 1.00 18.96 C
+ATOM 533 O ASP A 71 11.218 3.690 23.255 1.00 18.36 O
+ATOM 534 CB ASP A 71 13.919 1.914 23.527 1.00 19.16 C
+ATOM 535 CG ASP A 71 15.018 1.607 24.503 1.00 21.48 C
+ATOM 536 OD1 ASP A 71 14.724 1.621 25.726 1.00 24.29 O
+ATOM 537 OD2 ASP A 71 16.183 1.328 24.154 1.00 21.90 O
+ATOM 538 N ALA A 72 10.898 1.617 22.466 1.00 18.88 N
+ATOM 539 CA ALA A 72 9.835 2.050 21.579 1.00 18.84 C
+ATOM 540 C ALA A 72 8.594 2.459 22.368 1.00 18.83 C
+ATOM 541 O ALA A 72 7.869 3.362 21.934 1.00 18.46 O
+ATOM 542 CB ALA A 72 9.479 0.989 20.576 1.00 18.12 C
+ATOM 543 N ALA A 73 8.340 1.779 23.488 1.00 18.60 N
+ATOM 544 CA ALA A 73 7.220 2.130 24.358 1.00 19.45 C
+ATOM 545 C ALA A 73 7.462 3.547 24.951 1.00 19.36 C
+ATOM 546 O ALA A 73 6.558 4.359 25.045 1.00 18.85 O
+ATOM 547 CB ALA A 73 7.031 1.076 25.466 1.00 19.17 C
+ATOM 548 N PHE A 74 8.700 3.783 25.352 1.00 19.37 N
+ATOM 549 CA PHE A 74 9.152 5.061 25.866 1.00 20.59 C
+ATOM 550 C PHE A 74 8.879 6.209 24.870 1.00 20.61 C
+ATOM 551 O PHE A 74 8.440 7.296 25.235 1.00 21.23 O
+ATOM 552 CB PHE A 74 10.641 4.907 26.122 1.00 21.27 C
+ATOM 553 CG PHE A 74 11.292 6.105 26.684 1.00 22.78 C
+ATOM 554 CD1 PHE A 74 10.888 6.625 27.894 1.00 23.70 C
+ATOM 555 CD2 PHE A 74 12.352 6.689 26.013 1.00 24.12 C
+ATOM 556 CE1 PHE A 74 11.518 7.730 28.428 1.00 26.01 C
+ATOM 557 CE2 PHE A 74 12.974 7.796 26.525 1.00 25.97 C
+ATOM 558 CZ PHE A 74 12.561 8.317 27.739 1.00 26.67 C
+ATOM 559 N ALA A 75 9.123 5.937 23.599 1.00 20.09 N
+ATOM 560 CA ALA A 75 8.881 6.889 22.535 1.00 19.59 C
+ATOM 561 C ALA A 75 7.404 7.062 22.220 1.00 19.50 C
+ATOM 562 O ALA A 75 6.918 8.172 22.015 1.00 18.55 O
+ATOM 563 CB ALA A 75 9.585 6.440 21.300 1.00 19.94 C
+ATOM 564 N MET A 76 6.688 5.955 22.126 1.00 19.43 N
+ATOM 565 CA MET A 76 5.276 6.062 21.789 1.00 19.75 C
+ATOM 566 C MET A 76 4.543 6.903 22.821 1.00 19.64 C
+ATOM 567 O MET A 76 3.649 7.649 22.471 1.00 18.97 O
+ATOM 568 CB MET A 76 4.616 4.688 21.703 1.00 20.02 C
+ATOM 569 CG MET A 76 5.026 3.838 20.517 1.00 19.51 C
+ATOM 570 SD MET A 76 4.363 2.140 20.797 1.00 20.64 S
+ATOM 571 CE MET A 76 2.609 2.318 19.955 1.00 16.52 C
+ATOM 572 N GLN A 77 4.948 6.793 24.085 1.00 19.71 N
+ATOM 573 CA GLN A 77 4.258 7.476 25.163 1.00 21.09 C
+ATOM 574 C GLN A 77 4.602 8.973 25.155 1.00 21.42 C
+ATOM 575 O GLN A 77 3.981 9.752 25.856 1.00 21.43 O
+ATOM 576 CB GLN A 77 4.498 6.828 26.546 1.00 21.08 C
+ATOM 577 CG GLN A 77 5.942 6.783 27.038 1.00 21.96 C
+ATOM 578 CD GLN A 77 6.330 7.983 27.907 1.00 24.83 C
+ATOM 579 OE1 GLN A 77 5.535 8.481 28.702 1.00 26.22 O
+ATOM 580 NE2 GLN A 77 7.560 8.420 27.768 1.00 22.99 N
+ATOM 581 N ARG A 78 5.571 9.372 24.342 1.00 21.98 N
+ATOM 582 CA ARG A 78 5.848 10.798 24.254 1.00 23.42 C
+ATOM 583 C ARG A 78 4.736 11.540 23.526 1.00 23.85 C
+ATOM 584 O ARG A 78 4.507 12.696 23.819 1.00 24.07 O
+ATOM 585 CB ARG A 78 7.195 11.142 23.596 1.00 23.04 C
+ATOM 586 CG ARG A 78 8.427 10.762 24.406 1.00 26.06 C
+ATOM 587 CD ARG A 78 8.729 11.682 25.586 1.00 29.02 C
+ATOM 588 NE ARG A 78 8.409 13.080 25.315 1.00 33.61 N
+ATOM 589 CZ ARG A 78 8.098 13.967 26.255 1.00 33.87 C
+ATOM 590 NH1 ARG A 78 8.067 13.612 27.533 1.00 29.76 N
+ATOM 591 NH2 ARG A 78 7.819 15.214 25.908 1.00 36.63 N
+ATOM 592 N THR A 79 4.028 10.902 22.599 1.00 24.51 N
+ATOM 593 CA THR A 79 3.044 11.650 21.815 1.00 25.48 C
+ATOM 594 C THR A 79 1.644 11.076 21.720 1.00 25.54 C
+ATOM 595 O THR A 79 0.844 11.589 20.943 1.00 26.25 O
+ATOM 596 CB THR A 79 3.549 11.905 20.368 1.00 25.75 C
+ATOM 597 OG1 THR A 79 4.108 10.694 19.827 1.00 28.34 O
+ATOM 598 CG2 THR A 79 4.740 12.866 20.379 1.00 26.38 C
+ATOM 599 N ASN A 80 1.336 10.024 22.467 1.00 24.70 N
+ATOM 600 CA ASN A 80 -0.014 9.471 22.420 1.00 24.84 C
+ATOM 601 C ASN A 80 -0.531 9.158 23.820 1.00 25.06 C
+ATOM 602 O ASN A 80 0.187 8.558 24.627 1.00 24.85 O
+ATOM 603 CB ASN A 80 -0.066 8.175 21.598 1.00 24.79 C
+ATOM 604 CG ASN A 80 0.510 8.316 20.211 1.00 25.18 C
+ATOM 605 OD1 ASN A 80 -0.206 8.610 19.240 1.00 25.38 O
+ATOM 606 ND2 ASN A 80 1.812 8.050 20.089 1.00 23.46 N
+ATOM 607 N LYS A 81 -1.774 9.540 24.106 1.00 25.21 N
+ATOM 608 CA LYS A 81 -2.382 9.193 25.390 1.00 25.93 C
+ATOM 609 C LYS A 81 -2.466 7.678 25.573 1.00 24.64 C
+ATOM 610 O LYS A 81 -2.226 7.180 26.653 1.00 24.51 O
+ATOM 611 CB LYS A 81 -3.784 9.782 25.523 1.00 26.65 C
+ATOM 612 CG LYS A 81 -3.865 11.266 25.271 1.00 30.36 C
+ATOM 613 CD LYS A 81 -4.947 11.883 26.126 1.00 35.91 C
+ATOM 614 CE LYS A 81 -4.928 13.400 25.988 1.00 38.91 C
+ATOM 615 NZ LYS A 81 -4.995 13.779 24.546 1.00 42.52 N
+ATOM 616 N VAL A 82 -2.843 6.977 24.511 1.00 24.39 N
+ATOM 617 CA VAL A 82 -2.988 5.530 24.519 1.00 23.93 C
+ATOM 618 C VAL A 82 -2.103 4.902 23.445 1.00 23.87 C
+ATOM 619 O VAL A 82 -2.228 5.214 22.259 1.00 23.91 O
+ATOM 620 CB VAL A 82 -4.438 5.113 24.210 1.00 23.86 C
+ATOM 621 CG1 VAL A 82 -4.564 3.579 24.171 1.00 22.68 C
+ATOM 622 CG2 VAL A 82 -5.409 5.726 25.209 1.00 23.92 C
+ATOM 623 N SER A 83 -1.198 4.030 23.861 1.00 23.17 N
+ATOM 624 CA SER A 83 -0.328 3.336 22.924 1.00 23.14 C
+ATOM 625 C SER A 83 -0.461 1.852 23.166 1.00 22.45 C
+ATOM 626 O SER A 83 -0.341 1.432 24.310 1.00 23.16 O
+ATOM 627 CB SER A 83 1.126 3.745 23.148 1.00 22.72 C
+ATOM 628 OG SER A 83 1.325 5.106 22.863 1.00 23.97 O
+ATOM 629 N LEU A 84 -0.724 1.093 22.096 1.00 22.16 N
+ATOM 630 CA LEU A 84 -0.831 -0.374 22.120 1.00 21.95 C
+ATOM 631 C LEU A 84 0.365 -1.071 21.458 1.00 21.20 C
+ATOM 632 O LEU A 84 0.747 -0.734 20.334 1.00 20.32 O
+ATOM 633 CB LEU A 84 -2.084 -0.852 21.399 1.00 22.39 C
+ATOM 634 CG LEU A 84 -3.427 -0.289 21.884 1.00 25.29 C
+ATOM 635 CD1 LEU A 84 -4.590 -0.981 21.218 1.00 25.92 C
+ATOM 636 CD2 LEU A 84 -3.529 -0.427 23.394 1.00 27.71 C
+ATOM 637 N ILE A 85 0.929 -2.061 22.160 1.00 19.92 N
+ATOM 638 CA ILE A 85 2.027 -2.870 21.645 1.00 18.70 C
+ATOM 639 C ILE A 85 1.642 -4.333 21.629 1.00 18.78 C
+ATOM 640 O ILE A 85 1.077 -4.838 22.600 1.00 19.78 O
+ATOM 641 CB ILE A 85 3.281 -2.691 22.543 1.00 18.83 C
+ATOM 642 CG1 ILE A 85 3.857 -1.275 22.411 1.00 16.45 C
+ATOM 643 CG2 ILE A 85 4.350 -3.702 22.203 1.00 15.95 C
+ATOM 644 CD1 ILE A 85 4.989 -0.986 23.366 1.00 17.40 C
+ATOM 645 N VAL A 86 1.922 -5.026 20.537 1.00 18.89 N
+ATOM 646 CA VAL A 86 1.640 -6.456 20.492 1.00 18.71 C
+ATOM 647 C VAL A 86 2.918 -7.192 20.859 1.00 18.80 C
+ATOM 648 O VAL A 86 3.943 -6.981 20.227 1.00 17.42 O
+ATOM 649 CB VAL A 86 1.147 -6.941 19.116 1.00 19.34 C
+ATOM 650 CG1 VAL A 86 1.094 -8.477 19.066 1.00 17.98 C
+ATOM 651 CG2 VAL A 86 -0.242 -6.398 18.834 1.00 19.61 C
+ATOM 652 N CYS A 87 2.830 -8.019 21.905 1.00 18.22 N
+ATOM 653 CA CYS A 87 3.933 -8.843 22.375 1.00 18.16 C
+ATOM 654 C CYS A 87 3.426 -9.974 23.252 1.00 17.67 C
+ATOM 655 O CYS A 87 2.819 -9.776 24.303 1.00 18.19 O
+ATOM 656 CB CYS A 87 4.977 -8.023 23.137 1.00 18.33 C
+ATOM 657 SG CYS A 87 6.332 -9.055 23.762 1.00 20.46 S
+ATOM 658 N SER A 88 3.693 -11.180 22.820 1.00 17.82 N
+ATOM 659 CA SER A 88 3.217 -12.317 23.588 1.00 18.41 C
+ATOM 660 C SER A 88 3.604 -12.242 25.067 1.00 17.13 C
+ATOM 661 O SER A 88 2.793 -12.560 25.925 1.00 15.77 O
+ATOM 662 CB SER A 88 3.671 -13.639 22.965 1.00 18.66 C
+ATOM 663 OG SER A 88 5.077 -13.781 23.022 1.00 23.59 O
+ATOM 664 N ALA A 89 4.836 -11.814 25.347 1.00 16.60 N
+ATOM 665 CA ALA A 89 5.291 -11.581 26.720 1.00 16.74 C
+ATOM 666 C ALA A 89 5.040 -12.746 27.659 1.00 16.80 C
+ATOM 667 O ALA A 89 4.534 -12.551 28.752 1.00 16.34 O
+ATOM 668 CB ALA A 89 4.616 -10.320 27.280 1.00 16.41 C
+ATOM 669 N LEU A 90 5.401 -13.953 27.242 1.00 17.49 N
+ATOM 670 CA LEU A 90 5.057 -15.138 28.021 1.00 18.22 C
+ATOM 671 C LEU A 90 5.677 -15.251 29.400 1.00 18.33 C
+ATOM 672 O LEU A 90 5.032 -15.693 30.313 1.00 18.44 O
+ATOM 673 CB LEU A 90 5.349 -16.412 27.233 1.00 18.00 C
+ATOM 674 CG LEU A 90 4.567 -16.483 25.930 1.00 18.39 C
+ATOM 675 CD1 LEU A 90 4.934 -17.760 25.171 1.00 17.43 C
+ATOM 676 CD2 LEU A 90 3.032 -16.389 26.197 1.00 16.18 C
+ATOM 677 N LYS A 91 6.927 -14.854 29.542 1.00 19.63 N
+ATOM 678 CA LYS A 91 7.620 -15.004 30.804 1.00 20.62 C
+ATOM 679 C LYS A 91 7.549 -13.746 31.630 1.00 21.44 C
+ATOM 680 O LYS A 91 7.627 -12.633 31.075 1.00 21.62 O
+ATOM 681 CB LYS A 91 9.081 -15.377 30.551 1.00 21.10 C
+ATOM 682 CG LYS A 91 9.228 -16.633 29.684 1.00 23.15 C
+ATOM 683 CD LYS A 91 10.566 -17.355 29.918 1.00 27.36 C
+ATOM 684 CE LYS A 91 10.590 -18.698 29.227 1.00 26.03 C
+ATOM 685 NZ LYS A 91 11.996 -19.142 29.080 1.00 29.74 N
+ATOM 686 N LYS A 92 7.399 -13.903 32.946 1.00 21.53 N
+ATOM 687 CA LYS A 92 7.361 -12.736 33.803 1.00 23.02 C
+ATOM 688 C LYS A 92 8.565 -11.866 33.509 1.00 23.40 C
+ATOM 689 O LYS A 92 8.478 -10.641 33.406 1.00 23.29 O
+ATOM 690 CB LYS A 92 7.373 -13.086 35.298 1.00 23.23 C
+ATOM 691 CG LYS A 92 7.351 -11.797 36.190 1.00 24.83 C
+ATOM 692 CD LYS A 92 7.099 -12.049 37.703 1.00 29.78 C
+ATOM 693 CE LYS A 92 7.317 -10.747 38.554 1.00 32.47 C
+ATOM 694 NZ LYS A 92 8.766 -10.245 38.655 1.00 32.06 N
+ATOM 695 N HIS A 93 9.707 -12.517 33.401 1.00 23.43 N
+ATOM 696 CA HIS A 93 10.945 -11.803 33.202 1.00 24.02 C
+ATOM 697 C HIS A 93 10.922 -10.910 31.938 1.00 23.28 C
+ATOM 698 O HIS A 93 11.532 -9.841 31.931 1.00 23.87 O
+ATOM 699 CB HIS A 93 12.095 -12.822 33.260 1.00 25.43 C
+ATOM 700 CG HIS A 93 13.329 -12.392 32.562 1.00 27.89 C
+ATOM 701 ND1 HIS A 93 13.695 -12.905 31.339 1.00 30.85 N
+ATOM 702 CD2 HIS A 93 14.290 -11.501 32.908 1.00 32.73 C
+ATOM 703 CE1 HIS A 93 14.824 -12.338 30.951 1.00 33.41 C
+ATOM 704 NE2 HIS A 93 15.211 -11.484 31.886 1.00 33.61 N
+ATOM 705 N TYR A 94 10.192 -11.309 30.898 1.00 21.62 N
+ATOM 706 CA TYR A 94 10.044 -10.465 29.705 1.00 20.84 C
+ATOM 707 C TYR A 94 9.208 -9.234 30.071 1.00 20.45 C
+ATOM 708 O TYR A 94 9.415 -8.137 29.557 1.00 20.05 O
+ATOM 709 CB TYR A 94 9.303 -11.199 28.580 1.00 20.63 C
+ATOM 710 CG TYR A 94 9.891 -12.527 28.150 1.00 20.31 C
+ATOM 711 CD1 TYR A 94 11.174 -12.903 28.532 1.00 20.23 C
+ATOM 712 CD2 TYR A 94 9.159 -13.398 27.355 1.00 20.37 C
+ATOM 713 CE1 TYR A 94 11.714 -14.104 28.136 1.00 22.46 C
+ATOM 714 CE2 TYR A 94 9.683 -14.605 26.937 1.00 20.93 C
+ATOM 715 CZ TYR A 94 10.963 -14.973 27.344 1.00 24.21 C
+ATOM 716 OH TYR A 94 11.510 -16.199 26.952 1.00 24.38 O
+ATOM 717 N ARG A 95 8.239 -9.439 30.950 1.00 19.44 N
+ATOM 718 CA ARG A 95 7.364 -8.370 31.353 1.00 19.39 C
+ATOM 719 C ARG A 95 8.139 -7.336 32.176 1.00 19.62 C
+ATOM 720 O ARG A 95 8.010 -6.126 31.939 1.00 18.14 O
+ATOM 721 CB ARG A 95 6.145 -8.922 32.096 1.00 19.08 C
+ATOM 722 CG ARG A 95 5.326 -9.872 31.202 1.00 18.52 C
+ATOM 723 CD ARG A 95 3.971 -10.297 31.739 1.00 16.84 C
+ATOM 724 NE ARG A 95 4.039 -11.140 32.937 1.00 18.69 N
+ATOM 725 CZ ARG A 95 4.144 -12.469 32.938 1.00 20.02 C
+ATOM 726 NH1 ARG A 95 4.211 -13.158 31.793 1.00 19.73 N
+ATOM 727 NH2 ARG A 95 4.158 -13.119 34.095 1.00 17.25 N
+ATOM 728 N ASP A 96 8.966 -7.819 33.100 1.00 19.81 N
+ATOM 729 CA ASP A 96 9.847 -6.942 33.856 1.00 21.61 C
+ATOM 730 C ASP A 96 10.684 -6.095 32.925 1.00 21.83 C
+ATOM 731 O ASP A 96 10.800 -4.894 33.152 1.00 21.91 O
+ATOM 732 CB ASP A 96 10.818 -7.713 34.755 1.00 21.98 C
+ATOM 733 CG ASP A 96 10.132 -8.342 35.941 1.00 23.32 C
+ATOM 734 OD1 ASP A 96 8.977 -7.965 36.236 1.00 21.33 O
+ATOM 735 OD2 ASP A 96 10.683 -9.244 36.614 1.00 26.72 O
+ATOM 736 N LEU A 97 11.253 -6.712 31.881 1.00 22.28 N
+ATOM 737 CA LEU A 97 12.122 -5.967 30.956 1.00 22.76 C
+ATOM 738 C LEU A 97 11.333 -4.876 30.248 1.00 22.38 C
+ATOM 739 O LEU A 97 11.892 -3.838 29.923 1.00 23.22 O
+ATOM 740 CB LEU A 97 12.813 -6.871 29.926 1.00 22.79 C
+ATOM 741 CG LEU A 97 14.053 -7.686 30.338 1.00 25.85 C
+ATOM 742 CD1 LEU A 97 14.269 -8.878 29.383 1.00 22.81 C
+ATOM 743 CD2 LEU A 97 15.335 -6.815 30.447 1.00 25.95 C
+ATOM 744 N LEU A 98 10.043 -5.113 30.012 1.00 21.29 N
+ATOM 745 CA LEU A 98 9.214 -4.102 29.371 1.00 21.64 C
+ATOM 746 C LEU A 98 8.799 -3.011 30.342 1.00 21.52 C
+ATOM 747 O LEU A 98 8.636 -1.860 29.944 1.00 21.79 O
+ATOM 748 CB LEU A 98 7.971 -4.711 28.747 1.00 20.08 C
+ATOM 749 CG LEU A 98 8.322 -5.575 27.562 1.00 21.04 C
+ATOM 750 CD1 LEU A 98 7.108 -6.388 27.140 1.00 20.38 C
+ATOM 751 CD2 LEU A 98 8.887 -4.741 26.389 1.00 19.64 C
+ATOM 752 N ARG A 99 8.618 -3.395 31.607 1.00 21.85 N
+ATOM 753 CA ARG A 99 8.228 -2.480 32.671 1.00 21.78 C
+ATOM 754 C ARG A 99 9.290 -1.442 33.011 1.00 21.95 C
+ATOM 755 O ARG A 99 8.972 -0.352 33.442 1.00 21.52 O
+ATOM 756 CB ARG A 99 7.979 -3.267 33.961 1.00 21.83 C
+ATOM 757 CG ARG A 99 6.602 -3.873 34.145 1.00 19.72 C
+ATOM 758 CD ARG A 99 6.542 -4.832 35.320 1.00 18.33 C
+ATOM 759 NE ARG A 99 5.259 -5.513 35.326 1.00 17.66 N
+ATOM 760 CZ ARG A 99 5.110 -6.820 35.383 1.00 16.05 C
+ATOM 761 NH1 ARG A 99 6.174 -7.628 35.469 1.00 14.74 N
+ATOM 762 NH2 ARG A 99 3.895 -7.318 35.361 1.00 15.26 N
+ATOM 763 N GLU A 100 10.552 -1.821 32.863 1.00 22.67 N
+ATOM 764 CA GLU A 100 11.657 -0.998 33.327 1.00 24.03 C
+ATOM 765 C GLU A 100 11.665 0.408 32.734 1.00 23.51 C
+ATOM 766 O GLU A 100 11.724 0.595 31.515 1.00 23.20 O
+ATOM 767 CB GLU A 100 12.976 -1.718 33.053 1.00 24.73 C
+ATOM 768 CG GLU A 100 14.166 -1.187 33.833 1.00 29.90 C
+ATOM 769 CD GLU A 100 15.134 -2.313 34.124 1.00 37.44 C
+ATOM 770 OE1 GLU A 100 15.924 -2.673 33.195 1.00 36.80 O
+ATOM 771 OE2 GLU A 100 15.049 -2.868 35.260 1.00 38.87 O
+ATOM 772 N GLY A 101 11.576 1.397 33.612 1.00 23.32 N
+ATOM 773 CA GLY A 101 11.561 2.777 33.182 1.00 22.82 C
+ATOM 774 C GLY A 101 10.242 3.191 32.573 1.00 23.12 C
+ATOM 775 O GLY A 101 10.112 4.317 32.132 1.00 23.36 O
+ATOM 776 N ASN A 102 9.248 2.304 32.560 1.00 23.16 N
+ATOM 777 CA ASN A 102 7.953 2.652 31.990 1.00 22.82 C
+ATOM 778 C ASN A 102 6.829 2.431 33.022 1.00 23.02 C
+ATOM 779 O ASN A 102 6.005 1.533 32.859 1.00 22.28 O
+ATOM 780 CB ASN A 102 7.675 1.843 30.707 1.00 22.92 C
+ATOM 781 CG ASN A 102 8.698 2.099 29.570 1.00 22.73 C
+ATOM 782 OD1 ASN A 102 9.011 3.252 29.205 1.00 22.29 O
+ATOM 783 ND2 ASN A 102 9.182 1.015 28.982 1.00 22.70 N
+ATOM 784 N PRO A 103 6.772 3.268 34.066 1.00 23.04 N
+ATOM 785 CA PRO A 103 5.772 3.089 35.133 1.00 23.00 C
+ATOM 786 C PRO A 103 4.400 3.289 34.565 1.00 22.44 C
+ATOM 787 O PRO A 103 3.432 2.898 35.173 1.00 22.09 O
+ATOM 788 CB PRO A 103 6.042 4.247 36.118 1.00 22.80 C
+ATOM 789 CG PRO A 103 7.260 4.932 35.662 1.00 23.49 C
+ATOM 790 CD PRO A 103 7.610 4.459 34.276 1.00 22.89 C
+ATOM 791 N ASN A 104 4.315 3.941 33.415 1.00 22.10 N
+ATOM 792 CA ASN A 104 3.018 4.146 32.805 1.00 21.60 C
+ATOM 793 C ASN A 104 2.695 2.983 31.853 1.00 21.70 C
+ATOM 794 O ASN A 104 1.855 3.090 30.969 1.00 21.82 O
+ATOM 795 CB ASN A 104 2.908 5.545 32.154 1.00 21.83 C
+ATOM 796 CG ASN A 104 3.954 5.794 31.038 1.00 21.56 C
+ATOM 797 OD1 ASN A 104 4.965 5.127 30.958 1.00 21.19 O
+ATOM 798 ND2 ASN A 104 3.687 6.782 30.183 1.00 20.43 N
+ATOM 799 N LEU A 105 3.373 1.856 32.045 1.00 21.47 N
+ATOM 800 CA LEU A 105 3.093 0.695 31.220 1.00 21.16 C
+ATOM 801 C LEU A 105 2.277 -0.340 31.965 1.00 21.32 C
+ATOM 802 O LEU A 105 2.490 -0.592 33.154 1.00 21.50 O
+ATOM 803 CB LEU A 105 4.374 0.086 30.648 1.00 20.64 C
+ATOM 804 CG LEU A 105 4.252 -1.115 29.710 1.00 21.02 C
+ATOM 805 CD1 LEU A 105 5.297 -1.043 28.577 1.00 19.42 C
+ATOM 806 CD2 LEU A 105 4.342 -2.449 30.469 1.00 18.13 C
+ATOM 807 N SER A 106 1.311 -0.915 31.264 1.00 21.25 N
+ATOM 808 CA SER A 106 0.565 -2.017 31.811 1.00 22.01 C
+ATOM 809 C SER A 106 0.329 -3.115 30.745 1.00 20.71 C
+ATOM 810 O SER A 106 0.593 -2.928 29.555 1.00 20.25 O
+ATOM 811 CB SER A 106 -0.720 -1.488 32.446 1.00 22.52 C
+ATOM 812 OG SER A 106 -1.640 -1.162 31.459 1.00 27.80 O
+ATOM 813 N PHE A 107 -0.140 -4.281 31.168 1.00 19.79 N
+ATOM 814 CA PHE A 107 -0.457 -5.345 30.220 1.00 18.05 C
+ATOM 815 C PHE A 107 -1.953 -5.652 30.181 1.00 16.67 C
+ATOM 816 O PHE A 107 -2.665 -5.485 31.161 1.00 15.05 O
+ATOM 817 CB PHE A 107 0.288 -6.644 30.566 1.00 18.24 C
+ATOM 818 CG PHE A 107 1.748 -6.473 30.696 1.00 18.58 C
+ATOM 819 CD1 PHE A 107 2.282 -5.864 31.817 1.00 17.65 C
+ATOM 820 CD2 PHE A 107 2.600 -6.904 29.692 1.00 18.68 C
+ATOM 821 CE1 PHE A 107 3.655 -5.691 31.940 1.00 18.80 C
+ATOM 822 CE2 PHE A 107 3.968 -6.733 29.803 1.00 18.28 C
+ATOM 823 CZ PHE A 107 4.500 -6.133 30.930 1.00 17.92 C
+ATOM 824 N ILE A 108 -2.404 -6.120 29.024 1.00 16.36 N
+ATOM 825 CA ILE A 108 -3.749 -6.649 28.856 1.00 15.62 C
+ATOM 826 C ILE A 108 -3.537 -8.092 28.402 1.00 15.81 C
+ATOM 827 O ILE A 108 -3.103 -8.349 27.262 1.00 15.04 O
+ATOM 828 CB ILE A 108 -4.525 -5.841 27.810 1.00 16.96 C
+ATOM 829 CG1 ILE A 108 -4.700 -4.392 28.274 1.00 17.55 C
+ATOM 830 CG2 ILE A 108 -5.898 -6.498 27.433 1.00 13.85 C
+ATOM 831 CD1 ILE A 108 -5.392 -3.556 27.268 1.00 16.95 C
+ATOM 832 N TYR A 109 -3.795 -9.023 29.312 1.00 14.99 N
+ATOM 833 CA TYR A 109 -3.621 -10.422 29.053 1.00 16.15 C
+ATOM 834 C TYR A 109 -4.861 -10.997 28.401 1.00 16.65 C
+ATOM 835 O TYR A 109 -5.936 -11.016 28.985 1.00 16.52 O
+ATOM 836 CB TYR A 109 -3.295 -11.149 30.369 1.00 16.47 C
+ATOM 837 CG TYR A 109 -3.247 -12.675 30.331 1.00 17.72 C
+ATOM 838 CD1 TYR A 109 -3.054 -13.368 29.151 1.00 18.03 C
+ATOM 839 CD2 TYR A 109 -3.380 -13.423 31.514 1.00 19.84 C
+ATOM 840 CE1 TYR A 109 -3.007 -14.772 29.131 1.00 20.99 C
+ATOM 841 CE2 TYR A 109 -3.345 -14.827 31.499 1.00 19.60 C
+ATOM 842 CZ TYR A 109 -3.155 -15.492 30.312 1.00 20.38 C
+ATOM 843 OH TYR A 109 -3.113 -16.873 30.292 1.00 21.15 O
+ATOM 844 N LEU A 110 -4.715 -11.447 27.172 1.00 17.65 N
+ATOM 845 CA LEU A 110 -5.838 -12.053 26.484 1.00 19.18 C
+ATOM 846 C LEU A 110 -5.857 -13.507 26.913 1.00 20.35 C
+ATOM 847 O LEU A 110 -5.165 -14.355 26.313 1.00 19.71 O
+ATOM 848 CB LEU A 110 -5.641 -11.960 24.993 1.00 18.59 C
+ATOM 849 CG LEU A 110 -5.691 -10.545 24.465 1.00 21.03 C
+ATOM 850 CD1 LEU A 110 -5.577 -10.589 22.959 1.00 24.16 C
+ATOM 851 CD2 LEU A 110 -7.005 -9.904 24.872 1.00 24.05 C
+ATOM 852 N LYS A 111 -6.649 -13.795 27.940 1.00 21.06 N
+ATOM 853 CA LYS A 111 -6.610 -15.108 28.571 1.00 22.89 C
+ATOM 854 C LYS A 111 -7.635 -16.074 28.005 1.00 24.25 C
+ATOM 855 O LYS A 111 -8.834 -15.790 27.940 1.00 24.19 O
+ATOM 856 CB LYS A 111 -6.811 -14.948 30.072 1.00 23.08 C
+ATOM 857 CG LYS A 111 -6.627 -16.211 30.910 1.00 24.36 C
+ATOM 858 CD LYS A 111 -6.731 -15.821 32.373 1.00 25.90 C
+ATOM 859 CE LYS A 111 -6.503 -16.986 33.297 1.00 27.58 C
+ATOM 860 NZ LYS A 111 -6.584 -16.482 34.696 1.00 29.19 N
+ATOM 861 N GLY A 112 -7.151 -17.224 27.576 1.00 25.36 N
+ATOM 862 CA GLY A 112 -8.038 -18.246 27.087 1.00 26.80 C
+ATOM 863 C GLY A 112 -7.411 -19.573 27.389 1.00 28.06 C
+ATOM 864 O GLY A 112 -6.198 -19.680 27.590 1.00 27.23 O
+ATOM 865 N ASP A 113 -8.233 -20.601 27.454 1.00 29.60 N
+ATOM 866 CA ASP A 113 -7.653 -21.903 27.650 1.00 30.82 C
+ATOM 867 C ASP A 113 -7.339 -22.550 26.317 1.00 30.68 C
+ATOM 868 O ASP A 113 -7.772 -22.106 25.250 1.00 29.64 O
+ATOM 869 CB ASP A 113 -8.524 -22.785 28.517 1.00 32.51 C
+ATOM 870 CG ASP A 113 -9.714 -23.263 27.808 1.00 34.37 C
+ATOM 871 OD1 ASP A 113 -9.672 -23.281 26.571 1.00 38.96 O
+ATOM 872 OD2 ASP A 113 -10.734 -23.655 28.399 1.00 39.82 O
+ATOM 873 N PHE A 114 -6.541 -23.595 26.417 1.00 30.87 N
+ATOM 874 CA PHE A 114 -6.038 -24.325 25.288 1.00 31.38 C
+ATOM 875 C PHE A 114 -7.067 -24.701 24.225 1.00 31.52 C
+ATOM 876 O PHE A 114 -6.841 -24.450 23.042 1.00 30.63 O
+ATOM 877 CB PHE A 114 -5.300 -25.565 25.794 1.00 31.81 C
+ATOM 878 CG PHE A 114 -4.649 -26.365 24.710 1.00 31.94 C
+ATOM 879 CD1 PHE A 114 -3.289 -26.256 24.460 1.00 32.73 C
+ATOM 880 CD2 PHE A 114 -5.401 -27.228 23.941 1.00 32.78 C
+ATOM 881 CE1 PHE A 114 -2.696 -27.005 23.461 1.00 33.94 C
+ATOM 882 CE2 PHE A 114 -4.818 -27.994 22.946 1.00 33.70 C
+ATOM 883 CZ PHE A 114 -3.464 -27.893 22.705 1.00 34.29 C
+ATOM 884 N ASP A 115 -8.192 -25.289 24.619 1.00 32.10 N
+ATOM 885 CA ASP A 115 -9.117 -25.785 23.593 1.00 33.02 C
+ATOM 886 C ASP A 115 -9.749 -24.657 22.771 1.00 32.48 C
+ATOM 887 O ASP A 115 -9.935 -24.788 21.563 1.00 31.32 O
+ATOM 888 CB ASP A 115 -10.124 -26.837 24.141 1.00 33.58 C
+ATOM 889 CG ASP A 115 -9.433 -27.957 24.903 1.00 36.26 C
+ATOM 890 OD1 ASP A 115 -10.103 -28.645 25.711 1.00 37.75 O
+ATOM 891 OD2 ASP A 115 -8.203 -28.194 24.773 1.00 39.99 O
+ATOM 892 N VAL A 116 -10.014 -23.526 23.404 1.00 32.99 N
+ATOM 893 CA VAL A 116 -10.584 -22.408 22.674 1.00 33.32 C
+ATOM 894 C VAL A 116 -9.614 -21.874 21.619 1.00 33.35 C
+ATOM 895 O VAL A 116 -10.014 -21.580 20.490 1.00 33.34 O
+ATOM 896 CB VAL A 116 -10.972 -21.279 23.629 1.00 33.68 C
+ATOM 897 CG1 VAL A 116 -11.757 -20.191 22.897 1.00 33.91 C
+ATOM 898 CG2 VAL A 116 -11.766 -21.847 24.785 1.00 33.49 C
+ATOM 899 N ILE A 117 -8.341 -21.764 21.984 1.00 32.90 N
+ATOM 900 CA ILE A 117 -7.349 -21.194 21.091 1.00 32.90 C
+ATOM 901 C ILE A 117 -7.033 -22.168 19.984 1.00 33.79 C
+ATOM 902 O ILE A 117 -6.795 -21.782 18.843 1.00 33.21 O
+ATOM 903 CB ILE A 117 -6.061 -20.817 21.871 1.00 32.75 C
+ATOM 904 CG1 ILE A 117 -6.381 -19.762 22.928 1.00 31.26 C
+ATOM 905 CG2 ILE A 117 -4.976 -20.314 20.922 1.00 31.58 C
+ATOM 906 CD1 ILE A 117 -5.169 -19.207 23.621 1.00 31.96 C
+ATOM 907 N GLU A 118 -7.041 -23.447 20.328 1.00 35.07 N
+ATOM 908 CA GLU A 118 -6.732 -24.459 19.344 1.00 36.47 C
+ATOM 909 C GLU A 118 -7.724 -24.409 18.201 1.00 37.06 C
+ATOM 910 O GLU A 118 -7.318 -24.360 17.047 1.00 37.26 O
+ATOM 911 CB GLU A 118 -6.697 -25.852 19.967 1.00 36.60 C
+ATOM 912 CG GLU A 118 -6.414 -26.957 18.967 1.00 37.54 C
+ATOM 913 CD GLU A 118 -6.561 -28.320 19.590 1.00 39.16 C
+ATOM 914 OE1 GLU A 118 -5.608 -29.129 19.514 1.00 40.17 O
+ATOM 915 OE2 GLU A 118 -7.634 -28.569 20.168 1.00 40.48 O
+ATOM 916 N SER A 119 -9.015 -24.402 18.509 1.00 37.73 N
+ATOM 917 CA SER A 119 -10.000 -24.384 17.438 1.00 39.05 C
+ATOM 918 C SER A 119 -9.856 -23.117 16.616 1.00 39.36 C
+ATOM 919 O SER A 119 -9.999 -23.135 15.399 1.00 39.90 O
+ATOM 920 CB SER A 119 -11.443 -24.587 17.946 1.00 38.94 C
+ATOM 921 OG SER A 119 -11.974 -23.425 18.569 1.00 40.24 O
+ATOM 922 N ARG A 120 -9.548 -22.012 17.271 1.00 39.97 N
+ATOM 923 CA ARG A 120 -9.355 -20.772 16.534 1.00 40.36 C
+ATOM 924 C ARG A 120 -8.144 -20.844 15.605 1.00 40.63 C
+ATOM 925 O ARG A 120 -8.172 -20.295 14.507 1.00 40.21 O
+ATOM 926 CB ARG A 120 -9.265 -19.586 17.480 1.00 40.42 C
+ATOM 927 CG ARG A 120 -10.628 -19.146 17.971 1.00 40.77 C
+ATOM 928 CD ARG A 120 -10.537 -18.236 19.139 1.00 41.26 C
+ATOM 929 NE ARG A 120 -11.831 -17.777 19.605 1.00 41.50 N
+ATOM 930 CZ ARG A 120 -11.967 -16.826 20.506 1.00 40.37 C
+ATOM 931 NH1 ARG A 120 -10.890 -16.261 21.015 1.00 37.65 N
+ATOM 932 NH2 ARG A 120 -13.171 -16.436 20.891 1.00 42.93 N
+ATOM 933 N LEU A 121 -7.080 -21.517 16.028 1.00 40.80 N
+ATOM 934 CA LEU A 121 -5.964 -21.674 15.113 1.00 41.47 C
+ATOM 935 C LEU A 121 -6.333 -22.624 13.967 1.00 42.02 C
+ATOM 936 O LEU A 121 -5.938 -22.398 12.826 1.00 42.28 O
+ATOM 937 CB LEU A 121 -4.698 -22.138 15.832 1.00 41.33 C
+ATOM 938 CG LEU A 121 -3.937 -21.058 16.603 1.00 41.51 C
+ATOM 939 CD1 LEU A 121 -2.809 -21.700 17.367 1.00 41.19 C
+ATOM 940 CD2 LEU A 121 -3.410 -19.959 15.675 1.00 40.11 C
+ATOM 941 N LYS A 122 -7.106 -23.667 14.257 1.00 42.71 N
+ATOM 942 CA LYS A 122 -7.468 -24.643 13.228 1.00 44.14 C
+ATOM 943 C LYS A 122 -8.374 -24.056 12.146 1.00 44.81 C
+ATOM 944 O LYS A 122 -8.273 -24.411 10.975 1.00 45.10 O
+ATOM 945 CB LYS A 122 -8.157 -25.865 13.834 1.00 44.01 C
+ATOM 946 CG LYS A 122 -7.258 -26.817 14.607 1.00 45.61 C
+ATOM 947 CD LYS A 122 -7.751 -28.254 14.388 1.00 48.76 C
+ATOM 948 CE LYS A 122 -7.462 -29.179 15.558 1.00 49.80 C
+ATOM 949 NZ LYS A 122 -7.967 -30.566 15.280 1.00 49.58 N
+ATOM 950 N ALA A 123 -9.239 -23.137 12.548 1.00 45.56 N
+ATOM 951 CA ALA A 123 -10.252 -22.564 11.667 1.00 46.36 C
+ATOM 952 C ALA A 123 -9.751 -21.841 10.422 1.00 46.68 C
+ATOM 953 O ALA A 123 -10.560 -21.439 9.589 1.00 46.70 O
+ATOM 954 CB ALA A 123 -11.158 -21.635 12.469 1.00 46.67 C
+ATOM 955 N ARG A 124 -8.440 -21.653 10.312 1.00 47.08 N
+ATOM 956 CA ARG A 124 -7.840 -20.966 9.166 1.00 47.45 C
+ATOM 957 C ARG A 124 -7.625 -21.910 7.971 1.00 46.95 C
+ATOM 958 O ARG A 124 -6.793 -22.828 8.026 1.00 46.47 O
+ATOM 959 CB ARG A 124 -6.478 -20.373 9.548 1.00 48.23 C
+ATOM 960 CG ARG A 124 -6.398 -19.623 10.881 1.00 50.70 C
+ATOM 961 CD ARG A 124 -4.955 -19.404 11.332 1.00 54.43 C
+ATOM 962 NE ARG A 124 -4.773 -18.246 12.206 1.00 58.48 N
+ATOM 963 CZ ARG A 124 -3.578 -17.775 12.593 1.00 59.79 C
+ATOM 964 NH1 ARG A 124 -2.461 -18.373 12.181 1.00 58.54 N
+ATOM 965 NH2 ARG A 124 -3.501 -16.710 13.394 1.00 59.10 N
+ATOM 966 N LYS A 125 -8.351 -21.657 6.885 1.00 46.51 N
+ATOM 967 CA LYS A 125 -8.253 -22.470 5.678 1.00 46.03 C
+ATOM 968 C LYS A 125 -6.803 -22.603 5.245 1.00 45.74 C
+ATOM 969 O LYS A 125 -6.061 -21.618 5.210 1.00 45.51 O
+ATOM 970 CB LYS A 125 -9.042 -21.823 4.550 1.00 46.02 C
+ATOM 971 CG LYS A 125 -9.894 -22.783 3.766 1.00 46.18 C
+ATOM 972 CD LYS A 125 -10.643 -22.080 2.654 1.00 45.54 C
+ATOM 973 CE LYS A 125 -12.119 -22.413 2.718 1.00 46.31 C
+ATOM 974 NZ LYS A 125 -12.836 -22.132 1.447 1.00 46.46 N
+ATOM 975 N GLY A 126 -6.394 -23.824 4.928 1.00 45.12 N
+ATOM 976 CA GLY A 126 -5.043 -24.056 4.456 1.00 44.76 C
+ATOM 977 C GLY A 126 -3.951 -24.067 5.510 1.00 44.65 C
+ATOM 978 O GLY A 126 -2.784 -24.307 5.194 1.00 44.48 O
+ATOM 979 N HIS A 127 -4.301 -23.815 6.765 1.00 44.42 N
+ATOM 980 CA HIS A 127 -3.267 -23.801 7.782 1.00 44.60 C
+ATOM 981 C HIS A 127 -3.064 -25.144 8.451 1.00 44.21 C
+ATOM 982 O HIS A 127 -3.950 -25.631 9.151 1.00 43.90 O
+ATOM 983 CB HIS A 127 -3.545 -22.776 8.862 1.00 45.13 C
+ATOM 984 CG HIS A 127 -2.517 -22.796 9.941 1.00 46.52 C
+ATOM 985 ND1 HIS A 127 -2.813 -23.102 11.252 1.00 47.89 N
+ATOM 986 CD2 HIS A 127 -1.178 -22.605 9.890 1.00 47.72 C
+ATOM 987 CE1 HIS A 127 -1.703 -23.068 11.967 1.00 49.05 C
+ATOM 988 NE2 HIS A 127 -0.698 -22.764 11.165 1.00 49.06 N
+ATOM 989 N PHE A 128 -1.893 -25.738 8.256 1.00 43.73 N
+ATOM 990 CA PHE A 128 -1.640 -27.025 8.871 1.00 43.89 C
+ATOM 991 C PHE A 128 -1.286 -26.850 10.351 1.00 43.14 C
+ATOM 992 O PHE A 128 -0.238 -26.322 10.688 1.00 42.68 O
+ATOM 993 CB PHE A 128 -0.554 -27.798 8.128 1.00 44.26 C
+ATOM 994 CG PHE A 128 -0.252 -29.137 8.734 1.00 45.50 C
+ATOM 995 CD1 PHE A 128 0.933 -29.350 9.422 1.00 46.84 C
+ATOM 996 CD2 PHE A 128 -1.157 -30.172 8.635 1.00 46.38 C
+ATOM 997 CE1 PHE A 128 1.220 -30.585 9.988 1.00 47.32 C
+ATOM 998 CE2 PHE A 128 -0.883 -31.412 9.204 1.00 47.62 C
+ATOM 999 CZ PHE A 128 0.308 -31.618 9.878 1.00 47.35 C
+ATOM 1000 N PHE A 129 -2.173 -27.309 11.223 1.00 42.66 N
+ATOM 1001 CA PHE A 129 -2.002 -27.135 12.667 1.00 42.46 C
+ATOM 1002 C PHE A 129 -1.152 -28.180 13.388 1.00 42.20 C
+ATOM 1003 O PHE A 129 -1.474 -29.362 13.392 1.00 41.59 O
+ATOM 1004 CB PHE A 129 -3.371 -27.049 13.324 1.00 41.90 C
+ATOM 1005 CG PHE A 129 -3.326 -26.881 14.816 1.00 41.09 C
+ATOM 1006 CD1 PHE A 129 -3.071 -25.640 15.381 1.00 38.69 C
+ATOM 1007 CD2 PHE A 129 -3.580 -27.961 15.652 1.00 38.75 C
+ATOM 1008 CE1 PHE A 129 -3.056 -25.482 16.752 1.00 36.58 C
+ATOM 1009 CE2 PHE A 129 -3.568 -27.808 17.017 1.00 39.10 C
+ATOM 1010 CZ PHE A 129 -3.302 -26.561 17.572 1.00 37.88 C
+ATOM 1011 N LYS A 130 -0.070 -27.729 14.008 1.00 42.55 N
+ATOM 1012 CA LYS A 130 0.773 -28.618 14.807 1.00 42.83 C
+ATOM 1013 C LYS A 130 0.401 -28.413 16.265 1.00 42.62 C
+ATOM 1014 O LYS A 130 0.651 -27.351 16.841 1.00 42.72 O
+ATOM 1015 CB LYS A 130 2.254 -28.290 14.620 1.00 43.25 C
+ATOM 1016 CG LYS A 130 2.906 -28.829 13.359 1.00 44.57 C
+ATOM 1017 CD LYS A 130 4.243 -28.123 13.121 1.00 48.01 C
+ATOM 1018 CE LYS A 130 4.793 -28.364 11.705 1.00 50.77 C
+ATOM 1019 NZ LYS A 130 5.839 -27.355 11.298 1.00 51.03 N
+ATOM 1020 N THR A 131 -0.193 -29.426 16.876 1.00 42.14 N
+ATOM 1021 CA THR A 131 -0.603 -29.284 18.261 1.00 41.95 C
+ATOM 1022 C THR A 131 0.552 -28.944 19.224 1.00 41.19 C
+ATOM 1023 O THR A 131 0.397 -28.120 20.128 1.00 40.79 O
+ATOM 1024 CB THR A 131 -1.347 -30.531 18.713 1.00 42.21 C
+ATOM 1025 OG1 THR A 131 -2.331 -30.858 17.728 1.00 43.51 O
+ATOM 1026 CG2 THR A 131 -2.186 -30.217 19.935 1.00 42.36 C
+ATOM 1027 N GLN A 132 1.704 -29.566 19.007 1.00 40.09 N
+ATOM 1028 CA GLN A 132 2.870 -29.355 19.861 1.00 39.24 C
+ATOM 1029 C GLN A 132 3.296 -27.893 20.010 1.00 37.73 C
+ATOM 1030 O GLN A 132 3.806 -27.507 21.053 1.00 37.54 O
+ATOM 1031 CB GLN A 132 4.050 -30.200 19.371 1.00 39.54 C
+ATOM 1032 CG GLN A 132 5.343 -29.953 20.129 1.00 41.65 C
+ATOM 1033 CD GLN A 132 5.243 -30.403 21.571 1.00 44.60 C
+ATOM 1034 OE1 GLN A 132 4.689 -31.480 21.860 1.00 46.18 O
+ATOM 1035 NE2 GLN A 132 5.762 -29.583 22.485 1.00 43.69 N
+ATOM 1036 N MET A 133 3.098 -27.092 18.971 1.00 36.08 N
+ATOM 1037 CA MET A 133 3.440 -25.669 19.013 1.00 34.74 C
+ATOM 1038 C MET A 133 2.662 -24.960 20.121 1.00 32.98 C
+ATOM 1039 O MET A 133 3.222 -24.165 20.876 1.00 32.39 O
+ATOM 1040 CB MET A 133 3.153 -24.997 17.655 1.00 35.06 C
+ATOM 1041 CG MET A 133 3.459 -23.488 17.587 1.00 38.05 C
+ATOM 1042 SD MET A 133 2.307 -22.333 18.488 1.00 41.88 S
+ATOM 1043 CE MET A 133 0.923 -22.260 17.355 1.00 41.27 C
+ATOM 1044 N LEU A 134 1.377 -25.270 20.231 1.00 31.19 N
+ATOM 1045 CA LEU A 134 0.512 -24.626 21.218 1.00 30.08 C
+ATOM 1046 C LEU A 134 0.826 -25.123 22.620 1.00 29.38 C
+ATOM 1047 O LEU A 134 0.908 -24.334 23.567 1.00 29.58 O
+ATOM 1048 CB LEU A 134 -0.975 -24.843 20.861 1.00 29.56 C
+ATOM 1049 CG LEU A 134 -1.998 -24.069 21.687 1.00 28.48 C
+ATOM 1050 CD1 LEU A 134 -1.693 -22.562 21.619 1.00 27.89 C
+ATOM 1051 CD2 LEU A 134 -3.427 -24.353 21.227 1.00 27.23 C
+ATOM 1052 N VAL A 135 1.004 -26.441 22.737 1.00 29.01 N
+ATOM 1053 CA VAL A 135 1.369 -27.066 24.002 1.00 28.78 C
+ATOM 1054 C VAL A 135 2.517 -26.277 24.625 1.00 28.26 C
+ATOM 1055 O VAL A 135 2.406 -25.789 25.735 1.00 28.27 O
+ATOM 1056 CB VAL A 135 1.807 -28.571 23.835 1.00 29.09 C
+ATOM 1057 CG1 VAL A 135 2.421 -29.099 25.126 1.00 28.24 C
+ATOM 1058 CG2 VAL A 135 0.643 -29.472 23.387 1.00 29.55 C
+ATOM 1059 N THR A 136 3.611 -26.143 23.884 1.00 27.78 N
+ATOM 1060 CA THR A 136 4.791 -25.432 24.366 1.00 28.21 C
+ATOM 1061 C THR A 136 4.488 -23.968 24.751 1.00 27.52 C
+ATOM 1062 O THR A 136 4.976 -23.471 25.780 1.00 27.50 O
+ATOM 1063 CB THR A 136 5.923 -25.510 23.324 1.00 28.60 C
+ATOM 1064 OG1 THR A 136 6.190 -26.887 23.015 1.00 30.30 O
+ATOM 1065 CG2 THR A 136 7.232 -25.028 23.923 1.00 27.84 C
+ATOM 1066 N GLN A 137 3.675 -23.299 23.934 1.00 26.42 N
+ATOM 1067 CA GLN A 137 3.246 -21.945 24.244 1.00 25.55 C
+ATOM 1068 C GLN A 137 2.712 -21.936 25.665 1.00 24.98 C
+ATOM 1069 O GLN A 137 3.176 -21.162 26.501 1.00 23.53 O
+ATOM 1070 CB GLN A 137 2.180 -21.467 23.257 1.00 25.99 C
+ATOM 1071 CG GLN A 137 2.736 -21.125 21.896 1.00 25.03 C
+ATOM 1072 CD GLN A 137 3.374 -19.771 21.905 1.00 26.09 C
+ATOM 1073 OE1 GLN A 137 2.692 -18.777 22.169 1.00 25.26 O
+ATOM 1074 NE2 GLN A 137 4.687 -19.717 21.658 1.00 23.19 N
+ATOM 1075 N PHE A 138 1.758 -22.823 25.934 1.00 24.71 N
+ATOM 1076 CA PHE A 138 1.219 -22.972 27.282 1.00 25.89 C
+ATOM 1077 C PHE A 138 2.283 -23.406 28.316 1.00 25.83 C
+ATOM 1078 O PHE A 138 2.221 -23.012 29.464 1.00 26.66 O
+ATOM 1079 CB PHE A 138 -0.009 -23.897 27.297 1.00 25.47 C
+ATOM 1080 CG PHE A 138 -1.288 -23.180 26.958 1.00 26.86 C
+ATOM 1081 CD1 PHE A 138 -1.583 -22.848 25.653 1.00 26.10 C
+ATOM 1082 CD2 PHE A 138 -2.167 -22.802 27.952 1.00 27.42 C
+ATOM 1083 CE1 PHE A 138 -2.743 -22.159 25.342 1.00 29.26 C
+ATOM 1084 CE2 PHE A 138 -3.327 -22.126 27.646 1.00 29.25 C
+ATOM 1085 CZ PHE A 138 -3.620 -21.806 26.342 1.00 28.86 C
+ATOM 1086 N GLU A 139 3.259 -24.191 27.893 1.00 25.53 N
+ATOM 1087 CA GLU A 139 4.321 -24.627 28.781 1.00 26.26 C
+ATOM 1088 C GLU A 139 5.175 -23.438 29.134 1.00 24.91 C
+ATOM 1089 O GLU A 139 5.608 -23.295 30.276 1.00 24.13 O
+ATOM 1090 CB GLU A 139 5.223 -25.661 28.091 1.00 26.88 C
+ATOM 1091 CG GLU A 139 5.069 -27.099 28.553 1.00 32.28 C
+ATOM 1092 CD GLU A 139 6.381 -27.883 28.427 1.00 37.55 C
+ATOM 1093 OE1 GLU A 139 7.205 -27.554 27.541 1.00 41.02 O
+ATOM 1094 OE2 GLU A 139 6.607 -28.822 29.224 1.00 38.89 O
+ATOM 1095 N THR A 140 5.440 -22.601 28.133 1.00 23.87 N
+ATOM 1096 CA THR A 140 6.275 -21.428 28.337 1.00 23.07 C
+ATOM 1097 C THR A 140 5.517 -20.354 29.106 1.00 22.52 C
+ATOM 1098 O THR A 140 6.100 -19.618 29.896 1.00 21.74 O
+ATOM 1099 CB THR A 140 6.770 -20.877 27.000 1.00 23.40 C
+ATOM 1100 OG1 THR A 140 7.173 -21.954 26.146 1.00 24.34 O
+ATOM 1101 CG2 THR A 140 8.054 -20.114 27.184 1.00 24.20 C
+ATOM 1102 N LEU A 141 4.209 -20.283 28.895 1.00 21.88 N
+ATOM 1103 CA LEU A 141 3.407 -19.243 29.535 1.00 21.56 C
+ATOM 1104 C LEU A 141 3.573 -19.242 31.053 1.00 21.13 C
+ATOM 1105 O LEU A 141 3.374 -20.258 31.705 1.00 20.47 O
+ATOM 1106 CB LEU A 141 1.919 -19.395 29.189 1.00 20.59 C
+ATOM 1107 CG LEU A 141 0.973 -18.461 29.957 1.00 22.61 C
+ATOM 1108 CD1 LEU A 141 1.134 -16.997 29.548 1.00 22.05 C
+ATOM 1109 CD2 LEU A 141 -0.461 -18.865 29.758 1.00 23.92 C
+ATOM 1110 N GLN A 142 3.943 -18.091 31.598 1.00 20.97 N
+ATOM 1111 CA GLN A 142 3.990 -17.900 33.040 1.00 20.72 C
+ATOM 1112 C GLN A 142 2.884 -16.892 33.298 1.00 20.84 C
+ATOM 1113 O GLN A 142 3.084 -15.695 33.140 1.00 20.10 O
+ATOM 1114 CB GLN A 142 5.364 -17.347 33.469 1.00 21.16 C
+ATOM 1115 CG GLN A 142 6.574 -18.299 33.179 1.00 20.23 C
+ATOM 1116 CD GLN A 142 7.963 -17.733 33.605 1.00 23.64 C
+ATOM 1117 OE1 GLN A 142 8.086 -16.563 34.023 1.00 20.65 O
+ATOM 1118 NE2 GLN A 142 9.014 -18.579 33.485 1.00 22.34 N
+ATOM 1119 N GLU A 143 1.707 -17.377 33.648 1.00 21.16 N
+ATOM 1120 CA GLU A 143 0.558 -16.502 33.825 1.00 22.99 C
+ATOM 1121 C GLU A 143 0.811 -15.417 34.865 1.00 23.32 C
+ATOM 1122 O GLU A 143 1.278 -15.712 35.939 1.00 23.48 O
+ATOM 1123 CB GLU A 143 -0.718 -17.287 34.182 1.00 22.70 C
+ATOM 1124 CG GLU A 143 -1.335 -18.049 33.024 1.00 23.65 C
+ATOM 1125 CD GLU A 143 -2.761 -18.454 33.299 1.00 24.01 C
+ATOM 1126 OE1 GLU A 143 -3.627 -18.114 32.483 1.00 24.03 O
+ATOM 1127 OE2 GLU A 143 -3.019 -19.073 34.350 1.00 25.93 O
+ATOM 1128 N PRO A 144 0.516 -14.169 34.516 1.00 23.84 N
+ATOM 1129 CA PRO A 144 0.674 -13.055 35.440 1.00 24.82 C
+ATOM 1130 C PRO A 144 -0.379 -13.197 36.496 1.00 25.42 C
+ATOM 1131 O PRO A 144 -1.554 -13.055 36.185 1.00 25.96 O
+ATOM 1132 CB PRO A 144 0.328 -11.826 34.591 1.00 25.14 C
+ATOM 1133 CG PRO A 144 0.310 -12.293 33.193 1.00 23.96 C
+ATOM 1134 CD PRO A 144 0.016 -13.736 33.207 1.00 23.36 C
+ATOM 1135 N GLY A 145 0.035 -13.499 37.711 1.00 25.75 N
+ATOM 1136 CA GLY A 145 -0.882 -13.563 38.817 1.00 26.78 C
+ATOM 1137 C GLY A 145 -1.207 -12.191 39.386 1.00 27.18 C
+ATOM 1138 O GLY A 145 -0.770 -11.141 38.879 1.00 26.27 O
+ATOM 1139 N ALA A 146 -1.987 -12.221 40.463 1.00 27.96 N
+ATOM 1140 CA ALA A 146 -2.445 -11.015 41.154 1.00 27.81 C
+ATOM 1141 C ALA A 146 -1.297 -10.152 41.663 1.00 27.32 C
+ATOM 1142 O ALA A 146 -1.429 -8.945 41.713 1.00 27.44 O
+ATOM 1143 CB ALA A 146 -3.380 -11.383 42.287 1.00 28.39 C
+ATOM 1144 N ASP A 147 -0.184 -10.767 42.045 1.00 26.61 N
+ATOM 1145 CA ASP A 147 0.979 -9.995 42.451 1.00 26.30 C
+ATOM 1146 C ASP A 147 1.488 -9.073 41.318 1.00 25.62 C
+ATOM 1147 O ASP A 147 2.238 -8.151 41.584 1.00 25.15 O
+ATOM 1148 CB ASP A 147 2.105 -10.918 42.884 1.00 26.91 C
+ATOM 1149 CG ASP A 147 2.845 -11.499 41.711 1.00 29.05 C
+ATOM 1150 OD1 ASP A 147 2.231 -12.263 40.946 1.00 30.47 O
+ATOM 1151 OD2 ASP A 147 4.036 -11.216 41.455 1.00 33.24 O
+ATOM 1152 N GLU A 148 1.125 -9.348 40.061 1.00 24.18 N
+ATOM 1153 CA GLU A 148 1.489 -8.440 38.963 1.00 23.44 C
+ATOM 1154 C GLU A 148 0.306 -7.451 38.777 1.00 23.14 C
+ATOM 1155 O GLU A 148 -0.621 -7.704 38.005 1.00 22.18 O
+ATOM 1156 CB GLU A 148 1.851 -9.203 37.677 1.00 22.76 C
+ATOM 1157 CG GLU A 148 3.272 -9.783 37.679 1.00 23.55 C
+ATOM 1158 CD GLU A 148 3.628 -10.614 36.455 1.00 23.36 C
+ATOM 1159 OE1 GLU A 148 3.936 -10.037 35.377 1.00 22.92 O
+ATOM 1160 OE2 GLU A 148 3.626 -11.861 36.574 1.00 22.92 O
+ATOM 1161 N THR A 149 0.370 -6.319 39.476 1.00 22.60 N
+ATOM 1162 CA THR A 149 -0.768 -5.400 39.572 1.00 23.71 C
+ATOM 1163 C THR A 149 -0.993 -4.413 38.455 1.00 23.73 C
+ATOM 1164 O THR A 149 -1.915 -3.613 38.545 1.00 24.05 O
+ATOM 1165 CB THR A 149 -0.699 -4.617 40.869 1.00 24.02 C
+ATOM 1166 OG1 THR A 149 0.465 -3.757 40.835 1.00 24.08 O
+ATOM 1167 CG2 THR A 149 -0.455 -5.609 42.059 1.00 24.68 C
+ATOM 1168 N ASP A 150 -0.147 -4.445 37.435 1.00 23.34 N
+ATOM 1169 CA ASP A 150 -0.323 -3.602 36.265 1.00 23.42 C
+ATOM 1170 C ASP A 150 -0.816 -4.497 35.117 1.00 23.67 C
+ATOM 1171 O ASP A 150 -0.654 -4.181 33.941 1.00 23.62 O
+ATOM 1172 CB ASP A 150 0.990 -2.909 35.881 1.00 23.29 C
+ATOM 1173 CG ASP A 150 2.149 -3.895 35.718 1.00 22.07 C
+ATOM 1174 OD1 ASP A 150 1.910 -5.107 35.881 1.00 21.39 O
+ATOM 1175 OD2 ASP A 150 3.325 -3.561 35.425 1.00 19.54 O
+ATOM 1176 N VAL A 151 -1.413 -5.624 35.471 1.00 23.37 N
+ATOM 1177 CA VAL A 151 -1.911 -6.541 34.467 1.00 23.32 C
+ATOM 1178 C VAL A 151 -3.409 -6.578 34.497 1.00 23.64 C
+ATOM 1179 O VAL A 151 -3.995 -6.886 35.522 1.00 25.28 O
+ATOM 1180 CB VAL A 151 -1.405 -7.970 34.702 1.00 22.83 C
+ATOM 1181 CG1 VAL A 151 -2.251 -8.984 33.922 1.00 21.71 C
+ATOM 1182 CG2 VAL A 151 0.046 -8.062 34.342 1.00 21.35 C
+ATOM 1183 N LEU A 152 -4.029 -6.244 33.381 1.00 23.74 N
+ATOM 1184 CA LEU A 152 -5.479 -6.351 33.255 1.00 24.33 C
+ATOM 1185 C LEU A 152 -5.705 -7.625 32.438 1.00 24.37 C
+ATOM 1186 O LEU A 152 -4.827 -8.050 31.684 1.00 24.10 O
+ATOM 1187 CB LEU A 152 -6.037 -5.137 32.511 1.00 24.34 C
+ATOM 1188 CG LEU A 152 -5.662 -3.747 33.052 1.00 25.22 C
+ATOM 1189 CD1 LEU A 152 -5.827 -2.674 31.987 1.00 26.32 C
+ATOM 1190 CD2 LEU A 152 -6.510 -3.396 34.256 1.00 24.95 C
+ATOM 1191 N VAL A 153 -6.868 -8.241 32.585 1.00 24.53 N
+ATOM 1192 CA VAL A 153 -7.114 -9.530 31.967 1.00 24.38 C
+ATOM 1193 C VAL A 153 -8.424 -9.462 31.249 1.00 24.38 C
+ATOM 1194 O VAL A 153 -9.366 -8.922 31.773 1.00 24.88 O
+ATOM 1195 CB VAL A 153 -7.234 -10.621 33.036 1.00 24.81 C
+ATOM 1196 CG1 VAL A 153 -7.346 -12.011 32.387 1.00 24.84 C
+ATOM 1197 CG2 VAL A 153 -6.087 -10.541 34.024 1.00 23.62 C
+ATOM 1198 N VAL A 154 -8.489 -10.020 30.053 1.00 24.61 N
+ATOM 1199 CA VAL A 154 -9.690 -9.944 29.249 1.00 24.58 C
+ATOM 1200 C VAL A 154 -10.035 -11.358 28.813 1.00 24.80 C
+ATOM 1201 O VAL A 154 -9.143 -12.105 28.428 1.00 24.04 O
+ATOM 1202 CB VAL A 154 -9.450 -9.038 28.010 1.00 24.77 C
+ATOM 1203 CG1 VAL A 154 -10.419 -9.364 26.909 1.00 24.72 C
+ATOM 1204 CG2 VAL A 154 -9.514 -7.552 28.380 1.00 24.21 C
+ATOM 1205 N ASP A 155 -11.314 -11.727 28.885 1.00 25.16 N
+ATOM 1206 CA ASP A 155 -11.775 -13.086 28.545 1.00 26.07 C
+ATOM 1207 C ASP A 155 -11.844 -13.313 27.056 1.00 26.13 C
+ATOM 1208 O ASP A 155 -12.678 -12.700 26.390 1.00 27.15 O
+ATOM 1209 CB ASP A 155 -13.200 -13.287 29.073 1.00 26.43 C
+ATOM 1210 CG ASP A 155 -13.747 -14.697 28.817 1.00 27.68 C
+ATOM 1211 OD1 ASP A 155 -13.229 -15.458 27.955 1.00 27.24 O
+ATOM 1212 OD2 ASP A 155 -14.713 -15.142 29.468 1.00 30.23 O
+ATOM 1213 N ILE A 156 -11.044 -14.216 26.516 1.00 25.84 N
+ATOM 1214 CA ILE A 156 -11.141 -14.451 25.083 1.00 26.81 C
+ATOM 1215 C ILE A 156 -12.289 -15.346 24.602 1.00 27.70 C
+ATOM 1216 O ILE A 156 -12.610 -15.324 23.415 1.00 27.25 O
+ATOM 1217 CB ILE A 156 -9.813 -14.935 24.455 1.00 26.54 C
+ATOM 1218 CG1 ILE A 156 -9.454 -16.326 24.926 1.00 26.98 C
+ATOM 1219 CG2 ILE A 156 -8.657 -13.969 24.716 1.00 27.42 C
+ATOM 1220 CD1 ILE A 156 -8.237 -16.843 24.198 1.00 25.03 C
+ATOM 1221 N ASP A 157 -12.904 -16.132 25.483 1.00 28.44 N
+ATOM 1222 CA ASP A 157 -13.975 -17.021 25.035 1.00 30.25 C
+ATOM 1223 C ASP A 157 -15.213 -16.194 24.698 1.00 30.72 C
+ATOM 1224 O ASP A 157 -16.255 -16.255 25.365 1.00 31.19 O
+ATOM 1225 CB ASP A 157 -14.303 -18.103 26.064 1.00 30.43 C
+ATOM 1226 CG ASP A 157 -15.102 -19.234 25.457 1.00 31.48 C
+ATOM 1227 OD1 ASP A 157 -15.199 -19.262 24.215 1.00 29.61 O
+ATOM 1228 OD2 ASP A 157 -15.659 -20.136 26.130 1.00 35.30 O
+ATOM 1229 N GLN A 158 -15.086 -15.460 23.612 1.00 31.08 N
+ATOM 1230 CA GLN A 158 -16.038 -14.426 23.260 1.00 31.65 C
+ATOM 1231 C GLN A 158 -15.768 -14.165 21.785 1.00 31.75 C
+ATOM 1232 O GLN A 158 -14.661 -14.399 21.316 1.00 31.83 O
+ATOM 1233 CB GLN A 158 -15.705 -13.185 24.115 1.00 32.00 C
+ATOM 1234 CG GLN A 158 -16.783 -12.116 24.288 1.00 32.94 C
+ATOM 1235 CD GLN A 158 -16.465 -11.162 25.436 1.00 33.60 C
+ATOM 1236 OE1 GLN A 158 -17.235 -10.245 25.732 1.00 33.44 O
+ATOM 1237 NE2 GLN A 158 -15.338 -11.386 26.087 1.00 33.12 N
+ATOM 1238 N PRO A 159 -16.775 -13.764 21.021 1.00 31.92 N
+ATOM 1239 CA PRO A 159 -16.540 -13.408 19.617 1.00 32.06 C
+ATOM 1240 C PRO A 159 -15.596 -12.187 19.538 1.00 31.47 C
+ATOM 1241 O PRO A 159 -15.507 -11.430 20.491 1.00 30.83 O
+ATOM 1242 CB PRO A 159 -17.945 -13.022 19.093 1.00 32.38 C
+ATOM 1243 CG PRO A 159 -18.937 -13.529 20.109 1.00 32.82 C
+ATOM 1244 CD PRO A 159 -18.189 -13.623 21.425 1.00 32.17 C
+ATOM 1245 N LEU A 160 -14.925 -11.991 18.412 1.00 31.65 N
+ATOM 1246 CA LEU A 160 -13.978 -10.880 18.283 1.00 32.00 C
+ATOM 1247 C LEU A 160 -14.476 -9.543 18.840 1.00 32.39 C
+ATOM 1248 O LEU A 160 -13.752 -8.857 19.570 1.00 32.69 O
+ATOM 1249 CB LEU A 160 -13.535 -10.702 16.834 1.00 31.82 C
+ATOM 1250 CG LEU A 160 -12.659 -9.461 16.633 1.00 31.21 C
+ATOM 1251 CD1 LEU A 160 -11.376 -9.588 17.444 1.00 31.50 C
+ATOM 1252 CD2 LEU A 160 -12.331 -9.265 15.174 1.00 30.42 C
+ATOM 1253 N GLU A 161 -15.713 -9.179 18.509 1.00 32.79 N
+ATOM 1254 CA GLU A 161 -16.302 -7.929 18.986 1.00 33.36 C
+ATOM 1255 C GLU A 161 -16.294 -7.795 20.502 1.00 32.63 C
+ATOM 1256 O GLU A 161 -16.136 -6.699 21.029 1.00 33.14 O
+ATOM 1257 CB GLU A 161 -17.750 -7.803 18.504 1.00 33.90 C
+ATOM 1258 CG GLU A 161 -18.037 -8.629 17.268 1.00 36.41 C
+ATOM 1259 CD GLU A 161 -17.223 -8.166 16.094 1.00 39.78 C
+ATOM 1260 OE1 GLU A 161 -16.355 -7.296 16.306 1.00 44.07 O
+ATOM 1261 OE2 GLU A 161 -17.441 -8.665 14.979 1.00 39.48 O
+ATOM 1262 N GLY A 162 -16.488 -8.903 21.203 1.00 32.13 N
+ATOM 1263 CA GLY A 162 -16.538 -8.883 22.654 1.00 31.48 C
+ATOM 1264 C GLY A 162 -15.194 -8.600 23.292 1.00 30.89 C
+ATOM 1265 O GLY A 162 -15.073 -7.683 24.117 1.00 31.45 O
+ATOM 1266 N VAL A 163 -14.180 -9.368 22.905 1.00 30.26 N
+ATOM 1267 CA VAL A 163 -12.833 -9.150 23.417 1.00 30.08 C
+ATOM 1268 C VAL A 163 -12.359 -7.738 23.121 1.00 29.10 C
+ATOM 1269 O VAL A 163 -11.698 -7.132 23.948 1.00 29.83 O
+ATOM 1270 CB VAL A 163 -11.832 -10.181 22.841 1.00 30.21 C
+ATOM 1271 CG1 VAL A 163 -10.425 -9.875 23.328 1.00 30.35 C
+ATOM 1272 CG2 VAL A 163 -12.247 -11.608 23.206 1.00 31.36 C
+ATOM 1273 N VAL A 164 -12.682 -7.252 21.927 1.00 29.40 N
+ATOM 1274 CA VAL A 164 -12.409 -5.878 21.519 1.00 29.59 C
+ATOM 1275 C VAL A 164 -13.105 -4.938 22.493 1.00 29.92 C
+ATOM 1276 O VAL A 164 -12.517 -3.959 22.952 1.00 29.52 O
+ATOM 1277 CB VAL A 164 -12.951 -5.606 20.088 1.00 30.18 C
+ATOM 1278 CG1 VAL A 164 -12.808 -4.119 19.689 1.00 30.01 C
+ATOM 1279 CG2 VAL A 164 -12.255 -6.485 19.076 1.00 29.16 C
+ATOM 1280 N ALA A 165 -14.354 -5.258 22.828 1.00 29.90 N
+ATOM 1281 CA ALA A 165 -15.099 -4.404 23.750 1.00 30.40 C
+ATOM 1282 C ALA A 165 -14.490 -4.488 25.137 1.00 29.93 C
+ATOM 1283 O ALA A 165 -14.158 -3.473 25.728 1.00 30.30 O
+ATOM 1284 CB ALA A 165 -16.580 -4.749 23.777 1.00 30.44 C
+ATOM 1285 N SER A 166 -14.326 -5.702 25.649 1.00 29.66 N
+ATOM 1286 CA SER A 166 -13.694 -5.908 26.947 1.00 28.82 C
+ATOM 1287 C SER A 166 -12.328 -5.216 27.026 1.00 28.62 C
+ATOM 1288 O SER A 166 -11.944 -4.643 28.066 1.00 28.05 O
+ATOM 1289 CB SER A 166 -13.528 -7.395 27.190 1.00 29.26 C
+ATOM 1290 OG SER A 166 -14.779 -7.997 27.459 1.00 30.07 O
+ATOM 1291 N THR A 167 -11.596 -5.258 25.920 1.00 28.12 N
+ATOM 1292 CA THR A 167 -10.307 -4.612 25.901 1.00 28.72 C
+ATOM 1293 C THR A 167 -10.510 -3.108 26.014 1.00 28.95 C
+ATOM 1294 O THR A 167 -9.828 -2.428 26.783 1.00 28.05 O
+ATOM 1295 CB THR A 167 -9.525 -4.963 24.646 1.00 28.22 C
+ATOM 1296 OG1 THR A 167 -9.228 -6.358 24.663 1.00 27.93 O
+ATOM 1297 CG2 THR A 167 -8.139 -4.288 24.685 1.00 28.41 C
+ATOM 1298 N ILE A 168 -11.454 -2.591 25.243 1.00 30.07 N
+ATOM 1299 CA ILE A 168 -11.759 -1.174 25.347 1.00 31.25 C
+ATOM 1300 C ILE A 168 -12.182 -0.838 26.771 1.00 31.86 C
+ATOM 1301 O ILE A 168 -11.633 0.102 27.369 1.00 31.58 O
+ATOM 1302 CB ILE A 168 -12.781 -0.732 24.297 1.00 31.46 C
+ATOM 1303 CG1 ILE A 168 -12.055 -0.415 22.988 1.00 31.07 C
+ATOM 1304 CG2 ILE A 168 -13.500 0.497 24.752 1.00 32.44 C
+ATOM 1305 CD1 ILE A 168 -12.846 -0.735 21.750 1.00 30.54 C
+ATOM 1306 N GLU A 169 -13.082 -1.643 27.344 1.00 32.85 N
+ATOM 1307 CA GLU A 169 -13.548 -1.393 28.714 1.00 34.73 C
+ATOM 1308 C GLU A 169 -12.356 -1.327 29.651 1.00 35.27 C
+ATOM 1309 O GLU A 169 -12.235 -0.432 30.486 1.00 34.72 O
+ATOM 1310 CB GLU A 169 -14.512 -2.477 29.224 1.00 34.96 C
+ATOM 1311 CG GLU A 169 -15.495 -3.027 28.198 1.00 37.80 C
+ATOM 1312 CD GLU A 169 -16.583 -3.912 28.818 1.00 42.01 C
+ATOM 1313 OE1 GLU A 169 -17.116 -3.517 29.888 1.00 43.24 O
+ATOM 1314 OE2 GLU A 169 -16.921 -4.988 28.235 1.00 41.24 O
+ATOM 1315 N VAL A 170 -11.475 -2.300 29.493 1.00 36.15 N
+ATOM 1316 CA VAL A 170 -10.304 -2.401 30.322 1.00 37.51 C
+ATOM 1317 C VAL A 170 -9.415 -1.171 30.191 1.00 37.78 C
+ATOM 1318 O VAL A 170 -8.875 -0.688 31.178 1.00 37.02 O
+ATOM 1319 CB VAL A 170 -9.548 -3.686 29.972 1.00 37.79 C
+ATOM 1320 CG1 VAL A 170 -8.121 -3.603 30.398 1.00 37.98 C
+ATOM 1321 CG2 VAL A 170 -10.247 -4.862 30.631 1.00 39.00 C
+ATOM 1322 N ILE A 171 -9.292 -0.656 28.977 1.00 39.18 N
+ATOM 1323 CA ILE A 171 -8.475 0.528 28.739 1.00 41.07 C
+ATOM 1324 C ILE A 171 -9.116 1.774 29.341 1.00 43.24 C
+ATOM 1325 O ILE A 171 -8.434 2.578 29.981 1.00 43.48 O
+ATOM 1326 CB ILE A 171 -8.239 0.742 27.225 1.00 40.67 C
+ATOM 1327 CG1 ILE A 171 -7.377 -0.382 26.651 1.00 38.66 C
+ATOM 1328 CG2 ILE A 171 -7.611 2.121 26.963 1.00 40.05 C
+ATOM 1329 CD1 ILE A 171 -6.917 -0.126 25.249 1.00 36.66 C
+ATOM 1330 N LYS A 172 -10.426 1.920 29.148 1.00 45.61 N
+ATOM 1331 CA LYS A 172 -11.163 3.090 29.641 1.00 48.51 C
+ATOM 1332 C LYS A 172 -11.441 3.104 31.143 1.00 50.16 C
+ATOM 1333 O LYS A 172 -11.599 4.163 31.730 1.00 50.23 O
+ATOM 1334 CB LYS A 172 -12.472 3.279 28.862 1.00 48.53 C
+ATOM 1335 CG LYS A 172 -12.313 4.060 27.563 1.00 49.39 C
+ATOM 1336 CD LYS A 172 -13.615 4.111 26.779 1.00 51.55 C
+ATOM 1337 CE LYS A 172 -13.425 4.840 25.452 1.00 53.36 C
+ATOM 1338 NZ LYS A 172 -14.306 4.284 24.383 1.00 54.44 N
+ATOM 1339 N LYS A 173 -11.499 1.922 31.748 1.00 52.96 N
+ATOM 1340 CA LYS A 173 -11.732 1.743 33.188 1.00 55.62 C
+ATOM 1341 C LYS A 173 -10.859 2.694 34.007 1.00 56.94 C
+ATOM 1342 O LYS A 173 -10.924 2.713 35.243 1.00 57.66 O
+ATOM 1343 CB LYS A 173 -11.339 0.313 33.573 1.00 55.96 C
+ATOM 1344 CG LYS A 173 -12.341 -0.496 34.385 1.00 57.94 C
+ATOM 1345 CD LYS A 173 -11.855 -1.962 34.482 1.00 59.23 C
+ATOM 1346 CE LYS A 173 -12.885 -2.885 35.138 1.00 60.77 C
+ATOM 1347 NZ LYS A 173 -12.621 -4.345 34.875 1.00 60.35 N
+ATOM 1348 N GLY A 174 -10.017 3.455 33.317 1.00 58.18 N
+ATOM 1349 CA GLY A 174 -9.082 4.356 33.966 1.00 59.55 C
+ATOM 1350 C GLY A 174 -7.656 4.027 33.555 1.00 60.31 C
+ATOM 1351 O GLY A 174 -7.097 4.627 32.629 1.00 60.91 O
+TER 1352 GLY A 174
+HETATM 1353 MG MG A1001 -0.291 -12.139 15.940 1.00 25.12 MG
+HETATM 1354 PG ATP A 302 0.303 -14.897 16.967 1.00 27.28 P
+HETATM 1355 O1G ATP A 302 0.739 -16.269 16.695 1.00 27.81 O
+HETATM 1356 O2G ATP A 302 0.899 -14.379 18.294 1.00 30.64 O
+HETATM 1357 O3G ATP A 302 0.743 -13.936 15.877 1.00 23.38 O
+HETATM 1358 PB ATP A 302 -2.108 -13.793 17.800 1.00 18.75 P
+HETATM 1359 O1B ATP A 302 -1.686 -12.482 17.296 1.00 17.50 O
+HETATM 1360 O2B ATP A 302 -2.228 -13.812 19.330 1.00 22.40 O
+HETATM 1361 O3B ATP A 302 -1.266 -15.000 17.218 1.00 23.79 O
+HETATM 1362 PA ATP A 302 -4.353 -13.657 16.036 1.00 24.32 P
+HETATM 1363 O1A ATP A 302 -4.591 -12.246 16.298 1.00 24.57 O
+HETATM 1364 O2A ATP A 302 -3.607 -13.789 14.707 1.00 24.21 O
+HETATM 1365 O3A ATP A 302 -3.540 -14.295 17.267 1.00 23.34 O
+HETATM 1366 O5' ATP A 302 -5.694 -14.548 16.177 1.00 26.65 O
+HETATM 1367 C5' ATP A 302 -5.750 -15.952 15.995 1.00 26.53 C
+HETATM 1368 C4' ATP A 302 -6.852 -16.313 14.979 1.00 28.62 C
+HETATM 1369 O4' ATP A 302 -8.140 -16.323 15.553 1.00 28.06 O
+HETATM 1370 C3' ATP A 302 -6.951 -15.312 13.842 1.00 29.88 C
+HETATM 1371 O3' ATP A 302 -7.415 -16.042 12.747 1.00 33.14 O
+HETATM 1372 C2' ATP A 302 -8.039 -14.356 14.255 1.00 31.45 C
+HETATM 1373 O2' ATP A 302 -8.769 -13.867 13.151 1.00 34.25 O
+HETATM 1374 C1' ATP A 302 -8.930 -15.246 15.079 1.00 30.67 C
+HETATM 1375 N9 ATP A 302 -9.459 -14.575 16.270 1.00 32.02 N
+HETATM 1376 C8 ATP A 302 -8.820 -13.756 17.160 1.00 32.06 C
+HETATM 1377 N7 ATP A 302 -9.695 -13.418 18.144 1.00 31.52 N
+HETATM 1378 C5 ATP A 302 -10.873 -14.025 17.901 1.00 32.03 C
+HETATM 1379 C6 ATP A 302 -12.097 -14.037 18.556 1.00 31.13 C
+HETATM 1380 N6 ATP A 302 -12.237 -13.576 19.792 1.00 29.94 N
+HETATM 1381 N1 ATP A 302 -13.118 -14.788 18.023 1.00 31.81 N
+HETATM 1382 C2 ATP A 302 -12.951 -15.512 16.866 1.00 31.70 C
+HETATM 1383 N3 ATP A 302 -11.744 -15.481 16.207 1.00 32.79 N
+HETATM 1384 C4 ATP A 302 -10.726 -14.761 16.725 1.00 33.02 C
+HETATM 1385 O HOH A1002 3.449 -10.106 16.968 1.00 18.15 O
+HETATM 1386 O HOH A1003 -3.994 -30.626 11.578 1.00 28.70 O
+HETATM 1387 O HOH A1004 10.131 -15.322 34.217 1.00 18.41 O
+HETATM 1388 O HOH A1005 6.914 -14.328 24.919 1.00 15.64 O
+HETATM 1389 O HOH A1006 0.688 6.226 25.342 1.00 18.35 O
+HETATM 1390 O HOH A1007 13.290 5.484 22.727 1.00 27.04 O
+HETATM 1391 O HOH A1008 -14.867 -22.434 2.985 1.00 47.60 O
+HETATM 1392 O HOH A1009 2.680 -13.338 38.693 1.00 20.65 O
+HETATM 1393 O HOH A1010 11.175 0.800 36.548 1.00 35.20 O
+HETATM 1394 O HOH A1011 -1.381 -12.857 13.973 1.00 15.88 O
+HETATM 1395 O HOH A1012 3.603 -5.332 39.827 1.00 21.69 O
+HETATM 1396 O HOH A1013 -4.249 -18.047 27.963 1.00 13.22 O
+HETATM 1397 O HOH A1014 -13.229 -9.794 29.581 1.00 18.85 O
+HETATM 1398 O HOH A1015 13.848 -4.337 14.022 1.00 17.13 O
+HETATM 1399 O HOH A1016 -2.998 -16.433 26.084 1.00 19.64 O
+HETATM 1400 O HOH A1017 -6.219 -31.421 21.445 1.00 47.49 O
+HETATM 1401 O HOH A1018 1.068 -11.524 17.151 1.00 30.14 O
+HETATM 1402 O HOH A1019 11.476 -20.147 20.181 1.00 38.19 O
+HETATM 1403 O HOH A1020 21.520 -3.814 5.749 1.00 33.31 O
+HETATM 1404 O HOH A1021 7.401 5.456 29.658 1.00 24.38 O
+HETATM 1405 O HOH A1022 10.216 -2.426 37.164 1.00 31.48 O
+HETATM 1406 O HOH A1023 -5.663 5.105 28.884 1.00 24.97 O
+HETATM 1407 O HOH A1024 0.537 4.037 15.327 1.00 25.06 O
+HETATM 1408 O HOH A1025 -19.963 -3.066 25.295 1.00 36.69 O
+HETATM 1409 O HOH A1026 7.918 -20.989 31.846 1.00 26.08 O
+HETATM 1410 O HOH A1027 6.642 14.276 30.199 1.00 36.73 O
+HETATM 1411 O HOH A1028 2.928 2.411 14.476 1.00 24.63 O
+HETATM 1412 O HOH A1029 -2.654 8.352 19.505 1.00 21.06 O
+HETATM 1413 O HOH A1030 -8.655 -13.284 35.463 1.00 31.94 O
+HETATM 1414 O HOH A1031 11.829 3.291 29.750 1.00 30.78 O
+HETATM 1415 O HOH A1032 5.779 -12.339 13.434 1.00 29.33 O
+HETATM 1416 O HOH A1033 0.823 -11.572 14.445 1.00 13.33 O
+HETATM 1417 O HOH A1034 -6.499 9.701 19.774 1.00 40.15 O
+HETATM 1418 O HOH A1035 16.148 -3.970 17.424 1.00 19.59 O
+HETATM 1419 O HOH A1036 -10.816 -19.771 27.141 1.00 28.98 O
+HETATM 1420 O HOH A1037 -2.862 10.968 21.788 1.00 32.02 O
+HETATM 1421 O HOH A1038 -4.106 7.603 28.946 1.00 36.33 O
+HETATM 1422 O HOH A1039 -8.626 -7.450 34.882 1.00 34.72 O
+HETATM 1423 O HOH A1040 1.757 -20.139 34.582 1.00 32.14 O
+HETATM 1424 O HOH A1041 0.186 -7.791 15.414 1.00 26.16 O
+HETATM 1425 O HOH A1042 -12.340 -8.566 30.843 1.00 31.29 O
+HETATM 1426 O HOH A1043 -16.132 -0.594 25.615 1.00 36.83 O
+HETATM 1427 O HOH A1044 21.738 -8.126 25.594 1.00 35.22 O
+HETATM 1428 O HOH A1045 -15.523 -13.436 15.765 1.00 33.31 O
+HETATM 1429 O HOH A1046 3.651 6.492 35.574 1.00 23.08 O
+HETATM 1430 O HOH A1047 6.397 9.625 19.770 1.00 43.25 O
+HETATM 1431 O HOH A1048 22.183 -10.752 20.213 1.00 22.65 O
+HETATM 1432 O HOH A1049 4.036 -1.114 35.130 1.00 20.70 O
+HETATM 1433 O HOH A1050 22.553 -13.706 16.315 1.00 38.01 O
+HETATM 1434 O HOH A1051 11.727 -18.335 34.650 1.00 32.45 O
+HETATM 1435 O HOH A1052 3.131 15.914 23.254 1.00 40.54 O
+HETATM 1436 O HOH A1053 15.285 0.474 30.274 1.00 31.60 O
+HETATM 1437 O HOH A1054 -13.593 -20.226 10.507 1.00 40.24 O
+HETATM 1438 O HOH A1055 8.416 -12.445 18.151 1.00 26.50 O
+HETATM 1439 O HOH A1056 -3.914 8.225 22.200 1.00 18.97 O
+HETATM 1440 O HOH A1057 5.313 -11.662 20.561 1.00 24.21 O
+HETATM 1441 O HOH A1058 4.587 13.981 26.169 1.00 32.55 O
+HETATM 1442 O HOH A1059 -3.031 -9.009 37.994 1.00 35.66 O
+HETATM 1443 O HOH A1060 -0.354 8.030 16.362 1.00 31.45 O
+HETATM 1444 O HOH A1061 3.925 -4.976 42.272 1.00 26.12 O
+ATOM 1445 N THR B 3 17.047 -14.010 2.748 1.00 43.42 N
+ATOM 1446 CA THR B 3 16.207 -13.356 3.811 1.00 43.25 C
+ATOM 1447 C THR B 3 15.284 -12.274 3.266 1.00 42.65 C
+ATOM 1448 O THR B 3 14.232 -12.016 3.843 1.00 42.64 O
+ATOM 1449 CB THR B 3 17.071 -12.782 4.953 1.00 43.38 C
+ATOM 1450 OG1 THR B 3 17.782 -13.840 5.609 1.00 43.67 O
+ATOM 1451 CG2 THR B 3 16.173 -12.273 6.056 1.00 43.82 C
+ATOM 1452 N THR B 4 15.677 -11.629 2.172 1.00 42.14 N
+ATOM 1453 CA THR B 4 14.818 -10.626 1.554 1.00 41.34 C
+ATOM 1454 C THR B 4 13.707 -11.331 0.804 1.00 41.24 C
+ATOM 1455 O THR B 4 13.962 -12.003 -0.196 1.00 41.39 O
+ATOM 1456 CB THR B 4 15.596 -9.751 0.559 1.00 41.38 C
+ATOM 1457 OG1 THR B 4 16.466 -8.859 1.268 1.00 42.84 O
+ATOM 1458 CG2 THR B 4 14.639 -8.797 -0.160 1.00 40.30 C
+ATOM 1459 N ASN B 5 12.474 -11.219 1.277 1.00 40.70 N
+ATOM 1460 CA ASN B 5 11.397 -11.856 0.541 1.00 40.48 C
+ATOM 1461 C ASN B 5 10.985 -10.974 -0.629 1.00 40.10 C
+ATOM 1462 O ASN B 5 10.088 -10.140 -0.507 1.00 39.89 O
+ATOM 1463 CB ASN B 5 10.211 -12.212 1.436 1.00 40.46 C
+ATOM 1464 CG ASN B 5 9.245 -13.163 0.761 1.00 40.88 C
+ATOM 1465 OD1 ASN B 5 9.114 -13.162 -0.460 1.00 42.20 O
+ATOM 1466 ND2 ASN B 5 8.562 -13.978 1.553 1.00 41.87 N
+ATOM 1467 N HIS B 6 11.653 -11.178 -1.761 1.00 39.27 N
+ATOM 1468 CA HIS B 6 11.436 -10.362 -2.949 1.00 38.99 C
+ATOM 1469 C HIS B 6 9.980 -10.311 -3.453 1.00 38.61 C
+ATOM 1470 O HIS B 6 9.659 -9.535 -4.335 1.00 38.31 O
+ATOM 1471 CB HIS B 6 12.417 -10.766 -4.070 1.00 38.85 C
+ATOM 1472 CG HIS B 6 13.864 -10.531 -3.734 1.00 38.17 C
+ATOM 1473 ND1 HIS B 6 14.717 -11.549 -3.347 1.00 38.44 N
+ATOM 1474 CD2 HIS B 6 14.611 -9.399 -3.739 1.00 36.73 C
+ATOM 1475 CE1 HIS B 6 15.922 -11.050 -3.117 1.00 38.73 C
+ATOM 1476 NE2 HIS B 6 15.887 -9.749 -3.352 1.00 36.50 N
+ATOM 1477 N ASP B 7 9.105 -11.139 -2.896 1.00 38.71 N
+ATOM 1478 CA ASP B 7 7.696 -11.120 -3.295 1.00 38.90 C
+ATOM 1479 C ASP B 7 6.845 -10.226 -2.386 1.00 38.26 C
+ATOM 1480 O ASP B 7 5.684 -9.938 -2.678 1.00 38.24 O
+ATOM 1481 CB ASP B 7 7.122 -12.538 -3.320 1.00 39.91 C
+ATOM 1482 CG ASP B 7 7.540 -13.310 -4.557 1.00 42.10 C
+ATOM 1483 OD1 ASP B 7 7.187 -12.873 -5.678 1.00 43.75 O
+ATOM 1484 OD2 ASP B 7 8.235 -14.350 -4.504 1.00 45.28 O
+ATOM 1485 N HIS B 8 7.436 -9.801 -1.274 1.00 37.06 N
+ATOM 1486 CA HIS B 8 6.779 -8.917 -0.323 1.00 35.83 C
+ATOM 1487 C HIS B 8 7.273 -7.480 -0.542 1.00 34.45 C
+ATOM 1488 O HIS B 8 8.405 -7.277 -0.967 1.00 34.08 O
+ATOM 1489 CB HIS B 8 7.104 -9.396 1.098 1.00 35.89 C
+ATOM 1490 CG HIS B 8 6.379 -10.648 1.498 1.00 36.70 C
+ATOM 1491 ND1 HIS B 8 6.662 -11.336 2.659 1.00 37.57 N
+ATOM 1492 CD2 HIS B 8 5.367 -11.317 0.900 1.00 36.93 C
+ATOM 1493 CE1 HIS B 8 5.854 -12.375 2.756 1.00 36.77 C
+ATOM 1494 NE2 HIS B 8 5.052 -12.378 1.708 1.00 37.70 N
+ATOM 1495 N HIS B 9 6.453 -6.479 -0.238 1.00 32.80 N
+ATOM 1496 CA HIS B 9 6.906 -5.096 -0.436 1.00 31.20 C
+ATOM 1497 C HIS B 9 6.735 -4.149 0.767 1.00 29.75 C
+ATOM 1498 O HIS B 9 5.885 -4.376 1.629 1.00 29.72 O
+ATOM 1499 CB HIS B 9 6.230 -4.498 -1.667 1.00 31.19 C
+ATOM 1500 CG HIS B 9 7.116 -3.572 -2.432 1.00 31.39 C
+ATOM 1501 ND1 HIS B 9 7.934 -4.008 -3.451 1.00 30.97 N
+ATOM 1502 CD2 HIS B 9 7.338 -2.238 -2.312 1.00 30.93 C
+ATOM 1503 CE1 HIS B 9 8.618 -2.982 -3.932 1.00 30.03 C
+ATOM 1504 NE2 HIS B 9 8.275 -1.898 -3.259 1.00 31.02 N
+ATOM 1505 N ILE B 10 7.562 -3.107 0.819 1.00 27.86 N
+ATOM 1506 CA ILE B 10 7.481 -2.090 1.867 1.00 26.52 C
+ATOM 1507 C ILE B 10 7.302 -0.723 1.212 1.00 25.70 C
+ATOM 1508 O ILE B 10 8.009 -0.399 0.252 1.00 25.52 O
+ATOM 1509 CB ILE B 10 8.764 -2.063 2.727 1.00 26.91 C
+ATOM 1510 CG1 ILE B 10 8.990 -3.404 3.416 1.00 26.17 C
+ATOM 1511 CG2 ILE B 10 8.729 -0.925 3.764 1.00 25.73 C
+ATOM 1512 CD1 ILE B 10 10.449 -3.662 3.651 1.00 24.37 C
+ATOM 1513 N TYR B 11 6.352 0.058 1.721 1.00 24.36 N
+ATOM 1514 CA TYR B 11 6.094 1.377 1.205 1.00 23.67 C
+ATOM 1515 C TYR B 11 6.301 2.375 2.337 1.00 23.63 C
+ATOM 1516 O TYR B 11 5.703 2.266 3.412 1.00 23.24 O
+ATOM 1517 CB TYR B 11 4.677 1.492 0.623 1.00 23.56 C
+ATOM 1518 CG TYR B 11 4.403 0.522 -0.514 1.00 24.16 C
+ATOM 1519 CD1 TYR B 11 3.699 -0.646 -0.293 1.00 23.48 C
+ATOM 1520 CD2 TYR B 11 4.869 0.772 -1.800 1.00 24.37 C
+ATOM 1521 CE1 TYR B 11 3.451 -1.539 -1.318 1.00 26.55 C
+ATOM 1522 CE2 TYR B 11 4.643 -0.121 -2.834 1.00 27.13 C
+ATOM 1523 CZ TYR B 11 3.918 -1.275 -2.587 1.00 27.76 C
+ATOM 1524 OH TYR B 11 3.668 -2.177 -3.590 1.00 27.18 O
+ATOM 1525 N VAL B 12 7.189 3.332 2.093 1.00 23.24 N
+ATOM 1526 CA VAL B 12 7.462 4.382 3.041 1.00 22.68 C
+ATOM 1527 C VAL B 12 6.674 5.612 2.648 1.00 23.69 C
+ATOM 1528 O VAL B 12 7.068 6.332 1.728 1.00 23.89 O
+ATOM 1529 CB VAL B 12 8.931 4.791 3.001 1.00 22.53 C
+ATOM 1530 CG1 VAL B 12 9.168 5.938 3.978 1.00 21.73 C
+ATOM 1531 CG2 VAL B 12 9.848 3.589 3.298 1.00 20.70 C
+ATOM 1532 N LEU B 13 5.559 5.863 3.318 1.00 23.99 N
+ATOM 1533 CA LEU B 13 4.780 7.056 3.012 1.00 24.33 C
+ATOM 1534 C LEU B 13 5.607 8.248 3.512 1.00 24.07 C
+ATOM 1535 O LEU B 13 5.924 8.318 4.688 1.00 22.32 O
+ATOM 1536 CB LEU B 13 3.439 7.031 3.733 1.00 24.89 C
+ATOM 1537 CG LEU B 13 2.207 6.380 3.107 1.00 27.75 C
+ATOM 1538 CD1 LEU B 13 1.765 7.199 1.892 1.00 29.75 C
+ATOM 1539 CD2 LEU B 13 2.489 4.942 2.739 1.00 29.21 C
+ATOM 1540 N MET B 14 5.931 9.178 2.611 1.00 24.20 N
+ATOM 1541 CA MET B 14 6.786 10.326 2.919 1.00 24.20 C
+ATOM 1542 C MET B 14 6.098 11.620 2.500 1.00 24.35 C
+ATOM 1543 O MET B 14 5.042 11.600 1.868 1.00 25.33 O
+ATOM 1544 CB MET B 14 8.141 10.205 2.218 1.00 23.71 C
+ATOM 1545 CG MET B 14 8.031 10.247 0.701 1.00 23.68 C
+ATOM 1546 SD MET B 14 9.614 10.286 -0.147 1.00 25.78 S
+ATOM 1547 CE MET B 14 10.148 11.982 0.212 1.00 23.84 C
+ATOM 1548 N GLY B 15 6.707 12.746 2.840 1.00 24.56 N
+ATOM 1549 CA GLY B 15 6.088 14.036 2.595 1.00 24.42 C
+ATOM 1550 C GLY B 15 6.309 14.906 3.817 1.00 24.18 C
+ATOM 1551 O GLY B 15 6.669 14.398 4.881 1.00 23.18 O
+ATOM 1552 N VAL B 16 6.100 16.206 3.669 1.00 24.18 N
+ATOM 1553 CA VAL B 16 6.345 17.120 4.765 1.00 24.80 C
+ATOM 1554 C VAL B 16 5.259 17.004 5.811 1.00 25.25 C
+ATOM 1555 O VAL B 16 4.253 16.321 5.611 1.00 24.80 O
+ATOM 1556 CB VAL B 16 6.351 18.585 4.309 1.00 24.69 C
+ATOM 1557 CG1 VAL B 16 7.484 18.864 3.338 1.00 24.44 C
+ATOM 1558 CG2 VAL B 16 5.002 18.956 3.721 1.00 24.12 C
+ATOM 1559 N SER B 17 5.456 17.720 6.914 1.00 25.73 N
+ATOM 1560 CA SER B 17 4.489 17.721 8.001 1.00 26.08 C
+ATOM 1561 C SER B 17 3.179 18.268 7.495 1.00 25.94 C
+ATOM 1562 O SER B 17 3.133 19.348 6.929 1.00 26.04 O
+ATOM 1563 CB SER B 17 5.010 18.558 9.176 1.00 26.11 C
+ATOM 1564 OG SER B 17 4.124 18.517 10.284 1.00 26.25 O
+ATOM 1565 N GLY B 18 2.106 17.511 7.689 1.00 26.77 N
+ATOM 1566 CA GLY B 18 0.795 17.945 7.241 1.00 26.44 C
+ATOM 1567 C GLY B 18 0.400 17.453 5.851 1.00 26.99 C
+ATOM 1568 O GLY B 18 -0.702 17.760 5.357 1.00 26.57 O
+ATOM 1569 N SER B 19 1.273 16.678 5.213 1.00 26.18 N
+ATOM 1570 CA SER B 19 0.942 16.163 3.888 1.00 25.61 C
+ATOM 1571 C SER B 19 -0.109 15.059 3.956 1.00 25.84 C
+ATOM 1572 O SER B 19 -0.780 14.787 2.952 1.00 25.98 O
+ATOM 1573 CB SER B 19 2.184 15.692 3.140 1.00 25.48 C
+ATOM 1574 OG SER B 19 2.892 14.734 3.898 1.00 24.21 O
+ATOM 1575 N GLY B 20 -0.240 14.432 5.128 1.00 25.65 N
+ATOM 1576 CA GLY B 20 -1.249 13.411 5.381 1.00 25.82 C
+ATOM 1577 C GLY B 20 -0.732 12.011 5.672 1.00 25.97 C
+ATOM 1578 O GLY B 20 -1.511 11.037 5.738 1.00 25.29 O
+ATOM 1579 N LYS B 21 0.582 11.900 5.852 1.00 25.76 N
+ATOM 1580 CA LYS B 21 1.218 10.588 5.986 1.00 25.53 C
+ATOM 1581 C LYS B 21 0.466 9.679 6.946 1.00 25.87 C
+ATOM 1582 O LYS B 21 0.101 8.551 6.610 1.00 25.31 O
+ATOM 1583 CB LYS B 21 2.689 10.731 6.412 1.00 25.14 C
+ATOM 1584 CG LYS B 21 3.612 11.413 5.385 1.00 23.75 C
+ATOM 1585 CD LYS B 21 5.059 11.451 5.895 1.00 22.99 C
+ATOM 1586 CE LYS B 21 5.127 12.106 7.294 1.00 19.27 C
+ATOM 1587 NZ LYS B 21 4.696 13.521 7.200 1.00 17.38 N
+ATOM 1588 N SER B 22 0.247 10.175 8.155 1.00 26.25 N
+ATOM 1589 CA SER B 22 -0.413 9.381 9.184 1.00 26.95 C
+ATOM 1590 C SER B 22 -1.861 8.985 8.816 1.00 27.18 C
+ATOM 1591 O SER B 22 -2.237 7.816 8.890 1.00 26.05 O
+ATOM 1592 CB SER B 22 -0.385 10.140 10.525 1.00 26.78 C
+ATOM 1593 OG SER B 22 0.926 10.148 11.088 1.00 27.10 O
+ATOM 1594 N ALA B 23 -2.657 9.977 8.429 1.00 27.92 N
+ATOM 1595 CA ALA B 23 -4.076 9.766 8.176 1.00 29.18 C
+ATOM 1596 C ALA B 23 -4.257 8.801 7.033 1.00 30.10 C
+ATOM 1597 O ALA B 23 -5.165 7.990 7.041 1.00 30.58 O
+ATOM 1598 CB ALA B 23 -4.757 11.074 7.864 1.00 28.87 C
+ATOM 1599 N VAL B 24 -3.375 8.885 6.052 1.00 30.75 N
+ATOM 1600 CA VAL B 24 -3.482 8.030 4.882 1.00 31.41 C
+ATOM 1601 C VAL B 24 -2.938 6.624 5.166 1.00 31.76 C
+ATOM 1602 O VAL B 24 -3.591 5.616 4.848 1.00 31.91 O
+ATOM 1603 CB VAL B 24 -2.746 8.654 3.682 1.00 31.38 C
+ATOM 1604 CG1 VAL B 24 -2.747 7.713 2.490 1.00 31.16 C
+ATOM 1605 CG2 VAL B 24 -3.358 9.999 3.338 1.00 30.41 C
+ATOM 1606 N ALA B 25 -1.761 6.546 5.768 1.00 31.27 N
+ATOM 1607 CA ALA B 25 -1.203 5.235 6.049 1.00 32.12 C
+ATOM 1608 C ALA B 25 -2.123 4.420 6.947 1.00 32.61 C
+ATOM 1609 O ALA B 25 -2.306 3.237 6.715 1.00 32.56 O
+ATOM 1610 CB ALA B 25 0.186 5.335 6.636 1.00 31.69 C
+ATOM 1611 N SER B 26 -2.696 5.060 7.961 1.00 34.07 N
+ATOM 1612 CA SER B 26 -3.639 4.408 8.867 1.00 35.81 C
+ATOM 1613 C SER B 26 -4.781 3.721 8.119 1.00 36.88 C
+ATOM 1614 O SER B 26 -4.969 2.506 8.221 1.00 37.55 O
+ATOM 1615 CB SER B 26 -4.274 5.427 9.813 1.00 35.74 C
+ATOM 1616 OG SER B 26 -3.439 5.715 10.915 1.00 37.63 O
+ATOM 1617 N GLU B 27 -5.550 4.521 7.391 1.00 37.59 N
+ATOM 1618 CA GLU B 27 -6.719 4.041 6.676 1.00 38.61 C
+ATOM 1619 C GLU B 27 -6.327 3.002 5.623 1.00 38.82 C
+ATOM 1620 O GLU B 27 -7.023 2.010 5.426 1.00 38.48 O
+ATOM 1621 CB GLU B 27 -7.460 5.245 6.063 1.00 38.80 C
+ATOM 1622 CG GLU B 27 -8.629 4.926 5.143 1.00 40.06 C
+ATOM 1623 CD GLU B 27 -9.783 4.241 5.852 1.00 42.19 C
+ATOM 1624 OE1 GLU B 27 -10.171 4.681 6.956 1.00 42.41 O
+ATOM 1625 OE2 GLU B 27 -10.305 3.253 5.291 1.00 43.40 O
+ATOM 1626 N VAL B 28 -5.179 3.208 4.983 1.00 39.21 N
+ATOM 1627 CA VAL B 28 -4.749 2.302 3.936 1.00 39.54 C
+ATOM 1628 C VAL B 28 -4.349 0.943 4.456 1.00 39.83 C
+ATOM 1629 O VAL B 28 -4.588 -0.070 3.804 1.00 39.72 O
+ATOM 1630 CB VAL B 28 -3.591 2.861 3.118 1.00 39.61 C
+ATOM 1631 CG1 VAL B 28 -3.026 1.781 2.200 1.00 38.92 C
+ATOM 1632 CG2 VAL B 28 -4.067 4.019 2.296 1.00 39.43 C
+ATOM 1633 N ALA B 29 -3.718 0.917 5.621 1.00 40.12 N
+ATOM 1634 CA ALA B 29 -3.300 -0.354 6.187 1.00 40.18 C
+ATOM 1635 C ALA B 29 -4.558 -1.044 6.666 1.00 40.21 C
+ATOM 1636 O ALA B 29 -4.677 -2.255 6.617 1.00 39.90 O
+ATOM 1637 CB ALA B 29 -2.345 -0.140 7.339 1.00 39.83 C
+ATOM 1638 N HIS B 30 -5.498 -0.249 7.144 1.00 40.51 N
+ATOM 1639 CA HIS B 30 -6.745 -0.810 7.607 1.00 41.53 C
+ATOM 1640 C HIS B 30 -7.478 -1.519 6.469 1.00 41.14 C
+ATOM 1641 O HIS B 30 -7.886 -2.665 6.620 1.00 41.22 O
+ATOM 1642 CB HIS B 30 -7.646 0.252 8.217 1.00 41.67 C
+ATOM 1643 CG HIS B 30 -8.858 -0.324 8.863 1.00 44.54 C
+ATOM 1644 ND1 HIS B 30 -10.138 -0.048 8.433 1.00 46.43 N
+ATOM 1645 CD2 HIS B 30 -8.982 -1.209 9.881 1.00 47.61 C
+ATOM 1646 CE1 HIS B 30 -11.000 -0.711 9.181 1.00 48.31 C
+ATOM 1647 NE2 HIS B 30 -10.326 -1.423 10.066 1.00 49.10 N
+ATOM 1648 N GLN B 31 -7.622 -0.837 5.335 1.00 40.70 N
+ATOM 1649 CA GLN B 31 -8.293 -1.409 4.167 1.00 40.45 C
+ATOM 1650 C GLN B 31 -7.534 -2.583 3.522 1.00 40.05 C
+ATOM 1651 O GLN B 31 -8.159 -3.507 2.990 1.00 40.58 O
+ATOM 1652 CB GLN B 31 -8.631 -0.323 3.129 1.00 39.81 C
+ATOM 1653 CG GLN B 31 -9.749 0.624 3.590 1.00 41.63 C
+ATOM 1654 CD GLN B 31 -10.056 1.769 2.597 1.00 42.52 C
+ATOM 1655 OE1 GLN B 31 -9.719 1.687 1.417 1.00 42.34 O
+ATOM 1656 NE2 GLN B 31 -10.684 2.829 3.090 1.00 40.10 N
+ATOM 1657 N LEU B 32 -6.205 -2.568 3.561 1.00 39.05 N
+ATOM 1658 CA LEU B 32 -5.443 -3.631 2.896 1.00 38.07 C
+ATOM 1659 C LEU B 32 -5.001 -4.711 3.863 1.00 37.73 C
+ATOM 1660 O LEU B 32 -4.386 -5.690 3.463 1.00 38.04 O
+ATOM 1661 CB LEU B 32 -4.225 -3.073 2.151 1.00 37.75 C
+ATOM 1662 CG LEU B 32 -4.494 -2.070 1.020 1.00 37.46 C
+ATOM 1663 CD1 LEU B 32 -3.203 -1.630 0.323 1.00 33.80 C
+ATOM 1664 CD2 LEU B 32 -5.466 -2.670 0.018 1.00 37.47 C
+ATOM 1665 N HIS B 33 -5.311 -4.533 5.139 1.00 37.47 N
+ATOM 1666 CA HIS B 33 -4.867 -5.474 6.152 1.00 37.03 C
+ATOM 1667 C HIS B 33 -3.358 -5.600 6.064 1.00 35.79 C
+ATOM 1668 O HIS B 33 -2.801 -6.695 6.206 1.00 35.26 O
+ATOM 1669 CB HIS B 33 -5.530 -6.840 5.941 1.00 38.00 C
+ATOM 1670 CG HIS B 33 -7.003 -6.844 6.210 1.00 40.42 C
+ATOM 1671 ND1 HIS B 33 -7.944 -6.854 5.203 1.00 43.12 N
+ATOM 1672 CD2 HIS B 33 -7.698 -6.842 7.374 1.00 43.54 C
+ATOM 1673 CE1 HIS B 33 -9.156 -6.857 5.732 1.00 44.56 C
+ATOM 1674 NE2 HIS B 33 -9.035 -6.853 7.048 1.00 45.84 N
+ATOM 1675 N ALA B 34 -2.703 -4.468 5.814 1.00 34.13 N
+ATOM 1676 CA ALA B 34 -1.247 -4.418 5.697 1.00 32.62 C
+ATOM 1677 C ALA B 34 -0.603 -4.171 7.049 1.00 31.23 C
+ATOM 1678 O ALA B 34 -1.250 -3.690 7.962 1.00 30.60 O
+ATOM 1679 CB ALA B 34 -0.836 -3.305 4.725 1.00 32.58 C
+ATOM 1680 N ALA B 35 0.672 -4.510 7.173 1.00 30.04 N
+ATOM 1681 CA ALA B 35 1.405 -4.187 8.384 1.00 29.55 C
+ATOM 1682 C ALA B 35 1.702 -2.671 8.393 1.00 29.10 C
+ATOM 1683 O ALA B 35 1.806 -2.042 7.335 1.00 29.27 O
+ATOM 1684 CB ALA B 35 2.666 -4.983 8.457 1.00 29.79 C
+ATOM 1685 N PHE B 36 1.823 -2.079 9.575 1.00 28.36 N
+ATOM 1686 CA PHE B 36 1.975 -0.634 9.663 1.00 28.48 C
+ATOM 1687 C PHE B 36 2.900 -0.205 10.782 1.00 27.22 C
+ATOM 1688 O PHE B 36 2.729 -0.614 11.916 1.00 27.58 O
+ATOM 1689 CB PHE B 36 0.599 0.004 9.853 1.00 28.92 C
+ATOM 1690 CG PHE B 36 0.634 1.413 10.345 1.00 32.10 C
+ATOM 1691 CD1 PHE B 36 0.449 2.463 9.481 1.00 34.60 C
+ATOM 1692 CD2 PHE B 36 0.806 1.689 11.687 1.00 35.45 C
+ATOM 1693 CE1 PHE B 36 0.464 3.757 9.935 1.00 35.99 C
+ATOM 1694 CE2 PHE B 36 0.820 2.980 12.142 1.00 35.59 C
+ATOM 1695 CZ PHE B 36 0.652 4.015 11.274 1.00 36.19 C
+ATOM 1696 N LEU B 37 3.871 0.643 10.459 1.00 25.55 N
+ATOM 1697 CA LEU B 37 4.815 1.127 11.446 1.00 23.32 C
+ATOM 1698 C LEU B 37 4.974 2.636 11.355 1.00 22.12 C
+ATOM 1699 O LEU B 37 5.326 3.178 10.302 1.00 22.88 O
+ATOM 1700 CB LEU B 37 6.159 0.434 11.261 1.00 22.89 C
+ATOM 1701 CG LEU B 37 7.280 0.785 12.240 1.00 24.18 C
+ATOM 1702 CD1 LEU B 37 6.827 0.517 13.654 1.00 21.44 C
+ATOM 1703 CD2 LEU B 37 8.545 -0.004 11.930 1.00 23.43 C
+ATOM 1704 N ASP B 38 4.682 3.327 12.447 1.00 20.56 N
+ATOM 1705 CA ASP B 38 4.945 4.754 12.521 1.00 19.85 C
+ATOM 1706 C ASP B 38 6.438 4.846 12.871 1.00 19.48 C
+ATOM 1707 O ASP B 38 6.851 4.415 13.948 1.00 18.87 O
+ATOM 1708 CB ASP B 38 4.077 5.425 13.592 1.00 19.33 C
+ATOM 1709 CG ASP B 38 4.366 6.928 13.733 1.00 22.08 C
+ATOM 1710 OD1 ASP B 38 5.517 7.383 13.448 1.00 22.63 O
+ATOM 1711 OD2 ASP B 38 3.495 7.734 14.107 1.00 22.40 O
+ATOM 1712 N GLY B 39 7.238 5.382 11.953 1.00 19.05 N
+ATOM 1713 CA GLY B 39 8.683 5.465 12.115 1.00 19.22 C
+ATOM 1714 C GLY B 39 9.221 6.300 13.274 1.00 19.45 C
+ATOM 1715 O GLY B 39 10.373 6.129 13.634 1.00 19.50 O
+ATOM 1716 N ASP B 40 8.409 7.197 13.840 1.00 19.77 N
+ATOM 1717 CA ASP B 40 8.800 7.993 15.013 1.00 20.94 C
+ATOM 1718 C ASP B 40 9.010 7.096 16.221 1.00 21.24 C
+ATOM 1719 O ASP B 40 9.632 7.508 17.203 1.00 21.57 O
+ATOM 1720 CB ASP B 40 7.707 9.011 15.430 1.00 20.26 C
+ATOM 1721 CG ASP B 40 7.541 10.165 14.452 1.00 22.83 C
+ATOM 1722 OD1 ASP B 40 8.293 10.248 13.439 1.00 23.86 O
+ATOM 1723 OD2 ASP B 40 6.661 11.051 14.618 1.00 26.08 O
+ATOM 1724 N PHE B 41 8.464 5.885 16.181 1.00 21.14 N
+ATOM 1725 CA PHE B 41 8.553 5.023 17.352 1.00 21.33 C
+ATOM 1726 C PHE B 41 9.900 4.321 17.474 1.00 21.69 C
+ATOM 1727 O PHE B 41 10.178 3.696 18.496 1.00 21.75 O
+ATOM 1728 CB PHE B 41 7.392 4.016 17.403 1.00 20.75 C
+ATOM 1729 CG PHE B 41 6.008 4.658 17.378 1.00 21.15 C
+ATOM 1730 CD1 PHE B 41 4.897 3.930 17.001 1.00 20.64 C
+ATOM 1731 CD2 PHE B 41 5.824 5.973 17.751 1.00 21.41 C
+ATOM 1732 CE1 PHE B 41 3.640 4.506 16.985 1.00 21.55 C
+ATOM 1733 CE2 PHE B 41 4.572 6.559 17.735 1.00 20.31 C
+ATOM 1734 CZ PHE B 41 3.476 5.830 17.358 1.00 21.76 C
+ATOM 1735 N LEU B 42 10.731 4.428 16.437 1.00 22.10 N
+ATOM 1736 CA LEU B 42 12.040 3.764 16.405 1.00 22.82 C
+ATOM 1737 C LEU B 42 13.216 4.638 16.866 1.00 22.87 C
+ATOM 1738 O LEU B 42 14.362 4.205 16.789 1.00 22.59 O
+ATOM 1739 CB LEU B 42 12.358 3.250 14.989 1.00 23.12 C
+ATOM 1740 CG LEU B 42 11.935 1.843 14.547 1.00 23.37 C
+ATOM 1741 CD1 LEU B 42 12.873 0.790 15.125 1.00 24.72 C
+ATOM 1742 CD2 LEU B 42 10.490 1.564 14.943 1.00 23.24 C
+ATOM 1743 N HIS B 43 12.945 5.857 17.329 1.00 22.93 N
+ATOM 1744 CA HIS B 43 14.020 6.749 17.765 1.00 22.81 C
+ATOM 1745 C HIS B 43 14.724 6.147 18.966 1.00 23.34 C
+ATOM 1746 O HIS B 43 14.080 5.663 19.877 1.00 23.67 O
+ATOM 1747 CB HIS B 43 13.476 8.138 18.113 1.00 22.48 C
+ATOM 1748 CG HIS B 43 13.414 9.080 16.948 1.00 22.10 C
+ATOM 1749 ND1 HIS B 43 14.532 9.687 16.419 1.00 20.10 N
+ATOM 1750 CD2 HIS B 43 12.364 9.530 16.216 1.00 23.65 C
+ATOM 1751 CE1 HIS B 43 14.178 10.455 15.405 1.00 20.79 C
+ATOM 1752 NE2 HIS B 43 12.867 10.387 15.266 1.00 22.32 N
+ATOM 1753 N PRO B 44 16.051 6.166 18.972 1.00 24.15 N
+ATOM 1754 CA PRO B 44 16.814 5.701 20.136 1.00 24.72 C
+ATOM 1755 C PRO B 44 16.408 6.531 21.354 1.00 25.65 C
+ATOM 1756 O PRO B 44 15.946 7.680 21.220 1.00 25.07 O
+ATOM 1757 CB PRO B 44 18.274 6.047 19.796 1.00 24.92 C
+ATOM 1758 CG PRO B 44 18.306 6.528 18.402 1.00 24.42 C
+ATOM 1759 CD PRO B 44 16.903 6.669 17.887 1.00 24.02 C
+ATOM 1760 N ARG B 45 16.602 5.964 22.538 1.00 26.88 N
+ATOM 1761 CA ARG B 45 16.270 6.659 23.782 1.00 28.60 C
+ATOM 1762 C ARG B 45 16.771 8.114 23.840 1.00 28.68 C
+ATOM 1763 O ARG B 45 16.025 9.021 24.211 1.00 29.13 O
+ATOM 1764 CB ARG B 45 16.808 5.860 24.970 1.00 28.71 C
+ATOM 1765 CG ARG B 45 16.468 6.434 26.332 1.00 32.45 C
+ATOM 1766 CD ARG B 45 16.718 5.459 27.488 1.00 34.88 C
+ATOM 1767 NE ARG B 45 15.906 4.281 27.278 1.00 34.74 N
+ATOM 1768 CZ ARG B 45 14.724 4.078 27.849 1.00 35.02 C
+ATOM 1769 NH1 ARG B 45 14.214 4.966 28.703 1.00 29.94 N
+ATOM 1770 NH2 ARG B 45 14.048 2.968 27.556 1.00 35.25 N
+ATOM 1771 N ARG B 46 18.031 8.318 23.465 1.00 28.91 N
+ATOM 1772 CA ARG B 46 18.669 9.642 23.500 1.00 29.39 C
+ATOM 1773 C ARG B 46 17.989 10.694 22.628 1.00 28.10 C
+ATOM 1774 O ARG B 46 17.857 11.850 23.038 1.00 28.73 O
+ATOM 1775 CB ARG B 46 20.137 9.508 23.115 1.00 29.90 C
+ATOM 1776 CG ARG B 46 20.893 10.790 23.046 1.00 34.75 C
+ATOM 1777 CD ARG B 46 22.302 10.617 22.535 1.00 43.33 C
+ATOM 1778 NE ARG B 46 23.038 11.872 22.521 1.00 49.36 N
+ATOM 1779 CZ ARG B 46 22.547 13.028 22.083 1.00 52.53 C
+ATOM 1780 NH1 ARG B 46 21.307 13.102 21.623 1.00 53.91 N
+ATOM 1781 NH2 ARG B 46 23.293 14.117 22.114 1.00 55.63 N
+ATOM 1782 N ASN B 47 17.557 10.308 21.437 1.00 26.48 N
+ATOM 1783 CA ASN B 47 16.808 11.234 20.601 1.00 25.70 C
+ATOM 1784 C ASN B 47 15.544 11.695 21.314 1.00 25.21 C
+ATOM 1785 O ASN B 47 15.223 12.881 21.316 1.00 25.47 O
+ATOM 1786 CB ASN B 47 16.435 10.607 19.245 1.00 25.35 C
+ATOM 1787 CG ASN B 47 17.628 10.362 18.370 1.00 24.25 C
+ATOM 1788 OD1 ASN B 47 18.770 10.629 18.770 1.00 23.29 O
+ATOM 1789 ND2 ASN B 47 17.385 9.858 17.160 1.00 20.63 N
+ATOM 1790 N ILE B 48 14.824 10.766 21.926 1.00 24.95 N
+ATOM 1791 CA ILE B 48 13.575 11.115 22.599 1.00 25.30 C
+ATOM 1792 C ILE B 48 13.809 12.214 23.664 1.00 25.92 C
+ATOM 1793 O ILE B 48 13.073 13.198 23.738 1.00 25.56 O
+ATOM 1794 CB ILE B 48 12.929 9.849 23.232 1.00 24.66 C
+ATOM 1795 CG1 ILE B 48 12.648 8.771 22.174 1.00 24.53 C
+ATOM 1796 CG2 ILE B 48 11.644 10.192 23.951 1.00 24.38 C
+ATOM 1797 CD1 ILE B 48 11.526 9.118 21.208 1.00 22.02 C
+ATOM 1798 N GLU B 49 14.831 11.998 24.493 1.00 26.93 N
+ATOM 1799 CA GLU B 49 15.206 12.935 25.549 1.00 28.51 C
+ATOM 1800 C GLU B 49 15.615 14.265 24.943 1.00 28.30 C
+ATOM 1801 O GLU B 49 15.131 15.327 25.352 1.00 28.40 O
+ATOM 1802 CB GLU B 49 16.380 12.393 26.364 1.00 28.76 C
+ATOM 1803 CG GLU B 49 16.095 11.075 27.038 1.00 32.75 C
+ATOM 1804 CD GLU B 49 15.366 11.244 28.350 1.00 37.38 C
+ATOM 1805 OE1 GLU B 49 15.007 12.397 28.687 1.00 40.13 O
+ATOM 1806 OE2 GLU B 49 15.156 10.222 29.047 1.00 39.19 O
+ATOM 1807 N LYS B 50 16.514 14.186 23.959 1.00 28.07 N
+ATOM 1808 CA LYS B 50 16.963 15.387 23.270 1.00 28.52 C
+ATOM 1809 C LYS B 50 15.735 16.180 22.887 1.00 28.52 C
+ATOM 1810 O LYS B 50 15.633 17.356 23.222 1.00 29.62 O
+ATOM 1811 CB LYS B 50 17.818 15.101 22.020 1.00 27.97 C
+ATOM 1812 CG LYS B 50 18.352 16.390 21.380 1.00 26.95 C
+ATOM 1813 CD LYS B 50 19.334 16.121 20.253 1.00 25.06 C
+ATOM 1814 CE LYS B 50 20.232 17.321 19.967 1.00 24.48 C
+ATOM 1815 NZ LYS B 50 21.303 17.011 18.974 1.00 21.51 N
+ATOM 1816 N MET B 51 14.791 15.551 22.198 1.00 28.01 N
+ATOM 1817 CA MET B 51 13.572 16.256 21.784 1.00 27.48 C
+ATOM 1818 C MET B 51 12.686 16.605 22.984 1.00 27.94 C
+ATOM 1819 O MET B 51 12.027 17.642 22.980 1.00 27.75 O
+ATOM 1820 CB MET B 51 12.769 15.465 20.739 1.00 27.18 C
+ATOM 1821 CG MET B 51 13.430 15.304 19.363 1.00 25.83 C
+ATOM 1822 SD MET B 51 12.363 14.448 18.146 1.00 23.79 S
+ATOM 1823 CE MET B 51 12.382 12.698 18.794 1.00 20.68 C
+ATOM 1824 N ALA B 52 12.648 15.738 23.998 1.00 28.15 N
+ATOM 1825 CA ALA B 52 11.874 16.058 25.199 1.00 29.09 C
+ATOM 1826 C ALA B 52 12.341 17.423 25.716 1.00 30.10 C
+ATOM 1827 O ALA B 52 11.526 18.263 26.109 1.00 29.99 O
+ATOM 1828 CB ALA B 52 12.043 14.995 26.283 1.00 28.26 C
+ATOM 1829 N SER B 53 13.661 17.629 25.682 1.00 30.16 N
+ATOM 1830 CA SER B 53 14.276 18.852 26.169 1.00 31.05 C
+ATOM 1831 C SER B 53 14.022 20.084 25.279 1.00 31.46 C
+ATOM 1832 O SER B 53 14.448 21.202 25.613 1.00 31.60 O
+ATOM 1833 CB SER B 53 15.781 18.636 26.353 1.00 30.82 C
+ATOM 1834 OG SER B 53 16.487 19.049 25.194 1.00 31.81 O
+ATOM 1835 N GLY B 54 13.356 19.901 24.142 1.00 31.59 N
+ATOM 1836 CA GLY B 54 13.063 21.064 23.300 1.00 31.42 C
+ATOM 1837 C GLY B 54 14.052 21.291 22.169 1.00 30.87 C
+ATOM 1838 O GLY B 54 13.896 22.188 21.360 1.00 30.83 O
+ATOM 1839 N GLU B 55 15.079 20.461 22.098 1.00 30.45 N
+ATOM 1840 CA GLU B 55 16.066 20.626 21.047 1.00 29.79 C
+ATOM 1841 C GLU B 55 15.708 19.764 19.846 1.00 29.69 C
+ATOM 1842 O GLU B 55 15.216 18.655 20.014 1.00 29.44 O
+ATOM 1843 CB GLU B 55 17.454 20.280 21.582 1.00 29.17 C
+ATOM 1844 CG GLU B 55 17.914 21.234 22.668 1.00 30.31 C
+ATOM 1845 CD GLU B 55 17.878 22.683 22.205 1.00 32.74 C
+ATOM 1846 OE1 GLU B 55 18.141 22.927 21.017 1.00 29.40 O
+ATOM 1847 OE2 GLU B 55 17.593 23.585 23.029 1.00 35.98 O
+ATOM 1848 N PRO B 56 15.934 20.281 18.637 1.00 29.39 N
+ATOM 1849 CA PRO B 56 15.687 19.523 17.417 1.00 28.90 C
+ATOM 1850 C PRO B 56 16.848 18.593 17.103 1.00 28.65 C
+ATOM 1851 O PRO B 56 18.005 18.869 17.443 1.00 28.49 O
+ATOM 1852 CB PRO B 56 15.646 20.619 16.364 1.00 29.60 C
+ATOM 1853 CG PRO B 56 16.768 21.493 16.839 1.00 30.17 C
+ATOM 1854 CD PRO B 56 16.426 21.637 18.331 1.00 29.39 C
+ATOM 1855 N LEU B 57 16.528 17.499 16.420 1.00 27.97 N
+ATOM 1856 CA LEU B 57 17.530 16.520 16.033 1.00 27.26 C
+ATOM 1857 C LEU B 57 18.435 17.067 14.949 1.00 26.87 C
+ATOM 1858 O LEU B 57 18.022 17.900 14.153 1.00 26.18 O
+ATOM 1859 CB LEU B 57 16.850 15.251 15.530 1.00 26.77 C
+ATOM 1860 CG LEU B 57 15.989 14.531 16.571 1.00 26.82 C
+ATOM 1861 CD1 LEU B 57 15.731 13.121 16.120 1.00 24.97 C
+ATOM 1862 CD2 LEU B 57 16.688 14.550 17.937 1.00 25.83 C
+ATOM 1863 N ASN B 58 19.679 16.613 14.933 1.00 26.13 N
+ATOM 1864 CA ASN B 58 20.549 16.949 13.823 1.00 26.42 C
+ATOM 1865 C ASN B 58 20.732 15.637 13.029 1.00 26.22 C
+ATOM 1866 O ASN B 58 20.210 14.589 13.435 1.00 25.38 O
+ATOM 1867 CB ASN B 58 21.871 17.557 14.306 1.00 25.90 C
+ATOM 1868 CG ASN B 58 22.681 16.588 15.128 1.00 26.66 C
+ATOM 1869 OD1 ASN B 58 22.770 15.393 14.802 1.00 26.34 O
+ATOM 1870 ND2 ASN B 58 23.267 17.082 16.216 1.00 25.31 N
+ATOM 1871 N ASP B 59 21.436 15.687 11.908 1.00 26.32 N
+ATOM 1872 CA ASP B 59 21.578 14.483 11.093 1.00 27.80 C
+ATOM 1873 C ASP B 59 22.389 13.349 11.755 1.00 27.71 C
+ATOM 1874 O ASP B 59 22.186 12.181 11.429 1.00 27.53 O
+ATOM 1875 CB ASP B 59 22.042 14.786 9.650 1.00 27.94 C
+ATOM 1876 CG ASP B 59 20.917 15.359 8.781 1.00 29.92 C
+ATOM 1877 OD1 ASP B 59 19.752 15.389 9.243 1.00 31.36 O
+ATOM 1878 OD2 ASP B 59 21.097 15.793 7.616 1.00 32.14 O
+ATOM 1879 N ASP B 60 23.277 13.660 12.698 1.00 27.42 N
+ATOM 1880 CA ASP B 60 23.957 12.552 13.353 1.00 27.21 C
+ATOM 1881 C ASP B 60 22.950 11.781 14.210 1.00 25.95 C
+ATOM 1882 O ASP B 60 23.034 10.566 14.315 1.00 24.84 O
+ATOM 1883 CB ASP B 60 25.169 13.000 14.150 1.00 27.65 C
+ATOM 1884 CG ASP B 60 26.193 13.708 13.290 1.00 31.26 C
+ATOM 1885 OD1 ASP B 60 26.682 14.771 13.727 1.00 33.19 O
+ATOM 1886 OD2 ASP B 60 26.544 13.298 12.154 1.00 33.53 O
+ATOM 1887 N ASP B 61 22.000 12.496 14.811 1.00 24.99 N
+ATOM 1888 CA ASP B 61 20.979 11.852 15.636 1.00 24.61 C
+ATOM 1889 C ASP B 61 20.115 10.933 14.801 1.00 24.51 C
+ATOM 1890 O ASP B 61 19.691 9.905 15.281 1.00 24.23 O
+ATOM 1891 CB ASP B 61 20.031 12.865 16.272 1.00 23.77 C
+ATOM 1892 CG ASP B 61 20.746 13.865 17.156 1.00 23.86 C
+ATOM 1893 OD1 ASP B 61 21.740 13.504 17.829 1.00 18.59 O
+ATOM 1894 OD2 ASP B 61 20.361 15.040 17.226 1.00 23.83 O
+ATOM 1895 N ARG B 62 19.870 11.341 13.559 1.00 24.97 N
+ATOM 1896 CA ARG B 62 18.931 10.681 12.672 1.00 26.48 C
+ATOM 1897 C ARG B 62 19.449 9.349 12.100 1.00 27.22 C
+ATOM 1898 O ARG B 62 18.673 8.414 11.868 1.00 27.15 O
+ATOM 1899 CB ARG B 62 18.485 11.639 11.541 1.00 26.28 C
+ATOM 1900 CG ARG B 62 17.523 12.788 11.953 1.00 26.28 C
+ATOM 1901 CD ARG B 62 16.971 13.605 10.760 1.00 27.47 C
+ATOM 1902 NE ARG B 62 16.040 14.660 11.134 1.00 27.04 N
+ATOM 1903 CZ ARG B 62 16.399 15.910 11.467 1.00 29.67 C
+ATOM 1904 NH1 ARG B 62 17.684 16.267 11.464 1.00 28.27 N
+ATOM 1905 NH2 ARG B 62 15.472 16.813 11.807 1.00 26.88 N
+ATOM 1906 N LYS B 63 20.760 9.261 11.903 1.00 28.09 N
+ATOM 1907 CA LYS B 63 21.374 8.061 11.336 1.00 29.26 C
+ATOM 1908 C LYS B 63 20.930 6.749 12.002 1.00 29.33 C
+ATOM 1909 O LYS B 63 20.392 5.863 11.343 1.00 29.34 O
+ATOM 1910 CB LYS B 63 22.910 8.184 11.355 1.00 29.57 C
+ATOM 1911 CG LYS B 63 23.651 7.015 10.719 1.00 32.15 C
+ATOM 1912 CD LYS B 63 25.100 7.395 10.405 1.00 38.11 C
+ATOM 1913 CE LYS B 63 25.899 6.226 9.796 1.00 41.08 C
+ATOM 1914 NZ LYS B 63 27.376 6.505 9.788 1.00 42.31 N
+ATOM 1915 N PRO B 64 21.125 6.635 13.312 1.00 29.52 N
+ATOM 1916 CA PRO B 64 20.801 5.386 14.019 1.00 29.13 C
+ATOM 1917 C PRO B 64 19.294 5.212 14.065 1.00 28.91 C
+ATOM 1918 O PRO B 64 18.793 4.085 14.140 1.00 29.79 O
+ATOM 1919 CB PRO B 64 21.345 5.593 15.437 1.00 29.10 C
+ATOM 1920 CG PRO B 64 21.974 6.987 15.460 1.00 30.36 C
+ATOM 1921 CD PRO B 64 21.589 7.711 14.205 1.00 29.22 C
+ATOM 1922 N TRP B 65 18.574 6.326 14.048 1.00 27.77 N
+ATOM 1923 CA TRP B 65 17.133 6.258 13.975 1.00 26.58 C
+ATOM 1924 C TRP B 65 16.788 5.574 12.645 1.00 26.09 C
+ATOM 1925 O TRP B 65 16.121 4.552 12.613 1.00 24.77 O
+ATOM 1926 CB TRP B 65 16.508 7.651 14.030 1.00 25.57 C
+ATOM 1927 CG TRP B 65 15.095 7.616 13.630 1.00 24.70 C
+ATOM 1928 CD1 TRP B 65 14.164 6.710 14.041 1.00 24.45 C
+ATOM 1929 CD2 TRP B 65 14.423 8.482 12.710 1.00 24.44 C
+ATOM 1930 NE1 TRP B 65 12.953 6.970 13.456 1.00 20.77 N
+ATOM 1931 CE2 TRP B 65 13.079 8.053 12.636 1.00 22.48 C
+ATOM 1932 CE3 TRP B 65 14.810 9.591 11.956 1.00 25.13 C
+ATOM 1933 CZ2 TRP B 65 12.124 8.690 11.852 1.00 22.85 C
+ATOM 1934 CZ3 TRP B 65 13.849 10.228 11.156 1.00 26.49 C
+ATOM 1935 CH2 TRP B 65 12.527 9.771 11.113 1.00 24.88 C
+ATOM 1936 N LEU B 66 17.265 6.142 11.552 1.00 26.33 N
+ATOM 1937 CA LEU B 66 16.966 5.585 10.234 1.00 27.14 C
+ATOM 1938 C LEU B 66 17.482 4.144 10.051 1.00 27.24 C
+ATOM 1939 O LEU B 66 16.783 3.289 9.497 1.00 26.77 O
+ATOM 1940 CB LEU B 66 17.479 6.515 9.128 1.00 27.22 C
+ATOM 1941 CG LEU B 66 16.782 7.863 9.177 1.00 27.81 C
+ATOM 1942 CD1 LEU B 66 17.423 8.881 8.242 1.00 28.56 C
+ATOM 1943 CD2 LEU B 66 15.309 7.674 8.865 1.00 28.63 C
+ATOM 1944 N GLN B 67 18.686 3.870 10.527 1.00 27.24 N
+ATOM 1945 CA GLN B 67 19.212 2.508 10.438 1.00 28.63 C
+ATOM 1946 C GLN B 67 18.320 1.489 11.179 1.00 27.47 C
+ATOM 1947 O GLN B 67 18.158 0.325 10.755 1.00 27.28 O
+ATOM 1948 CB GLN B 67 20.646 2.440 10.976 1.00 29.32 C
+ATOM 1949 CG GLN B 67 21.144 1.004 11.158 1.00 34.86 C
+ATOM 1950 CD GLN B 67 21.510 0.342 9.823 1.00 41.94 C
+ATOM 1951 OE1 GLN B 67 22.075 0.991 8.942 1.00 45.36 O
+ATOM 1952 NE2 GLN B 67 21.170 -0.937 9.673 1.00 43.65 N
+ATOM 1953 N ALA B 68 17.742 1.931 12.283 1.00 26.00 N
+ATOM 1954 CA ALA B 68 16.848 1.076 13.046 1.00 25.55 C
+ATOM 1955 C ALA B 68 15.522 0.906 12.302 1.00 24.53 C
+ATOM 1956 O ALA B 68 14.933 -0.183 12.290 1.00 24.23 O
+ATOM 1957 CB ALA B 68 16.625 1.648 14.464 1.00 25.59 C
+ATOM 1958 N LEU B 69 15.072 1.975 11.654 1.00 23.38 N
+ATOM 1959 CA LEU B 69 13.851 1.895 10.860 1.00 23.04 C
+ATOM 1960 C LEU B 69 14.054 0.884 9.746 1.00 22.91 C
+ATOM 1961 O LEU B 69 13.142 0.137 9.404 1.00 22.62 O
+ATOM 1962 CB LEU B 69 13.518 3.240 10.239 1.00 22.51 C
+ATOM 1963 CG LEU B 69 12.081 3.665 10.510 1.00 23.86 C
+ATOM 1964 CD1 LEU B 69 11.608 4.759 9.550 1.00 21.89 C
+ATOM 1965 CD2 LEU B 69 11.173 2.445 10.488 1.00 21.81 C
+ATOM 1966 N ASN B 70 15.261 0.902 9.182 1.00 22.88 N
+ATOM 1967 CA ASN B 70 15.675 0.022 8.089 1.00 23.73 C
+ATOM 1968 C ASN B 70 15.514 -1.430 8.568 1.00 23.71 C
+ATOM 1969 O ASN B 70 14.871 -2.238 7.931 1.00 23.46 O
+ATOM 1970 CB ASN B 70 17.123 0.375 7.683 1.00 23.23 C
+ATOM 1971 CG ASN B 70 17.686 -0.502 6.572 1.00 23.76 C
+ATOM 1972 OD1 ASN B 70 18.142 0.000 5.524 1.00 27.24 O
+ATOM 1973 ND2 ASN B 70 17.737 -1.788 6.814 1.00 20.52 N
+ATOM 1974 N ASP B 71 16.062 -1.734 9.724 1.00 24.60 N
+ATOM 1975 CA ASP B 71 15.935 -3.079 10.254 1.00 25.79 C
+ATOM 1976 C ASP B 71 14.467 -3.370 10.520 1.00 26.24 C
+ATOM 1977 O ASP B 71 14.027 -4.510 10.392 1.00 27.03 O
+ATOM 1978 CB ASP B 71 16.767 -3.248 11.522 1.00 25.78 C
+ATOM 1979 CG ASP B 71 18.252 -3.000 11.279 1.00 28.68 C
+ATOM 1980 OD1 ASP B 71 18.626 -2.695 10.121 1.00 31.21 O
+ATOM 1981 OD2 ASP B 71 19.123 -3.080 12.172 1.00 29.94 O
+ATOM 1982 N ALA B 72 13.691 -2.352 10.876 1.00 25.54 N
+ATOM 1983 CA ALA B 72 12.297 -2.629 11.141 1.00 24.98 C
+ATOM 1984 C ALA B 72 11.575 -3.019 9.844 1.00 24.72 C
+ATOM 1985 O ALA B 72 10.787 -3.974 9.828 1.00 24.25 O
+ATOM 1986 CB ALA B 72 11.624 -1.452 11.847 1.00 25.18 C
+ATOM 1987 N ALA B 73 11.837 -2.285 8.763 1.00 24.15 N
+ATOM 1988 CA ALA B 73 11.265 -2.629 7.466 1.00 24.09 C
+ATOM 1989 C ALA B 73 11.711 -4.044 7.123 1.00 24.25 C
+ATOM 1990 O ALA B 73 10.943 -4.837 6.591 1.00 24.16 O
+ATOM 1991 CB ALA B 73 11.755 -1.683 6.395 1.00 23.66 C
+ATOM 1992 N PHE B 74 12.963 -4.349 7.445 1.00 24.24 N
+ATOM 1993 CA PHE B 74 13.543 -5.640 7.147 1.00 25.21 C
+ATOM 1994 C PHE B 74 12.754 -6.747 7.845 1.00 25.13 C
+ATOM 1995 O PHE B 74 12.425 -7.783 7.250 1.00 25.14 O
+ATOM 1996 CB PHE B 74 14.988 -5.648 7.607 1.00 25.71 C
+ATOM 1997 CG PHE B 74 15.701 -6.917 7.314 1.00 28.19 C
+ATOM 1998 CD1 PHE B 74 15.637 -7.483 6.048 1.00 30.42 C
+ATOM 1999 CD2 PHE B 74 16.439 -7.551 8.297 1.00 30.25 C
+ATOM 2000 CE1 PHE B 74 16.301 -8.667 5.763 1.00 30.63 C
+ATOM 2001 CE2 PHE B 74 17.101 -8.732 8.022 1.00 33.44 C
+ATOM 2002 CZ PHE B 74 17.035 -9.290 6.748 1.00 31.87 C
+ATOM 2003 N ALA B 75 12.422 -6.497 9.103 1.00 24.39 N
+ATOM 2004 CA ALA B 75 11.649 -7.438 9.886 1.00 24.68 C
+ATOM 2005 C ALA B 75 10.206 -7.578 9.369 1.00 24.11 C
+ATOM 2006 O ALA B 75 9.708 -8.686 9.258 1.00 23.77 O
+ATOM 2007 CB ALA B 75 11.682 -7.055 11.402 1.00 24.37 C
+ATOM 2008 N MET B 76 9.556 -6.464 9.042 1.00 24.21 N
+ATOM 2009 CA MET B 76 8.175 -6.475 8.537 1.00 25.04 C
+ATOM 2010 C MET B 76 7.995 -7.310 7.266 1.00 25.83 C
+ATOM 2011 O MET B 76 7.028 -8.046 7.135 1.00 25.86 O
+ATOM 2012 CB MET B 76 7.668 -5.044 8.249 1.00 24.46 C
+ATOM 2013 CG MET B 76 7.594 -4.120 9.467 1.00 24.50 C
+ATOM 2014 SD MET B 76 7.208 -2.372 9.067 1.00 23.94 S
+ATOM 2015 CE MET B 76 5.481 -2.504 8.769 1.00 22.02 C
+ATOM 2016 N GLN B 77 8.934 -7.193 6.336 1.00 26.81 N
+ATOM 2017 CA GLN B 77 8.817 -7.854 5.052 1.00 28.05 C
+ATOM 2018 C GLN B 77 8.989 -9.358 5.190 1.00 28.90 C
+ATOM 2019 O GLN B 77 8.773 -10.130 4.248 1.00 28.99 O
+ATOM 2020 CB GLN B 77 9.804 -7.257 4.045 1.00 27.81 C
+ATOM 2021 CG GLN B 77 11.258 -7.357 4.437 1.00 28.49 C
+ATOM 2022 CD GLN B 77 11.925 -8.614 3.922 1.00 27.57 C
+ATOM 2023 OE1 GLN B 77 11.832 -8.915 2.747 1.00 30.16 O
+ATOM 2024 NE2 GLN B 77 12.626 -9.322 4.789 1.00 26.16 N
+ATOM 2025 N ARG B 78 9.375 -9.774 6.382 1.00 29.85 N
+ATOM 2026 CA ARG B 78 9.481 -11.193 6.649 1.00 30.36 C
+ATOM 2027 C ARG B 78 8.103 -11.829 6.617 1.00 29.98 C
+ATOM 2028 O ARG B 78 7.934 -12.880 6.032 1.00 30.01 O
+ATOM 2029 CB ARG B 78 10.146 -11.436 7.999 1.00 30.62 C
+ATOM 2030 CG ARG B 78 11.623 -11.120 8.001 1.00 31.94 C
+ATOM 2031 CD ARG B 78 12.431 -12.015 7.059 1.00 34.57 C
+ATOM 2032 NE ARG B 78 11.880 -13.367 7.049 1.00 38.95 N
+ATOM 2033 CZ ARG B 78 12.227 -14.332 6.200 1.00 39.62 C
+ATOM 2034 NH1 ARG B 78 13.149 -14.127 5.275 1.00 40.32 N
+ATOM 2035 NH2 ARG B 78 11.648 -15.519 6.289 1.00 40.41 N
+ATOM 2036 N THR B 79 7.104 -11.168 7.192 1.00 30.30 N
+ATOM 2037 CA THR B 79 5.784 -11.806 7.343 1.00 30.62 C
+ATOM 2038 C THR B 79 4.571 -11.076 6.768 1.00 30.12 C
+ATOM 2039 O THR B 79 3.425 -11.483 6.971 1.00 29.67 O
+ATOM 2040 CB THR B 79 5.553 -12.074 8.814 1.00 30.53 C
+ATOM 2041 OG1 THR B 79 5.967 -10.919 9.551 1.00 31.85 O
+ATOM 2042 CG2 THR B 79 6.538 -13.136 9.283 1.00 31.45 C
+ATOM 2043 N ASN B 80 4.818 -9.999 6.046 1.00 30.02 N
+ATOM 2044 CA ASN B 80 3.725 -9.237 5.494 1.00 30.25 C
+ATOM 2045 C ASN B 80 3.962 -8.971 4.023 1.00 30.71 C
+ATOM 2046 O ASN B 80 5.086 -8.706 3.599 1.00 30.06 O
+ATOM 2047 CB ASN B 80 3.518 -7.952 6.301 1.00 29.87 C
+ATOM 2048 CG ASN B 80 3.249 -8.235 7.784 1.00 30.42 C
+ATOM 2049 OD1 ASN B 80 2.092 -8.211 8.246 1.00 31.32 O
+ATOM 2050 ND2 ASN B 80 4.313 -8.530 8.531 1.00 25.31 N
+ATOM 2051 N LYS B 81 2.900 -9.073 3.236 1.00 31.64 N
+ATOM 2052 CA LYS B 81 3.030 -8.874 1.802 1.00 32.47 C
+ATOM 2053 C LYS B 81 3.096 -7.373 1.532 1.00 31.53 C
+ATOM 2054 O LYS B 81 3.907 -6.911 0.732 1.00 32.02 O
+ATOM 2055 CB LYS B 81 1.898 -9.577 1.038 1.00 33.37 C
+ATOM 2056 CG LYS B 81 2.309 -10.885 0.384 1.00 37.74 C
+ATOM 2057 CD LYS B 81 1.097 -11.668 -0.091 1.00 43.64 C
+ATOM 2058 CE LYS B 81 1.491 -12.953 -0.803 1.00 47.94 C
+ATOM 2059 NZ LYS B 81 0.253 -13.661 -1.298 1.00 49.37 N
+ATOM 2060 N VAL B 82 2.259 -6.623 2.235 1.00 30.01 N
+ATOM 2061 CA VAL B 82 2.285 -5.180 2.143 1.00 28.54 C
+ATOM 2062 C VAL B 82 2.646 -4.622 3.517 1.00 28.36 C
+ATOM 2063 O VAL B 82 2.032 -4.973 4.536 1.00 27.92 O
+ATOM 2064 CB VAL B 82 0.950 -4.615 1.615 1.00 28.64 C
+ATOM 2065 CG1 VAL B 82 1.031 -3.142 1.471 1.00 27.90 C
+ATOM 2066 CG2 VAL B 82 0.609 -5.271 0.268 1.00 27.66 C
+ATOM 2067 N SER B 83 3.692 -3.797 3.531 1.00 27.50 N
+ATOM 2068 CA SER B 83 4.171 -3.117 4.731 1.00 26.66 C
+ATOM 2069 C SER B 83 4.186 -1.590 4.562 1.00 25.79 C
+ATOM 2070 O SER B 83 4.791 -1.072 3.636 1.00 25.38 O
+ATOM 2071 CB SER B 83 5.578 -3.605 5.071 1.00 26.11 C
+ATOM 2072 OG SER B 83 5.523 -4.808 5.810 1.00 26.62 O
+ATOM 2073 N LEU B 84 3.520 -0.879 5.458 1.00 24.96 N
+ATOM 2074 CA LEU B 84 3.536 0.577 5.408 1.00 24.52 C
+ATOM 2075 C LEU B 84 4.393 1.160 6.543 1.00 23.99 C
+ATOM 2076 O LEU B 84 4.348 0.690 7.677 1.00 24.15 O
+ATOM 2077 CB LEU B 84 2.122 1.155 5.446 1.00 24.36 C
+ATOM 2078 CG LEU B 84 1.103 0.689 4.388 1.00 26.23 C
+ATOM 2079 CD1 LEU B 84 -0.237 1.384 4.557 1.00 26.28 C
+ATOM 2080 CD2 LEU B 84 1.633 0.921 2.953 1.00 28.40 C
+ATOM 2081 N ILE B 85 5.190 2.169 6.222 1.00 23.01 N
+ATOM 2082 CA ILE B 85 6.001 2.856 7.219 1.00 22.14 C
+ATOM 2083 C ILE B 85 5.854 4.356 7.044 1.00 21.53 C
+ATOM 2084 O ILE B 85 6.001 4.853 5.946 1.00 21.28 O
+ATOM 2085 CB ILE B 85 7.479 2.475 7.059 1.00 22.58 C
+ATOM 2086 CG1 ILE B 85 7.698 1.024 7.506 1.00 20.43 C
+ATOM 2087 CG2 ILE B 85 8.362 3.414 7.859 1.00 21.64 C
+ATOM 2088 CD1 ILE B 85 9.060 0.514 7.185 1.00 18.36 C
+ATOM 2089 N VAL B 86 5.535 5.077 8.114 1.00 20.95 N
+ATOM 2090 CA VAL B 86 5.413 6.522 8.000 1.00 20.10 C
+ATOM 2091 C VAL B 86 6.752 7.120 8.380 1.00 19.77 C
+ATOM 2092 O VAL B 86 7.269 6.814 9.455 1.00 18.33 O
+ATOM 2093 CB VAL B 86 4.332 7.102 8.921 1.00 20.39 C
+ATOM 2094 CG1 VAL B 86 4.376 8.640 8.920 1.00 19.23 C
+ATOM 2095 CG2 VAL B 86 2.973 6.620 8.469 1.00 20.92 C
+ATOM 2096 N CYS B 87 7.298 7.948 7.477 1.00 19.04 N
+ATOM 2097 CA CYS B 87 8.568 8.637 7.664 1.00 19.52 C
+ATOM 2098 C CYS B 87 8.632 9.768 6.648 1.00 19.83 C
+ATOM 2099 O CYS B 87 8.635 9.548 5.448 1.00 19.25 O
+ATOM 2100 CB CYS B 87 9.737 7.676 7.464 1.00 19.34 C
+ATOM 2101 SG CYS B 87 11.379 8.363 7.771 1.00 21.21 S
+ATOM 2102 N SER B 88 8.692 10.996 7.110 1.00 20.51 N
+ATOM 2103 CA SER B 88 8.675 12.089 6.150 1.00 21.10 C
+ATOM 2104 C SER B 88 9.860 12.032 5.178 1.00 20.66 C
+ATOM 2105 O SER B 88 9.779 12.537 4.069 1.00 21.30 O
+ATOM 2106 CB SER B 88 8.612 13.390 6.901 1.00 20.80 C
+ATOM 2107 OG SER B 88 9.716 13.449 7.753 1.00 25.58 O
+ATOM 2108 N ALA B 89 10.950 11.394 5.591 1.00 20.86 N
+ATOM 2109 CA ALA B 89 12.117 11.172 4.729 1.00 21.38 C
+ATOM 2110 C ALA B 89 12.472 12.290 3.734 1.00 21.31 C
+ATOM 2111 O ALA B 89 12.750 12.004 2.571 1.00 20.88 O
+ATOM 2112 CB ALA B 89 11.934 9.861 3.971 1.00 21.48 C
+ATOM 2113 N LEU B 90 12.490 13.534 4.196 1.00 21.60 N
+ATOM 2114 CA LEU B 90 12.715 14.714 3.333 1.00 23.05 C
+ATOM 2115 C LEU B 90 14.003 14.739 2.535 1.00 23.90 C
+ATOM 2116 O LEU B 90 14.036 15.231 1.404 1.00 24.97 O
+ATOM 2117 CB LEU B 90 12.687 15.992 4.171 1.00 21.94 C
+ATOM 2118 CG LEU B 90 11.436 16.114 5.020 1.00 22.57 C
+ATOM 2119 CD1 LEU B 90 11.458 17.416 5.833 1.00 23.68 C
+ATOM 2120 CD2 LEU B 90 10.165 16.007 4.155 1.00 21.17 C
+ATOM 2121 N LYS B 91 15.070 14.250 3.145 1.00 24.61 N
+ATOM 2122 CA LYS B 91 16.368 14.314 2.518 1.00 25.74 C
+ATOM 2123 C LYS B 91 16.650 13.031 1.782 1.00 26.33 C
+ATOM 2124 O LYS B 91 16.312 11.929 2.251 1.00 25.83 O
+ATOM 2125 CB LYS B 91 17.478 14.571 3.556 1.00 25.62 C
+ATOM 2126 CG LYS B 91 17.703 16.061 3.891 1.00 26.14 C
+ATOM 2127 CD LYS B 91 18.676 16.226 5.054 1.00 27.22 C
+ATOM 2128 CE LYS B 91 18.711 17.660 5.584 1.00 28.41 C
+ATOM 2129 NZ LYS B 91 19.730 17.833 6.676 1.00 27.57 N
+ATOM 2130 N LYS B 92 17.271 13.195 0.619 1.00 26.32 N
+ATOM 2131 CA LYS B 92 17.659 12.076 -0.202 1.00 26.79 C
+ATOM 2132 C LYS B 92 18.428 11.100 0.660 1.00 26.43 C
+ATOM 2133 O LYS B 92 18.117 9.931 0.673 1.00 26.79 O
+ATOM 2134 CB LYS B 92 18.523 12.513 -1.386 1.00 27.30 C
+ATOM 2135 CG LYS B 92 19.029 11.333 -2.187 1.00 28.91 C
+ATOM 2136 CD LYS B 92 19.013 11.604 -3.674 1.00 34.22 C
+ATOM 2137 CE LYS B 92 19.390 10.338 -4.431 1.00 36.72 C
+ATOM 2138 NZ LYS B 92 20.244 10.674 -5.600 1.00 39.17 N
+ATOM 2139 N HIS B 93 19.423 11.580 1.392 1.00 26.69 N
+ATOM 2140 CA HIS B 93 20.236 10.736 2.259 1.00 27.24 C
+ATOM 2141 C HIS B 93 19.413 9.852 3.201 1.00 26.46 C
+ATOM 2142 O HIS B 93 19.758 8.698 3.417 1.00 25.86 O
+ATOM 2143 CB HIS B 93 21.174 11.606 3.085 1.00 28.08 C
+ATOM 2144 CG HIS B 93 22.013 10.843 4.061 1.00 31.29 C
+ATOM 2145 ND1 HIS B 93 21.900 11.015 5.425 1.00 33.72 N
+ATOM 2146 CD2 HIS B 93 22.991 9.920 3.875 1.00 34.46 C
+ATOM 2147 CE1 HIS B 93 22.773 10.233 6.037 1.00 36.16 C
+ATOM 2148 NE2 HIS B 93 23.451 9.558 5.121 1.00 35.72 N
+ATOM 2149 N TYR B 94 18.335 10.392 3.763 1.00 25.45 N
+ATOM 2150 CA TYR B 94 17.522 9.614 4.685 1.00 25.43 C
+ATOM 2151 C TYR B 94 16.934 8.433 3.907 1.00 24.82 C
+ATOM 2152 O TYR B 94 16.838 7.305 4.401 1.00 23.87 O
+ATOM 2153 CB TYR B 94 16.351 10.435 5.237 1.00 25.08 C
+ATOM 2154 CG TYR B 94 16.686 11.708 5.990 1.00 25.83 C
+ATOM 2155 CD1 TYR B 94 17.997 12.008 6.392 1.00 25.49 C
+ATOM 2156 CD2 TYR B 94 15.679 12.606 6.315 1.00 25.93 C
+ATOM 2157 CE1 TYR B 94 18.279 13.177 7.086 1.00 25.57 C
+ATOM 2158 CE2 TYR B 94 15.954 13.770 7.005 1.00 27.23 C
+ATOM 2159 CZ TYR B 94 17.257 14.050 7.386 1.00 26.84 C
+ATOM 2160 OH TYR B 94 17.514 15.207 8.077 1.00 27.34 O
+ATOM 2161 N ARG B 95 16.524 8.729 2.687 1.00 24.55 N
+ATOM 2162 CA ARG B 95 15.900 7.728 1.849 1.00 25.51 C
+ATOM 2163 C ARG B 95 16.891 6.625 1.464 1.00 25.74 C
+ATOM 2164 O ARG B 95 16.513 5.455 1.348 1.00 25.93 O
+ATOM 2165 CB ARG B 95 15.239 8.354 0.623 1.00 25.55 C
+ATOM 2166 CG ARG B 95 14.197 9.425 0.972 1.00 25.22 C
+ATOM 2167 CD ARG B 95 13.361 9.866 -0.205 1.00 24.98 C
+ATOM 2168 NE ARG B 95 14.167 10.659 -1.115 1.00 24.24 N
+ATOM 2169 CZ ARG B 95 14.186 11.990 -1.163 1.00 28.41 C
+ATOM 2170 NH1 ARG B 95 13.417 12.741 -0.365 1.00 27.40 N
+ATOM 2171 NH2 ARG B 95 14.987 12.586 -2.038 1.00 31.08 N
+ATOM 2172 N ASP B 96 18.158 6.994 1.278 1.00 25.42 N
+ATOM 2173 CA ASP B 96 19.175 5.985 0.967 1.00 26.32 C
+ATOM 2174 C ASP B 96 19.427 5.123 2.189 1.00 26.61 C
+ATOM 2175 O ASP B 96 19.626 3.913 2.078 1.00 26.68 O
+ATOM 2176 CB ASP B 96 20.483 6.621 0.510 1.00 26.57 C
+ATOM 2177 CG ASP B 96 20.356 7.305 -0.822 1.00 26.31 C
+ATOM 2178 OD1 ASP B 96 19.553 6.828 -1.665 1.00 25.85 O
+ATOM 2179 OD2 ASP B 96 21.007 8.328 -1.101 1.00 23.18 O
+ATOM 2180 N LEU B 97 19.429 5.762 3.353 1.00 26.60 N
+ATOM 2181 CA LEU B 97 19.575 5.036 4.589 1.00 27.27 C
+ATOM 2182 C LEU B 97 18.462 3.967 4.662 1.00 27.39 C
+ATOM 2183 O LEU B 97 18.707 2.835 5.039 1.00 27.72 O
+ATOM 2184 CB LEU B 97 19.544 6.009 5.782 1.00 27.55 C
+ATOM 2185 CG LEU B 97 20.735 6.973 6.028 1.00 28.18 C
+ATOM 2186 CD1 LEU B 97 20.407 7.980 7.093 1.00 27.10 C
+ATOM 2187 CD2 LEU B 97 22.037 6.263 6.398 1.00 29.21 C
+ATOM 2188 N LEU B 98 17.247 4.318 4.262 1.00 27.66 N
+ATOM 2189 CA LEU B 98 16.146 3.368 4.307 1.00 28.19 C
+ATOM 2190 C LEU B 98 16.280 2.277 3.249 1.00 28.61 C
+ATOM 2191 O LEU B 98 16.042 1.101 3.545 1.00 28.68 O
+ATOM 2192 CB LEU B 98 14.805 4.085 4.182 1.00 27.69 C
+ATOM 2193 CG LEU B 98 14.483 4.920 5.419 1.00 28.49 C
+ATOM 2194 CD1 LEU B 98 13.152 5.634 5.251 1.00 30.19 C
+ATOM 2195 CD2 LEU B 98 14.472 4.029 6.660 1.00 27.82 C
+ATOM 2196 N ARG B 99 16.697 2.669 2.043 1.00 28.84 N
+ATOM 2197 CA ARG B 99 16.885 1.753 0.910 1.00 29.68 C
+ATOM 2198 C ARG B 99 17.852 0.617 1.127 1.00 30.28 C
+ATOM 2199 O ARG B 99 17.640 -0.455 0.620 1.00 31.12 O
+ATOM 2200 CB ARG B 99 17.461 2.492 -0.296 1.00 29.05 C
+ATOM 2201 CG ARG B 99 16.476 3.129 -1.179 1.00 27.97 C
+ATOM 2202 CD ARG B 99 17.074 4.105 -2.152 1.00 26.02 C
+ATOM 2203 NE ARG B 99 16.001 4.820 -2.834 1.00 27.49 N
+ATOM 2204 CZ ARG B 99 15.917 6.140 -2.933 1.00 25.00 C
+ATOM 2205 NH1 ARG B 99 16.856 6.917 -2.403 1.00 24.22 N
+ATOM 2206 NH2 ARG B 99 14.897 6.674 -3.572 1.00 23.26 N
+ATOM 2207 N GLU B 100 18.947 0.889 1.819 1.00 31.40 N
+ATOM 2208 CA GLU B 100 20.059 -0.047 1.944 1.00 32.90 C
+ATOM 2209 C GLU B 100 19.704 -1.467 2.427 1.00 32.32 C
+ATOM 2210 O GLU B 100 19.368 -1.662 3.588 1.00 32.22 O
+ATOM 2211 CB GLU B 100 21.123 0.578 2.843 1.00 33.87 C
+ATOM 2212 CG GLU B 100 22.547 0.095 2.638 1.00 38.98 C
+ATOM 2213 CD GLU B 100 23.539 1.159 3.084 1.00 47.10 C
+ATOM 2214 OE1 GLU B 100 23.741 1.312 4.315 1.00 48.50 O
+ATOM 2215 OE2 GLU B 100 24.088 1.877 2.213 1.00 49.83 O
+ATOM 2216 N GLY B 101 19.794 -2.448 1.527 1.00 32.17 N
+ATOM 2217 CA GLY B 101 19.523 -3.851 1.855 1.00 31.19 C
+ATOM 2218 C GLY B 101 18.046 -4.178 1.762 1.00 30.67 C
+ATOM 2219 O GLY B 101 17.608 -5.267 2.128 1.00 30.65 O
+ATOM 2220 N ASN B 102 17.277 -3.215 1.265 1.00 29.95 N
+ATOM 2221 CA ASN B 102 15.837 -3.372 1.112 1.00 29.22 C
+ATOM 2222 C ASN B 102 15.377 -3.100 -0.333 1.00 29.12 C
+ATOM 2223 O ASN B 102 14.606 -2.177 -0.570 1.00 29.09 O
+ATOM 2224 CB ASN B 102 15.093 -2.480 2.125 1.00 29.30 C
+ATOM 2225 CG ASN B 102 15.338 -2.901 3.583 1.00 28.82 C
+ATOM 2226 OD1 ASN B 102 15.226 -4.085 3.925 1.00 27.84 O
+ATOM 2227 ND2 ASN B 102 15.651 -1.927 4.447 1.00 24.76 N
+ATOM 2228 N PRO B 103 15.796 -3.951 -1.280 1.00 28.58 N
+ATOM 2229 CA PRO B 103 15.506 -3.734 -2.703 1.00 28.11 C
+ATOM 2230 C PRO B 103 14.041 -3.850 -2.924 1.00 27.73 C
+ATOM 2231 O PRO B 103 13.567 -3.412 -3.965 1.00 26.98 O
+ATOM 2232 CB PRO B 103 16.217 -4.898 -3.404 1.00 28.34 C
+ATOM 2233 CG PRO B 103 16.336 -5.960 -2.357 1.00 28.55 C
+ATOM 2234 CD PRO B 103 16.515 -5.213 -1.051 1.00 28.81 C
+ATOM 2235 N ASN B 104 13.332 -4.436 -1.959 1.00 27.10 N
+ATOM 2236 CA ASN B 104 11.886 -4.524 -2.053 1.00 27.08 C
+ATOM 2237 C ASN B 104 11.160 -3.378 -1.332 1.00 26.93 C
+ATOM 2238 O ASN B 104 9.968 -3.454 -1.061 1.00 26.58 O
+ATOM 2239 CB ASN B 104 11.349 -5.908 -1.666 1.00 27.56 C
+ATOM 2240 CG ASN B 104 11.496 -6.236 -0.176 1.00 28.39 C
+ATOM 2241 OD1 ASN B 104 12.487 -5.894 0.458 1.00 29.12 O
+ATOM 2242 ND2 ASN B 104 10.507 -6.952 0.372 1.00 30.42 N
+ATOM 2243 N LEU B 105 11.893 -2.306 -1.049 1.00 26.50 N
+ATOM 2244 CA LEU B 105 11.293 -1.135 -0.426 1.00 26.27 C
+ATOM 2245 C LEU B 105 11.112 -0.046 -1.474 1.00 25.87 C
+ATOM 2246 O LEU B 105 11.941 0.112 -2.366 1.00 25.35 O
+ATOM 2247 CB LEU B 105 12.162 -0.634 0.742 1.00 25.86 C
+ATOM 2248 CG LEU B 105 11.676 0.494 1.665 1.00 27.01 C
+ATOM 2249 CD1 LEU B 105 12.089 0.256 3.131 1.00 27.72 C
+ATOM 2250 CD2 LEU B 105 12.170 1.846 1.170 1.00 28.26 C
+ATOM 2251 N SER B 106 10.022 0.702 -1.370 1.00 25.49 N
+ATOM 2252 CA SER B 106 9.851 1.833 -2.247 1.00 25.51 C
+ATOM 2253 C SER B 106 9.184 3.038 -1.512 1.00 25.42 C
+ATOM 2254 O SER B 106 8.750 2.914 -0.368 1.00 25.06 O
+ATOM 2255 CB SER B 106 9.218 1.384 -3.580 1.00 25.54 C
+ATOM 2256 OG SER B 106 7.833 1.213 -3.516 1.00 26.67 O
+ATOM 2257 N PHE B 107 9.175 4.225 -2.100 1.00 24.75 N
+ATOM 2258 CA PHE B 107 8.589 5.352 -1.389 1.00 24.57 C
+ATOM 2259 C PHE B 107 7.289 5.798 -2.029 1.00 24.18 C
+ATOM 2260 O PHE B 107 7.118 5.666 -3.218 1.00 23.89 O
+ATOM 2261 CB PHE B 107 9.557 6.548 -1.307 1.00 24.74 C
+ATOM 2262 CG PHE B 107 10.870 6.221 -0.663 1.00 24.58 C
+ATOM 2263 CD1 PHE B 107 11.875 5.615 -1.398 1.00 23.87 C
+ATOM 2264 CD2 PHE B 107 11.094 6.495 0.678 1.00 22.45 C
+ATOM 2265 CE1 PHE B 107 13.076 5.286 -0.811 1.00 24.24 C
+ATOM 2266 CE2 PHE B 107 12.299 6.165 1.274 1.00 21.70 C
+ATOM 2267 CZ PHE B 107 13.291 5.563 0.529 1.00 23.50 C
+ATOM 2268 N ILE B 108 6.365 6.315 -1.229 1.00 24.35 N
+ATOM 2269 CA ILE B 108 5.138 6.855 -1.776 1.00 24.91 C
+ATOM 2270 C ILE B 108 5.095 8.295 -1.347 1.00 25.30 C
+ATOM 2271 O ILE B 108 4.765 8.598 -0.203 1.00 25.33 O
+ATOM 2272 CB ILE B 108 3.911 6.104 -1.267 1.00 25.05 C
+ATOM 2273 CG1 ILE B 108 3.960 4.636 -1.692 1.00 25.70 C
+ATOM 2274 CG2 ILE B 108 2.646 6.713 -1.847 1.00 25.14 C
+ATOM 2275 CD1 ILE B 108 2.609 3.926 -1.542 1.00 25.19 C
+ATOM 2276 N TYR B 109 5.452 9.184 -2.257 1.00 25.25 N
+ATOM 2277 CA TYR B 109 5.497 10.613 -1.960 1.00 26.66 C
+ATOM 2278 C TYR B 109 4.123 11.308 -1.971 1.00 27.24 C
+ATOM 2279 O TYR B 109 3.496 11.411 -3.016 1.00 27.34 O
+ATOM 2280 CB TYR B 109 6.460 11.289 -2.948 1.00 26.34 C
+ATOM 2281 CG TYR B 109 6.627 12.774 -2.794 1.00 27.59 C
+ATOM 2282 CD1 TYR B 109 6.281 13.421 -1.606 1.00 26.00 C
+ATOM 2283 CD2 TYR B 109 7.132 13.547 -3.851 1.00 27.36 C
+ATOM 2284 CE1 TYR B 109 6.424 14.790 -1.478 1.00 25.27 C
+ATOM 2285 CE2 TYR B 109 7.293 14.914 -3.720 1.00 27.27 C
+ATOM 2286 CZ TYR B 109 6.934 15.535 -2.529 1.00 26.91 C
+ATOM 2287 OH TYR B 109 7.109 16.903 -2.385 1.00 26.26 O
+ATOM 2288 N LEU B 110 3.657 11.769 -0.808 1.00 27.82 N
+ATOM 2289 CA LEU B 110 2.395 12.509 -0.718 1.00 28.19 C
+ATOM 2290 C LEU B 110 2.662 13.986 -1.058 1.00 29.20 C
+ATOM 2291 O LEU B 110 2.880 14.842 -0.189 1.00 29.22 O
+ATOM 2292 CB LEU B 110 1.782 12.370 0.672 1.00 28.02 C
+ATOM 2293 CG LEU B 110 1.154 11.015 1.007 1.00 28.69 C
+ATOM 2294 CD1 LEU B 110 0.555 11.032 2.412 1.00 29.33 C
+ATOM 2295 CD2 LEU B 110 0.102 10.662 -0.032 1.00 28.48 C
+ATOM 2296 N LYS B 111 2.627 14.270 -2.348 1.00 29.75 N
+ATOM 2297 CA LYS B 111 3.038 15.548 -2.873 1.00 30.88 C
+ATOM 2298 C LYS B 111 1.919 16.585 -2.941 1.00 31.35 C
+ATOM 2299 O LYS B 111 0.775 16.281 -3.298 1.00 31.32 O
+ATOM 2300 CB LYS B 111 3.639 15.291 -4.260 1.00 31.50 C
+ATOM 2301 CG LYS B 111 4.041 16.500 -5.084 1.00 32.83 C
+ATOM 2302 CD LYS B 111 4.679 16.036 -6.396 1.00 34.45 C
+ATOM 2303 CE LYS B 111 5.380 17.183 -7.083 1.00 37.39 C
+ATOM 2304 NZ LYS B 111 6.138 16.717 -8.272 1.00 39.06 N
+ATOM 2305 N GLY B 112 2.266 17.812 -2.593 1.00 31.73 N
+ATOM 2306 CA GLY B 112 1.336 18.926 -2.661 1.00 33.06 C
+ATOM 2307 C GLY B 112 2.096 20.163 -2.240 1.00 33.80 C
+ATOM 2308 O GLY B 112 3.180 20.051 -1.672 1.00 33.47 O
+ATOM 2309 N ASP B 113 1.559 21.347 -2.498 1.00 35.07 N
+ATOM 2310 CA ASP B 113 2.317 22.531 -2.116 1.00 36.17 C
+ATOM 2311 C ASP B 113 1.898 23.173 -0.818 1.00 35.88 C
+ATOM 2312 O ASP B 113 0.950 22.748 -0.156 1.00 35.69 O
+ATOM 2313 CB ASP B 113 2.312 23.586 -3.213 1.00 37.57 C
+ATOM 2314 CG ASP B 113 0.932 24.004 -3.589 1.00 39.21 C
+ATOM 2315 OD1 ASP B 113 0.096 24.159 -2.666 1.00 40.01 O
+ATOM 2316 OD2 ASP B 113 0.597 24.175 -4.787 1.00 43.19 O
+ATOM 2317 N PHE B 114 2.638 24.217 -0.486 1.00 35.66 N
+ATOM 2318 CA PHE B 114 2.437 24.983 0.727 1.00 36.17 C
+ATOM 2319 C PHE B 114 0.985 25.349 1.017 1.00 36.12 C
+ATOM 2320 O PHE B 114 0.408 24.873 1.992 1.00 35.98 O
+ATOM 2321 CB PHE B 114 3.278 26.253 0.672 1.00 36.15 C
+ATOM 2322 CG PHE B 114 3.441 26.908 1.994 1.00 38.00 C
+ATOM 2323 CD1 PHE B 114 4.351 26.413 2.909 1.00 38.47 C
+ATOM 2324 CD2 PHE B 114 2.670 28.002 2.338 1.00 38.63 C
+ATOM 2325 CE1 PHE B 114 4.500 27.010 4.135 1.00 39.98 C
+ATOM 2326 CE2 PHE B 114 2.812 28.595 3.560 1.00 38.84 C
+ATOM 2327 CZ PHE B 114 3.723 28.103 4.463 1.00 39.72 C
+ATOM 2328 N ASP B 115 0.394 26.187 0.173 1.00 36.23 N
+ATOM 2329 CA ASP B 115 -0.966 26.653 0.420 1.00 36.54 C
+ATOM 2330 C ASP B 115 -1.875 25.490 0.818 1.00 36.28 C
+ATOM 2331 O ASP B 115 -2.640 25.580 1.777 1.00 35.76 O
+ATOM 2332 CB ASP B 115 -1.529 27.410 -0.793 1.00 36.94 C
+ATOM 2333 CG ASP B 115 -0.749 28.674 -1.108 1.00 39.36 C
+ATOM 2334 OD1 ASP B 115 0.126 29.032 -0.284 1.00 42.50 O
+ATOM 2335 OD2 ASP B 115 -0.930 29.365 -2.151 1.00 39.90 O
+ATOM 2336 N VAL B 116 -1.771 24.375 0.107 1.00 36.63 N
+ATOM 2337 CA VAL B 116 -2.650 23.258 0.414 1.00 36.91 C
+ATOM 2338 C VAL B 116 -2.366 22.655 1.778 1.00 37.14 C
+ATOM 2339 O VAL B 116 -3.285 22.348 2.537 1.00 36.94 O
+ATOM 2340 CB VAL B 116 -2.560 22.133 -0.621 1.00 36.83 C
+ATOM 2341 CG1 VAL B 116 -3.581 21.068 -0.281 1.00 36.41 C
+ATOM 2342 CG2 VAL B 116 -2.807 22.675 -2.010 1.00 36.55 C
+ATOM 2343 N ILE B 117 -1.090 22.480 2.092 1.00 37.58 N
+ATOM 2344 CA ILE B 117 -0.737 21.878 3.364 1.00 38.59 C
+ATOM 2345 C ILE B 117 -1.069 22.861 4.479 1.00 38.58 C
+ATOM 2346 O ILE B 117 -1.671 22.497 5.478 1.00 38.51 O
+ATOM 2347 CB ILE B 117 0.744 21.442 3.379 1.00 38.84 C
+ATOM 2348 CG1 ILE B 117 0.988 20.437 2.246 1.00 40.15 C
+ATOM 2349 CG2 ILE B 117 1.126 20.873 4.751 1.00 38.97 C
+ATOM 2350 CD1 ILE B 117 2.197 19.549 2.415 1.00 42.06 C
+ATOM 2351 N GLU B 118 -0.720 24.118 4.269 1.00 38.73 N
+ATOM 2352 CA GLU B 118 -1.005 25.158 5.239 1.00 39.50 C
+ATOM 2353 C GLU B 118 -2.481 25.113 5.615 1.00 39.42 C
+ATOM 2354 O GLU B 118 -2.835 24.903 6.775 1.00 39.20 O
+ATOM 2355 CB GLU B 118 -0.607 26.509 4.657 1.00 39.61 C
+ATOM 2356 CG GLU B 118 -1.286 27.726 5.257 1.00 42.05 C
+ATOM 2357 CD GLU B 118 -0.725 29.008 4.672 1.00 44.65 C
+ATOM 2358 OE1 GLU B 118 -0.825 29.206 3.436 1.00 46.33 O
+ATOM 2359 OE2 GLU B 118 -0.157 29.800 5.442 1.00 46.21 O
+ATOM 2360 N SER B 119 -3.348 25.266 4.629 1.00 39.48 N
+ATOM 2361 CA SER B 119 -4.761 25.234 4.919 1.00 39.88 C
+ATOM 2362 C SER B 119 -5.053 24.076 5.852 1.00 40.17 C
+ATOM 2363 O SER B 119 -5.621 24.274 6.918 1.00 40.29 O
+ATOM 2364 CB SER B 119 -5.598 25.107 3.637 1.00 40.20 C
+ATOM 2365 OG SER B 119 -5.952 23.757 3.382 1.00 39.65 O
+ATOM 2366 N ARG B 120 -4.649 22.866 5.473 1.00 40.48 N
+ATOM 2367 CA ARG B 120 -4.981 21.684 6.283 1.00 40.75 C
+ATOM 2368 C ARG B 120 -4.459 21.672 7.736 1.00 40.57 C
+ATOM 2369 O ARG B 120 -5.147 21.228 8.653 1.00 40.58 O
+ATOM 2370 CB ARG B 120 -4.578 20.400 5.560 1.00 40.86 C
+ATOM 2371 CG ARG B 120 -5.574 19.974 4.508 1.00 41.38 C
+ATOM 2372 CD ARG B 120 -4.940 19.306 3.331 1.00 42.72 C
+ATOM 2373 NE ARG B 120 -5.860 19.112 2.220 1.00 42.79 N
+ATOM 2374 CZ ARG B 120 -5.705 18.150 1.321 1.00 44.19 C
+ATOM 2375 NH1 ARG B 120 -4.669 17.329 1.415 1.00 42.65 N
+ATOM 2376 NH2 ARG B 120 -6.571 18.000 0.330 1.00 43.56 N
+ATOM 2377 N LEU B 121 -3.241 22.137 7.945 1.00 40.34 N
+ATOM 2378 CA LEU B 121 -2.705 22.170 9.297 1.00 40.51 C
+ATOM 2379 C LEU B 121 -3.555 23.113 10.124 1.00 40.40 C
+ATOM 2380 O LEU B 121 -3.964 22.784 11.228 1.00 39.76 O
+ATOM 2381 CB LEU B 121 -1.257 22.642 9.281 1.00 40.18 C
+ATOM 2382 CG LEU B 121 -0.301 21.539 8.841 1.00 40.33 C
+ATOM 2383 CD1 LEU B 121 1.080 22.102 8.618 1.00 38.47 C
+ATOM 2384 CD2 LEU B 121 -0.296 20.410 9.873 1.00 38.49 C
+ATOM 2385 N LYS B 122 -3.827 24.279 9.543 1.00 41.00 N
+ATOM 2386 CA LYS B 122 -4.642 25.311 10.156 1.00 41.44 C
+ATOM 2387 C LYS B 122 -6.041 24.833 10.532 1.00 41.55 C
+ATOM 2388 O LYS B 122 -6.623 25.338 11.487 1.00 41.54 O
+ATOM 2389 CB LYS B 122 -4.800 26.487 9.200 1.00 42.00 C
+ATOM 2390 CG LYS B 122 -3.622 27.419 9.084 1.00 43.26 C
+ATOM 2391 CD LYS B 122 -4.143 28.820 8.864 1.00 46.91 C
+ATOM 2392 CE LYS B 122 -3.052 29.778 8.420 1.00 50.41 C
+ATOM 2393 NZ LYS B 122 -3.566 31.183 8.320 1.00 51.32 N
+ATOM 2394 N ALA B 123 -6.596 23.887 9.780 1.00 41.20 N
+ATOM 2395 CA ALA B 123 -7.954 23.427 10.078 1.00 41.34 C
+ATOM 2396 C ALA B 123 -8.019 22.477 11.265 1.00 41.33 C
+ATOM 2397 O ALA B 123 -9.078 21.911 11.542 1.00 40.85 O
+ATOM 2398 CB ALA B 123 -8.624 22.791 8.849 1.00 41.19 C
+ATOM 2399 N ARG B 124 -6.893 22.282 11.949 1.00 41.12 N
+ATOM 2400 CA ARG B 124 -6.905 21.451 13.142 1.00 41.49 C
+ATOM 2401 C ARG B 124 -7.550 22.288 14.245 1.00 40.91 C
+ATOM 2402 O ARG B 124 -7.090 23.387 14.559 1.00 40.30 O
+ATOM 2403 CB ARG B 124 -5.494 21.030 13.560 1.00 42.54 C
+ATOM 2404 CG ARG B 124 -4.710 20.195 12.535 1.00 45.02 C
+ATOM 2405 CD ARG B 124 -3.339 19.734 13.040 1.00 49.18 C
+ATOM 2406 NE ARG B 124 -2.828 18.598 12.278 1.00 53.56 N
+ATOM 2407 CZ ARG B 124 -1.674 17.980 12.528 1.00 55.42 C
+ATOM 2408 NH1 ARG B 124 -0.905 18.391 13.531 1.00 56.69 N
+ATOM 2409 NH2 ARG B 124 -1.284 16.959 11.773 1.00 54.54 N
+ATOM 2410 N LYS B 125 -8.626 21.767 14.819 1.00 40.15 N
+ATOM 2411 CA LYS B 125 -9.359 22.495 15.833 1.00 39.31 C
+ATOM 2412 C LYS B 125 -8.423 22.736 16.999 1.00 38.86 C
+ATOM 2413 O LYS B 125 -7.729 21.824 17.446 1.00 38.79 O
+ATOM 2414 CB LYS B 125 -10.600 21.696 16.245 1.00 39.34 C
+ATOM 2415 CG LYS B 125 -11.718 22.523 16.848 1.00 38.57 C
+ATOM 2416 CD LYS B 125 -13.108 21.896 16.607 1.00 34.84 C
+ATOM 2417 CE LYS B 125 -14.053 22.316 17.701 1.00 32.21 C
+ATOM 2418 NZ LYS B 125 -15.469 21.905 17.531 1.00 26.62 N
+ATOM 2419 N GLY B 126 -8.359 23.976 17.465 1.00 38.06 N
+ATOM 2420 CA GLY B 126 -7.500 24.300 18.591 1.00 37.53 C
+ATOM 2421 C GLY B 126 -6.028 24.508 18.263 1.00 37.24 C
+ATOM 2422 O GLY B 126 -5.266 24.969 19.105 1.00 37.17 O
+ATOM 2423 N HIS B 127 -5.617 24.177 17.047 1.00 36.65 N
+ATOM 2424 CA HIS B 127 -4.228 24.339 16.678 1.00 36.62 C
+ATOM 2425 C HIS B 127 -3.854 25.770 16.272 1.00 36.16 C
+ATOM 2426 O HIS B 127 -4.422 26.328 15.339 1.00 35.16 O
+ATOM 2427 CB HIS B 127 -3.838 23.384 15.552 1.00 37.16 C
+ATOM 2428 CG HIS B 127 -2.394 23.488 15.181 1.00 39.32 C
+ATOM 2429 ND1 HIS B 127 -1.964 24.000 13.974 1.00 41.27 N
+ATOM 2430 CD2 HIS B 127 -1.277 23.216 15.896 1.00 40.75 C
+ATOM 2431 CE1 HIS B 127 -0.644 24.008 13.952 1.00 41.94 C
+ATOM 2432 NE2 HIS B 127 -0.203 23.536 15.104 1.00 41.63 N
+ATOM 2433 N PHE B 128 -2.898 26.357 16.983 1.00 36.14 N
+ATOM 2434 CA PHE B 128 -2.399 27.670 16.616 1.00 36.55 C
+ATOM 2435 C PHE B 128 -1.303 27.468 15.587 1.00 36.84 C
+ATOM 2436 O PHE B 128 -0.190 27.077 15.929 1.00 36.83 O
+ATOM 2437 CB PHE B 128 -1.858 28.449 17.817 1.00 36.40 C
+ATOM 2438 CG PHE B 128 -1.625 29.913 17.523 1.00 37.45 C
+ATOM 2439 CD1 PHE B 128 -2.645 30.841 17.703 1.00 37.10 C
+ATOM 2440 CD2 PHE B 128 -0.396 30.356 17.033 1.00 38.36 C
+ATOM 2441 CE1 PHE B 128 -2.446 32.191 17.426 1.00 38.09 C
+ATOM 2442 CE2 PHE B 128 -0.182 31.704 16.746 1.00 39.91 C
+ATOM 2443 CZ PHE B 128 -1.219 32.626 16.941 1.00 39.51 C
+ATOM 2444 N PHE B 129 -1.623 27.717 14.327 1.00 37.28 N
+ATOM 2445 CA PHE B 129 -0.670 27.496 13.247 1.00 38.49 C
+ATOM 2446 C PHE B 129 0.546 28.438 13.250 1.00 39.09 C
+ATOM 2447 O PHE B 129 0.412 29.663 13.222 1.00 39.07 O
+ATOM 2448 CB PHE B 129 -1.362 27.550 11.896 1.00 37.98 C
+ATOM 2449 CG PHE B 129 -0.416 27.451 10.742 1.00 39.33 C
+ATOM 2450 CD1 PHE B 129 0.169 26.234 10.413 1.00 39.83 C
+ATOM 2451 CD2 PHE B 129 -0.085 28.581 9.995 1.00 39.09 C
+ATOM 2452 CE1 PHE B 129 1.053 26.142 9.348 1.00 39.54 C
+ATOM 2453 CE2 PHE B 129 0.796 28.497 8.931 1.00 37.99 C
+ATOM 2454 CZ PHE B 129 1.367 27.279 8.605 1.00 38.86 C
+ATOM 2455 N LYS B 130 1.731 27.842 13.276 1.00 39.87 N
+ATOM 2456 CA LYS B 130 2.991 28.579 13.252 1.00 40.80 C
+ATOM 2457 C LYS B 130 3.605 28.441 11.863 1.00 41.12 C
+ATOM 2458 O LYS B 130 4.109 27.376 11.495 1.00 41.33 O
+ATOM 2459 CB LYS B 130 3.927 28.024 14.329 1.00 41.12 C
+ATOM 2460 CG LYS B 130 3.471 28.375 15.740 1.00 43.15 C
+ATOM 2461 CD LYS B 130 4.276 27.691 16.831 1.00 47.32 C
+ATOM 2462 CE LYS B 130 4.408 28.617 18.039 1.00 49.25 C
+ATOM 2463 NZ LYS B 130 4.684 27.904 19.317 1.00 49.58 N
+ATOM 2464 N THR B 131 3.537 29.513 11.084 1.00 41.13 N
+ATOM 2465 CA THR B 131 4.013 29.494 9.706 1.00 41.70 C
+ATOM 2466 C THR B 131 5.421 28.933 9.490 1.00 41.34 C
+ATOM 2467 O THR B 131 5.646 28.141 8.571 1.00 41.35 O
+ATOM 2468 CB THR B 131 3.916 30.897 9.078 1.00 41.87 C
+ATOM 2469 OG1 THR B 131 2.565 31.358 9.131 1.00 43.91 O
+ATOM 2470 CG2 THR B 131 4.152 30.820 7.599 1.00 42.99 C
+ATOM 2471 N GLN B 132 6.356 29.340 10.338 1.00 41.18 N
+ATOM 2472 CA GLN B 132 7.771 29.006 10.161 1.00 40.86 C
+ATOM 2473 C GLN B 132 8.058 27.507 10.059 1.00 40.40 C
+ATOM 2474 O GLN B 132 8.940 27.080 9.300 1.00 40.29 O
+ATOM 2475 CB GLN B 132 8.610 29.661 11.265 1.00 40.90 C
+ATOM 2476 CG GLN B 132 10.083 29.855 10.922 1.00 42.44 C
+ATOM 2477 CD GLN B 132 10.321 30.788 9.731 1.00 45.23 C
+ATOM 2478 OE1 GLN B 132 9.383 31.373 9.164 1.00 46.47 O
+ATOM 2479 NE2 GLN B 132 11.578 30.926 9.353 1.00 46.52 N
+ATOM 2480 N MET B 133 7.299 26.724 10.817 1.00 39.75 N
+ATOM 2481 CA MET B 133 7.418 25.278 10.826 1.00 39.12 C
+ATOM 2482 C MET B 133 7.332 24.740 9.399 1.00 38.12 C
+ATOM 2483 O MET B 133 8.275 24.128 8.889 1.00 37.83 O
+ATOM 2484 CB MET B 133 6.297 24.679 11.684 1.00 39.26 C
+ATOM 2485 CG MET B 133 6.393 23.176 11.933 1.00 41.79 C
+ATOM 2486 SD MET B 133 5.808 22.087 10.566 1.00 43.96 S
+ATOM 2487 CE MET B 133 4.049 22.232 10.740 1.00 44.07 C
+ATOM 2488 N LEU B 134 6.197 24.992 8.756 1.00 36.81 N
+ATOM 2489 CA LEU B 134 5.960 24.488 7.419 1.00 35.58 C
+ATOM 2490 C LEU B 134 6.977 25.041 6.449 1.00 35.04 C
+ATOM 2491 O LEU B 134 7.426 24.340 5.556 1.00 34.37 O
+ATOM 2492 CB LEU B 134 4.547 24.817 6.940 1.00 35.26 C
+ATOM 2493 CG LEU B 134 4.190 24.140 5.620 1.00 35.02 C
+ATOM 2494 CD1 LEU B 134 4.441 22.633 5.687 1.00 33.14 C
+ATOM 2495 CD2 LEU B 134 2.736 24.418 5.212 1.00 36.62 C
+ATOM 2496 N VAL B 135 7.323 26.313 6.617 1.00 34.60 N
+ATOM 2497 CA VAL B 135 8.327 26.929 5.764 1.00 34.11 C
+ATOM 2498 C VAL B 135 9.632 26.138 5.854 1.00 34.07 C
+ATOM 2499 O VAL B 135 10.276 25.888 4.835 1.00 34.25 O
+ATOM 2500 CB VAL B 135 8.589 28.414 6.127 1.00 34.11 C
+ATOM 2501 CG1 VAL B 135 9.955 28.870 5.585 1.00 33.29 C
+ATOM 2502 CG2 VAL B 135 7.457 29.336 5.600 1.00 33.86 C
+ATOM 2503 N THR B 136 10.012 25.726 7.059 1.00 33.81 N
+ATOM 2504 CA THR B 136 11.259 24.981 7.214 1.00 34.06 C
+ATOM 2505 C THR B 136 11.103 23.598 6.582 1.00 33.86 C
+ATOM 2506 O THR B 136 12.031 23.067 5.979 1.00 33.82 O
+ATOM 2507 CB THR B 136 11.713 24.901 8.700 1.00 34.25 C
+ATOM 2508 OG1 THR B 136 12.003 26.217 9.186 1.00 34.68 O
+ATOM 2509 CG2 THR B 136 13.076 24.220 8.819 1.00 34.39 C
+ATOM 2510 N GLN B 137 9.909 23.033 6.671 1.00 33.47 N
+ATOM 2511 CA GLN B 137 9.691 21.740 6.068 1.00 33.19 C
+ATOM 2512 C GLN B 137 9.990 21.794 4.572 1.00 33.36 C
+ATOM 2513 O GLN B 137 10.721 20.935 4.057 1.00 33.04 O
+ATOM 2514 CB GLN B 137 8.276 21.241 6.336 1.00 33.29 C
+ATOM 2515 CG GLN B 137 8.050 20.869 7.793 1.00 32.37 C
+ATOM 2516 CD GLN B 137 8.709 19.563 8.151 1.00 31.37 C
+ATOM 2517 OE1 GLN B 137 8.295 18.518 7.672 1.00 33.91 O
+ATOM 2518 NE2 GLN B 137 9.728 19.614 8.985 1.00 29.96 N
+ATOM 2519 N PHE B 138 9.469 22.811 3.887 1.00 33.03 N
+ATOM 2520 CA PHE B 138 9.692 22.915 2.449 1.00 33.74 C
+ATOM 2521 C PHE B 138 11.141 23.216 2.066 1.00 34.04 C
+ATOM 2522 O PHE B 138 11.637 22.714 1.059 1.00 34.81 O
+ATOM 2523 CB PHE B 138 8.680 23.844 1.759 1.00 33.56 C
+ATOM 2524 CG PHE B 138 7.390 23.152 1.386 1.00 33.21 C
+ATOM 2525 CD1 PHE B 138 6.475 22.815 2.358 1.00 34.79 C
+ATOM 2526 CD2 PHE B 138 7.098 22.836 0.071 1.00 34.96 C
+ATOM 2527 CE1 PHE B 138 5.288 22.182 2.043 1.00 35.65 C
+ATOM 2528 CE2 PHE B 138 5.905 22.180 -0.256 1.00 36.35 C
+ATOM 2529 CZ PHE B 138 5.005 21.854 0.735 1.00 36.08 C
+ATOM 2530 N GLU B 139 11.818 24.020 2.876 1.00 34.37 N
+ATOM 2531 CA GLU B 139 13.229 24.294 2.660 1.00 34.83 C
+ATOM 2532 C GLU B 139 13.973 22.964 2.722 1.00 34.53 C
+ATOM 2533 O GLU B 139 14.840 22.676 1.895 1.00 34.21 O
+ATOM 2534 CB GLU B 139 13.798 25.223 3.748 1.00 35.14 C
+ATOM 2535 CG GLU B 139 13.059 26.545 3.939 1.00 38.40 C
+ATOM 2536 CD GLU B 139 13.724 27.465 4.961 1.00 41.87 C
+ATOM 2537 OE1 GLU B 139 14.147 26.965 6.036 1.00 42.44 O
+ATOM 2538 OE2 GLU B 139 13.813 28.695 4.691 1.00 42.48 O
+ATOM 2539 N THR B 140 13.614 22.145 3.701 1.00 33.74 N
+ATOM 2540 CA THR B 140 14.335 20.906 3.924 1.00 34.03 C
+ATOM 2541 C THR B 140 14.028 19.836 2.873 1.00 33.73 C
+ATOM 2542 O THR B 140 14.861 18.975 2.600 1.00 33.75 O
+ATOM 2543 CB THR B 140 14.040 20.373 5.342 1.00 33.87 C
+ATOM 2544 OG1 THR B 140 14.318 21.395 6.299 1.00 34.48 O
+ATOM 2545 CG2 THR B 140 14.999 19.275 5.721 1.00 33.16 C
+ATOM 2546 N LEU B 141 12.842 19.911 2.282 1.00 33.33 N
+ATOM 2547 CA LEU B 141 12.393 18.928 1.298 1.00 32.59 C
+ATOM 2548 C LEU B 141 13.265 18.835 0.056 1.00 32.63 C
+ATOM 2549 O LEU B 141 13.498 19.816 -0.644 1.00 32.54 O
+ATOM 2550 CB LEU B 141 10.965 19.235 0.863 1.00 32.51 C
+ATOM 2551 CG LEU B 141 10.371 18.234 -0.127 1.00 31.85 C
+ATOM 2552 CD1 LEU B 141 10.473 16.826 0.415 1.00 30.15 C
+ATOM 2553 CD2 LEU B 141 8.941 18.621 -0.337 1.00 30.70 C
+ATOM 2554 N GLN B 142 13.743 17.633 -0.212 1.00 32.04 N
+ATOM 2555 CA GLN B 142 14.513 17.391 -1.403 1.00 31.38 C
+ATOM 2556 C GLN B 142 13.635 16.427 -2.148 1.00 30.70 C
+ATOM 2557 O GLN B 142 13.628 15.230 -1.859 1.00 30.05 O
+ATOM 2558 CB GLN B 142 15.859 16.770 -1.046 1.00 31.62 C
+ATOM 2559 CG GLN B 142 16.798 17.731 -0.324 1.00 32.99 C
+ATOM 2560 CD GLN B 142 18.110 17.061 0.033 1.00 37.22 C
+ATOM 2561 OE1 GLN B 142 18.204 15.815 0.041 1.00 38.34 O
+ATOM 2562 NE2 GLN B 142 19.129 17.867 0.315 1.00 37.92 N
+ATOM 2563 N GLU B 143 12.846 16.965 -3.068 1.00 30.03 N
+ATOM 2564 CA GLU B 143 11.910 16.141 -3.803 1.00 30.25 C
+ATOM 2565 C GLU B 143 12.650 15.028 -4.565 1.00 29.62 C
+ATOM 2566 O GLU B 143 13.738 15.238 -5.105 1.00 29.41 O
+ATOM 2567 CB GLU B 143 10.997 16.983 -4.712 1.00 30.16 C
+ATOM 2568 CG GLU B 143 9.971 17.807 -3.939 1.00 31.16 C
+ATOM 2569 CD GLU B 143 8.952 18.481 -4.837 1.00 33.75 C
+ATOM 2570 OE1 GLU B 143 7.749 18.148 -4.758 1.00 35.24 O
+ATOM 2571 OE2 GLU B 143 9.351 19.345 -5.633 1.00 36.63 O
+ATOM 2572 N PRO B 144 12.120 13.820 -4.491 1.00 28.96 N
+ATOM 2573 CA PRO B 144 12.686 12.717 -5.259 1.00 28.92 C
+ATOM 2574 C PRO B 144 12.438 12.983 -6.727 1.00 28.74 C
+ATOM 2575 O PRO B 144 11.290 13.010 -7.173 1.00 28.45 O
+ATOM 2576 CB PRO B 144 11.875 11.493 -4.794 1.00 28.89 C
+ATOM 2577 CG PRO B 144 11.194 11.925 -3.490 1.00 28.73 C
+ATOM 2578 CD PRO B 144 11.004 13.401 -3.623 1.00 28.74 C
+ATOM 2579 N GLY B 145 13.507 13.212 -7.471 1.00 29.07 N
+ATOM 2580 CA GLY B 145 13.392 13.369 -8.907 1.00 29.43 C
+ATOM 2581 C GLY B 145 13.223 12.011 -9.576 1.00 29.51 C
+ATOM 2582 O GLY B 145 13.129 10.982 -8.906 1.00 28.90 O
+ATOM 2583 N ALA B 146 13.200 12.027 -10.908 1.00 29.82 N
+ATOM 2584 CA ALA B 146 13.011 10.850 -11.739 1.00 29.42 C
+ATOM 2585 C ALA B 146 14.094 9.792 -11.555 1.00 29.27 C
+ATOM 2586 O ALA B 146 13.839 8.624 -11.731 1.00 28.72 O
+ATOM 2587 CB ALA B 146 12.941 11.263 -13.179 1.00 30.07 C
+ATOM 2588 N ASP B 147 15.303 10.219 -11.221 1.00 28.93 N
+ATOM 2589 CA ASP B 147 16.387 9.297 -10.965 1.00 29.36 C
+ATOM 2590 C ASP B 147 16.132 8.410 -9.725 1.00 29.21 C
+ATOM 2591 O ASP B 147 16.824 7.435 -9.514 1.00 28.96 O
+ATOM 2592 CB ASP B 147 17.661 10.097 -10.764 1.00 29.71 C
+ATOM 2593 CG ASP B 147 17.533 11.101 -9.622 1.00 30.63 C
+ATOM 2594 OD1 ASP B 147 16.552 11.882 -9.603 1.00 31.71 O
+ATOM 2595 OD2 ASP B 147 18.345 11.153 -8.691 1.00 29.17 O
+ATOM 2596 N GLU B 148 15.168 8.757 -8.878 1.00 29.30 N
+ATOM 2597 CA GLU B 148 14.856 7.872 -7.749 1.00 29.22 C
+ATOM 2598 C GLU B 148 13.733 6.988 -8.244 1.00 29.56 C
+ATOM 2599 O GLU B 148 12.564 7.322 -8.136 1.00 30.47 O
+ATOM 2600 CB GLU B 148 14.505 8.646 -6.464 1.00 28.77 C
+ATOM 2601 CG GLU B 148 15.673 9.479 -5.927 1.00 28.79 C
+ATOM 2602 CD GLU B 148 15.386 10.206 -4.613 1.00 28.30 C
+ATOM 2603 OE1 GLU B 148 15.169 9.536 -3.573 1.00 26.52 O
+ATOM 2604 OE2 GLU B 148 15.411 11.457 -4.615 1.00 25.82 O
+ATOM 2605 N THR B 149 14.101 5.854 -8.817 1.00 29.60 N
+ATOM 2606 CA THR B 149 13.130 4.996 -9.490 1.00 29.20 C
+ATOM 2607 C THR B 149 12.225 4.173 -8.597 1.00 29.41 C
+ATOM 2608 O THR B 149 11.283 3.560 -9.090 1.00 29.16 O
+ATOM 2609 CB THR B 149 13.862 4.091 -10.486 1.00 29.46 C
+ATOM 2610 OG1 THR B 149 14.871 3.319 -9.803 1.00 28.22 O
+ATOM 2611 CG2 THR B 149 14.665 4.979 -11.468 1.00 28.76 C
+ATOM 2612 N ASP B 150 12.506 4.155 -7.297 1.00 29.33 N
+ATOM 2613 CA ASP B 150 11.678 3.413 -6.347 1.00 29.76 C
+ATOM 2614 C ASP B 150 10.612 4.322 -5.732 1.00 29.73 C
+ATOM 2615 O ASP B 150 10.001 3.964 -4.722 1.00 28.86 O
+ATOM 2616 CB ASP B 150 12.539 2.743 -5.245 1.00 29.64 C
+ATOM 2617 CG ASP B 150 13.472 3.737 -4.537 1.00 29.84 C
+ATOM 2618 OD1 ASP B 150 13.301 4.963 -4.754 1.00 32.04 O
+ATOM 2619 OD2 ASP B 150 14.400 3.400 -3.759 1.00 27.36 O
+ATOM 2620 N VAL B 151 10.378 5.480 -6.359 1.00 30.14 N
+ATOM 2621 CA VAL B 151 9.409 6.449 -5.841 1.00 30.48 C
+ATOM 2622 C VAL B 151 8.097 6.569 -6.610 1.00 31.27 C
+ATOM 2623 O VAL B 151 8.093 6.856 -7.806 1.00 32.31 O
+ATOM 2624 CB VAL B 151 10.025 7.851 -5.730 1.00 30.41 C
+ATOM 2625 CG1 VAL B 151 8.962 8.861 -5.297 1.00 31.25 C
+ATOM 2626 CG2 VAL B 151 11.177 7.853 -4.753 1.00 28.16 C
+ATOM 2627 N LEU B 152 6.980 6.362 -5.914 1.00 31.58 N
+ATOM 2628 CA LEU B 152 5.647 6.521 -6.489 1.00 31.87 C
+ATOM 2629 C LEU B 152 5.074 7.846 -5.997 1.00 32.32 C
+ATOM 2630 O LEU B 152 5.361 8.244 -4.878 1.00 32.73 O
+ATOM 2631 CB LEU B 152 4.741 5.386 -6.041 1.00 31.61 C
+ATOM 2632 CG LEU B 152 5.172 3.952 -6.379 1.00 33.10 C
+ATOM 2633 CD1 LEU B 152 4.292 2.963 -5.643 1.00 33.48 C
+ATOM 2634 CD2 LEU B 152 5.128 3.678 -7.889 1.00 33.99 C
+ATOM 2635 N VAL B 153 4.265 8.530 -6.806 1.00 32.44 N
+ATOM 2636 CA VAL B 153 3.748 9.838 -6.395 1.00 32.41 C
+ATOM 2637 C VAL B 153 2.240 9.917 -6.357 1.00 32.89 C
+ATOM 2638 O VAL B 153 1.550 9.426 -7.249 1.00 33.28 O
+ATOM 2639 CB VAL B 153 4.312 11.003 -7.246 1.00 32.61 C
+ATOM 2640 CG1 VAL B 153 3.651 12.329 -6.851 1.00 31.60 C
+ATOM 2641 CG2 VAL B 153 5.832 11.096 -7.098 1.00 31.40 C
+ATOM 2642 N VAL B 154 1.736 10.520 -5.288 1.00 33.02 N
+ATOM 2643 CA VAL B 154 0.313 10.653 -5.075 1.00 33.29 C
+ATOM 2644 C VAL B 154 -0.056 12.110 -4.811 1.00 34.05 C
+ATOM 2645 O VAL B 154 0.649 12.826 -4.094 1.00 33.39 O
+ATOM 2646 CB VAL B 154 -0.149 9.759 -3.932 1.00 33.05 C
+ATOM 2647 CG1 VAL B 154 -1.502 10.184 -3.437 1.00 33.49 C
+ATOM 2648 CG2 VAL B 154 -0.194 8.326 -4.393 1.00 32.82 C
+ATOM 2649 N ASP B 155 -1.171 12.518 -5.411 1.00 34.93 N
+ATOM 2650 CA ASP B 155 -1.709 13.869 -5.360 1.00 36.31 C
+ATOM 2651 C ASP B 155 -2.426 14.148 -4.052 1.00 36.62 C
+ATOM 2652 O ASP B 155 -3.519 13.621 -3.837 1.00 36.34 O
+ATOM 2653 CB ASP B 155 -2.749 13.978 -6.473 1.00 36.79 C
+ATOM 2654 CG ASP B 155 -2.994 15.396 -6.931 1.00 39.25 C
+ATOM 2655 OD1 ASP B 155 -3.003 16.333 -6.092 1.00 40.96 O
+ATOM 2656 OD2 ASP B 155 -3.212 15.652 -8.136 1.00 41.31 O
+ATOM 2657 N ILE B 156 -1.866 14.988 -3.184 1.00 37.08 N
+ATOM 2658 CA ILE B 156 -2.584 15.264 -1.934 1.00 38.54 C
+ATOM 2659 C ILE B 156 -3.738 16.261 -2.054 1.00 39.47 C
+ATOM 2660 O ILE B 156 -4.573 16.332 -1.155 1.00 39.78 O
+ATOM 2661 CB ILE B 156 -1.650 15.666 -0.770 1.00 38.23 C
+ATOM 2662 CG1 ILE B 156 -1.088 17.078 -0.976 1.00 39.41 C
+ATOM 2663 CG2 ILE B 156 -0.575 14.618 -0.554 1.00 37.72 C
+ATOM 2664 CD1 ILE B 156 -0.037 17.458 0.039 1.00 40.59 C
+ATOM 2665 N ASP B 157 -3.795 17.015 -3.151 1.00 40.23 N
+ATOM 2666 CA ASP B 157 -4.841 18.020 -3.323 1.00 41.49 C
+ATOM 2667 C ASP B 157 -6.158 17.394 -3.734 1.00 42.01 C
+ATOM 2668 O ASP B 157 -6.815 17.834 -4.670 1.00 42.19 O
+ATOM 2669 CB ASP B 157 -4.437 19.045 -4.372 1.00 41.51 C
+ATOM 2670 CG ASP B 157 -5.347 20.246 -4.370 1.00 42.77 C
+ATOM 2671 OD1 ASP B 157 -6.218 20.324 -3.471 1.00 41.76 O
+ATOM 2672 OD2 ASP B 157 -5.266 21.156 -5.222 1.00 44.12 O
+ATOM 2673 N GLN B 158 -6.549 16.384 -2.988 1.00 42.77 N
+ATOM 2674 CA GLN B 158 -7.682 15.559 -3.318 1.00 43.70 C
+ATOM 2675 C GLN B 158 -8.188 15.160 -1.953 1.00 43.95 C
+ATOM 2676 O GLN B 158 -7.418 15.117 -1.012 1.00 44.33 O
+ATOM 2677 CB GLN B 158 -7.126 14.375 -4.138 1.00 43.48 C
+ATOM 2678 CG GLN B 158 -7.903 13.081 -4.237 1.00 44.01 C
+ATOM 2679 CD GLN B 158 -7.195 12.098 -5.175 1.00 45.15 C
+ATOM 2680 OE1 GLN B 158 -7.833 11.364 -5.933 1.00 46.55 O
+ATOM 2681 NE2 GLN B 158 -5.874 12.109 -5.143 1.00 44.60 N
+ATOM 2682 N PRO B 159 -9.481 14.950 -1.793 1.00 44.32 N
+ATOM 2683 CA PRO B 159 -9.991 14.511 -0.494 1.00 44.40 C
+ATOM 2684 C PRO B 159 -9.271 13.259 0.018 1.00 44.20 C
+ATOM 2685 O PRO B 159 -8.920 12.358 -0.752 1.00 43.86 O
+ATOM 2686 CB PRO B 159 -11.469 14.234 -0.775 1.00 44.74 C
+ATOM 2687 CG PRO B 159 -11.791 15.166 -1.915 1.00 44.73 C
+ATOM 2688 CD PRO B 159 -10.554 15.153 -2.780 1.00 44.37 C
+ATOM 2689 N LEU B 160 -9.045 13.241 1.328 1.00 44.45 N
+ATOM 2690 CA LEU B 160 -8.399 12.141 2.038 1.00 44.68 C
+ATOM 2691 C LEU B 160 -8.643 10.789 1.409 1.00 44.61 C
+ATOM 2692 O LEU B 160 -7.713 10.071 1.039 1.00 44.72 O
+ATOM 2693 CB LEU B 160 -8.925 12.112 3.476 1.00 44.33 C
+ATOM 2694 CG LEU B 160 -8.528 10.900 4.317 1.00 44.73 C
+ATOM 2695 CD1 LEU B 160 -7.010 10.785 4.397 1.00 43.94 C
+ATOM 2696 CD2 LEU B 160 -9.133 10.976 5.705 1.00 45.31 C
+ATOM 2697 N GLU B 161 -9.916 10.451 1.292 1.00 45.00 N
+ATOM 2698 CA GLU B 161 -10.299 9.125 0.832 1.00 45.16 C
+ATOM 2699 C GLU B 161 -9.899 8.892 -0.634 1.00 44.40 C
+ATOM 2700 O GLU B 161 -9.646 7.764 -1.059 1.00 44.09 O
+ATOM 2701 CB GLU B 161 -11.775 8.890 1.152 1.00 45.53 C
+ATOM 2702 CG GLU B 161 -12.296 9.845 2.235 1.00 48.45 C
+ATOM 2703 CD GLU B 161 -11.750 9.585 3.648 1.00 51.59 C
+ATOM 2704 OE1 GLU B 161 -10.943 8.636 3.860 1.00 50.19 O
+ATOM 2705 OE2 GLU B 161 -12.142 10.353 4.568 1.00 51.98 O
+ATOM 2706 N GLY B 162 -9.780 9.976 -1.391 1.00 43.53 N
+ATOM 2707 CA GLY B 162 -9.238 9.866 -2.732 1.00 42.57 C
+ATOM 2708 C GLY B 162 -7.729 9.661 -2.646 1.00 41.56 C
+ATOM 2709 O GLY B 162 -7.133 8.881 -3.405 1.00 41.79 O
+ATOM 2710 N VAL B 163 -7.098 10.359 -1.709 1.00 40.35 N
+ATOM 2711 CA VAL B 163 -5.659 10.221 -1.533 1.00 39.13 C
+ATOM 2712 C VAL B 163 -5.422 8.778 -1.162 1.00 38.39 C
+ATOM 2713 O VAL B 163 -4.506 8.130 -1.646 1.00 37.76 O
+ATOM 2714 CB VAL B 163 -5.123 11.117 -0.408 1.00 38.83 C
+ATOM 2715 CG1 VAL B 163 -3.667 10.794 -0.133 1.00 38.69 C
+ATOM 2716 CG2 VAL B 163 -5.286 12.549 -0.768 1.00 38.00 C
+ATOM 2717 N VAL B 164 -6.290 8.281 -0.301 1.00 37.89 N
+ATOM 2718 CA VAL B 164 -6.221 6.898 0.110 1.00 38.21 C
+ATOM 2719 C VAL B 164 -6.238 6.015 -1.122 1.00 38.02 C
+ATOM 2720 O VAL B 164 -5.292 5.268 -1.374 1.00 37.90 O
+ATOM 2721 CB VAL B 164 -7.412 6.520 1.009 1.00 38.58 C
+ATOM 2722 CG1 VAL B 164 -7.395 5.049 1.317 1.00 38.33 C
+ATOM 2723 CG2 VAL B 164 -7.385 7.323 2.296 1.00 38.81 C
+ATOM 2724 N ALA B 165 -7.311 6.128 -1.905 1.00 38.08 N
+ATOM 2725 CA ALA B 165 -7.468 5.320 -3.109 1.00 37.95 C
+ATOM 2726 C ALA B 165 -6.294 5.480 -4.061 1.00 37.93 C
+ATOM 2727 O ALA B 165 -5.792 4.501 -4.612 1.00 38.08 O
+ATOM 2728 CB ALA B 165 -8.797 5.638 -3.824 1.00 38.51 C
+ATOM 2729 N SER B 166 -5.845 6.707 -4.269 1.00 37.38 N
+ATOM 2730 CA SER B 166 -4.708 6.879 -5.149 1.00 37.19 C
+ATOM 2731 C SER B 166 -3.503 6.124 -4.569 1.00 36.99 C
+ATOM 2732 O SER B 166 -2.677 5.570 -5.317 1.00 36.19 O
+ATOM 2733 CB SER B 166 -4.395 8.356 -5.344 1.00 37.09 C
+ATOM 2734 OG SER B 166 -5.558 9.049 -5.747 1.00 37.38 O
+ATOM 2735 N THR B 167 -3.413 6.100 -3.240 1.00 36.64 N
+ATOM 2736 CA THR B 167 -2.324 5.399 -2.583 1.00 37.20 C
+ATOM 2737 C THR B 167 -2.556 3.927 -2.800 1.00 38.02 C
+ATOM 2738 O THR B 167 -1.671 3.184 -3.213 1.00 37.67 O
+ATOM 2739 CB THR B 167 -2.291 5.679 -1.065 1.00 36.70 C
+ATOM 2740 OG1 THR B 167 -2.237 7.093 -0.830 1.00 36.58 O
+ATOM 2741 CG2 THR B 167 -0.994 5.161 -0.472 1.00 34.46 C
+ATOM 2742 N ILE B 168 -3.766 3.506 -2.500 1.00 39.60 N
+ATOM 2743 CA ILE B 168 -4.125 2.123 -2.714 1.00 41.90 C
+ATOM 2744 C ILE B 168 -3.870 1.739 -4.177 1.00 43.20 C
+ATOM 2745 O ILE B 168 -3.379 0.652 -4.459 1.00 43.21 O
+ATOM 2746 CB ILE B 168 -5.595 1.899 -2.316 1.00 41.82 C
+ATOM 2747 CG1 ILE B 168 -5.705 1.879 -0.794 1.00 41.64 C
+ATOM 2748 CG2 ILE B 168 -6.140 0.609 -2.949 1.00 41.99 C
+ATOM 2749 CD1 ILE B 168 -7.090 1.644 -0.281 1.00 43.17 C
+ATOM 2750 N GLU B 169 -4.172 2.654 -5.095 1.00 44.98 N
+ATOM 2751 CA GLU B 169 -3.993 2.398 -6.522 1.00 47.02 C
+ATOM 2752 C GLU B 169 -2.505 2.206 -6.886 1.00 47.68 C
+ATOM 2753 O GLU B 169 -2.150 1.282 -7.623 1.00 47.11 O
+ATOM 2754 CB GLU B 169 -4.659 3.505 -7.358 1.00 47.15 C
+ATOM 2755 CG GLU B 169 -5.037 3.092 -8.781 1.00 50.67 C
+ATOM 2756 CD GLU B 169 -5.569 4.244 -9.635 1.00 53.67 C
+ATOM 2757 OE1 GLU B 169 -4.962 4.529 -10.691 1.00 54.10 O
+ATOM 2758 OE2 GLU B 169 -6.595 4.864 -9.258 1.00 55.81 O
+ATOM 2759 N VAL B 170 -1.629 3.052 -6.355 1.00 48.81 N
+ATOM 2760 CA VAL B 170 -0.218 2.901 -6.674 1.00 50.68 C
+ATOM 2761 C VAL B 170 0.388 1.678 -6.001 1.00 51.70 C
+ATOM 2762 O VAL B 170 1.359 1.113 -6.490 1.00 51.58 O
+ATOM 2763 CB VAL B 170 0.615 4.136 -6.322 1.00 50.85 C
+ATOM 2764 CG1 VAL B 170 1.984 3.982 -6.906 1.00 51.40 C
+ATOM 2765 CG2 VAL B 170 -0.015 5.384 -6.892 1.00 51.03 C
+ATOM 2766 N ILE B 171 -0.195 1.272 -4.880 1.00 53.49 N
+ATOM 2767 CA ILE B 171 0.264 0.091 -4.164 1.00 55.46 C
+ATOM 2768 C ILE B 171 -0.118 -1.162 -4.939 1.00 57.44 C
+ATOM 2769 O ILE B 171 0.670 -2.112 -5.057 1.00 57.37 O
+ATOM 2770 CB ILE B 171 -0.352 0.042 -2.752 1.00 55.36 C
+ATOM 2771 CG1 ILE B 171 0.467 0.892 -1.771 1.00 55.19 C
+ATOM 2772 CG2 ILE B 171 -0.434 -1.381 -2.248 1.00 54.82 C
+ATOM 2773 CD1 ILE B 171 -0.006 0.777 -0.344 1.00 54.30 C
+ATOM 2774 N LYS B 172 -1.333 -1.163 -5.474 1.00 59.75 N
+ATOM 2775 CA LYS B 172 -1.823 -2.316 -6.215 1.00 62.11 C
+ATOM 2776 C LYS B 172 -1.381 -2.307 -7.678 1.00 63.77 C
+ATOM 2777 O LYS B 172 -1.440 -3.329 -8.357 1.00 63.92 O
+ATOM 2778 CB LYS B 172 -3.338 -2.426 -6.090 1.00 61.97 C
+ATOM 2779 CG LYS B 172 -3.787 -3.141 -4.828 1.00 62.19 C
+ATOM 2780 CD LYS B 172 -5.199 -2.745 -4.463 1.00 62.87 C
+ATOM 2781 CE LYS B 172 -5.978 -3.908 -3.876 1.00 63.81 C
+ATOM 2782 NZ LYS B 172 -7.365 -3.496 -3.514 1.00 64.19 N
+ATOM 2783 N LYS B 173 -0.916 -1.150 -8.143 1.00 65.96 N
+ATOM 2784 CA LYS B 173 -0.435 -0.999 -9.510 1.00 68.00 C
+ATOM 2785 C LYS B 173 0.567 -2.096 -9.839 1.00 68.93 C
+ATOM 2786 O LYS B 173 0.809 -2.405 -11.008 1.00 69.34 O
+ATOM 2787 CB LYS B 173 0.215 0.377 -9.696 1.00 68.41 C
+ATOM 2788 CG LYS B 173 0.758 0.633 -11.100 1.00 70.55 C
+ATOM 2789 CD LYS B 173 1.341 2.041 -11.256 1.00 73.74 C
+ATOM 2790 CE LYS B 173 0.256 3.079 -11.524 1.00 75.78 C
+ATOM 2791 NZ LYS B 173 0.836 4.418 -11.862 1.00 77.25 N
+ATOM 2792 N GLY B 174 1.149 -2.689 -8.802 1.00 69.88 N
+ATOM 2793 CA GLY B 174 2.119 -3.754 -8.984 1.00 70.73 C
+ATOM 2794 C GLY B 174 2.752 -4.184 -7.675 1.00 71.24 C
+ATOM 2795 O GLY B 174 2.122 -4.827 -6.835 1.00 71.68 O
+TER 2796 GLY B 174
+HETATM 2797 MG MG B1002 1.955 12.234 11.064 1.00 28.40 MG
+HETATM 2798 PG ATP B 303 2.930 15.082 10.703 1.00 29.50 P
+HETATM 2799 O1G ATP B 303 3.070 16.428 11.274 1.00 27.19 O
+HETATM 2800 O2G ATP B 303 4.227 14.547 10.072 1.00 31.85 O
+HETATM 2801 O3G ATP B 303 2.421 14.068 11.723 1.00 29.10 O
+HETATM 2802 PB ATP B 303 1.336 14.041 8.650 1.00 24.02 P
+HETATM 2803 O1B ATP B 303 1.311 12.770 9.398 1.00 23.68 O
+HETATM 2804 O2B ATP B 303 2.034 13.946 7.285 1.00 26.37 O
+HETATM 2805 O3B ATP B 303 1.892 15.268 9.501 1.00 28.80 O
+HETATM 2806 PA ATP B 303 -1.499 14.142 9.044 1.00 27.19 P
+HETATM 2807 O1A ATP B 303 -1.829 12.766 8.607 1.00 24.88 O
+HETATM 2808 O2A ATP B 303 -1.501 14.319 10.576 1.00 25.41 O
+HETATM 2809 O3A ATP B 303 -0.122 14.631 8.374 1.00 26.08 O
+HETATM 2810 O5' ATP B 303 -2.533 15.167 8.364 1.00 28.49 O
+HETATM 2811 C5' ATP B 303 -2.513 16.574 8.490 1.00 28.82 C
+HETATM 2812 C4' ATP B 303 -3.965 17.015 8.732 1.00 31.93 C
+HETATM 2813 O4' ATP B 303 -4.695 17.115 7.527 1.00 31.82 O
+HETATM 2814 C3' ATP B 303 -4.656 15.956 9.559 1.00 32.92 C
+HETATM 2815 O3' ATP B 303 -5.475 16.602 10.491 1.00 35.35 O
+HETATM 2816 C2' ATP B 303 -5.527 15.179 8.605 1.00 33.47 C
+HETATM 2817 O2' ATP B 303 -6.710 14.858 9.308 1.00 33.75 O
+HETATM 2818 C1' ATP B 303 -5.743 16.154 7.456 1.00 34.63 C
+HETATM 2819 N9 ATP B 303 -5.688 15.549 6.097 1.00 37.28 N
+HETATM 2820 C8 ATP B 303 -4.796 14.620 5.642 1.00 36.76 C
+HETATM 2821 N7 ATP B 303 -5.054 14.356 4.347 1.00 36.02 N
+HETATM 2822 C5 ATP B 303 -6.082 15.115 3.946 1.00 38.02 C
+HETATM 2823 C6 ATP B 303 -6.739 15.216 2.719 1.00 38.88 C
+HETATM 2824 N6 ATP B 303 -6.091 14.856 1.616 1.00 38.60 N
+HETATM 2825 N1 ATP B 303 -7.790 16.095 2.604 1.00 38.38 N
+HETATM 2826 C2 ATP B 303 -8.174 16.842 3.701 1.00 37.92 C
+HETATM 2827 N3 ATP B 303 -7.523 16.718 4.905 1.00 36.77 N
+HETATM 2828 C4 ATP B 303 -6.487 15.875 5.030 1.00 37.23 C
+HETATM 2829 O HOH B1003 16.199 2.740 18.055 1.00 18.12 O
+HETATM 2830 O HOH B1004 17.508 3.465 22.490 1.00 19.35 O
+HETATM 2831 O HOH B1005 4.737 16.654 1.307 1.00 27.77 O
+HETATM 2832 O HOH B1006 12.463 13.678 7.198 1.00 18.92 O
+HETATM 2833 O HOH B1007 -3.827 29.647 13.549 1.00 30.06 O
+HETATM 2834 O HOH B1008 6.036 -6.238 3.153 1.00 26.28 O
+HETATM 2835 O HOH B1009 11.028 -7.156 -4.974 1.00 29.17 O
+HETATM 2836 O HOH B1010 3.604 -9.849 10.604 1.00 22.73 O
+HETATM 2837 O HOH B1011 20.938 -1.845 -1.485 1.00 32.12 O
+HETATM 2838 O HOH B1012 1.679 8.218 12.181 1.00 26.66 O
+HETATM 2839 O HOH B1013 -11.647 22.415 10.868 1.00 36.96 O
+HETATM 2840 O HOH B1014 12.516 3.433 19.866 1.00 17.60 O
+HETATM 2841 O HOH B1015 22.702 9.607 -0.203 1.00 41.65 O
+HETATM 2842 O HOH B1016 11.373 -0.152 -7.693 1.00 31.86 O
+HETATM 2843 O HOH B1017 -5.391 26.474 -1.384 1.00 32.21 O
+HETATM 2844 O HOH B1018 19.956 20.548 17.579 1.00 43.33 O
+HETATM 2845 O HOH B1019 4.674 -14.498 4.782 1.00 25.38 O
+HETATM 2846 O HOH B1020 8.826 8.570 11.011 1.00 18.39 O
+HETATM 2847 O HOH B1021 -2.456 6.943 -7.905 1.00 31.16 O
+HETATM 2848 O HOH B1022 -16.164 18.735 17.294 1.00 40.89 O
+HETATM 2849 O HOH B1023 8.256 16.303 8.734 1.00 25.09 O
+HETATM 2850 O HOH B1024 -10.362 18.491 1.533 1.00 57.63 O
+HETATM 2851 O HOH B1025 0.107 12.993 11.918 1.00 13.03 O
+HETATM 2852 O HOH B1026 19.207 7.609 -7.999 1.00 23.34 O
+HETATM 2853 O HOH B1027 21.269 3.757 18.851 1.00 25.81 O
+HETATM 2854 O HOH B1028 15.790 2.691 -7.154 1.00 36.24 O
+HETATM 2855 O HOH B1029 1.112 6.518 15.210 1.00 33.82 O
+HETATM 2856 O HOH B1030 0.322 -7.873 3.767 1.00 25.68 O
+HETATM 2857 O HOH B1031 14.211 -6.421 2.717 1.00 32.58 O
+HETATM 2858 O HOH B1032 9.954 27.137 2.128 1.00 29.28 O
+HETATM 2859 O HOH B1033 -3.430 8.885 12.746 1.00 31.83 O
+HETATM 2860 O HOH B1034 1.649 26.808 -2.528 1.00 39.40 O
+HETATM 2861 O HOH B1035 2.045 11.873 13.009 1.00 17.16 O
+HETATM 2862 O HOH B1036 3.518 11.607 10.908 1.00 28.35 O
+CONECT 1354 1355 1356 1357 1361
+CONECT 1355 1354
+CONECT 1356 1354
+CONECT 1357 1354
+CONECT 1358 1359 1360 1361 1365
+CONECT 1359 1358
+CONECT 1360 1358
+CONECT 1361 1354 1358
+CONECT 1362 1363 1364 1365 1366
+CONECT 1363 1362
+CONECT 1364 1362
+CONECT 1365 1358 1362
+CONECT 1366 1362 1367
+CONECT 1367 1366 1368
+CONECT 1368 1367 1369 1370
+CONECT 1369 1368 1374
+CONECT 1370 1368 1371 1372
+CONECT 1371 1370
+CONECT 1372 1370 1373 1374
+CONECT 1373 1372
+CONECT 1374 1369 1372 1375
+CONECT 1375 1374 1376 1384
+CONECT 1376 1375 1377
+CONECT 1377 1376 1378
+CONECT 1378 1377 1379 1384
+CONECT 1379 1378 1380 1381
+CONECT 1380 1379
+CONECT 1381 1379 1382
+CONECT 1382 1381 1383
+CONECT 1383 1382 1384
+CONECT 1384 1375 1378 1383
+CONECT 2798 2799 2800 2801 2805
+CONECT 2799 2798
+CONECT 2800 2798
+CONECT 2801 2798
+CONECT 2802 2803 2804 2805 2809
+CONECT 2803 2802
+CONECT 2804 2802
+CONECT 2805 2798 2802
+CONECT 2806 2807 2808 2809 2810
+CONECT 2807 2806
+CONECT 2808 2806
+CONECT 2809 2802 2806
+CONECT 2810 2806 2811
+CONECT 2811 2810 2812
+CONECT 2812 2811 2813 2814
+CONECT 2813 2812 2818
+CONECT 2814 2812 2815 2816
+CONECT 2815 2814
+CONECT 2816 2814 2817 2818
+CONECT 2817 2816
+CONECT 2818 2813 2816 2819
+CONECT 2819 2818 2820 2828
+CONECT 2820 2819 2821
+CONECT 2821 2820 2822
+CONECT 2822 2821 2823 2828
+CONECT 2823 2822 2824 2825
+CONECT 2824 2823
+CONECT 2825 2823 2826
+CONECT 2826 2825 2827
+CONECT 2827 2826 2828
+CONECT 2828 2819 2822 2827
+END
diff --git a/doc/tests/data/2IYW.pdb b/doc/tests/data/2IYW.pdb
new file mode 100644
index 0000000000000000000000000000000000000000..8c01e0acd3484636496a09fbe274ee37b9150012
--- /dev/null
+++ b/doc/tests/data/2IYW.pdb
@@ -0,0 +1,1645 @@
+ATOM 1 N ALA A 2 11.967 20.925 2.908 1.00 23.50 N
+ATOM 2 CA ALA A 2 12.980 21.586 2.027 1.00 22.36 C
+ATOM 3 C ALA A 2 14.366 21.137 2.439 1.00 19.46 C
+ATOM 4 O ALA A 2 14.597 20.855 3.611 1.00 18.97 O
+ATOM 5 CB ALA A 2 12.885 23.092 2.124 1.00 23.06 C
+ATOM 6 N PRO A 3 15.298 21.060 1.478 1.00 14.92 N
+ATOM 7 CA PRO A 3 16.630 20.599 1.853 1.00 13.44 C
+ATOM 8 C PRO A 3 17.270 21.431 2.957 1.00 11.41 C
+ATOM 9 O PRO A 3 17.071 22.651 3.032 1.00 13.66 O
+ATOM 10 CB PRO A 3 17.416 20.701 0.532 1.00 12.13 C
+ATOM 11 CG PRO A 3 16.412 20.585 -0.500 1.00 13.11 C
+ATOM 12 CD PRO A 3 15.202 21.302 0.027 1.00 15.39 C
+ATOM 13 N LYS A 4 18.027 20.776 3.824 1.00 12.49 N
+ATOM 14 CA LYS A 4 18.866 21.479 4.779 1.00 12.14 C
+ATOM 15 C LYS A 4 19.899 22.361 4.076 1.00 10.81 C
+ATOM 16 O LYS A 4 20.204 23.451 4.539 1.00 10.33 O
+ATOM 17 CB LYS A 4 19.559 20.512 5.746 1.00 13.75 C
+ATOM 18 CG LYS A 4 18.610 19.643 6.579 1.00 18.60 C
+ATOM 19 CD LYS A 4 17.551 20.430 7.370 1.00 24.95 C
+ATOM 20 CE LYS A 4 16.203 19.686 7.440 1.00 27.71 C
+ATOM 21 NZ LYS A 4 15.307 19.916 6.244 1.00 27.73 N
+ATOM 22 N ALA A 5 20.420 21.898 2.949 1.00 9.45 N
+ATOM 23 CA ALA A 5 21.393 22.681 2.179 1.00 8.90 C
+ATOM 24 C ALA A 5 21.361 22.198 0.736 1.00 7.11 C
+ATOM 25 O ALA A 5 21.256 21.005 0.510 1.00 8.55 O
+ATOM 26 CB ALA A 5 22.782 22.479 2.750 1.00 9.59 C
+ATOM 27 N VAL A 6 21.428 23.144 -0.205 1.00 7.26 N
+ATOM 28 CA VAL A 6 21.587 22.877 -1.640 1.00 6.73 C
+ATOM 29 C VAL A 6 23.003 23.316 -2.014 1.00 7.23 C
+ATOM 30 O VAL A 6 23.343 24.490 -1.854 1.00 8.71 O
+ATOM 31 CB VAL A 6 20.573 23.684 -2.484 1.00 6.96 C
+ATOM 32 CG1 VAL A 6 20.668 23.305 -3.955 1.00 10.21 C
+ATOM 33 CG2 VAL A 6 19.137 23.456 -1.968 1.00 9.06 C
+ATOM 34 N LEU A 7 23.832 22.380 -2.459 1.00 7.37 N
+ATOM 35 CA LEU A 7 25.220 22.691 -2.813 1.00 8.02 C
+ATOM 36 C LEU A 7 25.351 23.021 -4.296 1.00 8.44 C
+ATOM 37 O LEU A 7 24.847 22.297 -5.133 1.00 6.96 O
+ATOM 38 CB LEU A 7 26.149 21.521 -2.468 1.00 8.68 C
+ATOM 39 CG LEU A 7 26.111 20.987 -1.036 1.00 10.01 C
+ATOM 40 CD1 LEU A 7 27.099 19.852 -0.883 1.00 10.06 C
+ATOM 41 CD2 LEU A 7 26.420 22.076 -0.035 1.00 11.54 C
+ATOM 42 N VAL A 8 26.029 24.122 -4.605 1.00 9.12 N
+ATOM 43 CA VAL A 8 26.313 24.501 -5.997 1.00 8.97 C
+ATOM 44 C VAL A 8 27.777 24.869 -6.137 1.00 8.74 C
+ATOM 45 O VAL A 8 28.411 25.260 -5.161 1.00 8.45 O
+ATOM 46 CB VAL A 8 25.439 25.694 -6.477 1.00 8.99 C
+ATOM 47 CG1 VAL A 8 23.939 25.358 -6.360 1.00 11.02 C
+ATOM 48 CG2 VAL A 8 25.771 26.978 -5.723 1.00 7.36 C
+ATOM 49 N GLY A 9 28.321 24.725 -7.343 1.00 8.80 N
+ATOM 50 CA GLY A 9 29.721 25.053 -7.579 1.00 9.76 C
+ATOM 51 C GLY A 9 30.256 24.437 -8.847 1.00 9.85 C
+ATOM 52 O GLY A 9 29.619 23.584 -9.449 1.00 10.90 O
+ATOM 53 N LEU A 10 31.448 24.864 -9.235 1.00 10.91 N
+ATOM 54 CA LEU A 10 32.100 24.324 -10.436 1.00 11.30 C
+ATOM 55 C LEU A 10 32.567 22.875 -10.281 1.00 12.07 C
+ATOM 56 O LEU A 10 32.561 22.322 -9.173 1.00 12.44 O
+ATOM 57 CB LEU A 10 33.307 25.184 -10.769 1.00 11.16 C
+ATOM 58 CG LEU A 10 33.005 26.624 -11.148 1.00 12.41 C
+ATOM 59 CD1 LEU A 10 34.303 27.468 -11.090 1.00 13.49 C
+ATOM 60 CD2 LEU A 10 32.392 26.665 -12.515 1.00 12.07 C
+ATOM 61 N PRO A 11 33.023 22.262 -11.391 1.00 12.98 N
+ATOM 62 CA PRO A 11 33.591 20.924 -11.266 1.00 12.45 C
+ATOM 63 C PRO A 11 34.815 20.950 -10.356 1.00 12.66 C
+ATOM 64 O PRO A 11 35.650 21.853 -10.439 1.00 13.17 O
+ATOM 65 CB PRO A 11 33.955 20.538 -12.724 1.00 11.77 C
+ATOM 66 CG PRO A 11 33.157 21.478 -13.577 1.00 13.86 C
+ATOM 67 CD PRO A 11 33.051 22.741 -12.785 1.00 12.55 C
+ATOM 68 N GLY A 12 34.876 19.987 -9.451 1.00 13.49 N
+ATOM 69 CA GLY A 12 35.948 19.908 -8.473 1.00 13.10 C
+ATOM 70 C GLY A 12 35.769 20.762 -7.234 1.00 12.70 C
+ATOM 71 O GLY A 12 36.599 20.704 -6.330 1.00 12.76 O
+ATOM 72 N SER A 13 34.688 21.548 -7.159 1.00 10.66 N
+ATOM 73 CA SER A 13 34.466 22.399 -5.997 1.00 8.47 C
+ATOM 74 C SER A 13 34.160 21.607 -4.718 1.00 9.48 C
+ATOM 75 O SER A 13 34.333 22.117 -3.610 1.00 10.04 O
+ATOM 76 CB SER A 13 33.353 23.416 -6.262 1.00 8.10 C
+ATOM 77 OG SER A 13 32.122 22.818 -6.578 1.00 8.57 O
+ATOM 78 N GLY A 14 33.691 20.377 -4.872 1.00 9.46 N
+ATOM 79 CA GLY A 14 33.421 19.506 -3.727 1.00 9.82 C
+ATOM 80 C GLY A 14 31.973 19.105 -3.532 1.00 11.40 C
+ATOM 81 O GLY A 14 31.601 18.632 -2.460 1.00 11.61 O
+ATOM 82 N LYS A 15 31.146 19.248 -4.562 1.00 11.03 N
+ATOM 83 CA LYS A 15 29.714 18.906 -4.421 1.00 13.00 C
+ATOM 84 C LYS A 15 29.504 17.461 -3.920 1.00 12.89 C
+ATOM 85 O LYS A 15 28.676 17.210 -3.040 1.00 12.78 O
+ATOM 86 CB LYS A 15 28.974 19.147 -5.731 1.00 12.66 C
+ATOM 87 CG LYS A 15 28.893 20.625 -6.123 1.00 13.04 C
+ATOM 88 CD LYS A 15 28.119 20.824 -7.434 1.00 14.68 C
+ATOM 89 CE LYS A 15 28.748 20.146 -8.643 1.00 14.92 C
+ATOM 90 NZ LYS A 15 30.209 20.488 -8.860 1.00 14.66 N
+ATOM 91 N SER A 16 30.289 16.525 -4.436 1.00 13.46 N
+ATOM 92 CA SER A 16 30.173 15.119 -4.014 1.00 13.24 C
+ATOM 93 C SER A 16 30.776 14.888 -2.634 1.00 13.01 C
+ATOM 94 O SER A 16 30.120 14.381 -1.721 1.00 11.59 O
+ATOM 95 CB SER A 16 30.851 14.221 -5.044 1.00 13.75 C
+ATOM 96 OG SER A 16 30.166 14.310 -6.267 1.00 13.25 O
+ATOM 97 N THR A 17 32.036 15.283 -2.489 1.00 12.02 N
+ATOM 98 CA THR A 17 32.780 15.148 -1.223 1.00 12.25 C
+ATOM 99 C THR A 17 32.111 15.838 -0.042 1.00 11.87 C
+ATOM 100 O THR A 17 31.906 15.236 1.022 1.00 10.95 O
+ATOM 101 CB THR A 17 34.186 15.739 -1.393 1.00 12.67 C
+ATOM 102 OG1 THR A 17 34.819 15.123 -2.521 1.00 14.69 O
+ATOM 103 CG2 THR A 17 35.016 15.515 -0.151 1.00 15.06 C
+ATOM 104 N ILE A 18 31.779 17.114 -0.227 1.00 11.25 N
+ATOM 105 CA ILE A 18 31.101 17.880 0.811 1.00 10.45 C
+ATOM 106 C ILE A 18 29.654 17.404 1.018 1.00 10.83 C
+ATOM 107 O ILE A 18 29.168 17.367 2.151 1.00 11.45 O
+ATOM 108 CB ILE A 18 31.126 19.385 0.490 1.00 10.65 C
+ATOM 109 CG1 ILE A 18 32.581 19.858 0.292 1.00 9.73 C
+ATOM 110 CG2 ILE A 18 30.420 20.197 1.580 1.00 8.70 C
+ATOM 111 CD1 ILE A 18 33.527 19.626 1.481 1.00 9.51 C
+ATOM 112 N GLY A 19 28.984 17.071 -0.079 1.00 10.17 N
+ATOM 113 CA GLY A 19 27.659 16.435 -0.036 1.00 10.98 C
+ATOM 114 C GLY A 19 27.627 15.237 0.912 1.00 11.08 C
+ATOM 115 O GLY A 19 26.811 15.185 1.840 1.00 11.42 O
+ATOM 116 N ARG A 20 28.531 14.287 0.707 1.00 12.25 N
+ATOM 117 CA ARG A 20 28.585 13.101 1.561 1.00 13.64 C
+ATOM 118 C ARG A 20 28.919 13.450 2.999 1.00 13.24 C
+ATOM 119 O ARG A 20 28.232 13.019 3.916 1.00 12.27 O
+ATOM 120 CB ARG A 20 29.630 12.106 1.060 1.00 14.88 C
+ATOM 121 CG ARG A 20 29.283 11.449 -0.261 1.00 21.78 C
+ATOM 122 CD ARG A 20 30.299 10.361 -0.603 1.00 29.42 C
+ATOM 123 NE ARG A 20 31.478 10.904 -1.280 1.00 34.66 N
+ATOM 124 CZ ARG A 20 31.648 10.954 -2.603 1.00 38.60 C
+ATOM 125 NH1 ARG A 20 30.720 10.486 -3.442 1.00 39.52 N
+ATOM 126 NH2 ARG A 20 32.765 11.471 -3.099 1.00 40.42 N
+ATOM 127 N ARG A 21 29.980 14.226 3.200 1.00 11.77 N
+ATOM 128 CA ARG A 21 30.439 14.519 4.547 1.00 12.68 C
+ATOM 129 C ARG A 21 29.425 15.339 5.352 1.00 11.67 C
+ATOM 130 O ARG A 21 29.258 15.110 6.546 1.00 10.99 O
+ATOM 131 CB AARG A 21 31.787 15.238 4.499 0.50 13.34 C
+ATOM 131 CB BARG A 21 31.779 15.261 4.509 0.50 13.36 C
+ATOM 132 CG AARG A 21 32.900 14.373 3.960 0.50 17.78 C
+ATOM 132 CG BARG A 21 32.954 14.397 4.134 0.50 17.72 C
+ATOM 133 CD AARG A 21 34.202 15.131 3.937 0.50 22.71 C
+ATOM 133 CD BARG A 21 34.176 15.256 3.883 0.50 22.48 C
+ATOM 134 NE AARG A 21 34.727 15.299 5.291 0.50 25.41 N
+ATOM 134 NE BARG A 21 35.398 14.465 3.742 0.50 24.76 N
+ATOM 135 CZ AARG A 21 35.909 14.859 5.721 0.50 27.97 C
+ATOM 135 CZ BARG A 21 36.341 14.332 4.676 0.50 28.25 C
+ATOM 136 NH1AARG A 21 36.748 14.224 4.903 0.50 29.79 N
+ATOM 136 NH1BARG A 21 36.235 14.931 5.865 0.50 28.29 N
+ATOM 137 NH2AARG A 21 36.267 15.071 6.984 0.50 27.94 N
+ATOM 137 NH2BARG A 21 37.410 13.592 4.417 0.50 29.88 N
+ATOM 138 N LEU A 22 28.776 16.305 4.702 1.00 10.51 N
+ATOM 139 CA LEU A 22 27.766 17.139 5.355 1.00 11.80 C
+ATOM 140 C LEU A 22 26.515 16.316 5.717 1.00 10.72 C
+ATOM 141 O LEU A 22 25.957 16.455 6.803 1.00 11.35 O
+ATOM 142 CB LEU A 22 27.375 18.312 4.450 1.00 12.23 C
+ATOM 143 CG LEU A 22 26.398 19.346 5.025 1.00 11.77 C
+ATOM 144 CD1 LEU A 22 26.989 20.050 6.283 1.00 9.28 C
+ATOM 145 CD2 LEU A 22 25.998 20.360 3.947 1.00 11.93 C
+ATOM 146 N ALA A 23 26.073 15.487 4.777 1.00 10.32 N
+ATOM 147 CA ALA A 23 24.929 14.609 5.003 1.00 10.27 C
+ATOM 148 C ALA A 23 25.220 13.607 6.130 1.00 10.73 C
+ATOM 149 O ALA A 23 24.360 13.294 6.963 1.00 11.25 O
+ATOM 150 CB ALA A 23 24.537 13.898 3.694 1.00 9.63 C
+ATOM 151 N LYS A 24 26.453 13.131 6.192 1.00 10.84 N
+ATOM 152 CA LYS A 24 26.849 12.273 7.301 1.00 11.88 C
+ATOM 153 C LYS A 24 26.814 13.015 8.622 1.00 12.46 C
+ATOM 154 O LYS A 24 26.261 12.524 9.580 1.00 12.48 O
+ATOM 155 CB ALYS A 24 28.230 11.662 7.072 0.34 12.79 C
+ATOM 155 CB BLYS A 24 28.219 11.732 6.937 0.33 12.07 C
+ATOM 155 CB CLYS A 24 28.262 11.704 7.157 0.33 12.63 C
+ATOM 156 CG ALYS A 24 28.259 10.735 5.869 0.34 15.24 C
+ATOM 156 CG BLYS A 24 28.915 10.892 7.945 0.33 11.59 C
+ATOM 156 CG CLYS A 24 28.467 10.726 6.046 0.33 14.56 C
+ATOM 157 CD ALYS A 24 29.597 10.061 5.649 0.34 18.90 C
+ATOM 157 CD BLYS A 24 30.019 10.084 7.253 0.33 14.72 C
+ATOM 157 CD CLYS A 24 29.878 10.154 6.157 0.33 17.29 C
+ATOM 158 CE ALYS A 24 30.153 9.518 6.946 0.34 20.00 C
+ATOM 158 CE BLYS A 24 29.783 9.932 5.731 0.33 17.30 C
+ATOM 158 CE CLYS A 24 30.060 8.871 5.370 0.33 18.16 C
+ATOM 159 NZ ALYS A 24 30.926 10.569 7.686 0.34 20.82 N
+ATOM 159 NZ BLYS A 24 30.659 8.879 5.101 0.33 23.65 N
+ATOM 159 NZ CLYS A 24 30.349 9.126 3.929 0.33 18.85 N
+ATOM 160 N ALA A 25 27.390 14.209 8.667 1.00 12.46 N
+ATOM 161 CA ALA A 25 27.396 15.014 9.888 1.00 12.95 C
+ATOM 162 C ALA A 25 25.989 15.341 10.373 1.00 12.60 C
+ATOM 163 O ALA A 25 25.722 15.351 11.569 1.00 13.32 O
+ATOM 164 CB ALA A 25 28.210 16.300 9.672 1.00 12.88 C
+ATOM 165 N LEU A 26 25.078 15.613 9.451 1.00 11.68 N
+ATOM 166 CA LEU A 26 23.713 16.004 9.827 1.00 12.19 C
+ATOM 167 C LEU A 26 22.810 14.793 10.069 1.00 12.01 C
+ATOM 168 O LEU A 26 21.725 14.936 10.633 1.00 13.35 O
+ATOM 169 CB LEU A 26 23.090 16.873 8.735 1.00 11.77 C
+ATOM 170 CG LEU A 26 23.624 18.294 8.502 1.00 13.22 C
+ATOM 171 CD1 LEU A 26 23.086 18.854 7.181 1.00 15.45 C
+ATOM 172 CD2 LEU A 26 23.280 19.209 9.664 1.00 15.54 C
+ATOM 173 N GLY A 27 23.224 13.621 9.591 1.00 10.81 N
+ATOM 174 CA GLY A 27 22.390 12.416 9.690 1.00 11.78 C
+ATOM 175 C GLY A 27 21.180 12.511 8.778 1.00 10.50 C
+ATOM 176 O GLY A 27 20.059 12.202 9.176 1.00 11.73 O
+ATOM 177 N VAL A 28 21.407 12.960 7.544 1.00 10.19 N
+ATOM 178 CA VAL A 28 20.320 13.136 6.587 1.00 9.28 C
+ATOM 179 C VAL A 28 20.650 12.495 5.241 1.00 6.55 C
+ATOM 180 O VAL A 28 21.799 12.117 4.986 1.00 8.06 O
+ATOM 181 CB VAL A 28 19.953 14.640 6.358 1.00 9.76 C
+ATOM 182 CG1 VAL A 28 19.509 15.304 7.648 1.00 9.89 C
+ATOM 183 CG2 VAL A 28 21.118 15.394 5.748 1.00 10.76 C
+ATOM 184 N GLY A 29 19.635 12.410 4.379 1.00 6.82 N
+ATOM 185 CA GLY A 29 19.789 11.839 3.045 1.00 7.15 C
+ATOM 186 C GLY A 29 20.523 12.766 2.086 1.00 7.96 C
+ATOM 187 O GLY A 29 20.509 13.975 2.253 1.00 8.71 O
+ATOM 188 N LEU A 30 21.165 12.176 1.091 1.00 8.46 N
+ATOM 189 CA LEU A 30 21.916 12.919 0.088 1.00 9.22 C
+ATOM 190 C LEU A 30 21.344 12.586 -1.281 1.00 9.97 C
+ATOM 191 O LEU A 30 21.218 11.413 -1.654 1.00 9.20 O
+ATOM 192 CB LEU A 30 23.420 12.588 0.160 1.00 10.45 C
+ATOM 193 CG LEU A 30 24.304 13.194 -0.947 1.00 10.81 C
+ATOM 194 CD1 LEU A 30 24.335 14.712 -0.856 1.00 11.17 C
+ATOM 195 CD2 LEU A 30 25.720 12.623 -0.919 1.00 13.20 C
+ATOM 196 N LEU A 31 20.996 13.632 -2.011 1.00 9.44 N
+ATOM 197 CA LEU A 31 20.480 13.502 -3.346 1.00 11.12 C
+ATOM 198 C LEU A 31 21.281 14.405 -4.296 1.00 11.39 C
+ATOM 199 O LEU A 31 21.514 15.569 -4.003 1.00 11.37 O
+ATOM 200 CB LEU A 31 19.003 13.901 -3.324 1.00 11.93 C
+ATOM 201 CG LEU A 31 18.118 13.514 -4.498 1.00 16.80 C
+ATOM 202 CD1 LEU A 31 18.204 12.011 -4.784 1.00 20.00 C
+ATOM 203 CD2 LEU A 31 16.695 13.951 -4.148 1.00 18.33 C
+ATOM 204 N ASP A 32 21.698 13.842 -5.422 1.00 10.75 N
+ATOM 205 CA ASP A 32 22.413 14.571 -6.463 1.00 12.68 C
+ATOM 206 C ASP A 32 21.542 14.631 -7.703 1.00 12.49 C
+ATOM 207 O ASP A 32 21.086 13.592 -8.178 1.00 12.00 O
+ATOM 208 CB AASP A 32 23.734 13.917 -6.797 0.50 12.58 C
+ATOM 208 CB BASP A 32 23.715 13.797 -6.733 0.50 12.46 C
+ATOM 209 CG AASP A 32 24.469 14.668 -7.865 0.50 15.07 C
+ATOM 209 CG BASP A 32 24.548 14.363 -7.877 0.50 14.52 C
+ATOM 210 OD1AASP A 32 25.018 15.751 -7.555 0.50 15.22 O
+ATOM 210 OD1BASP A 32 24.000 15.003 -8.802 0.50 15.14 O
+ATOM 211 OD2AASP A 32 24.451 14.195 -9.018 0.50 15.65 O
+ATOM 211 OD2BASP A 32 25.782 14.127 -7.851 0.50 12.22 O
+ATOM 212 N THR A 33 21.292 15.831 -8.234 1.00 12.07 N
+ATOM 213 CA THR A 33 20.281 15.954 -9.295 1.00 12.68 C
+ATOM 214 C THR A 33 20.675 15.271 -10.597 1.00 13.45 C
+ATOM 215 O THR A 33 19.803 14.783 -11.321 1.00 11.90 O
+ATOM 216 CB THR A 33 19.829 17.409 -9.577 1.00 13.32 C
+ATOM 217 OG1 THR A 33 20.926 18.188 -10.037 1.00 12.77 O
+ATOM 218 CG2 THR A 33 19.224 18.025 -8.327 1.00 14.97 C
+ATOM 219 N ASP A 34 21.972 15.211 -10.892 1.00 13.29 N
+ATOM 220 CA ASP A 34 22.431 14.464 -12.059 1.00 14.97 C
+ATOM 221 C ASP A 34 22.111 12.977 -11.935 1.00 14.97 C
+ATOM 222 O ASP A 34 21.616 12.368 -12.868 1.00 15.12 O
+ATOM 223 CB ASP A 34 23.933 14.652 -12.280 1.00 15.71 C
+ATOM 224 CG ASP A 34 24.270 15.984 -12.941 1.00 18.95 C
+ATOM 225 OD1 ASP A 34 23.365 16.623 -13.518 1.00 19.11 O
+ATOM 226 OD2 ASP A 34 25.449 16.380 -12.883 1.00 25.14 O
+ATOM 227 N VAL A 35 22.411 12.400 -10.780 1.00 14.33 N
+ATOM 228 CA VAL A 35 22.056 11.012 -10.497 1.00 13.55 C
+ATOM 229 C VAL A 35 20.532 10.815 -10.567 1.00 12.34 C
+ATOM 230 O VAL A 35 20.050 9.858 -11.183 1.00 14.05 O
+ATOM 231 CB VAL A 35 22.605 10.578 -9.126 1.00 13.86 C
+ATOM 232 CG1 VAL A 35 22.129 9.179 -8.768 1.00 16.60 C
+ATOM 233 CG2 VAL A 35 24.136 10.672 -9.113 1.00 14.83 C
+ATOM 234 N ALA A 36 19.785 11.742 -9.972 1.00 10.84 N
+ATOM 235 CA ALA A 36 18.318 11.701 -9.988 1.00 10.36 C
+ATOM 236 C ALA A 36 17.714 11.724 -11.406 1.00 10.54 C
+ATOM 237 O ALA A 36 16.713 11.059 -11.675 1.00 10.24 O
+ATOM 238 CB ALA A 36 17.753 12.867 -9.150 1.00 10.01 C
+ATOM 239 N ILE A 37 18.326 12.482 -12.316 1.00 9.04 N
+ATOM 240 CA ILE A 37 17.873 12.513 -13.691 1.00 10.51 C
+ATOM 241 C ILE A 37 18.065 11.137 -14.322 1.00 10.15 C
+ATOM 242 O ILE A 37 17.185 10.630 -15.011 1.00 11.68 O
+ATOM 243 CB ILE A 37 18.642 13.550 -14.524 1.00 10.90 C
+ATOM 244 CG1 ILE A 37 18.209 14.972 -14.147 1.00 10.71 C
+ATOM 245 CG2 ILE A 37 18.412 13.326 -16.014 1.00 11.57 C
+ATOM 246 CD1 ILE A 37 19.169 16.040 -14.604 1.00 10.50 C
+ATOM 247 N GLU A 38 19.235 10.555 -14.106 1.00 11.34 N
+ATOM 248 CA GLU A 38 19.508 9.223 -14.658 1.00 11.73 C
+ATOM 249 C GLU A 38 18.576 8.164 -14.060 1.00 12.38 C
+ATOM 250 O GLU A 38 18.137 7.228 -14.752 1.00 12.74 O
+ATOM 251 CB GLU A 38 20.972 8.856 -14.440 1.00 12.89 C
+ATOM 252 CG GLU A 38 21.916 9.754 -15.249 1.00 14.03 C
+ATOM 253 CD GLU A 38 23.349 9.315 -15.206 1.00 20.67 C
+ATOM 254 OE1 GLU A 38 23.699 8.568 -14.280 1.00 24.27 O
+ATOM 255 OE2 GLU A 38 24.131 9.737 -16.093 1.00 23.54 O
+ATOM 256 N GLN A 39 18.271 8.316 -12.775 1.00 13.01 N
+ATOM 257 CA GLN A 39 17.378 7.390 -12.078 1.00 13.64 C
+ATOM 258 C GLN A 39 15.912 7.500 -12.526 1.00 13.27 C
+ATOM 259 O GLN A 39 15.165 6.527 -12.449 1.00 14.96 O
+ATOM 260 CB GLN A 39 17.474 7.618 -10.568 1.00 13.83 C
+ATOM 261 CG GLN A 39 18.772 7.122 -9.960 1.00 16.12 C
+ATOM 262 CD GLN A 39 18.858 7.393 -8.462 1.00 19.97 C
+ATOM 263 OE1 GLN A 39 18.476 8.461 -7.990 1.00 25.10 O
+ATOM 264 NE2 GLN A 39 19.392 6.439 -7.721 1.00 23.17 N
+ATOM 265 N ARG A 40 15.509 8.686 -12.969 1.00 13.67 N
+ATOM 266 CA ARG A 40 14.124 8.976 -13.365 1.00 16.09 C
+ATOM 267 C ARG A 40 13.836 8.667 -14.844 1.00 15.66 C
+ATOM 268 O ARG A 40 12.687 8.458 -15.224 1.00 17.08 O
+ATOM 269 CB ARG A 40 13.813 10.463 -13.080 1.00 17.82 C
+ATOM 270 CG ARG A 40 12.336 10.846 -13.095 1.00 24.92 C
+ATOM 271 CD ARG A 40 11.613 10.384 -11.828 1.00 32.94 C
+ATOM 272 NE ARG A 40 10.154 10.441 -11.959 1.00 38.36 N
+ATOM 273 CZ ARG A 40 9.415 9.548 -12.624 1.00 44.20 C
+ATOM 274 NH1 ARG A 40 9.980 8.511 -13.241 1.00 45.04 N
+ATOM 275 NH2 ARG A 40 8.095 9.693 -12.683 1.00 49.94 N
+ATOM 276 N THR A 41 14.881 8.663 -15.666 1.00 14.88 N
+ATOM 277 CA THR A 41 14.763 8.474 -17.110 1.00 15.52 C
+ATOM 278 C THR A 41 15.355 7.158 -17.623 1.00 15.57 C
+ATOM 279 O THR A 41 14.983 6.699 -18.703 1.00 17.75 O
+ATOM 280 CB THR A 41 15.498 9.600 -17.882 1.00 14.53 C
+ATOM 281 OG1 THR A 41 16.909 9.532 -17.609 1.00 12.51 O
+ATOM 282 CG2 THR A 41 14.961 10.965 -17.518 1.00 17.20 C
+ATOM 283 N GLY A 42 16.309 6.580 -16.891 1.00 16.29 N
+ATOM 284 CA GLY A 42 17.065 5.426 -17.370 1.00 17.38 C
+ATOM 285 C GLY A 42 17.968 5.757 -18.556 1.00 18.63 C
+ATOM 286 O GLY A 42 18.289 4.886 -19.355 1.00 19.27 O
+ATOM 287 N ARG A 43 18.373 7.024 -18.664 1.00 18.32 N
+ATOM 288 CA ARG A 43 19.248 7.502 -19.738 1.00 17.86 C
+ATOM 289 C ARG A 43 20.429 8.268 -19.135 1.00 17.66 C
+ATOM 290 O ARG A 43 20.242 9.029 -18.191 1.00 17.20 O
+ATOM 291 CB ARG A 43 18.467 8.419 -20.647 1.00 17.75 C
+ATOM 292 CG ARG A 43 17.193 7.794 -21.228 1.00 18.89 C
+ATOM 293 CD ARG A 43 16.316 8.843 -21.821 1.00 22.67 C
+ATOM 294 NE ARG A 43 16.981 9.502 -22.940 1.00 26.45 N
+ATOM 295 CZ ARG A 43 16.594 10.646 -23.494 1.00 26.64 C
+ATOM 296 NH1 ARG A 43 15.537 11.306 -23.033 1.00 29.17 N
+ATOM 297 NH2 ARG A 43 17.284 11.135 -24.517 1.00 29.98 N
+ATOM 298 N SER A 44 21.637 8.070 -19.662 1.00 17.02 N
+ATOM 299 CA SER A 44 22.798 8.813 -19.176 1.00 15.89 C
+ATOM 300 C SER A 44 22.645 10.295 -19.508 1.00 15.33 C
+ATOM 301 O SER A 44 22.001 10.638 -20.502 1.00 16.37 O
+ATOM 302 CB SER A 44 24.084 8.303 -19.814 1.00 17.08 C
+ATOM 303 OG SER A 44 24.137 8.710 -21.164 1.00 19.55 O
+ATOM 304 N ILE A 45 23.279 11.154 -18.712 1.00 15.86 N
+ATOM 305 CA ILE A 45 23.294 12.604 -18.968 1.00 17.35 C
+ATOM 306 C ILE A 45 23.813 12.879 -20.383 1.00 17.39 C
+ATOM 307 O ILE A 45 23.201 13.616 -21.150 1.00 18.11 O
+ATOM 308 CB ILE A 45 24.189 13.365 -17.970 1.00 18.23 C
+ATOM 309 CG1 ILE A 45 23.709 13.200 -16.519 1.00 20.06 C
+ATOM 310 CG2 ILE A 45 24.279 14.851 -18.341 1.00 20.02 C
+ATOM 311 CD1 ILE A 45 22.262 13.485 -16.275 1.00 21.11 C
+ATOM 312 N ALA A 46 24.930 12.250 -20.722 1.00 20.51 N
+ATOM 313 CA ALA A 46 25.528 12.405 -22.046 1.00 21.50 C
+ATOM 314 C ALA A 46 24.557 12.054 -23.175 1.00 21.27 C
+ATOM 315 O ALA A 46 24.463 12.790 -24.152 1.00 21.28 O
+ATOM 316 CB ALA A 46 26.800 11.570 -22.156 1.00 22.23 C
+ATOM 317 N ASP A 47 23.831 10.943 -23.041 1.00 20.37 N
+ATOM 318 CA ASP A 47 22.844 10.556 -24.044 1.00 19.50 C
+ATOM 319 C ASP A 47 21.692 11.541 -24.176 1.00 19.21 C
+ATOM 320 O ASP A 47 21.221 11.820 -25.281 1.00 20.25 O
+ATOM 321 CB ASP A 47 22.288 9.144 -23.772 1.00 20.61 C
+ATOM 322 CG ASP A 47 23.208 8.029 -24.290 1.00 23.21 C
+ATOM 323 OD1 ASP A 47 24.191 8.327 -25.003 1.00 27.45 O
+ATOM 324 OD2 ASP A 47 22.945 6.847 -23.988 1.00 23.93 O
+ATOM 325 N ILE A 48 21.200 12.054 -23.054 1.00 18.54 N
+ATOM 326 CA ILE A 48 20.137 13.029 -23.137 1.00 17.19 C
+ATOM 327 C ILE A 48 20.623 14.248 -23.921 1.00 17.35 C
+ATOM 328 O ILE A 48 19.938 14.736 -24.814 1.00 18.39 O
+ATOM 329 CB ILE A 48 19.615 13.459 -21.749 1.00 18.43 C
+ATOM 330 CG1 ILE A 48 19.129 12.230 -20.962 1.00 18.78 C
+ATOM 331 CG2 ILE A 48 18.484 14.467 -21.938 1.00 18.28 C
+ATOM 332 CD1 ILE A 48 18.805 12.483 -19.465 1.00 20.85 C
+ATOM 333 N PHE A 49 21.802 14.747 -23.577 1.00 20.36 N
+ATOM 334 CA PHE A 49 22.406 15.858 -24.331 1.00 21.76 C
+ATOM 335 C PHE A 49 22.582 15.584 -25.814 1.00 22.70 C
+ATOM 336 O PHE A 49 22.146 16.366 -26.662 1.00 24.42 O
+ATOM 337 CB PHE A 49 23.769 16.195 -23.755 1.00 22.42 C
+ATOM 338 CG PHE A 49 23.740 17.325 -22.797 1.00 24.97 C
+ATOM 339 CD1 PHE A 49 23.829 18.629 -23.254 1.00 27.60 C
+ATOM 340 CD2 PHE A 49 23.624 17.093 -21.434 1.00 28.02 C
+ATOM 341 CE1 PHE A 49 23.813 19.684 -22.367 1.00 27.88 C
+ATOM 342 CE2 PHE A 49 23.601 18.144 -20.539 1.00 29.57 C
+ATOM 343 CZ PHE A 49 23.696 19.447 -21.007 1.00 28.93 C
+ATOM 344 N ALA A 50 23.247 14.477 -26.127 1.00 22.95 N
+ATOM 345 CA ALA A 50 23.534 14.136 -27.515 1.00 23.21 C
+ATOM 346 C ALA A 50 22.250 13.922 -28.307 1.00 23.14 C
+ATOM 347 O ALA A 50 22.146 14.319 -29.464 1.00 22.93 O
+ATOM 348 CB ALA A 50 24.403 12.891 -27.584 1.00 23.65 C
+ATOM 349 N THR A 51 21.270 13.281 -27.684 1.00 22.64 N
+ATOM 350 CA THR A 51 20.074 12.881 -28.396 1.00 22.71 C
+ATOM 351 C THR A 51 19.025 13.980 -28.434 1.00 23.09 C
+ATOM 352 O THR A 51 18.460 14.247 -29.482 1.00 22.29 O
+ATOM 353 CB THR A 51 19.462 11.607 -27.776 1.00 23.33 C
+ATOM 354 OG1 THR A 51 20.489 10.622 -27.619 1.00 22.53 O
+ATOM 355 CG2 THR A 51 18.370 11.048 -28.658 1.00 24.03 C
+ATOM 356 N ASP A 52 18.756 14.610 -27.291 1.00 23.40 N
+ATOM 357 CA ASP A 52 17.637 15.562 -27.171 1.00 23.67 C
+ATOM 358 C ASP A 52 18.042 17.024 -27.299 1.00 22.83 C
+ATOM 359 O ASP A 52 17.197 17.886 -27.579 1.00 23.75 O
+ATOM 360 CB ASP A 52 16.932 15.386 -25.823 1.00 24.88 C
+ATOM 361 CG ASP A 52 16.284 14.022 -25.662 1.00 27.98 C
+ATOM 362 OD1 ASP A 52 16.249 13.252 -26.639 1.00 32.17 O
+ATOM 363 OD2 ASP A 52 15.809 13.724 -24.545 1.00 32.73 O
+ATOM 364 N GLY A 53 19.316 17.308 -27.051 1.00 22.12 N
+ATOM 365 CA GLY A 53 19.830 18.679 -27.057 1.00 22.47 C
+ATOM 366 C GLY A 53 19.822 19.302 -25.665 1.00 21.81 C
+ATOM 367 O GLY A 53 19.103 18.848 -24.763 1.00 20.55 O
+ATOM 368 N GLU A 54 20.623 20.347 -25.494 1.00 22.71 N
+ATOM 369 CA GLU A 54 20.792 20.988 -24.186 1.00 23.25 C
+ATOM 370 C GLU A 54 19.481 21.514 -23.618 1.00 22.52 C
+ATOM 371 O GLU A 54 19.245 21.417 -22.418 1.00 18.66 O
+ATOM 372 CB GLU A 54 21.816 22.131 -24.269 1.00 24.06 C
+ATOM 373 CG GLU A 54 22.086 22.844 -22.928 1.00 25.80 C
+ATOM 374 CD GLU A 54 23.423 23.571 -22.884 1.00 30.09 C
+ATOM 375 OE1 GLU A 54 24.034 23.792 -23.957 1.00 39.19 O
+ATOM 376 OE2 GLU A 54 23.869 23.922 -21.766 1.00 32.05 O
+ATOM 377 N GLN A 55 18.624 22.072 -24.464 1.00 23.75 N
+ATOM 378 CA GLN A 55 17.378 22.670 -23.965 1.00 24.66 C
+ATOM 379 C GLN A 55 16.412 21.655 -23.366 1.00 23.36 C
+ATOM 380 O GLN A 55 15.791 21.925 -22.345 1.00 22.18 O
+ATOM 381 CB GLN A 55 16.689 23.530 -25.031 1.00 26.10 C
+ATOM 382 CG GLN A 55 17.409 24.860 -25.297 1.00 30.16 C
+ATOM 383 CD GLN A 55 17.973 25.517 -24.030 1.00 50.73 C
+ATOM 384 OE1 GLN A 55 19.192 25.614 -23.857 1.00 55.52 O
+ATOM 385 NE2 GLN A 55 17.087 25.953 -23.137 1.00 37.68 N
+ATOM 386 N GLU A 56 16.287 20.485 -23.980 1.00 21.87 N
+ATOM 387 CA GLU A 56 15.452 19.448 -23.409 1.00 21.66 C
+ATOM 388 C GLU A 56 16.116 18.844 -22.178 1.00 19.45 C
+ATOM 389 O GLU A 56 15.418 18.469 -21.244 1.00 17.79 O
+ATOM 390 CB GLU A 56 15.095 18.368 -24.446 1.00 22.75 C
+ATOM 391 CG GLU A 56 14.489 17.082 -23.866 1.00 25.71 C
+ATOM 392 CD GLU A 56 13.147 17.262 -23.155 1.00 30.10 C
+ATOM 393 OE1 GLU A 56 12.603 18.386 -23.104 1.00 33.26 O
+ATOM 394 OE2 GLU A 56 12.623 16.241 -22.653 1.00 32.59 O
+ATOM 395 N PHE A 57 17.448 18.748 -22.159 1.00 17.03 N
+ATOM 396 CA PHE A 57 18.124 18.347 -20.918 1.00 15.07 C
+ATOM 397 C PHE A 57 17.785 19.314 -19.763 1.00 13.56 C
+ATOM 398 O PHE A 57 17.495 18.879 -18.641 1.00 13.25 O
+ATOM 399 CB PHE A 57 19.644 18.268 -21.064 1.00 15.21 C
+ATOM 400 CG PHE A 57 20.318 17.909 -19.786 1.00 14.05 C
+ATOM 401 CD1 PHE A 57 20.317 16.594 -19.345 1.00 15.81 C
+ATOM 402 CD2 PHE A 57 20.872 18.889 -18.973 1.00 17.03 C
+ATOM 403 CE1 PHE A 57 20.893 16.253 -18.136 1.00 17.97 C
+ATOM 404 CE2 PHE A 57 21.461 18.554 -17.757 1.00 18.50 C
+ATOM 405 CZ PHE A 57 21.474 17.234 -17.337 1.00 18.48 C
+ATOM 406 N ARG A 58 17.840 20.617 -20.046 1.00 14.46 N
+ATOM 407 CA ARG A 58 17.530 21.642 -19.044 1.00 14.01 C
+ATOM 408 C ARG A 58 16.094 21.557 -18.559 1.00 14.67 C
+ATOM 409 O ARG A 58 15.827 21.802 -17.383 1.00 12.76 O
+ATOM 410 CB ARG A 58 17.830 23.053 -19.567 1.00 15.14 C
+ATOM 411 CG ARG A 58 19.315 23.339 -19.843 1.00 14.76 C
+ATOM 412 CD ARG A 58 20.221 23.309 -18.616 1.00 16.11 C
+ATOM 413 NE ARG A 58 21.621 23.423 -19.012 1.00 15.63 N
+ATOM 414 CZ ARG A 58 22.642 22.752 -18.482 1.00 18.73 C
+ATOM 415 NH1 ARG A 58 22.473 21.893 -17.492 1.00 18.57 N
+ATOM 416 NH2 ARG A 58 23.856 22.946 -18.960 1.00 19.49 N
+ATOM 417 N ARG A 59 15.173 21.182 -19.448 1.00 14.25 N
+ATOM 418 CA ARG A 59 13.774 20.984 -19.091 1.00 16.16 C
+ATOM 419 C ARG A 59 13.602 19.836 -18.099 1.00 15.12 C
+ATOM 420 O ARG A 59 12.932 19.984 -17.076 1.00 15.53 O
+ATOM 421 CB ARG A 59 12.925 20.699 -20.346 1.00 17.23 C
+ATOM 422 CG ARG A 59 11.399 20.790 -20.130 1.00 22.10 C
+ATOM 423 CD ARG A 59 10.789 19.571 -19.394 1.00 26.54 C
+ATOM 424 NE ARG A 59 10.849 18.342 -20.182 1.00 29.00 N
+ATOM 425 CZ ARG A 59 10.618 17.115 -19.716 1.00 29.94 C
+ATOM 426 NH1 ARG A 59 10.324 16.906 -18.436 1.00 26.80 N
+ATOM 427 NH2 ARG A 59 10.700 16.076 -20.540 1.00 31.61 N
+ATOM 428 N ILE A 60 14.181 18.684 -18.425 1.00 14.42 N
+ATOM 429 CA ILE A 60 14.140 17.503 -17.563 1.00 14.45 C
+ATOM 430 C ILE A 60 14.791 17.812 -16.227 1.00 13.73 C
+ATOM 431 O ILE A 60 14.250 17.486 -15.157 1.00 13.47 O
+ATOM 432 CB ILE A 60 14.878 16.313 -18.230 1.00 15.07 C
+ATOM 433 CG1 ILE A 60 14.067 15.811 -19.424 1.00 18.91 C
+ATOM 434 CG2 ILE A 60 15.120 15.176 -17.222 1.00 17.28 C
+ATOM 435 CD1 ILE A 60 14.845 14.885 -20.366 1.00 21.09 C
+ATOM 436 N GLU A 61 15.955 18.453 -16.312 1.00 13.32 N
+ATOM 437 CA GLU A 61 16.713 18.894 -15.149 1.00 11.86 C
+ATOM 438 C GLU A 61 15.895 19.809 -14.228 1.00 11.31 C
+ATOM 439 O GLU A 61 15.891 19.617 -13.016 1.00 10.10 O
+ATOM 440 CB GLU A 61 17.984 19.609 -15.592 1.00 12.21 C
+ATOM 441 CG GLU A 61 18.882 20.028 -14.428 1.00 12.80 C
+ATOM 442 CD GLU A 61 20.185 20.646 -14.866 1.00 13.14 C
+ATOM 443 OE1 GLU A 61 20.149 21.533 -15.743 1.00 13.70 O
+ATOM 444 OE2 GLU A 61 21.250 20.263 -14.321 1.00 14.63 O
+ATOM 445 N GLU A 62 15.231 20.811 -14.794 1.00 12.22 N
+ATOM 446 CA GLU A 62 14.433 21.713 -13.979 1.00 13.13 C
+ATOM 447 C GLU A 62 13.308 20.968 -13.243 1.00 13.34 C
+ATOM 448 O GLU A 62 13.095 21.192 -12.047 1.00 12.19 O
+ATOM 449 CB GLU A 62 13.896 22.879 -14.801 1.00 13.81 C
+ATOM 450 CG GLU A 62 13.088 23.857 -13.962 1.00 14.30 C
+ATOM 451 CD GLU A 62 12.644 25.071 -14.718 1.00 16.67 C
+ATOM 452 OE1 GLU A 62 13.265 25.414 -15.742 1.00 18.04 O
+ATOM 453 OE2 GLU A 62 11.677 25.709 -14.258 1.00 18.79 O
+ATOM 454 N ASP A 63 12.596 20.072 -13.926 1.00 13.64 N
+ATOM 455 CA ASP A 63 11.563 19.268 -13.242 1.00 13.90 C
+ATOM 456 C ASP A 63 12.123 18.469 -12.059 1.00 12.70 C
+ATOM 457 O ASP A 63 11.520 18.416 -10.975 1.00 11.25 O
+ATOM 458 CB ASP A 63 10.883 18.304 -14.224 1.00 15.54 C
+ATOM 459 CG ASP A 63 9.836 18.977 -15.086 1.00 18.54 C
+ATOM 460 OD1 ASP A 63 9.214 19.969 -14.651 1.00 19.65 O
+ATOM 461 OD2 ASP A 63 9.618 18.501 -16.217 1.00 24.23 O
+ATOM 462 N VAL A 64 13.285 17.850 -12.262 1.00 11.26 N
+ATOM 463 CA VAL A 64 13.924 17.052 -11.204 1.00 11.48 C
+ATOM 464 C VAL A 64 14.349 17.924 -10.012 1.00 10.09 C
+ATOM 465 O VAL A 64 14.179 17.535 -8.851 1.00 10.24 O
+ATOM 466 CB VAL A 64 15.144 16.262 -11.765 1.00 11.20 C
+ATOM 467 CG1 VAL A 64 16.030 15.698 -10.639 1.00 12.42 C
+ATOM 468 CG2 VAL A 64 14.657 15.141 -12.653 1.00 14.44 C
+ATOM 469 N VAL A 65 14.913 19.091 -10.315 1.00 10.55 N
+ATOM 470 CA VAL A 65 15.343 20.053 -9.291 1.00 10.41 C
+ATOM 471 C VAL A 65 14.127 20.511 -8.501 1.00 9.63 C
+ATOM 472 O VAL A 65 14.145 20.505 -7.271 1.00 11.28 O
+ATOM 473 CB VAL A 65 16.079 21.281 -9.916 1.00 11.09 C
+ATOM 474 CG1 VAL A 65 16.299 22.387 -8.910 1.00 13.02 C
+ATOM 475 CG2 VAL A 65 17.428 20.871 -10.477 1.00 11.95 C
+ATOM 476 N ARG A 66 13.071 20.910 -9.201 1.00 10.39 N
+ATOM 477 CA ARG A 66 11.870 21.392 -8.510 1.00 10.44 C
+ATOM 478 C ARG A 66 11.278 20.334 -7.601 1.00 11.10 C
+ATOM 479 O ARG A 66 10.906 20.622 -6.457 1.00 11.13 O
+ATOM 480 CB ARG A 66 10.828 21.901 -9.507 1.00 11.95 C
+ATOM 481 CG ARG A 66 11.139 23.272 -10.058 1.00 12.56 C
+ATOM 482 CD ARG A 66 10.163 23.650 -11.168 1.00 16.72 C
+ATOM 483 NE ARG A 66 10.402 25.003 -11.683 1.00 18.63 N
+ATOM 484 CZ ARG A 66 10.041 26.134 -11.071 1.00 20.16 C
+ATOM 485 NH1 ARG A 66 9.421 26.113 -9.901 1.00 17.46 N
+ATOM 486 NH2 ARG A 66 10.312 27.308 -11.627 1.00 23.84 N
+ATOM 487 N ALA A 67 11.210 19.094 -8.088 1.00 11.53 N
+ATOM 488 CA ALA A 67 10.703 17.993 -7.272 1.00 10.41 C
+ATOM 489 C ALA A 67 11.545 17.774 -6.022 1.00 11.86 C
+ATOM 490 O ALA A 67 11.012 17.596 -4.932 1.00 12.64 O
+ATOM 491 CB ALA A 67 10.616 16.704 -8.099 1.00 12.07 C
+ATOM 492 N ALA A 68 12.866 17.770 -6.184 1.00 11.40 N
+ATOM 493 CA ALA A 68 13.779 17.589 -5.064 1.00 11.68 C
+ATOM 494 C ALA A 68 13.694 18.718 -4.041 1.00 10.23 C
+ATOM 495 O ALA A 68 13.751 18.469 -2.851 1.00 11.29 O
+ATOM 496 CB ALA A 68 15.220 17.419 -5.574 1.00 10.94 C
+ATOM 497 N LEU A 69 13.567 19.966 -4.496 1.00 10.26 N
+ATOM 498 CA LEU A 69 13.418 21.101 -3.569 1.00 9.46 C
+ATOM 499 C LEU A 69 12.151 20.968 -2.732 1.00 11.32 C
+ATOM 500 O LEU A 69 12.100 21.390 -1.573 1.00 12.74 O
+ATOM 501 CB LEU A 69 13.429 22.426 -4.334 1.00 9.23 C
+ATOM 502 CG LEU A 69 14.768 22.783 -4.985 1.00 7.66 C
+ATOM 503 CD1 LEU A 69 14.611 23.990 -5.900 1.00 7.88 C
+ATOM 504 CD2 LEU A 69 15.831 23.059 -3.938 1.00 10.62 C
+ATOM 505 N ALA A 70 11.130 20.358 -3.324 1.00 12.27 N
+ATOM 506 CA ALA A 70 9.846 20.186 -2.664 1.00 14.05 C
+ATOM 507 C ALA A 70 9.859 19.014 -1.682 1.00 14.76 C
+ATOM 508 O ALA A 70 9.292 19.105 -0.597 1.00 15.64 O
+ATOM 509 CB ALA A 70 8.774 19.984 -3.689 1.00 14.53 C
+ATOM 510 N ASP A 71 10.498 17.927 -2.084 1.00 14.41 N
+ATOM 511 CA ASP A 71 10.333 16.631 -1.438 1.00 15.49 C
+ATOM 512 C ASP A 71 11.497 16.184 -0.563 1.00 13.99 C
+ATOM 513 O ASP A 71 11.290 15.337 0.285 1.00 13.35 O
+ATOM 514 CB ASP A 71 10.117 15.526 -2.481 1.00 16.38 C
+ATOM 515 CG ASP A 71 8.886 15.739 -3.334 1.00 20.87 C
+ATOM 516 OD1 ASP A 71 7.881 16.266 -2.815 1.00 26.64 O
+ATOM 517 OD2 ASP A 71 8.938 15.359 -4.526 1.00 27.12 O
+ATOM 518 N HIS A 72 12.708 16.705 -0.773 1.00 12.06 N
+ATOM 519 CA HIS A 72 13.899 16.199 -0.072 1.00 12.03 C
+ATOM 520 C HIS A 72 14.237 17.058 1.135 1.00 12.67 C
+ATOM 521 O HIS A 72 14.335 18.270 1.025 1.00 14.67 O
+ATOM 522 CB HIS A 72 15.077 16.138 -1.031 1.00 12.47 C
+ATOM 523 CG HIS A 72 16.301 15.484 -0.468 1.00 10.76 C
+ATOM 524 ND1 HIS A 72 16.309 14.191 0.015 1.00 11.99 N
+ATOM 525 CD2 HIS A 72 17.569 15.943 -0.329 1.00 11.06 C
+ATOM 526 CE1 HIS A 72 17.524 13.885 0.437 1.00 12.53 C
+ATOM 527 NE2 HIS A 72 18.310 14.928 0.239 1.00 8.81 N
+ATOM 528 N ASP A 73 14.429 16.417 2.289 1.00 10.25 N
+ATOM 529 CA ASP A 73 14.684 17.130 3.540 1.00 11.72 C
+ATOM 530 C ASP A 73 16.168 17.216 3.887 1.00 11.35 C
+ATOM 531 O ASP A 73 16.536 17.895 4.821 1.00 11.77 O
+ATOM 532 CB ASP A 73 13.953 16.440 4.696 1.00 13.95 C
+ATOM 533 CG ASP A 73 12.509 16.891 4.847 1.00 18.61 C
+ATOM 534 OD1 ASP A 73 12.023 17.740 4.065 1.00 24.67 O
+ATOM 535 OD2 ASP A 73 11.871 16.393 5.788 1.00 26.15 O
+ATOM 536 N GLY A 74 17.006 16.519 3.138 1.00 10.18 N
+ATOM 537 CA GLY A 74 18.432 16.396 3.460 1.00 10.52 C
+ATOM 538 C GLY A 74 19.341 17.345 2.693 1.00 10.37 C
+ATOM 539 O GLY A 74 19.015 18.522 2.503 1.00 11.39 O
+ATOM 540 N VAL A 75 20.506 16.843 2.276 1.00 8.72 N
+ATOM 541 CA VAL A 75 21.403 17.622 1.428 1.00 8.12 C
+ATOM 542 C VAL A 75 21.122 17.324 -0.041 1.00 8.83 C
+ATOM 543 O VAL A 75 20.980 16.174 -0.448 1.00 9.43 O
+ATOM 544 CB VAL A 75 22.902 17.352 1.762 1.00 8.27 C
+ATOM 545 CG1 VAL A 75 23.840 18.143 0.821 1.00 7.06 C
+ATOM 546 CG2 VAL A 75 23.192 17.673 3.238 1.00 8.80 C
+ATOM 547 N LEU A 76 21.076 18.382 -0.833 1.00 7.94 N
+ATOM 548 CA LEU A 76 20.878 18.284 -2.269 1.00 8.90 C
+ATOM 549 C LEU A 76 22.068 18.905 -2.976 1.00 8.81 C
+ATOM 550 O LEU A 76 22.492 19.997 -2.628 1.00 10.68 O
+ATOM 551 CB LEU A 76 19.611 19.069 -2.652 1.00 9.64 C
+ATOM 552 CG LEU A 76 19.145 19.045 -4.111 1.00 10.29 C
+ATOM 553 CD1 LEU A 76 18.836 17.657 -4.544 1.00 13.09 C
+ATOM 554 CD2 LEU A 76 17.906 19.948 -4.292 1.00 12.25 C
+ATOM 555 N SER A 77 22.629 18.209 -3.948 1.00 9.13 N
+ATOM 556 CA SER A 77 23.663 18.811 -4.788 1.00 10.14 C
+ATOM 557 C SER A 77 23.160 18.968 -6.222 1.00 11.14 C
+ATOM 558 O SER A 77 22.518 18.060 -6.791 1.00 11.54 O
+ATOM 559 CB ASER A 77 24.990 18.059 -4.714 0.50 10.37 C
+ATOM 559 CB BSER A 77 24.905 17.918 -4.747 0.50 10.69 C
+ATOM 560 OG ASER A 77 24.896 16.775 -5.259 0.50 9.05 O
+ATOM 560 OG BSER A 77 25.803 18.200 -5.798 0.50 13.17 O
+ATOM 561 N LEU A 78 23.437 20.135 -6.793 1.00 11.58 N
+ATOM 562 CA LEU A 78 22.960 20.486 -8.127 1.00 12.54 C
+ATOM 563 C LEU A 78 24.040 20.263 -9.184 1.00 12.17 C
+ATOM 564 O LEU A 78 25.205 20.656 -9.004 1.00 11.72 O
+ATOM 565 CB LEU A 78 22.503 21.950 -8.169 1.00 13.39 C
+ATOM 566 CG LEU A 78 21.014 22.278 -8.252 1.00 17.89 C
+ATOM 567 CD1 LEU A 78 20.173 21.499 -7.251 1.00 21.00 C
+ATOM 568 CD2 LEU A 78 20.833 23.784 -8.073 1.00 18.10 C
+ATOM 569 N GLY A 79 23.641 19.647 -10.291 1.00 12.89 N
+ATOM 570 CA GLY A 79 24.489 19.554 -11.472 1.00 13.87 C
+ATOM 571 C GLY A 79 24.904 20.948 -11.905 1.00 14.36 C
+ATOM 572 O GLY A 79 24.128 21.920 -11.756 1.00 11.79 O
+ATOM 573 N GLY A 80 26.111 21.041 -12.464 1.00 14.37 N
+ATOM 574 CA GLY A 80 26.796 22.325 -12.682 1.00 15.02 C
+ATOM 575 C GLY A 80 26.042 23.381 -13.467 1.00 15.39 C
+ATOM 576 O GLY A 80 26.169 24.581 -13.200 1.00 16.65 O
+ATOM 577 N GLY A 81 25.255 22.937 -14.437 1.00 14.00 N
+ATOM 578 CA GLY A 81 24.578 23.850 -15.340 1.00 13.44 C
+ATOM 579 C GLY A 81 23.147 24.172 -15.006 1.00 12.66 C
+ATOM 580 O GLY A 81 22.524 24.945 -15.728 1.00 12.28 O
+ATOM 581 N ALA A 82 22.615 23.602 -13.924 1.00 11.79 N
+ATOM 582 CA ALA A 82 21.212 23.847 -13.553 1.00 10.89 C
+ATOM 583 C ALA A 82 20.920 25.331 -13.364 1.00 10.71 C
+ATOM 584 O ALA A 82 19.852 25.813 -13.739 1.00 10.93 O
+ATOM 585 CB ALA A 82 20.846 23.083 -12.270 1.00 11.39 C
+ATOM 586 N VAL A 83 21.859 26.066 -12.778 1.00 9.25 N
+ATOM 587 CA VAL A 83 21.628 27.492 -12.518 1.00 11.04 C
+ATOM 588 C VAL A 83 21.518 28.339 -13.789 1.00 11.63 C
+ATOM 589 O VAL A 83 21.098 29.481 -13.706 1.00 11.80 O
+ATOM 590 CB VAL A 83 22.694 28.141 -11.563 1.00 10.96 C
+ATOM 591 CG1 VAL A 83 22.626 27.522 -10.181 1.00 13.12 C
+ATOM 592 CG2 VAL A 83 24.087 28.058 -12.143 1.00 11.34 C
+ATOM 593 N THR A 84 21.884 27.793 -14.953 1.00 12.54 N
+ATOM 594 CA THR A 84 21.670 28.504 -16.214 1.00 11.87 C
+ATOM 595 C THR A 84 20.177 28.613 -16.594 1.00 13.37 C
+ATOM 596 O THR A 84 19.825 29.412 -17.461 1.00 14.46 O
+ATOM 597 CB THR A 84 22.435 27.880 -17.406 1.00 11.92 C
+ATOM 598 OG1 THR A 84 21.868 26.618 -17.748 1.00 11.90 O
+ATOM 599 CG2 THR A 84 23.902 27.727 -17.102 1.00 13.36 C
+ATOM 600 N SER A 85 19.315 27.803 -15.974 1.00 13.82 N
+ATOM 601 CA SER A 85 17.862 27.864 -16.224 1.00 14.11 C
+ATOM 602 C SER A 85 17.215 28.913 -15.338 1.00 14.47 C
+ATOM 603 O SER A 85 17.277 28.802 -14.123 1.00 12.75 O
+ATOM 604 CB SER A 85 17.190 26.509 -15.984 1.00 14.72 C
+ATOM 605 OG SER A 85 17.596 25.563 -16.965 1.00 13.82 O
+ATOM 606 N PRO A 86 16.564 29.933 -15.933 1.00 16.26 N
+ATOM 607 CA PRO A 86 15.903 30.937 -15.088 1.00 16.28 C
+ATOM 608 C PRO A 86 14.883 30.349 -14.109 1.00 15.18 C
+ATOM 609 O PRO A 86 14.739 30.856 -12.991 1.00 15.20 O
+ATOM 610 CB PRO A 86 15.203 31.856 -16.106 1.00 17.29 C
+ATOM 611 CG PRO A 86 15.925 31.645 -17.373 1.00 18.27 C
+ATOM 612 CD PRO A 86 16.396 30.229 -17.368 1.00 17.26 C
+ATOM 613 N GLY A 87 14.183 29.295 -14.528 1.00 14.32 N
+ATOM 614 CA GLY A 87 13.207 28.628 -13.682 1.00 13.62 C
+ATOM 615 C GLY A 87 13.830 27.934 -12.484 1.00 13.08 C
+ATOM 616 O GLY A 87 13.200 27.815 -11.428 1.00 12.46 O
+ATOM 617 N VAL A 88 15.063 27.452 -12.651 1.00 12.64 N
+ATOM 618 CA VAL A 88 15.793 26.850 -11.531 1.00 11.74 C
+ATOM 619 C VAL A 88 16.219 27.943 -10.536 1.00 11.00 C
+ATOM 620 O VAL A 88 16.090 27.774 -9.315 1.00 9.36 O
+ATOM 621 CB VAL A 88 17.010 26.068 -12.025 1.00 10.46 C
+ATOM 622 CG1 VAL A 88 18.001 25.770 -10.873 1.00 9.57 C
+ATOM 623 CG2 VAL A 88 16.566 24.781 -12.705 1.00 10.82 C
+ATOM 624 N ARG A 89 16.726 29.059 -11.055 1.00 10.75 N
+ATOM 625 CA ARG A 89 17.034 30.207 -10.192 1.00 9.62 C
+ATOM 626 C ARG A 89 15.794 30.691 -9.438 1.00 10.41 C
+ATOM 627 O ARG A 89 15.877 31.026 -8.262 1.00 10.48 O
+ATOM 628 CB ARG A 89 17.717 31.343 -10.975 1.00 9.39 C
+ATOM 629 CG ARG A 89 19.053 30.932 -11.609 1.00 12.47 C
+ATOM 630 CD ARG A 89 19.846 32.108 -12.161 1.00 13.72 C
+ATOM 631 NE ARG A 89 19.108 32.887 -13.163 1.00 14.28 N
+ATOM 632 CZ ARG A 89 19.205 32.751 -14.484 1.00 17.53 C
+ATOM 633 NH1 ARG A 89 19.981 31.830 -15.026 1.00 16.02 N
+ATOM 634 NH2 ARG A 89 18.493 33.544 -15.276 1.00 20.11 N
+ATOM 635 N ALA A 90 14.632 30.685 -10.094 1.00 11.00 N
+ATOM 636 CA ALA A 90 13.390 31.054 -9.429 1.00 12.62 C
+ATOM 637 C ALA A 90 13.033 30.048 -8.339 1.00 12.43 C
+ATOM 638 O ALA A 90 12.705 30.423 -7.213 1.00 13.09 O
+ATOM 639 CB ALA A 90 12.264 31.180 -10.441 1.00 12.36 C
+ATOM 640 N ALA A 91 13.123 28.759 -8.670 1.00 11.81 N
+ATOM 641 CA ALA A 91 12.795 27.687 -7.721 1.00 10.44 C
+ATOM 642 C ALA A 91 13.653 27.702 -6.465 1.00 9.60 C
+ATOM 643 O ALA A 91 13.184 27.332 -5.383 1.00 10.11 O
+ATOM 644 CB ALA A 91 12.911 26.314 -8.419 1.00 10.93 C
+ATOM 645 N LEU A 92 14.916 28.112 -6.605 1.00 8.94 N
+ATOM 646 CA LEU A 92 15.850 28.097 -5.490 1.00 9.33 C
+ATOM 647 C LEU A 92 15.597 29.198 -4.465 1.00 9.83 C
+ATOM 648 O LEU A 92 15.976 29.049 -3.303 1.00 10.59 O
+ATOM 649 CB LEU A 92 17.290 28.232 -5.981 1.00 9.74 C
+ATOM 650 CG LEU A 92 17.909 26.998 -6.620 1.00 8.70 C
+ATOM 651 CD1 LEU A 92 19.198 27.380 -7.333 1.00 12.18 C
+ATOM 652 CD2 LEU A 92 18.146 25.885 -5.575 1.00 10.26 C
+ATOM 653 N ALA A 93 14.962 30.286 -4.900 1.00 11.00 N
+ATOM 654 CA ALA A 93 14.769 31.463 -4.045 1.00 10.59 C
+ATOM 655 C ALA A 93 14.012 31.069 -2.782 1.00 11.92 C
+ATOM 656 O ALA A 93 12.913 30.523 -2.860 1.00 13.41 O
+ATOM 657 CB ALA A 93 14.019 32.540 -4.793 1.00 11.31 C
+ATOM 658 N GLY A 94 14.614 31.315 -1.625 1.00 11.39 N
+ATOM 659 CA GLY A 94 14.033 30.923 -0.351 1.00 12.46 C
+ATOM 660 C GLY A 94 14.736 29.741 0.288 1.00 12.47 C
+ATOM 661 O GLY A 94 14.605 29.515 1.487 1.00 13.92 O
+ATOM 662 N HIS A 95 15.475 28.973 -0.500 1.00 11.03 N
+ATOM 663 CA HIS A 95 16.221 27.840 0.035 1.00 9.91 C
+ATOM 664 C HIS A 95 17.585 28.251 0.566 1.00 9.63 C
+ATOM 665 O HIS A 95 18.080 29.335 0.289 1.00 7.91 O
+ATOM 666 CB HIS A 95 16.373 26.767 -1.042 1.00 10.84 C
+ATOM 667 CG HIS A 95 15.078 26.106 -1.400 1.00 12.15 C
+ATOM 668 ND1 HIS A 95 14.562 25.058 -0.669 1.00 14.32 N
+ATOM 669 CD2 HIS A 95 14.184 26.357 -2.384 1.00 13.58 C
+ATOM 670 CE1 HIS A 95 13.406 24.689 -1.190 1.00 15.53 C
+ATOM 671 NE2 HIS A 95 13.154 25.461 -2.232 1.00 14.31 N
+ATOM 672 N THR A 96 18.195 27.350 1.329 1.00 9.16 N
+ATOM 673 CA THR A 96 19.563 27.509 1.773 1.00 8.14 C
+ATOM 674 C THR A 96 20.485 26.986 0.681 1.00 9.59 C
+ATOM 675 O THR A 96 20.512 25.781 0.431 1.00 9.40 O
+ATOM 676 CB THR A 96 19.747 26.740 3.072 1.00 10.19 C
+ATOM 677 OG1 THR A 96 18.893 27.333 4.056 1.00 11.88 O
+ATOM 678 CG2 THR A 96 21.199 26.802 3.549 1.00 10.71 C
+ATOM 679 N VAL A 97 21.217 27.904 0.036 1.00 8.48 N
+ATOM 680 CA VAL A 97 22.057 27.608 -1.124 1.00 8.24 C
+ATOM 681 C VAL A 97 23.514 27.954 -0.804 1.00 8.67 C
+ATOM 682 O VAL A 97 23.880 29.129 -0.616 1.00 8.69 O
+ATOM 683 CB VAL A 97 21.583 28.351 -2.387 1.00 8.38 C
+ATOM 684 CG1 VAL A 97 22.394 27.912 -3.604 1.00 9.99 C
+ATOM 685 CG2 VAL A 97 20.097 28.072 -2.629 1.00 8.42 C
+ATOM 686 N VAL A 98 24.322 26.900 -0.731 1.00 8.81 N
+ATOM 687 CA VAL A 98 25.727 26.977 -0.337 1.00 9.26 C
+ATOM 688 C VAL A 98 26.593 26.865 -1.593 1.00 8.45 C
+ATOM 689 O VAL A 98 26.614 25.827 -2.257 1.00 8.50 O
+ATOM 690 CB VAL A 98 26.093 25.849 0.657 1.00 9.94 C
+ATOM 691 CG1 VAL A 98 27.566 25.924 1.054 1.00 11.18 C
+ATOM 692 CG2 VAL A 98 25.230 25.914 1.903 1.00 11.02 C
+ATOM 693 N TYR A 99 27.310 27.951 -1.897 1.00 8.19 N
+ATOM 694 CA TYR A 99 28.172 28.036 -3.056 1.00 8.22 C
+ATOM 695 C TYR A 99 29.573 27.660 -2.603 1.00 9.68 C
+ATOM 696 O TYR A 99 30.210 28.392 -1.861 1.00 8.59 O
+ATOM 697 CB TYR A 99 28.134 29.463 -3.597 1.00 9.27 C
+ATOM 698 CG TYR A 99 29.130 29.829 -4.695 1.00 9.13 C
+ATOM 699 CD1 TYR A 99 29.699 28.860 -5.540 1.00 10.14 C
+ATOM 700 CD2 TYR A 99 29.441 31.168 -4.932 1.00 11.05 C
+ATOM 701 CE1 TYR A 99 30.591 29.227 -6.546 1.00 10.11 C
+ATOM 702 CE2 TYR A 99 30.329 31.529 -5.937 1.00 13.01 C
+ATOM 703 CZ TYR A 99 30.887 30.557 -6.741 1.00 11.81 C
+ATOM 704 OH TYR A 99 31.768 30.924 -7.744 1.00 13.68 O
+ATOM 705 N LEU A 100 30.032 26.499 -3.052 1.00 9.55 N
+ATOM 706 CA LEU A 100 31.414 26.051 -2.823 1.00 9.08 C
+ATOM 707 C LEU A 100 32.321 26.716 -3.848 1.00 9.21 C
+ATOM 708 O LEU A 100 32.302 26.368 -5.041 1.00 8.41 O
+ATOM 709 CB LEU A 100 31.488 24.525 -2.952 1.00 10.20 C
+ATOM 710 CG LEU A 100 30.549 23.667 -2.097 1.00 9.87 C
+ATOM 711 CD1 LEU A 100 30.665 22.182 -2.448 1.00 11.12 C
+ATOM 712 CD2 LEU A 100 30.809 23.881 -0.625 1.00 11.47 C
+ATOM 713 N GLU A 101 33.095 27.695 -3.390 1.00 10.02 N
+ATOM 714 CA GLU A 101 33.925 28.508 -4.267 1.00 10.07 C
+ATOM 715 C GLU A 101 35.288 27.869 -4.497 1.00 11.38 C
+ATOM 716 O GLU A 101 35.881 27.295 -3.588 1.00 10.96 O
+ATOM 717 CB GLU A 101 34.133 29.899 -3.679 1.00 10.82 C
+ATOM 718 CG GLU A 101 32.873 30.689 -3.415 1.00 12.61 C
+ATOM 719 CD GLU A 101 33.152 31.993 -2.693 1.00 19.93 C
+ATOM 720 OE1 GLU A 101 34.068 32.030 -1.845 1.00 26.10 O
+ATOM 721 OE2 GLU A 101 32.448 32.978 -2.959 1.00 23.36 O
+ATOM 722 N ILE A 102 35.791 27.985 -5.719 1.00 11.03 N
+ATOM 723 CA ILE A 102 37.114 27.449 -6.050 1.00 12.65 C
+ATOM 724 C ILE A 102 37.743 28.297 -7.146 1.00 13.44 C
+ATOM 725 O ILE A 102 37.026 28.896 -7.933 1.00 12.01 O
+ATOM 726 CB ILE A 102 37.002 25.954 -6.472 1.00 12.74 C
+ATOM 727 CG1 ILE A 102 38.380 25.311 -6.585 1.00 14.99 C
+ATOM 728 CG2 ILE A 102 36.202 25.785 -7.761 1.00 13.41 C
+ATOM 729 CD1 ILE A 102 38.331 23.818 -6.758 1.00 15.72 C
+ATOM 730 N SER A 103 39.077 28.375 -7.185 1.00 14.66 N
+ATOM 731 CA SER A 103 39.757 29.061 -8.295 1.00 15.42 C
+ATOM 732 C SER A 103 39.872 28.141 -9.513 1.00 15.29 C
+ATOM 733 O SER A 103 39.674 26.943 -9.413 1.00 15.60 O
+ATOM 734 CB SER A 103 41.163 29.511 -7.874 1.00 16.58 C
+ATOM 735 OG SER A 103 42.010 28.386 -7.655 1.00 16.49 O
+ATOM 736 N ALA A 104 40.221 28.721 -10.661 1.00 13.95 N
+ATOM 737 CA ALA A 104 40.446 27.958 -11.881 1.00 14.19 C
+ATOM 738 C ALA A 104 41.599 26.960 -11.691 1.00 13.66 C
+ATOM 739 O ALA A 104 41.486 25.776 -12.043 1.00 15.36 O
+ATOM 740 CB ALA A 104 40.737 28.908 -13.058 1.00 14.04 C
+ATOM 741 N ALA A 105 42.694 27.432 -11.110 1.00 14.22 N
+ATOM 742 CA ALA A 105 43.878 26.597 -10.942 1.00 14.78 C
+ATOM 743 C ALA A 105 43.557 25.398 -10.070 1.00 14.45 C
+ATOM 744 O ALA A 105 43.972 24.281 -10.370 1.00 13.84 O
+ATOM 745 CB ALA A 105 45.013 27.403 -10.319 1.00 15.71 C
+ATOM 746 N GLU A 106 42.828 25.638 -8.984 1.00 12.76 N
+ATOM 747 CA GLU A 106 42.450 24.547 -8.072 1.00 13.48 C
+ATOM 748 C GLU A 106 41.399 23.617 -8.663 1.00 11.98 C
+ATOM 749 O GLU A 106 41.443 22.416 -8.443 1.00 11.61 O
+ATOM 750 CB GLU A 106 42.030 25.088 -6.711 1.00 14.96 C
+ATOM 751 CG GLU A 106 43.187 25.758 -5.984 1.00 20.12 C
+ATOM 752 CD GLU A 106 44.439 24.887 -5.974 1.00 32.39 C
+ATOM 753 OE1 GLU A 106 44.353 23.770 -5.424 1.00 26.33 O
+ATOM 754 OE2 GLU A 106 45.482 25.299 -6.538 1.00 27.88 O
+ATOM 755 N GLY A 107 40.476 24.178 -9.443 1.00 12.85 N
+ATOM 756 CA GLY A 107 39.449 23.393 -10.099 1.00 12.51 C
+ATOM 757 C GLY A 107 40.026 22.438 -11.119 1.00 12.98 C
+ATOM 758 O GLY A 107 39.643 21.281 -11.171 1.00 13.28 O
+ATOM 759 N VAL A 108 40.986 22.926 -11.898 1.00 12.96 N
+ATOM 760 CA VAL A 108 41.695 22.086 -12.861 1.00 12.38 C
+ATOM 761 C VAL A 108 42.481 20.969 -12.148 1.00 11.03 C
+ATOM 762 O VAL A 108 42.382 19.797 -12.522 1.00 11.34 O
+ATOM 763 CB VAL A 108 42.606 22.966 -13.743 1.00 12.51 C
+ATOM 764 CG1 VAL A 108 43.537 22.122 -14.628 1.00 12.75 C
+ATOM 765 CG2 VAL A 108 41.755 23.862 -14.609 1.00 14.35 C
+ATOM 766 N ARG A 109 43.226 21.325 -11.101 1.00 12.64 N
+ATOM 767 CA ARG A 109 43.970 20.326 -10.315 1.00 12.26 C
+ATOM 768 C ARG A 109 43.055 19.239 -9.772 1.00 13.82 C
+ATOM 769 O ARG A 109 43.354 18.049 -9.885 1.00 12.50 O
+ATOM 770 CB ARG A 109 44.690 20.981 -9.154 1.00 14.15 C
+ATOM 771 CG ARG A 109 45.602 20.027 -8.408 1.00 15.60 C
+ATOM 772 CD ARG A 109 46.219 20.687 -7.201 1.00 16.34 C
+ATOM 773 NE ARG A 109 45.274 20.955 -6.107 1.00 16.14 N
+ATOM 774 CZ ARG A 109 44.732 20.044 -5.301 1.00 12.49 C
+ATOM 775 NH1 ARG A 109 44.972 18.755 -5.462 1.00 19.37 N
+ATOM 776 NH2 ARG A 109 43.936 20.433 -4.323 1.00 20.38 N
+ATOM 777 N ARG A 110 41.938 19.668 -9.178 1.00 14.73 N
+ATOM 778 CA ARG A 110 40.980 18.761 -8.538 1.00 16.15 C
+ATOM 779 C ARG A 110 40.068 17.994 -9.504 1.00 16.66 C
+ATOM 780 O ARG A 110 39.255 17.170 -9.075 1.00 19.08 O
+ATOM 781 CB ARG A 110 40.188 19.526 -7.460 1.00 15.99 C
+ATOM 782 CG ARG A 110 41.024 19.696 -6.185 1.00 18.46 C
+ATOM 783 CD ARG A 110 40.749 20.919 -5.325 1.00 20.89 C
+ATOM 784 NE ARG A 110 39.355 21.060 -4.932 1.00 18.97 N
+ATOM 785 CZ ARG A 110 38.910 21.858 -3.960 1.00 19.80 C
+ATOM 786 NH1 ARG A 110 39.745 22.596 -3.242 1.00 20.98 N
+ATOM 787 NH2 ARG A 110 37.609 21.938 -3.720 1.00 17.52 N
+ATOM 788 N THR A 111 40.214 18.235 -10.801 1.00 15.93 N
+ATOM 789 CA THR A 111 39.493 17.468 -11.802 1.00 16.42 C
+ATOM 790 C THR A 111 40.444 16.753 -12.784 1.00 17.11 C
+ATOM 791 O THR A 111 40.109 16.556 -13.939 1.00 18.05 O
+ATOM 792 CB THR A 111 38.459 18.333 -12.551 1.00 16.26 C
+ATOM 793 OG1 THR A 111 39.089 19.476 -13.147 1.00 15.94 O
+ATOM 794 CG2 THR A 111 37.385 18.799 -11.595 1.00 17.44 C
+ATOM 795 N GLY A 112 41.619 16.373 -12.299 1.00 18.19 N
+ATOM 796 CA GLY A 112 42.560 15.550 -13.066 1.00 18.69 C
+ATOM 797 C GLY A 112 43.740 16.278 -13.682 1.00 18.36 C
+ATOM 798 O GLY A 112 44.614 15.646 -14.287 1.00 18.39 O
+ATOM 799 N GLY A 113 43.779 17.599 -13.555 1.00 17.36 N
+ATOM 800 CA GLY A 113 44.894 18.383 -14.093 1.00 17.44 C
+ATOM 801 C GLY A 113 44.671 18.841 -15.525 1.00 18.42 C
+ATOM 802 O GLY A 113 43.637 18.586 -16.121 1.00 16.75 O
+ATOM 803 N ASN A 114 45.643 19.553 -16.064 1.00 20.40 N
+ATOM 804 CA ASN A 114 45.563 20.074 -17.434 1.00 21.80 C
+ATOM 805 C ASN A 114 45.900 18.971 -18.445 1.00 24.68 C
+ATOM 806 O ASN A 114 46.428 17.930 -18.072 1.00 23.45 O
+ATOM 807 CB ASN A 114 46.499 21.285 -17.557 1.00 20.83 C
+ATOM 808 CG ASN A 114 46.276 22.103 -18.822 1.00 22.45 C
+ATOM 809 OD1 ASN A 114 45.198 22.092 -19.416 1.00 21.44 O
+ATOM 810 ND2 ASN A 114 47.315 22.830 -19.234 1.00 20.02 N
+ATOM 811 N THR A 115 45.562 19.197 -19.714 1.00 28.67 N
+ATOM 812 CA THR A 115 45.738 18.206 -20.791 1.00 31.91 C
+ATOM 813 C THR A 115 46.794 18.645 -21.808 1.00 33.68 C
+ATOM 814 O THR A 115 47.187 19.815 -21.839 1.00 33.08 O
+ATOM 815 CB THR A 115 44.423 18.023 -21.572 1.00 32.40 C
+ATOM 816 OG1 THR A 115 43.954 19.308 -22.017 1.00 33.99 O
+ATOM 817 CG2 THR A 115 43.372 17.371 -20.711 1.00 33.95 C
+ATOM 818 N VAL A 116 47.236 17.702 -22.645 1.00 36.37 N
+ATOM 819 CA VAL A 116 48.083 18.028 -23.802 1.00 38.80 C
+ATOM 820 C VAL A 116 47.316 18.957 -24.741 1.00 41.14 C
+ATOM 821 O VAL A 116 46.120 18.774 -24.974 1.00 40.68 O
+ATOM 822 CB VAL A 116 48.562 16.760 -24.591 1.00 38.84 C
+ATOM 823 CG1 VAL A 116 47.388 16.004 -25.216 1.00 39.47 C
+ATOM 824 CG2 VAL A 116 49.593 17.138 -25.671 1.00 37.82 C
+ATOM 825 N ARG A 117 48.017 19.960 -25.261 1.00 44.27 N
+ATOM 826 CA ARG A 117 47.426 20.928 -26.178 1.00 46.70 C
+ATOM 827 C ARG A 117 47.727 20.500 -27.617 1.00 48.58 C
+ATOM 828 O ARG A 117 48.880 20.586 -28.057 1.00 48.84 O
+ATOM 829 CB ARG A 117 47.990 22.319 -25.904 1.00 47.01 C
+ATOM 830 CG ARG A 117 47.364 23.425 -26.739 1.00 48.26 C
+ATOM 831 CD ARG A 117 48.281 24.620 -26.796 1.00 49.91 C
+ATOM 832 NE ARG A 117 48.567 25.134 -25.458 1.00 52.12 N
+ATOM 833 CZ ARG A 117 47.825 26.030 -24.811 1.00 54.45 C
+ATOM 834 NH1 ARG A 117 46.732 26.537 -25.371 1.00 55.35 N
+ATOM 835 NH2 ARG A 117 48.185 26.428 -23.594 1.00 54.85 N
+ATOM 836 N PRO A 118 46.694 20.037 -28.355 1.00 50.84 N
+ATOM 837 CA PRO A 118 46.892 19.555 -29.732 1.00 52.43 C
+ATOM 838 C PRO A 118 47.539 20.594 -30.648 1.00 53.56 C
+ATOM 839 O PRO A 118 48.520 20.294 -31.328 1.00 54.00 O
+ATOM 840 CB PRO A 118 45.470 19.245 -30.209 1.00 52.54 C
+ATOM 841 CG PRO A 118 44.674 19.059 -28.972 1.00 52.12 C
+ATOM 842 CD PRO A 118 45.282 19.944 -27.940 1.00 50.73 C
+ATOM 843 N LEU A 119 46.985 21.802 -30.650 1.00 54.44 N
+ATOM 844 CA LEU A 119 47.517 22.909 -31.447 1.00 54.81 C
+ATOM 845 C LEU A 119 47.828 24.129 -30.578 1.00 53.97 C
+ATOM 846 O LEU A 119 46.983 24.586 -29.796 1.00 53.15 O
+ATOM 847 CB LEU A 119 46.567 23.286 -32.603 1.00 55.36 C
+ATOM 848 CG LEU A 119 45.113 22.797 -32.656 1.00 56.38 C
+ATOM 849 CD1 LEU A 119 44.267 23.373 -31.550 1.00 57.45 C
+ATOM 850 CD2 LEU A 119 44.515 23.168 -34.005 1.00 56.05 C
+ATOM 851 N LEU A 120 49.047 24.650 -30.732 1.00 53.08 N
+ATOM 852 CA LEU A 120 49.498 25.855 -30.021 1.00 52.41 C
+ATOM 853 C LEU A 120 48.480 26.998 -30.118 1.00 51.55 C
+ATOM 854 O LEU A 120 48.267 27.732 -29.146 1.00 51.02 O
+ATOM 855 CB LEU A 120 50.855 26.318 -30.564 1.00 52.42 C
+ATOM 856 CG LEU A 120 51.295 27.738 -30.201 1.00 52.54 C
+ATOM 857 N ALA A 121 47.852 27.130 -31.287 1.00 50.36 N
+ATOM 858 CA ALA A 121 46.861 28.185 -31.533 1.00 49.37 C
+ATOM 859 C ALA A 121 45.464 27.904 -30.944 1.00 47.90 C
+ATOM 860 O ALA A 121 44.610 28.794 -30.943 1.00 48.08 O
+ATOM 861 CB ALA A 121 46.753 28.453 -33.020 1.00 49.51 C
+ATOM 862 N GLY A 122 45.236 26.688 -30.440 1.00 45.83 N
+ATOM 863 CA GLY A 122 43.945 26.316 -29.845 1.00 44.13 C
+ATOM 864 C GLY A 122 43.998 26.133 -28.339 1.00 42.52 C
+ATOM 865 O GLY A 122 45.073 26.225 -27.749 1.00 42.81 O
+ATOM 866 N PRO A 123 42.834 25.858 -27.709 1.00 40.09 N
+ATOM 867 CA PRO A 123 42.717 25.837 -26.244 1.00 37.60 C
+ATOM 868 C PRO A 123 43.049 24.498 -25.578 1.00 34.55 C
+ATOM 869 O PRO A 123 42.879 23.441 -26.185 1.00 35.07 O
+ATOM 870 CB PRO A 123 41.243 26.198 -26.010 1.00 38.08 C
+ATOM 871 CG PRO A 123 40.522 25.723 -27.251 1.00 39.27 C
+ATOM 872 CD PRO A 123 41.542 25.555 -28.360 1.00 40.07 C
+ATOM 873 N ASP A 124 43.522 24.562 -24.335 1.00 29.64 N
+ATOM 874 CA ASP A 124 43.751 23.355 -23.525 1.00 27.02 C
+ATOM 875 C ASP A 124 42.681 23.262 -22.427 1.00 24.75 C
+ATOM 876 O ASP A 124 41.844 24.161 -22.291 1.00 22.43 O
+ATOM 877 CB ASP A 124 45.175 23.339 -22.940 1.00 26.81 C
+ATOM 878 CG ASP A 124 45.451 24.485 -21.970 1.00 27.97 C
+ATOM 879 OD1 ASP A 124 44.536 25.276 -21.647 1.00 27.50 O
+ATOM 880 OD2 ASP A 124 46.615 24.607 -21.530 1.00 30.39 O
+ATOM 881 N ARG A 125 42.711 22.188 -21.647 1.00 22.74 N
+ATOM 882 CA ARG A 125 41.708 21.962 -20.607 1.00 22.43 C
+ATOM 883 C ARG A 125 41.590 23.122 -19.612 1.00 20.53 C
+ATOM 884 O ARG A 125 40.487 23.503 -19.214 1.00 19.50 O
+ATOM 885 CB ARG A 125 42.018 20.673 -19.860 1.00 23.04 C
+ATOM 886 CG ARG A 125 40.942 20.288 -18.900 1.00 25.97 C
+ATOM 887 CD ARG A 125 41.033 18.837 -18.476 1.00 27.26 C
+ATOM 888 NE ARG A 125 39.884 18.557 -17.641 1.00 27.67 N
+ATOM 889 CZ ARG A 125 39.790 18.854 -16.350 1.00 28.84 C
+ATOM 890 NH1 ARG A 125 40.808 19.407 -15.685 1.00 24.23 N
+ATOM 891 NH2 ARG A 125 38.661 18.574 -15.721 1.00 31.18 N
+ATOM 892 N ALA A 126 42.722 23.688 -19.228 1.00 19.00 N
+ATOM 893 CA ALA A 126 42.734 24.793 -18.287 1.00 18.39 C
+ATOM 894 C ALA A 126 41.983 25.984 -18.858 1.00 17.69 C
+ATOM 895 O ALA A 126 41.230 26.634 -18.150 1.00 15.90 O
+ATOM 896 CB ALA A 126 44.146 25.163 -17.915 1.00 18.37 C
+ATOM 897 N GLU A 127 42.128 26.238 -20.158 1.00 17.57 N
+ATOM 898 CA GLU A 127 41.448 27.394 -20.767 1.00 17.30 C
+ATOM 899 C GLU A 127 39.928 27.179 -20.899 1.00 16.89 C
+ATOM 900 O GLU A 127 39.141 28.100 -20.704 1.00 16.26 O
+ATOM 901 CB GLU A 127 42.103 27.725 -22.117 1.00 19.18 C
+ATOM 902 CG GLU A 127 43.479 28.378 -21.933 1.00 24.41 C
+ATOM 903 CD GLU A 127 44.492 28.056 -23.028 1.00 40.15 C
+ATOM 904 OE1 GLU A 127 44.117 27.445 -24.047 1.00 34.19 O
+ATOM 905 OE2 GLU A 127 45.680 28.416 -22.858 1.00 34.25 O
+ATOM 906 N LYS A 128 39.526 25.953 -21.213 1.00 15.77 N
+ATOM 907 CA LYS A 128 38.113 25.604 -21.278 1.00 16.59 C
+ATOM 908 C LYS A 128 37.466 25.760 -19.893 1.00 15.56 C
+ATOM 909 O LYS A 128 36.336 26.209 -19.771 1.00 15.31 O
+ATOM 910 CB LYS A 128 37.940 24.173 -21.770 1.00 17.23 C
+ATOM 911 CG LYS A 128 38.414 23.958 -23.201 1.00 20.39 C
+ATOM 912 CD LYS A 128 38.254 22.514 -23.633 1.00 25.64 C
+ATOM 913 CE LYS A 128 38.788 22.316 -25.043 1.00 28.94 C
+ATOM 914 NZ LYS A 128 38.794 20.883 -25.442 1.00 31.40 N
+ATOM 915 N TYR A 129 38.184 25.355 -18.858 1.00 14.86 N
+ATOM 916 CA TYR A 129 37.706 25.536 -17.491 1.00 15.61 C
+ATOM 917 C TYR A 129 37.527 27.016 -17.152 1.00 16.69 C
+ATOM 918 O TYR A 129 36.527 27.429 -16.542 1.00 17.62 O
+ATOM 919 CB TYR A 129 38.679 24.893 -16.511 1.00 14.92 C
+ATOM 920 CG TYR A 129 38.090 24.708 -15.149 1.00 12.14 C
+ATOM 921 CD1 TYR A 129 38.001 25.778 -14.258 1.00 13.20 C
+ATOM 922 CD2 TYR A 129 37.603 23.469 -14.739 1.00 13.64 C
+ATOM 923 CE1 TYR A 129 37.450 25.615 -12.991 1.00 12.14 C
+ATOM 924 CE2 TYR A 129 37.051 23.306 -13.457 1.00 13.79 C
+ATOM 925 CZ TYR A 129 36.980 24.383 -12.594 1.00 13.19 C
+ATOM 926 OH TYR A 129 36.437 24.223 -11.316 1.00 11.46 O
+ATOM 927 N ARG A 130 38.500 27.819 -17.559 1.00 16.44 N
+ATOM 928 CA ARG A 130 38.447 29.255 -17.327 1.00 17.27 C
+ATOM 929 C ARG A 130 37.186 29.848 -17.964 1.00 16.40 C
+ATOM 930 O ARG A 130 36.519 30.703 -17.379 1.00 16.48 O
+ATOM 931 CB ARG A 130 39.728 29.914 -17.862 1.00 18.90 C
+ATOM 932 CG ARG A 130 39.970 31.311 -17.364 1.00 24.79 C
+ATOM 933 CD ARG A 130 41.382 31.783 -17.677 1.00 33.30 C
+ATOM 934 NE ARG A 130 41.562 32.090 -19.097 1.00 40.27 N
+ATOM 935 CZ ARG A 130 41.463 33.304 -19.645 1.00 48.42 C
+ATOM 936 NH1 ARG A 130 41.176 34.377 -18.910 1.00 48.91 N
+ATOM 937 NH2 ARG A 130 41.656 33.445 -20.953 1.00 48.73 N
+ATOM 938 N ALA A 131 36.840 29.357 -19.145 1.00 14.84 N
+ATOM 939 CA ALA A 131 35.631 29.805 -19.842 1.00 14.58 C
+ATOM 940 C ALA A 131 34.343 29.417 -19.097 1.00 14.14 C
+ATOM 941 O ALA A 131 33.413 30.216 -19.003 1.00 13.76 O
+ATOM 942 CB ALA A 131 35.601 29.244 -21.247 1.00 15.54 C
+ATOM 943 N LEU A 132 34.295 28.182 -18.593 1.00 14.17 N
+ATOM 944 CA LEU A 132 33.117 27.685 -17.863 1.00 13.53 C
+ATOM 945 C LEU A 132 32.929 28.507 -16.574 1.00 12.86 C
+ATOM 946 O LEU A 132 31.815 28.900 -16.221 1.00 13.17 O
+ATOM 947 CB LEU A 132 33.298 26.208 -17.530 1.00 14.09 C
+ATOM 948 CG LEU A 132 32.189 25.530 -16.715 1.00 12.95 C
+ATOM 949 CD1 LEU A 132 30.915 25.369 -17.534 1.00 13.62 C
+ATOM 950 CD2 LEU A 132 32.654 24.188 -16.165 1.00 16.87 C
+ATOM 951 N MET A 133 34.044 28.768 -15.898 1.00 12.97 N
+ATOM 952 CA MET A 133 34.055 29.563 -14.679 1.00 15.27 C
+ATOM 953 C MET A 133 33.505 30.956 -14.921 1.00 16.07 C
+ATOM 954 O MET A 133 32.605 31.426 -14.208 1.00 14.06 O
+ATOM 955 CB MET A 133 35.471 29.643 -14.131 1.00 16.72 C
+ATOM 956 CG MET A 133 35.588 30.532 -12.922 1.00 20.45 C
+ATOM 957 SD MET A 133 37.154 30.332 -12.049 1.00 27.53 S
+ATOM 958 CE MET A 133 36.628 30.839 -10.409 1.00 30.30 C
+ATOM 959 N ALA A 134 34.049 31.617 -15.940 1.00 16.57 N
+ATOM 960 CA ALA A 134 33.612 32.953 -16.326 1.00 17.21 C
+ATOM 961 C ALA A 134 32.100 33.055 -16.518 1.00 16.82 C
+ATOM 962 O ALA A 134 31.496 34.082 -16.181 1.00 17.34 O
+ATOM 963 CB ALA A 134 34.350 33.406 -17.615 1.00 17.56 C
+ATOM 964 N LYS A 135 31.484 31.999 -17.044 1.00 16.67 N
+ATOM 965 CA LYS A 135 30.034 31.985 -17.308 1.00 16.60 C
+ATOM 966 C LYS A 135 29.175 31.525 -16.124 1.00 15.41 C
+ATOM 967 O LYS A 135 28.069 32.011 -15.939 1.00 15.08 O
+ATOM 968 CB LYS A 135 29.718 31.061 -18.486 1.00 17.79 C
+ATOM 969 CG LYS A 135 30.210 31.543 -19.825 1.00 22.59 C
+ATOM 970 CD LYS A 135 29.652 30.693 -20.974 1.00 27.89 C
+ATOM 971 CE LYS A 135 29.824 29.202 -20.747 1.00 30.43 C
+ATOM 972 NZ LYS A 135 29.728 28.443 -22.025 1.00 32.83 N
+ATOM 973 N ARG A 136 29.670 30.563 -15.356 1.00 13.80 N
+ATOM 974 CA ARG A 136 28.892 29.948 -14.255 1.00 12.94 C
+ATOM 975 C ARG A 136 28.996 30.689 -12.933 1.00 12.21 C
+ATOM 976 O ARG A 136 28.014 30.798 -12.197 1.00 10.19 O
+ATOM 977 CB ARG A 136 29.349 28.505 -14.043 1.00 12.27 C
+ATOM 978 CG ARG A 136 29.007 27.577 -15.178 1.00 13.07 C
+ATOM 979 CD ARG A 136 27.519 27.340 -15.329 1.00 15.48 C
+ATOM 980 NE ARG A 136 27.293 26.239 -16.262 1.00 16.15 N
+ATOM 981 CZ ARG A 136 27.174 26.339 -17.587 1.00 17.48 C
+ATOM 982 NH1 ARG A 136 27.218 27.510 -18.202 1.00 18.43 N
+ATOM 983 NH2 ARG A 136 26.991 25.245 -18.310 1.00 18.66 N
+ATOM 984 N ALA A 137 30.187 31.195 -12.624 1.00 12.80 N
+ATOM 985 CA ALA A 137 30.469 31.759 -11.305 1.00 12.82 C
+ATOM 986 C ALA A 137 29.543 32.918 -10.937 1.00 12.43 C
+ATOM 987 O ALA A 137 29.083 33.000 -9.789 1.00 11.89 O
+ATOM 988 CB ALA A 137 31.937 32.188 -11.199 1.00 13.85 C
+ATOM 989 N PRO A 138 29.257 33.826 -11.890 1.00 12.91 N
+ATOM 990 CA PRO A 138 28.308 34.901 -11.557 1.00 14.31 C
+ATOM 991 C PRO A 138 26.916 34.386 -11.171 1.00 13.49 C
+ATOM 992 O PRO A 138 26.254 35.003 -10.344 1.00 11.29 O
+ATOM 993 CB PRO A 138 28.238 35.720 -12.847 1.00 14.94 C
+ATOM 994 CG PRO A 138 29.512 35.384 -13.564 1.00 15.63 C
+ATOM 995 CD PRO A 138 29.766 33.958 -13.262 1.00 14.50 C
+ATOM 996 N LEU A 139 26.492 33.269 -11.760 1.00 12.15 N
+ATOM 997 CA LEU A 139 25.175 32.695 -11.473 1.00 12.01 C
+ATOM 998 C LEU A 139 25.143 32.021 -10.099 1.00 11.53 C
+ATOM 999 O LEU A 139 24.141 32.133 -9.382 1.00 11.68 O
+ATOM 1000 CB LEU A 139 24.740 31.700 -12.563 1.00 12.25 C
+ATOM 1001 CG LEU A 139 24.698 32.250 -14.001 1.00 13.91 C
+ATOM 1002 CD1 LEU A 139 24.295 31.192 -15.001 1.00 18.07 C
+ATOM 1003 CD2 LEU A 139 23.754 33.437 -14.075 1.00 17.91 C
+ATOM 1004 N TYR A 140 26.213 31.312 -9.736 1.00 9.97 N
+ATOM 1005 CA TYR A 140 26.321 30.753 -8.382 1.00 11.11 C
+ATOM 1006 C TYR A 140 26.312 31.874 -7.347 1.00 11.73 C
+ATOM 1007 O TYR A 140 25.676 31.749 -6.299 1.00 11.24 O
+ATOM 1008 CB TYR A 140 27.586 29.900 -8.192 1.00 12.10 C
+ATOM 1009 CG TYR A 140 27.722 28.722 -9.144 1.00 10.57 C
+ATOM 1010 CD1 TYR A 140 26.656 27.866 -9.401 1.00 9.37 C
+ATOM 1011 CD2 TYR A 140 28.938 28.448 -9.759 1.00 13.48 C
+ATOM 1012 CE1 TYR A 140 26.787 26.792 -10.276 1.00 12.16 C
+ATOM 1013 CE2 TYR A 140 29.073 27.382 -10.626 1.00 13.63 C
+ATOM 1014 CZ TYR A 140 28.000 26.561 -10.883 1.00 12.13 C
+ATOM 1015 OH TYR A 140 28.161 25.512 -11.770 1.00 14.62 O
+ATOM 1016 N ARG A 141 27.040 32.938 -7.600 1.00 11.73 N
+ATOM 1017 CA ARG A 141 26.983 34.096 -6.714 1.00 13.41 C
+ATOM 1018 C ARG A 141 25.570 34.654 -6.541 1.00 11.78 C
+ATOM 1019 O ARG A 141 25.171 34.994 -5.485 1.00 13.53 O
+ATOM 1020 CB AARG A 141 27.897 35.252 -7.184 0.33 13.73 C
+ATOM 1020 CB BARG A 141 27.906 35.259 -7.176 0.33 12.85 C
+ATOM 1020 CB CARG A 141 27.885 35.269 -7.015 0.33 13.69 C
+ATOM 1021 CG AARG A 141 29.383 34.993 -7.062 0.33 18.09 C
+ATOM 1021 CG BARG A 141 29.388 34.952 -7.133 0.33 14.25 C
+ATOM 1021 CG CARG A 141 29.292 34.907 -7.060 0.33 18.01 C
+ATOM 1022 CD AARG A 141 30.162 36.254 -7.409 0.33 23.06 C
+ATOM 1022 CD BARG A 141 30.236 36.226 -7.180 0.33 14.63 C
+ATOM 1022 CD CARG A 141 30.146 36.041 -7.561 0.33 22.97 C
+ATOM 1023 NE AARG A 141 29.843 37.345 -6.483 0.33 26.15 N
+ATOM 1023 NE BARG A 141 30.136 36.963 -8.445 0.33 12.15 N
+ATOM 1023 NE CARG A 141 30.085 37.253 -6.778 0.33 26.06 N
+ATOM 1024 CZ AARG A 141 30.661 37.846 -5.556 0.33 28.33 C
+ATOM 1024 CZ BARG A 141 30.762 36.643 -9.576 0.33 12.73 C
+ATOM 1024 CZ CARG A 141 29.832 37.362 -5.487 0.33 27.86 C
+ATOM 1025 NH1AARG A 141 31.900 37.389 -5.407 0.33 27.80 N
+ATOM 1025 NH1BARG A 141 31.527 35.558 -9.646 0.33 12.42 N
+ATOM 1025 NH1CARG A 141 29.550 36.305 -4.734 0.33 28.39 N
+ATOM 1026 NH2AARG A 141 30.238 38.834 -4.773 0.33 29.98 N
+ATOM 1026 NH2BARG A 141 30.598 37.400 -10.658 0.33 11.04 N
+ATOM 1026 NH2CARG A 141 29.836 38.567 -4.954 0.33 28.54 N
+ATOM 1027 N ARG A 142 24.856 34.800 -7.616 1.00 12.09 N
+ATOM 1028 CA ARG A 142 23.474 35.342 -7.591 1.00 13.23 C
+ATOM 1029 C ARG A 142 22.564 34.527 -6.695 1.00 11.21 C
+ATOM 1030 O ARG A 142 21.822 35.070 -5.889 1.00 11.70 O
+ATOM 1031 CB AARG A 142 22.862 35.391 -8.998 0.50 13.75 C
+ATOM 1031 CB BARG A 142 22.853 35.344 -8.992 0.50 13.54 C
+ATOM 1032 CG AARG A 142 23.327 36.550 -9.849 0.50 18.13 C
+ATOM 1032 CG BARG A 142 23.166 36.548 -9.838 0.50 17.15 C
+ATOM 1033 CD AARG A 142 22.549 36.622 -11.163 0.50 21.94 C
+ATOM 1033 CD BARG A 142 22.675 36.345 -11.271 0.50 19.73 C
+ATOM 1034 NE AARG A 142 21.247 37.269 -10.997 0.50 23.30 N
+ATOM 1034 NE BARG A 142 21.229 36.119 -11.363 0.50 20.08 N
+ATOM 1035 CZ AARG A 142 21.062 38.580 -10.850 0.50 23.29 C
+ATOM 1035 CZ BARG A 142 20.547 36.059 -12.507 0.50 20.28 C
+ATOM 1036 NH1AARG A 142 22.097 39.419 -10.830 0.50 22.50 N
+ATOM 1036 NH1BARG A 142 21.169 36.195 -13.677 0.50 16.19 N
+ATOM 1037 NH2AARG A 142 19.832 39.058 -10.702 0.50 22.43 N
+ATOM 1037 NH2BARG A 142 19.236 35.862 -12.489 0.50 21.78 N
+ATOM 1038 N VAL A 143 22.590 33.210 -6.870 1.00 9.03 N
+ATOM 1039 CA VAL A 143 21.670 32.338 -6.124 1.00 8.07 C
+ATOM 1040 C VAL A 143 22.103 31.995 -4.693 1.00 7.75 C
+ATOM 1041 O VAL A 143 21.284 31.496 -3.914 1.00 8.41 O
+ATOM 1042 CB VAL A 143 21.372 30.995 -6.873 1.00 6.58 C
+ATOM 1043 CG1 VAL A 143 20.812 31.264 -8.247 1.00 7.87 C
+ATOM 1044 CG2 VAL A 143 22.617 30.096 -6.937 1.00 6.39 C
+ATOM 1045 N ALA A 144 23.373 32.219 -4.350 1.00 7.72 N
+ATOM 1046 CA ALA A 144 23.874 31.793 -3.059 1.00 8.17 C
+ATOM 1047 C ALA A 144 23.221 32.527 -1.877 1.00 8.88 C
+ATOM 1048 O ALA A 144 22.848 33.689 -1.984 1.00 9.91 O
+ATOM 1049 CB ALA A 144 25.406 31.965 -2.980 1.00 8.84 C
+ATOM 1050 N THR A 145 23.109 31.817 -0.758 1.00 9.92 N
+ATOM 1051 CA THR A 145 22.816 32.421 0.550 1.00 10.77 C
+ATOM 1052 C THR A 145 23.985 32.259 1.513 1.00 11.06 C
+ATOM 1053 O THR A 145 24.037 32.939 2.537 1.00 12.14 O
+ATOM 1054 CB THR A 145 21.533 31.857 1.203 1.00 10.96 C
+ATOM 1055 OG1 THR A 145 21.687 30.458 1.477 1.00 9.25 O
+ATOM 1056 CG2 THR A 145 20.344 32.070 0.291 1.00 11.94 C
+ATOM 1057 N MET A 146 24.906 31.352 1.188 1.00 11.02 N
+ATOM 1058 CA MET A 146 26.155 31.176 1.927 1.00 11.81 C
+ATOM 1059 C MET A 146 27.262 30.911 0.905 1.00 11.49 C
+ATOM 1060 O MET A 146 27.106 30.059 0.042 1.00 11.22 O
+ATOM 1061 CB MET A 146 26.036 29.985 2.879 1.00 11.92 C
+ATOM 1062 CG MET A 146 27.204 29.825 3.851 1.00 13.96 C
+ATOM 1063 SD MET A 146 27.268 28.196 4.664 1.00 15.02 S
+ATOM 1064 CE MET A 146 25.611 28.001 5.292 1.00 14.63 C
+ATOM 1065 N ARG A 147 28.372 31.647 0.989 1.00 11.76 N
+ATOM 1066 CA ARG A 147 29.542 31.377 0.134 1.00 12.81 C
+ATOM 1067 C ARG A 147 30.712 30.836 0.953 1.00 12.94 C
+ATOM 1068 O ARG A 147 31.059 31.408 1.964 1.00 12.91 O
+ATOM 1069 CB ARG A 147 29.955 32.636 -0.610 1.00 14.74 C
+ATOM 1070 CG ARG A 147 28.809 33.214 -1.398 1.00 17.29 C
+ATOM 1071 CD ARG A 147 29.248 34.124 -2.522 1.00 26.23 C
+ATOM 1072 NE ARG A 147 29.433 35.493 -2.059 1.00 31.61 N
+ATOM 1073 CZ ARG A 147 30.567 36.001 -1.583 1.00 36.22 C
+ATOM 1074 NH1 ARG A 147 31.669 35.265 -1.482 1.00 38.73 N
+ATOM 1075 NH2 ARG A 147 30.597 37.268 -1.202 1.00 36.55 N
+ATOM 1076 N VAL A 148 31.287 29.714 0.526 1.00 11.31 N
+ATOM 1077 CA VAL A 148 32.379 29.080 1.252 1.00 12.57 C
+ATOM 1078 C VAL A 148 33.605 28.872 0.342 1.00 13.13 C
+ATOM 1079 O VAL A 148 33.545 28.128 -0.625 1.00 12.08 O
+ATOM 1080 CB AVAL A 148 31.958 27.750 1.961 0.50 12.56 C
+ATOM 1080 CB BVAL A 148 31.916 27.714 1.839 0.50 11.45 C
+ATOM 1081 CG1AVAL A 148 31.359 26.761 0.998 0.50 14.11 C
+ATOM 1081 CG1BVAL A 148 32.983 27.124 2.759 0.50 13.28 C
+ATOM 1082 CG2AVAL A 148 33.149 27.126 2.708 0.50 14.10 C
+ATOM 1082 CG2BVAL A 148 30.575 27.865 2.591 0.50 10.06 C
+ATOM 1083 N ASP A 149 34.713 29.536 0.671 1.00 14.36 N
+ATOM 1084 CA ASP A 149 35.970 29.348 -0.064 1.00 14.64 C
+ATOM 1085 C ASP A 149 36.557 27.977 0.254 1.00 14.93 C
+ATOM 1086 O ASP A 149 36.867 27.681 1.405 1.00 16.56 O
+ATOM 1087 CB ASP A 149 36.981 30.454 0.293 1.00 15.26 C
+ATOM 1088 CG ASP A 149 38.134 30.542 -0.701 1.00 18.64 C
+ATOM 1089 OD1 ASP A 149 38.456 29.538 -1.358 1.00 17.41 O
+ATOM 1090 OD2 ASP A 149 38.725 31.631 -0.826 1.00 25.48 O
+ATOM 1091 N THR A 150 36.707 27.138 -0.767 1.00 13.78 N
+ATOM 1092 CA THR A 150 37.287 25.802 -0.576 1.00 12.92 C
+ATOM 1093 C THR A 150 38.751 25.727 -1.026 1.00 14.51 C
+ATOM 1094 O THR A 150 39.348 24.659 -0.956 1.00 14.74 O
+ATOM 1095 CB THR A 150 36.509 24.719 -1.319 1.00 13.13 C
+ATOM 1096 OG1 THR A 150 36.783 24.794 -2.722 1.00 13.09 O
+ATOM 1097 CG2 THR A 150 34.993 24.854 -1.051 1.00 12.10 C
+ATOM 1098 N ASN A 151 39.314 26.834 -1.506 1.00 15.77 N
+ATOM 1099 CA ASN A 151 40.681 26.795 -2.037 1.00 16.37 C
+ATOM 1100 C ASN A 151 41.707 26.412 -0.974 1.00 18.99 C
+ATOM 1101 O ASN A 151 42.652 25.682 -1.262 1.00 19.32 O
+ATOM 1102 CB ASN A 151 41.068 28.128 -2.667 1.00 16.99 C
+ATOM 1103 CG ASN A 151 40.364 28.376 -3.963 1.00 15.61 C
+ATOM 1104 OD1 ASN A 151 40.455 27.573 -4.902 1.00 18.89 O
+ATOM 1105 ND2 ASN A 151 39.631 29.487 -4.032 1.00 16.94 N
+ATOM 1106 N ARG A 152 41.507 26.905 0.245 1.00 19.43 N
+ATOM 1107 CA ARG A 152 42.464 26.694 1.344 1.00 22.67 C
+ATOM 1108 C ARG A 152 41.826 26.087 2.600 1.00 22.47 C
+ATOM 1109 O ARG A 152 42.343 26.232 3.703 1.00 24.41 O
+ATOM 1110 CB ARG A 152 43.129 28.031 1.701 1.00 23.44 C
+ATOM 1111 CG ARG A 152 43.958 28.631 0.556 1.00 29.99 C
+ATOM 1112 CD ARG A 152 44.620 29.945 0.945 1.00 37.73 C
+ATOM 1113 NE ARG A 152 45.415 29.825 2.169 1.00 45.01 N
+ATOM 1114 CZ ARG A 152 46.619 29.256 2.252 1.00 51.41 C
+ATOM 1115 NH1 ARG A 152 47.208 28.735 1.177 1.00 58.04 N
+ATOM 1116 NH2 ARG A 152 47.241 29.207 3.428 1.00 53.02 N
+ATOM 1117 N ARG A 153 40.697 25.414 2.427 1.00 21.97 N
+ATOM 1118 CA ARG A 153 40.089 24.624 3.489 1.00 21.87 C
+ATOM 1119 C ARG A 153 39.969 23.206 2.983 1.00 21.35 C
+ATOM 1120 O ARG A 153 39.488 22.994 1.869 1.00 21.86 O
+ATOM 1121 CB ARG A 153 38.684 25.129 3.824 1.00 22.52 C
+ATOM 1122 CG ARG A 153 38.606 26.437 4.522 1.00 24.30 C
+ATOM 1123 CD ARG A 153 37.190 26.653 5.059 1.00 26.68 C
+ATOM 1124 NE ARG A 153 37.036 27.951 5.710 1.00 29.31 N
+ATOM 1125 CZ ARG A 153 36.634 29.070 5.113 1.00 31.85 C
+ATOM 1126 NH1 ARG A 153 36.322 29.082 3.826 1.00 33.82 N
+ATOM 1127 NH2 ARG A 153 36.541 30.190 5.816 1.00 33.00 N
+ATOM 1128 N ASN A 154 40.385 22.239 3.795 1.00 19.93 N
+ATOM 1129 CA ASN A 154 40.161 20.826 3.479 1.00 20.26 C
+ATOM 1130 C ASN A 154 38.671 20.486 3.712 1.00 18.81 C
+ATOM 1131 O ASN A 154 37.945 21.313 4.282 1.00 18.95 O
+ATOM 1132 CB ASN A 154 41.109 19.925 4.289 1.00 20.94 C
+ATOM 1133 CG ASN A 154 40.945 20.085 5.794 1.00 23.94 C
+ATOM 1134 OD1 ASN A 154 39.847 19.964 6.329 1.00 25.16 O
+ATOM 1135 ND2 ASN A 154 42.050 20.346 6.484 1.00 33.88 N
+ATOM 1136 N PRO A 155 38.196 19.310 3.251 1.00 18.68 N
+ATOM 1137 CA PRO A 155 36.751 19.015 3.372 1.00 17.25 C
+ATOM 1138 C PRO A 155 36.170 19.071 4.793 1.00 16.07 C
+ATOM 1139 O PRO A 155 35.056 19.565 4.981 1.00 14.39 O
+ATOM 1140 CB PRO A 155 36.638 17.609 2.784 1.00 18.28 C
+ATOM 1141 CG PRO A 155 37.751 17.532 1.845 1.00 17.87 C
+ATOM 1142 CD PRO A 155 38.888 18.229 2.532 1.00 18.70 C
+ATOM 1143 N GLY A 156 36.915 18.597 5.785 1.00 14.38 N
+ATOM 1144 CA GLY A 156 36.465 18.645 7.178 1.00 13.41 C
+ATOM 1145 C GLY A 156 36.222 20.071 7.647 1.00 13.46 C
+ATOM 1146 O GLY A 156 35.216 20.364 8.312 1.00 12.50 O
+ATOM 1147 N ALA A 157 37.151 20.958 7.292 1.00 12.52 N
+ATOM 1148 CA ALA A 157 37.026 22.396 7.584 1.00 13.17 C
+ATOM 1149 C ALA A 157 35.850 23.080 6.870 1.00 12.94 C
+ATOM 1150 O ALA A 157 35.166 23.935 7.452 1.00 12.81 O
+ATOM 1151 CB ALA A 157 38.319 23.105 7.255 1.00 14.38 C
+ATOM 1152 N VAL A 158 35.638 22.719 5.608 1.00 11.64 N
+ATOM 1153 CA VAL A 158 34.490 23.201 4.848 1.00 12.61 C
+ATOM 1154 C VAL A 158 33.179 22.763 5.519 1.00 11.91 C
+ATOM 1155 O VAL A 158 32.262 23.569 5.691 1.00 12.87 O
+ATOM 1156 CB VAL A 158 34.550 22.704 3.370 1.00 12.61 C
+ATOM 1157 CG1 VAL A 158 33.281 23.058 2.599 1.00 9.06 C
+ATOM 1158 CG2 VAL A 158 35.756 23.284 2.660 1.00 13.66 C
+ATOM 1159 N VAL A 159 33.096 21.497 5.914 1.00 12.68 N
+ATOM 1160 CA VAL A 159 31.869 20.994 6.547 1.00 13.59 C
+ATOM 1161 C VAL A 159 31.632 21.703 7.892 1.00 13.20 C
+ATOM 1162 O VAL A 159 30.513 22.107 8.205 1.00 12.68 O
+ATOM 1163 CB VAL A 159 31.895 19.449 6.671 1.00 13.56 C
+ATOM 1164 CG1 VAL A 159 30.769 18.931 7.553 1.00 13.21 C
+ATOM 1165 CG2 VAL A 159 31.790 18.828 5.289 1.00 14.15 C
+ATOM 1166 N ARG A 160 32.679 21.873 8.687 1.00 14.46 N
+ATOM 1167 CA ARG A 160 32.515 22.568 9.986 1.00 15.36 C
+ATOM 1168 C ARG A 160 32.064 24.030 9.819 1.00 13.81 C
+ATOM 1169 O ARG A 160 31.243 24.523 10.584 1.00 14.06 O
+ATOM 1170 CB AARG A 160 33.808 22.498 10.809 0.50 15.75 C
+ATOM 1170 CB BARG A 160 33.801 22.483 10.814 0.50 15.54 C
+ATOM 1171 CG AARG A 160 33.978 21.191 11.566 0.50 19.51 C
+ATOM 1171 CG BARG A 160 34.062 21.099 11.395 0.50 18.69 C
+ATOM 1172 CD AARG A 160 35.208 21.211 12.474 0.50 23.63 C
+ATOM 1172 CD BARG A 160 35.155 21.131 12.461 0.50 21.94 C
+ATOM 1173 NE AARG A 160 36.408 20.737 11.786 0.50 26.16 N
+ATOM 1173 NE BARG A 160 36.390 21.747 11.978 0.50 23.23 N
+ATOM 1174 CZ AARG A 160 37.367 21.505 11.265 0.50 29.01 C
+ATOM 1174 CZ BARG A 160 37.353 21.119 11.299 0.50 26.49 C
+ATOM 1175 NH1AARG A 160 37.315 22.835 11.327 0.50 28.71 N
+ATOM 1175 NH1BARG A 160 37.247 19.829 10.988 0.50 25.82 N
+ATOM 1176 NH2AARG A 160 38.401 20.926 10.670 0.50 30.56 N
+ATOM 1176 NH2BARG A 160 38.433 21.793 10.921 0.50 28.31 N
+ATOM 1177 N HIS A 161 32.590 24.712 8.801 1.00 12.71 N
+ATOM 1178 CA HIS A 161 32.192 26.085 8.450 1.00 12.95 C
+ATOM 1179 C HIS A 161 30.710 26.171 8.090 1.00 11.67 C
+ATOM 1180 O HIS A 161 29.990 27.031 8.565 1.00 12.19 O
+ATOM 1181 CB HIS A 161 33.066 26.583 7.285 1.00 13.57 C
+ATOM 1182 CG HIS A 161 32.784 27.989 6.844 1.00 15.56 C
+ATOM 1183 ND1 HIS A 161 33.655 29.028 7.089 1.00 19.01 N
+ATOM 1184 CD2 HIS A 161 31.761 28.519 6.128 1.00 17.44 C
+ATOM 1185 CE1 HIS A 161 33.172 30.143 6.563 1.00 20.56 C
+ATOM 1186 NE2 HIS A 161 32.023 29.862 5.974 1.00 19.15 N
+ATOM 1187 N ILE A 162 30.244 25.244 7.265 1.00 10.82 N
+ATOM 1188 CA ILE A 162 28.836 25.207 6.886 1.00 10.31 C
+ATOM 1189 C ILE A 162 27.937 24.903 8.088 1.00 11.20 C
+ATOM 1190 O ILE A 162 26.947 25.582 8.324 1.00 12.96 O
+ATOM 1191 CB ILE A 162 28.600 24.149 5.764 1.00 8.76 C
+ATOM 1192 CG1 ILE A 162 29.352 24.550 4.475 1.00 10.30 C
+ATOM 1193 CG2 ILE A 162 27.122 24.005 5.480 1.00 8.38 C
+ATOM 1194 CD1 ILE A 162 29.450 23.435 3.428 1.00 9.43 C
+ATOM 1195 N LEU A 163 28.294 23.889 8.857 1.00 12.51 N
+ATOM 1196 CA LEU A 163 27.476 23.479 10.006 1.00 14.13 C
+ATOM 1197 C LEU A 163 27.279 24.616 10.978 1.00 14.70 C
+ATOM 1198 O LEU A 163 26.178 24.817 11.510 1.00 16.10 O
+ATOM 1199 CB LEU A 163 28.125 22.306 10.739 1.00 14.83 C
+ATOM 1200 CG LEU A 163 28.131 20.962 10.024 1.00 12.65 C
+ATOM 1201 CD1 LEU A 163 29.048 19.996 10.778 1.00 14.63 C
+ATOM 1202 CD2 LEU A 163 26.720 20.411 9.896 1.00 15.51 C
+ATOM 1203 N SER A 164 28.341 25.380 11.199 1.00 15.99 N
+ATOM 1204 CA SER A 164 28.288 26.542 12.112 1.00 17.50 C
+ATOM 1205 C SER A 164 27.340 27.657 11.632 1.00 17.53 C
+ATOM 1206 O SER A 164 27.020 28.570 12.394 1.00 18.50 O
+ATOM 1207 CB ASER A 164 29.698 27.103 12.352 0.50 17.21 C
+ATOM 1207 CB BSER A 164 29.695 27.112 12.306 0.50 17.41 C
+ATOM 1208 OG ASER A 164 30.143 27.875 11.260 0.50 16.60 O
+ATOM 1208 OG BSER A 164 30.575 26.096 12.742 0.50 18.86 O
+ATOM 1209 N ARG A 165 26.903 27.567 10.373 1.00 17.64 N
+ATOM 1210 CA ARG A 165 26.036 28.558 9.747 1.00 16.77 C
+ATOM 1211 C ARG A 165 24.708 27.991 9.254 1.00 17.74 C
+ATOM 1212 O ARG A 165 23.969 28.694 8.564 1.00 18.24 O
+ATOM 1213 CB ARG A 165 26.770 29.222 8.588 1.00 17.62 C
+ATOM 1214 CG ARG A 165 27.908 30.067 9.055 1.00 16.04 C
+ATOM 1215 CD ARG A 165 28.855 30.391 7.944 1.00 19.32 C
+ATOM 1216 NE ARG A 165 29.901 31.275 8.440 1.00 22.51 N
+ATOM 1217 CZ ARG A 165 30.956 30.894 9.159 1.00 24.14 C
+ATOM 1218 NH1 ARG A 165 31.145 29.621 9.475 1.00 23.03 N
+ATOM 1219 NH2 ARG A 165 31.835 31.806 9.565 1.00 26.81 N
+ATOM 1220 N LEU A 166 24.415 26.746 9.640 1.00 19.06 N
+ATOM 1221 CA LEU A 166 23.151 26.057 9.328 1.00 20.75 C
+ATOM 1222 C LEU A 166 22.383 25.611 10.579 1.00 20.75 C
+ATOM 1223 O LEU A 166 21.509 24.757 10.490 1.00 22.41 O
+ATOM 1224 CB LEU A 166 23.446 24.777 8.521 1.00 22.24 C
+ATOM 1225 CG LEU A 166 23.821 24.831 7.053 1.00 26.36 C
+ATOM 1226 CD1 LEU A 166 23.873 23.407 6.501 1.00 29.10 C
+ATOM 1227 CD2 LEU A 166 22.845 25.654 6.279 1.00 28.81 C
+ATOM 1228 N GLN A 167 22.692 26.185 11.733 1.00 19.69 N
+ATOM 1229 CA GLN A 167 22.189 25.642 12.991 1.00 18.66 C
+ATOM 1230 C GLN A 167 20.670 25.823 13.119 1.00 19.16 C
+ATOM 1231 O GLN A 167 20.078 26.748 12.558 1.00 17.55 O
+ATOM 1232 CB GLN A 167 22.919 26.252 14.181 1.00 17.82 C
+ATOM 1233 CG GLN A 167 24.435 26.150 14.095 1.00 16.42 C
+ATOM 1234 CD GLN A 167 25.100 26.639 15.345 1.00 13.15 C
+ATOM 1235 OE1 GLN A 167 24.828 26.124 16.425 1.00 18.65 O
+ATOM 1236 NE2 GLN A 167 25.964 27.640 15.222 1.00 14.17 N
+ATOM 1237 N VAL A 168 20.036 24.897 13.824 1.00 20.18 N
+ATOM 1238 CA VAL A 168 18.595 24.943 14.018 1.00 21.88 C
+ATOM 1239 C VAL A 168 18.297 24.819 15.513 1.00 24.58 C
+ATOM 1240 O VAL A 168 18.524 23.760 16.091 1.00 25.22 O
+ATOM 1241 CB VAL A 168 17.891 23.798 13.253 1.00 23.04 C
+ATOM 1242 CG1 VAL A 168 16.400 23.776 13.567 1.00 24.70 C
+ATOM 1243 CG2 VAL A 168 18.126 23.927 11.744 1.00 24.48 C
+ATOM 1244 N PRO A 169 17.780 25.889 16.147 1.00 27.30 N
+ATOM 1245 CA PRO A 169 17.465 25.756 17.579 1.00 29.04 C
+ATOM 1246 C PRO A 169 16.358 24.713 17.802 1.00 31.64 C
+ATOM 1247 O PRO A 169 15.412 24.645 17.010 1.00 31.49 O
+ATOM 1248 CB PRO A 169 16.971 27.156 17.989 1.00 28.88 C
+ATOM 1249 CG PRO A 169 17.153 28.049 16.807 1.00 28.08 C
+ATOM 1250 CD PRO A 169 17.457 27.220 15.602 1.00 27.22 C
+ATOM 1251 N SER A 170 16.472 23.910 18.852 1.00 36.13 N
+ATOM 1252 CA SER A 170 15.414 22.942 19.175 1.00 39.75 C
+ATOM 1253 C SER A 170 14.261 23.625 19.903 1.00 41.87 C
+ATOM 1254 O SER A 170 14.456 24.143 20.996 1.00 41.13 O
+ATOM 1255 CB SER A 170 15.941 21.810 20.051 1.00 40.15 C
+ATOM 1256 OG SER A 170 14.873 20.956 20.444 1.00 41.53 O
+ATOM 1257 N PRO A 171 13.048 23.595 19.326 1.00 45.45 N
+ATOM 1258 CA PRO A 171 11.921 24.288 19.972 1.00 47.19 C
+ATOM 1259 C PRO A 171 11.496 23.692 21.324 1.00 47.74 C
+ATOM 1260 O PRO A 171 10.928 24.398 22.158 1.00 48.11 O
+ATOM 1261 CB PRO A 171 10.779 24.144 18.952 1.00 47.49 C
+ATOM 1262 CG PRO A 171 11.416 23.683 17.690 1.00 47.18 C
+ATOM 1263 CD PRO A 171 12.631 22.922 18.086 1.00 45.84 C
+ATOM 1264 N SER A 172 11.773 22.407 21.527 1.00 47.89 N
+ATOM 1265 CA SER A 172 11.427 21.720 22.772 1.00 47.91 C
+ATOM 1266 C SER A 172 12.609 21.648 23.750 1.00 47.28 C
+ATOM 1267 O SER A 172 12.581 20.875 24.710 1.00 47.08 O
+ATOM 1268 CB SER A 172 10.933 20.308 22.449 1.00 48.16 C
+ATOM 1269 OG SER A 172 11.938 19.567 21.771 1.00 47.70 O
+ATOM 1270 N GLU A 173 13.635 22.461 23.509 1.00 46.38 N
+ATOM 1271 CA GLU A 173 14.881 22.415 24.277 1.00 45.81 C
+ATOM 1272 C GLU A 173 14.667 22.569 25.784 1.00 44.41 C
+ATOM 1273 O GLU A 173 15.124 21.744 26.576 1.00 43.99 O
+ATOM 1274 CB GLU A 173 15.820 23.513 23.775 1.00 46.16 C
+ATOM 1275 CG GLU A 173 17.040 23.771 24.642 1.00 46.53 C
+ATOM 1276 CD GLU A 173 17.821 24.974 24.165 1.00 46.26 C
+ATOM 1277 OE1 GLU A 173 18.395 24.883 23.057 1.00 47.14 O
+ATOM 1278 OE2 GLU A 173 17.859 26.001 24.889 1.00 41.39 O
+ATOM 1279 N ALA A 174 13.985 23.642 26.164 1.00 43.24 N
+ATOM 1280 CA ALA A 174 13.697 23.939 27.571 1.00 42.56 C
+ATOM 1281 C ALA A 174 12.995 22.759 28.247 1.00 41.65 C
+ATOM 1282 O ALA A 174 13.496 22.203 29.228 1.00 41.45 O
+ATOM 1283 CB ALA A 174 12.832 25.197 27.676 1.00 42.79 C
+ATOM 1284 N ALA A 175 11.845 22.381 27.695 1.00 40.25 N
+ATOM 1285 CA ALA A 175 11.028 21.286 28.226 1.00 38.86 C
+ATOM 1286 C ALA A 175 11.818 19.980 28.391 1.00 37.15 C
+ATOM 1287 O ALA A 175 11.679 19.301 29.404 1.00 36.72 O
+ATOM 1288 CB ALA A 175 9.799 21.060 27.338 1.00 39.09 C
+ATOM 1289 N THR A 176 12.655 19.641 27.411 1.00 34.82 N
+ATOM 1290 CA THR A 176 13.503 18.437 27.490 1.00 34.13 C
+ATOM 1291 C THR A 176 14.307 18.345 28.803 1.00 31.77 C
+ATOM 1292 O THR A 176 14.376 17.288 29.441 1.00 31.24 O
+ATOM 1293 CB THR A 176 14.493 18.382 26.302 1.00 34.77 C
+ATOM 1294 OG1 THR A 176 13.773 18.510 25.066 1.00 36.33 O
+ATOM 1295 CG2 THR A 176 15.285 17.073 26.299 1.00 36.38 C
+ATOM 1296 N LEU A 177 14.921 19.456 29.199 1.00 29.62 N
+ATOM 1297 CA LEU A 177 15.676 19.512 30.455 1.00 28.56 C
+ATOM 1298 C LEU A 177 14.815 19.247 31.687 1.00 28.37 C
+ATOM 1299 O LEU A 177 15.349 18.937 32.748 1.00 26.75 O
+ATOM 1300 CB LEU A 177 16.351 20.875 30.622 1.00 28.94 C
+ATOM 1301 CG LEU A 177 17.528 21.227 29.708 1.00 30.64 C
+ATOM 1302 CD1 LEU A 177 17.870 22.702 29.858 1.00 30.61 C
+ATOM 1303 CD2 LEU A 177 18.747 20.380 30.007 1.00 32.13 C
+ATOM 1304 N GLU A 178 13.493 19.379 31.554 1.00 27.98 N
+ATOM 1305 CA GLU A 178 12.584 19.258 32.692 1.00 29.39 C
+ATOM 1306 C GLU A 178 11.958 17.871 32.834 1.00 32.86 C
+ATOM 1307 O GLU A 178 11.151 17.646 33.742 1.00 33.54 O
+ATOM 1308 CB GLU A 178 11.480 20.327 32.590 1.00 29.06 C
+ATOM 1309 CG GLU A 178 12.005 21.760 32.678 1.00 25.62 C
+ATOM 1310 CD GLU A 178 10.915 22.815 32.546 1.00 23.98 C
+ATOM 1311 OE1 GLU A 178 10.081 22.732 31.610 1.00 20.87 O
+ATOM 1312 OE2 GLU A 178 10.899 23.741 33.371 1.00 15.93 O
+ATOM 1313 N HIS A 179 12.316 16.950 31.940 1.00 36.33 N
+ATOM 1314 CA HIS A 179 11.715 15.607 31.923 1.00 39.11 C
+ATOM 1315 C HIS A 179 12.773 14.513 32.065 1.00 39.82 C
+ATOM 1316 O HIS A 179 13.973 14.792 32.106 1.00 40.89 O
+ATOM 1317 CB HIS A 179 10.916 15.390 30.631 1.00 39.62 C
+ATOM 1318 CG HIS A 179 10.018 16.535 30.270 1.00 40.58 C
+TER 1319 HIS A 179
+HETATM 1320 PG ATP A 201 32.020 17.261 -10.269 1.00 25.11 P
+HETATM 1321 O1G ATP A 201 31.057 16.174 -9.817 1.00 24.48 O
+HETATM 1322 O2G ATP A 201 31.315 18.553 -10.632 1.00 24.06 O
+HETATM 1323 O3G ATP A 201 32.997 16.830 -11.334 1.00 24.38 O
+HETATM 1324 PB ATP A 201 32.510 17.799 -7.497 1.00 14.19 P
+HETATM 1325 O1B ATP A 201 31.577 16.667 -7.113 1.00 14.26 O
+HETATM 1326 O2B ATP A 201 32.130 19.246 -7.222 1.00 14.41 O
+HETATM 1327 O3B ATP A 201 32.977 17.632 -9.026 1.00 17.39 O
+HETATM 1328 PA ATP A 201 34.444 16.290 -5.961 1.00 15.67 P
+HETATM 1329 O1A ATP A 201 33.740 16.191 -4.630 1.00 16.51 O
+HETATM 1330 O2A ATP A 201 34.356 15.148 -6.923 1.00 16.00 O
+HETATM 1331 O3A ATP A 201 33.946 17.594 -6.768 1.00 12.65 O
+HETATM 1332 O5' ATP A 201 35.977 16.646 -5.633 1.00 15.79 O
+HETATM 1333 C5' ATP A 201 36.994 16.627 -6.631 1.00 18.36 C
+HETATM 1334 C4' ATP A 201 38.351 16.322 -6.005 1.00 18.18 C
+HETATM 1335 O4' ATP A 201 38.757 17.379 -5.132 1.00 15.38 O
+HETATM 1336 C3' ATP A 201 38.361 15.054 -5.173 1.00 18.30 C
+HETATM 1337 O3' ATP A 201 39.629 14.414 -5.361 1.00 22.45 O
+HETATM 1338 C2' ATP A 201 38.222 15.553 -3.752 1.00 16.55 C
+HETATM 1339 O2' ATP A 201 38.822 14.699 -2.792 1.00 18.88 O
+HETATM 1340 C1' ATP A 201 38.935 16.881 -3.810 1.00 13.61 C
+HETATM 1341 N9 ATP A 201 38.398 17.885 -2.890 1.00 13.87 N
+HETATM 1342 C8 ATP A 201 37.099 18.176 -2.707 1.00 13.81 C
+HETATM 1343 N7 ATP A 201 36.974 19.163 -1.803 1.00 12.17 N
+HETATM 1344 C5 ATP A 201 38.206 19.533 -1.409 1.00 13.54 C
+HETATM 1345 C6 ATP A 201 38.768 20.506 -0.465 1.00 16.52 C
+HETATM 1346 N6 ATP A 201 37.969 21.327 0.248 1.00 14.41 N
+HETATM 1347 N1 ATP A 201 40.109 20.561 -0.342 1.00 19.10 N
+HETATM 1348 C2 ATP A 201 40.918 19.755 -1.050 1.00 18.85 C
+HETATM 1349 N3 ATP A 201 40.472 18.838 -1.925 1.00 17.78 N
+HETATM 1350 C4 ATP A 201 39.145 18.682 -2.133 1.00 17.12 C
+HETATM 1351 MG MG A 202 30.500 15.258 -8.074 1.00 16.72 MG
+HETATM 1352 O HOH A2001 16.394 24.875 1.602 1.00 13.79 O
+HETATM 1353 O HOH A2002 15.733 23.864 5.777 1.00 39.92 O
+HETATM 1354 O HOH A2003 14.840 25.961 3.341 1.00 30.82 O
+HETATM 1355 O HOH A2004 18.711 25.122 5.938 1.00 16.52 O
+HETATM 1356 O HOH A2005 26.918 13.226 -4.130 1.00 43.54 O
+HETATM 1357 O HOH A2006 29.838 21.597 -11.935 1.00 23.94 O
+HETATM 1358 O HOH A2007 32.710 26.692 -7.704 1.00 8.44 O
+HETATM 1359 O HOH A2008 34.508 12.599 10.062 1.00 45.55 O
+HETATM 1360 O HOH A2009 26.516 15.724 -3.379 1.00 30.09 O
+HETATM 1361 O HOH A2010 28.679 16.189 -7.983 1.00 22.66 O
+HETATM 1362 O HOH A2011 33.272 12.651 1.335 1.00 33.20 O
+HETATM 1363 O HOH A2012 36.278 12.733 -2.459 1.00 39.41 O
+HETATM 1364 O HOH A2013 23.707 5.660 -7.616 1.00 46.64 O
+HETATM 1365 O HOH A2014 10.853 14.593 -12.521 1.00 38.41 O
+HETATM 1366 O HOH A2015 34.103 12.817 -5.098 1.00 48.19 O
+HETATM 1367 O HOH A2016 11.899 12.694 -19.572 1.00 41.43 O
+HETATM 1368 O HOH A2017 31.150 14.326 8.173 1.00 20.48 O
+HETATM 1369 O HOH A2018 37.363 13.327 1.241 1.00 53.25 O
+HETATM 1370 O HOH A2019 38.802 15.311 9.085 1.00 62.70 O
+HETATM 1371 O HOH A2020 33.473 16.201 7.669 1.00 27.71 O
+HETATM 1372 O HOH A2021 13.554 20.669 -26.505 1.00 34.40 O
+HETATM 1373 O HOH A2022 11.764 22.747 -23.255 1.00 33.25 O
+HETATM 1374 O HOH A2023 33.744 11.695 7.552 1.00 48.46 O
+HETATM 1375 O HOH A2024 26.574 12.211 12.254 1.00 29.52 O
+HETATM 1376 O HOH A2025 32.828 7.348 2.585 1.00 42.69 O
+HETATM 1377 O HOH A2026 32.799 8.158 8.728 1.00 43.51 O
+HETATM 1378 O HOH A2027 32.301 11.102 3.654 1.00 37.76 O
+HETATM 1379 O HOH A2028 8.033 24.235 -15.736 1.00 35.81 O
+HETATM 1380 O HOH A2029 27.404 13.991 14.074 1.00 55.22 O
+HETATM 1381 O HOH A2030 12.770 14.224 -5.206 1.00 26.64 O
+HETATM 1382 O HOH A2031 20.940 9.273 -3.567 1.00 32.89 O
+HETATM 1383 O HOH A2032 27.036 13.821 -10.102 1.00 24.19 O
+HETATM 1384 O HOH A2033 26.160 17.800 -8.520 1.00 33.36 O
+HETATM 1385 O HOH A2034 27.226 15.260 -6.080 1.00 37.46 O
+HETATM 1386 O HOH A2035 21.642 11.104 -5.700 1.00 18.76 O
+HETATM 1387 O HOH A2036 21.530 18.184 -12.535 1.00 16.58 O
+HETATM 1388 O HOH A2037 24.417 31.184 -18.688 1.00 37.44 O
+HETATM 1389 O HOH A2038 25.151 18.211 -15.207 1.00 26.65 O
+HETATM 1390 O HOH A2039 27.435 16.839 -10.452 1.00 51.67 O
+HETATM 1391 O HOH A2040 14.917 10.333 -9.718 1.00 27.33 O
+HETATM 1392 O HOH A2041 12.307 26.370 2.751 1.00 57.55 O
+HETATM 1393 O HOH A2042 26.661 9.805 -16.783 1.00 32.26 O
+HETATM 1394 O HOH A2043 21.818 4.739 -9.472 1.00 40.19 O
+HETATM 1395 O HOH A2044 19.630 3.642 -8.659 1.00 35.02 O
+HETATM 1396 O HOH A2045 11.041 13.326 -10.330 1.00 42.47 O
+HETATM 1397 O HOH A2046 10.841 9.557 -17.371 1.00 43.93 O
+HETATM 1398 O HOH A2047 45.756 25.576 -14.043 1.00 33.13 O
+HETATM 1399 O HOH A2048 46.028 22.613 -1.665 1.00 26.35 O
+HETATM 1400 O HOH A2049 13.368 7.759 -20.328 1.00 39.43 O
+HETATM 1401 O HOH A2050 38.831 13.944 -11.351 1.00 39.08 O
+HETATM 1402 O HOH A2051 43.704 13.171 -10.480 1.00 43.18 O
+HETATM 1403 O HOH A2052 13.321 11.144 -20.742 1.00 36.97 O
+HETATM 1404 O HOH A2053 18.614 8.880 -25.099 1.00 51.93 O
+HETATM 1405 O HOH A2054 44.200 14.956 -23.482 1.00 57.63 O
+HETATM 1406 O HOH A2055 26.249 7.363 -22.085 1.00 32.19 O
+HETATM 1407 O HOH A2056 26.681 13.983 -25.055 1.00 32.76 O
+HETATM 1408 O HOH A2057 26.646 10.803 -19.131 1.00 26.73 O
+HETATM 1409 O HOH A2058 21.976 5.943 -21.792 1.00 30.99 O
+HETATM 1410 O HOH A2059 22.847 17.928 -28.584 1.00 46.43 O
+HETATM 1411 O HOH A2060 24.454 16.042 -30.490 1.00 54.17 O
+HETATM 1412 O HOH A2061 18.223 12.821 -32.020 1.00 36.70 O
+HETATM 1413 O HOH A2062 16.730 20.451 -26.704 1.00 22.31 O
+HETATM 1414 O HOH A2063 13.370 13.698 -23.694 1.00 38.16 O
+HETATM 1415 O HOH A2064 35.082 34.227 -11.689 1.00 42.83 O
+HETATM 1416 O HOH A2065 22.098 21.232 -27.737 1.00 35.11 O
+HETATM 1417 O HOH A2066 25.718 22.923 -26.016 1.00 52.52 O
+HETATM 1418 O HOH A2067 21.786 26.036 -20.889 1.00 49.69 O
+HETATM 1419 O HOH A2068 26.265 25.085 -21.335 1.00 39.68 O
+HETATM 1420 O HOH A2069 27.891 32.993 5.178 1.00 50.98 O
+HETATM 1421 O HOH A2070 18.617 22.277 -27.541 1.00 37.40 O
+HETATM 1422 O HOH A2071 15.406 24.604 -21.837 1.00 43.11 O
+HETATM 1423 O HOH A2072 12.071 20.349 -24.371 1.00 31.13 O
+HETATM 1424 O HOH A2073 34.916 26.650 11.151 1.00 48.39 O
+HETATM 1425 O HOH A2074 10.892 22.039 -17.002 1.00 26.70 O
+HETATM 1426 O HOH A2075 12.270 15.390 -15.148 1.00 47.35 O
+HETATM 1427 O HOH A2076 23.874 20.517 -15.106 1.00 21.31 O
+HETATM 1428 O HOH A2077 13.697 27.823 -16.874 1.00 17.73 O
+HETATM 1429 O HOH A2078 14.465 24.598 -17.741 1.00 37.49 O
+HETATM 1430 O HOH A2079 11.869 24.008 -18.257 1.00 45.37 O
+HETATM 1431 O HOH A2080 10.131 27.369 -15.485 1.00 49.88 O
+HETATM 1432 O HOH A2081 7.812 21.032 -12.584 1.00 19.67 O
+HETATM 1433 O HOH A2082 9.765 22.493 -14.852 1.00 29.32 O
+HETATM 1434 O HOH A2083 8.851 18.858 -11.009 1.00 13.81 O
+HETATM 1435 O HOH A2084 13.847 14.839 -7.845 1.00 20.07 O
+HETATM 1436 O HOH A2085 10.173 23.095 -5.893 1.00 12.34 O
+HETATM 1437 O HOH A2086 9.151 29.892 -12.347 1.00 33.23 O
+HETATM 1438 O HOH A2087 9.164 29.029 -8.822 1.00 21.89 O
+HETATM 1439 O HOH A2088 10.249 23.242 -0.213 1.00 33.01 O
+HETATM 1440 O HOH A2089 36.851 14.924 -12.150 1.00 30.56 O
+HETATM 1441 O HOH A2090 43.876 11.270 -5.452 1.00 39.92 O
+HETATM 1442 O HOH A2091 13.828 12.563 0.336 1.00 18.43 O
+HETATM 1443 O HOH A2092 9.988 17.822 2.322 1.00 37.21 O
+HETATM 1444 O HOH A2093 26.224 23.430 -9.214 1.00 12.21 O
+HETATM 1445 O HOH A2094 23.998 24.394 -10.935 1.00 16.97 O
+HETATM 1446 O HOH A2095 19.452 26.527 -19.205 1.00 35.39 O
+HETATM 1447 O HOH A2096 21.529 31.594 -18.033 1.00 39.19 O
+HETATM 1448 O HOH A2097 15.831 26.337 -18.874 1.00 46.73 O
+HETATM 1449 O HOH A2098 17.830 23.176 -15.847 1.00 13.61 O
+HETATM 1450 O HOH A2099 14.836 33.414 -12.591 1.00 35.17 O
+HETATM 1451 O HOH A2100 17.715 31.974 -6.403 1.00 10.55 O
+HETATM 1452 O HOH A2101 19.536 33.170 -17.989 1.00 35.17 O
+HETATM 1453 O HOH A2102 11.079 30.059 -4.962 0.66 13.25 O
+HETATM 1454 O HOH A2103 11.407 25.512 -4.523 1.00 35.93 O
+HETATM 1455 O HOH A2104 11.252 28.570 -1.476 1.00 49.35 O
+HETATM 1456 O HOH A2105 11.866 27.406 0.633 1.00 41.35 O
+HETATM 1457 O HOH A2106 17.541 31.566 -1.491 1.00 6.96 O
+HETATM 1458 O HOH A2107 19.956 30.084 4.612 1.00 25.85 O
+HETATM 1459 O HOH A2108 33.935 29.326 -7.870 1.00 15.58 O
+HETATM 1460 O HOH A2109 32.479 33.428 -7.722 1.00 26.65 O
+HETATM 1461 O HOH A2110 33.794 33.489 0.338 1.00 32.93 O
+HETATM 1462 O HOH A2111 32.580 34.495 -5.127 1.00 44.58 O
+HETATM 1463 O HOH A2112 44.395 29.159 -6.542 1.00 48.72 O
+HETATM 1464 O HOH A2113 40.584 31.724 -10.610 1.00 28.81 O
+HETATM 1465 O HOH A2114 45.887 23.588 -12.217 1.00 15.68 O
+HETATM 1466 O HOH A2115 43.333 30.323 -10.642 1.00 22.77 O
+HETATM 1467 O HOH A2116 46.511 27.814 -7.051 1.00 48.30 O
+HETATM 1468 O HOH A2117 46.871 23.489 -3.968 1.00 33.49 O
+HETATM 1469 O HOH A2118 47.377 24.079 -7.985 1.00 19.93 O
+HETATM 1470 O HOH A2119 42.596 23.114 -3.565 1.00 38.36 O
+HETATM 1471 O HOH A2120 45.787 16.927 -10.397 1.00 25.49 O
+HETATM 1472 O HOH A2121 44.544 20.105 -1.255 1.00 41.40 O
+HETATM 1473 O HOH A2122 46.153 16.891 -7.115 1.00 27.43 O
+HETATM 1474 O HOH A2123 39.529 13.732 -8.991 1.00 45.97 O
+HETATM 1475 O HOH A2124 38.764 15.052 -16.490 1.00 45.94 O
+HETATM 1476 O HOH A2125 42.408 15.099 -9.762 1.00 26.15 O
+HETATM 1477 O HOH A2126 47.348 15.871 -15.100 1.00 43.01 O
+HETATM 1478 O HOH A2127 44.690 13.113 -14.481 1.00 51.52 O
+HETATM 1479 O HOH A2128 46.564 15.128 -21.983 1.00 40.69 O
+HETATM 1480 O HOH A2129 44.253 17.104 -25.930 1.00 56.58 O
+HETATM 1481 O HOH A2130 51.356 19.341 -28.242 1.00 53.19 O
+HETATM 1482 O HOH A2131 51.509 24.563 -25.082 1.00 42.32 O
+HETATM 1483 O HOH A2132 48.273 22.526 -22.371 1.00 33.67 O
+HETATM 1484 O HOH A2133 36.596 17.306 -17.545 1.00 43.10 O
+HETATM 1485 O HOH A2134 39.731 30.555 -21.669 1.00 39.41 O
+HETATM 1486 O HOH A2135 39.997 19.612 -23.171 1.00 40.53 O
+HETATM 1487 O HOH A2136 37.537 32.698 -15.757 1.00 25.34 O
+HETATM 1488 O HOH A2137 32.835 36.113 -14.927 1.00 27.30 O
+HETATM 1489 O HOH A2138 29.304 35.719 -18.227 1.00 31.41 O
+HETATM 1490 O HOH A2139 27.049 34.187 -16.767 1.00 28.02 O
+HETATM 1491 O HOH A2140 26.436 30.120 -17.249 1.00 20.72 O
+HETATM 1492 O HOH A2141 26.777 27.768 -21.343 1.00 36.86 O
+HETATM 1493 O HOH A2142 26.778 37.588 -10.008 1.00 16.89 O
+HETATM 1494 O HOH A2143 25.906 35.793 -2.699 1.00 24.95 O
+HETATM 1495 O HOH A2144 33.070 35.850 -12.278 1.00 50.14 O
+HETATM 1496 O HOH A2145 31.687 35.865 -10.107 0.66 33.83 O
+HETATM 1497 O HOH A2146 16.616 34.824 -13.119 1.00 34.19 O
+HETATM 1498 O HOH A2147 19.171 42.406 -11.209 1.00 29.64 O
+HETATM 1499 O HOH A2148 22.283 42.388 -11.496 0.50 35.05 O
+HETATM 1500 O HOH A2149 19.518 35.735 -11.872 0.50 24.55 O
+HETATM 1501 O HOH A2150 18.709 39.381 -11.423 0.50 17.89 O
+HETATM 1502 O HOH A2151 18.633 30.849 -3.961 1.00 7.00 O
+HETATM 1503 O HOH A2152 22.666 35.930 -3.434 1.00 13.60 O
+HETATM 1504 O HOH A2153 24.290 32.148 5.169 1.00 27.25 O
+HETATM 1505 O HOH A2154 25.864 35.252 2.751 1.00 34.46 O
+HETATM 1506 O HOH A2155 22.230 30.224 4.066 1.00 21.92 O
+HETATM 1507 O HOH A2156 28.498 33.848 2.754 1.00 17.87 O
+HETATM 1508 O HOH A2157 31.250 34.937 2.265 1.00 36.25 O
+HETATM 1509 O HOH A2158 41.520 31.449 -1.700 1.00 44.59 O
+HETATM 1510 O HOH A2159 37.937 31.128 -5.473 1.00 31.10 O
+HETATM 1511 O HOH A2160 41.561 27.990 5.939 1.00 48.67 O
+HETATM 1512 O HOH A2161 39.606 28.452 1.695 1.00 25.22 O
+HETATM 1513 O HOH A2162 34.837 31.395 2.917 1.00 25.13 O
+HETATM 1514 O HOH A2163 37.314 26.958 8.256 1.00 43.12 O
+HETATM 1515 O HOH A2164 39.553 17.010 5.827 1.00 26.47 O
+HETATM 1516 O HOH A2165 41.726 23.017 6.303 1.00 25.86 O
+HETATM 1517 O HOH A2166 34.043 18.037 9.578 1.00 30.44 O
+HETATM 1518 O HOH A2167 36.068 25.280 9.566 1.00 23.02 O
+HETATM 1519 O HOH A2168 39.881 19.136 9.290 1.00 50.82 O
+HETATM 1520 O HOH A2169 38.636 24.848 11.134 0.50 34.09 O
+HETATM 1521 O HOH A2170 36.268 17.063 11.054 1.00 64.79 O
+HETATM 1522 O HOH A2171 30.384 31.575 4.657 1.00 28.89 O
+HETATM 1523 O HOH A2172 35.979 28.995 9.040 1.00 44.56 O
+HETATM 1524 O HOH A2173 24.593 22.659 12.185 1.00 21.20 O
+HETATM 1525 O HOH A2174 30.515 23.451 13.324 1.00 40.31 O
+HETATM 1526 O HOH A2175 23.451 31.247 7.732 1.00 31.89 O
+HETATM 1527 O HOH A2176 34.870 30.587 10.789 1.00 55.67 O
+HETATM 1528 O HOH A2177 33.466 28.680 11.358 1.00 35.67 O
+HETATM 1529 O HOH A2178 22.080 21.784 11.893 1.00 43.22 O
+HETATM 1530 O HOH A2179 20.285 22.217 9.608 1.00 42.56 O
+HETATM 1531 O HOH A2180 17.580 27.909 11.758 1.00 26.94 O
+HETATM 1532 O HOH A2181 23.412 23.994 16.832 1.00 32.42 O
+HETATM 1533 O HOH A2182 21.299 22.650 14.520 1.00 25.24 O
+HETATM 1534 O HOH A2183 20.617 24.229 18.259 1.00 38.08 O
+HETATM 1535 O HOH A2184 12.667 25.568 24.261 1.00 55.59 O
+HETATM 1536 O HOH A2185 16.830 25.889 27.131 1.00 26.11 O
+HETATM 1537 O HOH A2186 19.567 28.245 24.397 1.00 38.32 O
+HETATM 1538 O HOH A2187 18.428 26.237 20.724 1.00 42.09 O
+HETATM 1539 O HOH A2188 17.413 20.324 26.170 1.00 47.93 O
+HETATM 1540 O HOH A2189 10.680 24.048 25.504 1.00 50.18 O
+HETATM 1541 O HOH A2190 17.906 18.497 33.264 1.00 28.68 O
+HETATM 1542 O HOH A2191 14.495 17.448 34.756 1.00 44.69 O
+HETATM 1543 O HOH A2192 12.349 24.075 35.467 1.00 26.49 O
+HETATM 1544 O HOH A2193 9.900 18.633 35.810 1.00 26.39 O
+HETATM 1545 O HOH A2194 8.227 20.845 30.994 1.00 28.22 O
+HETATM 1546 O HOH A2195 35.297 21.327 -1.002 1.00 14.75 O
+HETATM 1547 O HOH A2196 42.652 17.660 -3.271 1.00 26.75 O
+HETATM 1548 O HOH A2197 32.220 14.146 -8.096 1.00 17.10 O
+HETATM 1549 O HOH A2198 35.492 15.416 -10.176 1.00 34.29 O
+HETATM 1550 O HOH A2199 42.117 16.085 -5.806 1.00 32.91 O
+HETATM 1551 O HOH A2200 41.712 22.844 -0.070 1.00 27.53 O
+HETATM 1552 O HOH A2201 29.650 13.756 -9.193 1.00 17.92 O
+HETATM 1553 O HOH A2202 30.263 19.021 -12.969 1.00 48.87 O
+HETATM 1554 O HOH A2203 29.101 15.076 -12.152 1.00 46.00 O
+HETATM 1555 O HOH A2204 32.843 13.652 -11.392 1.00 45.38 O
+HETATM 1556 O HOH A2205 41.188 11.478 -5.277 1.00 42.49 O
+HETATM 1557 O HOH A2206 34.829 16.723 -13.249 1.00 30.94 O
+CONECT 1320 1321 1322 1323 1327
+CONECT 1321 1320
+CONECT 1322 1320
+CONECT 1323 1320
+CONECT 1324 1325 1326 1327 1331
+CONECT 1325 1324
+CONECT 1326 1324
+CONECT 1327 1320 1324
+CONECT 1328 1329 1330 1331 1332
+CONECT 1329 1328
+CONECT 1330 1328
+CONECT 1331 1324 1328
+CONECT 1332 1328 1333
+CONECT 1333 1332 1334
+CONECT 1334 1333 1335 1336
+CONECT 1335 1334 1340
+CONECT 1336 1334 1337 1338
+CONECT 1337 1336
+CONECT 1338 1336 1339 1340
+CONECT 1339 1338
+CONECT 1340 1335 1338 1341
+CONECT 1341 1340 1342 1350
+CONECT 1342 1341 1343
+CONECT 1343 1342 1344
+CONECT 1344 1343 1345 1350
+CONECT 1345 1344 1346 1347
+CONECT 1346 1345
+CONECT 1347 1345 1348
+CONECT 1348 1347 1349
+CONECT 1349 1348 1350
+CONECT 1350 1341 1344 1349
+END
diff --git a/doc/tests/scripts/loop_structure_db.py b/doc/tests/scripts/loop_structure_db.py
index 09258a9236b4c8dc6e27dfb866c83df17c6067e4..1359eb6e2c51a6aa9039a02d0ce77effbae6c52e 100644
--- a/doc/tests/scripts/loop_structure_db.py
+++ b/doc/tests/scripts/loop_structure_db.py
@@ -66,16 +66,9 @@ structure_db_two.PrintStatistics()
for i in range(structure_db_one.GetNumCoords()):
- # get the CoordInfo for chain with index 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)
-
# 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)
+ bb_list = structure_db_one.GetBackboneList(i)
+ res_depths = structure_db_one.GetResidueDepths(i)
# generate structure profiles based on structure_db_two
prof = structure_db_two.GenerateStructureProfile(bb_list,
diff --git a/doc/tests/scripts/modelling_motif_finder.py b/doc/tests/scripts/modelling_motif_finder.py
new file mode 100644
index 0000000000000000000000000000000000000000..ff072d3466e55ab1626c01b45e3cf926f17995f8
--- /dev/null
+++ b/doc/tests/scripts/modelling_motif_finder.py
@@ -0,0 +1,59 @@
+# Example script that loads protein structures that contain ATP and
+# generates motif queries describing their binding pockets.
+# In a second step, those pockets are matched against a protein
+# structure that only contains an ATP analog. The ATP from every
+# match is transformed and stored to disk for further processing.
+
+from ost import io, geom, mol
+from promod3 import modelling
+
+files = ['data/1E2Q.pdb', 'data/1KO5.pdb', 'data/2IYW.pdb']
+
+atp_list = list()
+query_list = list()
+
+for f in files:
+
+ prot = io.LoadPDB(f)
+ peptide_sel = prot.Select("peptide=true")
+ atp_sel = prot.Select("rname=ATP")
+
+ # generate a single query for each ATP pocket
+ for atp_idx, atp_r in enumerate(atp_sel.residues):
+ pocket_view = peptide_sel.CreateEmptyView()
+ for atp_at in atp_r.atoms:
+ close_at = peptide_sel.FindWithin(atp_at.GetPos(), 4.5)
+ for at in close_at:
+ r = at.handle.GetResidue()
+ add_flag = mol.INCLUDE_ATOMS | mol.CHECK_DUPLICATES
+ pocket_view.AddResidue(r, add_flag)
+
+ ca_positions = geom.Vec3List()
+ for res in pocket_view.residues:
+ ca_positions.append(res.FindAtom("CA").GetPos())
+ i = "%s_%i"%(f, atp_idx)
+ query = modelling.MotifQuery(ca_positions, i, 4.0, 9.0, 1.0)
+ query_list.append(query)
+
+ # create an entity from atp for later use
+ atp_view = prot.CreateEmptyView()
+ atp_view.AddResidue(atp_r, mol.INCLUDE_ATOMS)
+ atp_list.append(mol.CreateEntityFromView(atp_view, True))
+
+# That's it, let's combine the single queries
+full_query = modelling.MotifQuery(query_list)
+
+prot = io.LoadPDB("data/1AKE.pdb")
+peptide_sel = prot.Select("peptide=true")
+ca_positions = geom.Vec3List()
+for r in peptide_sel.residues:
+ ca_positions.append(r.FindAtom("CA").GetPos())
+
+# search all matches, fetch the corresponding atps,
+# transform them onto the 1ake binding site and dump them to disk
+matches = modelling.FindMotifs(full_query, ca_positions)
+for m_idx, m in enumerate(matches):
+ atp = atp_list[m.query_idx].Copy()
+ atp.EditXCS().ApplyTransform(m.mat)
+ io.SavePDB(atp, "m_%i.pdb"%(m_idx))
+
diff --git a/doc/tests/test_doctests.py b/doc/tests/test_doctests.py
index 42d8071136c6a94d82d91cdcaded36bdcf36d819..d988f653f1558b27a727c26623a5cc05efbb99b3 100644
--- a/doc/tests/test_doctests.py
+++ b/doc/tests/test_doctests.py
@@ -261,7 +261,7 @@ class DocTests(unittest.TestCase):
import matplotlib.pyplot as plt
import numpy as np
except ImportError:
- print 'Missing python libraries, skipping testLoopFragDB...'
+ print 'Missing python libraries, skipping testLoopTorsionSampler...'
return
# run it
self.checkPMRun('loop_torsion_sampler.py', [], 0)
@@ -392,6 +392,21 @@ class DocTests(unittest.TestCase):
# clean up
os.remove('aa_relax_test.pdb')
+ def testModellingMotifFinder(self):
+ # run it
+ self.checkPMRun('modelling_motif_finder.py', [], 0)
+ # check that result exists and is readable, cleanup afterwards
+ for i in range(12):
+ io.LoadPDB("m_%i.pdb"%(i))
+ os.remove("m_%i.pdb"%(i))
+
+ # check whether the script suddenly found more hits
+ try:
+ io.LoadPDB("m_12.pdb")
+ raise RuntimeError("Expect exactly 12 hits in motif finder example")
+ except:
+ pass
+
################################################################
def testSidechainSteps(self):
diff --git a/loop/doc/backbone.rst b/loop/doc/backbone.rst
index 3acc2f8e1a2b74a97e559c050e71eb97c777802e..e5e2d9964cfb6cd7cce133bd1cd5869c3bd19d19 100644
--- a/loop/doc/backbone.rst
+++ b/loop/doc/backbone.rst
@@ -79,6 +79,22 @@ The BackboneList class
code which is not one of the 20 default amino acids or if
*sequence* and *dihedral_angles* are inconsistent in size.
+ .. method:: BackboneList(residues)
+
+ Creates a BackboneList with positions and sequence extracted from
+ *residues*.
+
+ :param residues: List of :class:`ost.mol.ResidueHandle` objects from
+ which the backbone positions and one letter codes
+ are extracted.
+
+ :type residues: :class:`list`
+
+ :raises: :exc:`~exceptions.RuntimeError` if a residue in *residues*
+ contains a one letter code which is not one of the 20 default
+ amino acids or when there is a residue not providing all
+ required positions.
+
.. method:: BackboneList(sequence, residues)
Creates a BackboneList from given *sequence* and positions extracted from
diff --git a/loop/doc/structure_db.rst b/loop/doc/structure_db.rst
index b3089c7248bc40d5f4bd292125795b2edde82204..756afe78cd46954025953926e787eb618c2f5f58 100644
--- a/loop/doc/structure_db.rst
+++ b/loop/doc/structure_db.rst
@@ -141,6 +141,7 @@ database, you might want to consider two things:
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.
+ For the bare minimum (only backbone coordinates and sequence), use Minimal.
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 :class:`StructureDB`). One important note:
@@ -148,8 +149,8 @@ database, you might want to consider two things:
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
+ Minimal, All, Dihedrals, SolventAccessibilities, ResidueDepths, DSSP,
+ AAFrequencies, AAFrequenciesStruct
.. class:: StructureDB(data_to_store)
@@ -249,7 +250,8 @@ database, you might want to consider two things:
:type id: :class:`str`
:type chain_name: :class:`str`
- :type ent: :class:`ost.mol.EntityView`
+ :type ent: :class:`ost.mol.EntityHandle` /
+ :class:`ost.mol.EntityView`
:type seqres: :class:`ost.seq.SequenceHandle`
:type prof: :class:`ost.seq.ProfileHandle`
:type only_longest_strech: :class:`bool`
@@ -314,14 +316,22 @@ database, you might want to consider two things:
.. method:: GetBackboneList(fragment, sequence)
- GetBackboneList(n_stem, c_stem, fragment, sequence)
+ GetBackboneList(n_stem, c_stem, fragment, sequence="")
+ GetBackboneList(coord_idx, sequence="")
+ GetBackboneList(n_stem, c_stem, coord_idx, sequence="")
- :returns: Backbone list with positions extracted from *fragment*.
+
+ :returns: Backbone list with positions extracted from *fragment* or
+ full entry at *coord_idx*
:rtype: :class:`BackboneList`
:param fragment: Fragment definition from which to extract positions.
:type fragment: :class:`FragmentInfo`
- :param sequence: Sequence to set for the returned backbone list.
+ :param coord_idx: Idx of entry from which to extract positions.
+ :type coord_idx: :class:`int`
+ :param sequence: Sequence of the returned backbone list. If not
+ set, the original sequence at specified location in the
+ database is used.
:type sequence: :class:`str`
:param n_stem: Positions on which the backbone list's N-terminus should be
superposed onto.
@@ -330,89 +340,116 @@ database, you might want to consider two things:
superposed onto.
: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 connected
- stretches in the database) or if *sequence* contains a one letter
- code which is not one of the 20 default amino acids.
-
+ :raises: :exc:`~exceptions.RuntimeError` if the length of *sequence* does
+ not match with the desired backbone list, if *sequence* contains
+ a character which does not belong to the 20 proteinogenic amino
+ acids or if *fragment* or *coord_idx* is invalid. Fragment can
+ be invalid when it does not fully fit into one of the connected
+ stretches of residues in the database.
.. method:: GetSequence(fragment)
+ GetSequence(coord_idx)
- :returns: The sequence of *fragment*
+ :returns: The sequence of *fragment* or full entry at *coord_idx*
:rtype: :class:`str`
:param fragment: Fragment definition from which to extract the sequence.
:type fragment: :class:`FragmentInfo`
- :raises: :exc:`~exceptions.RuntimeError` if fragment is invalid. This is
- the case when the fragment does not fully fit into one of the
- connected stretches of residues in the database.
+ :param coord_idx: Idx of entry from which to extract the sequence
+ :type coord_idx: :class:`int`
+
+ :raises: :exc:`~exceptions.RuntimeError` if fragment or coord_idx is
+ invalid. Fragment can be invalid when it does not fully fit into
+ one of the connected stretches of residues in the database.
.. method:: GetDSSPStates(fragment)
+ GetDSSPStates(coord_idx)
- :returns: The dssp states of *fragment*
+ :returns: The dssp states of *fragment* or full entry at *coord_idx*
:rtype: :class:`str`
:param fragment: Fragment definition from which to extract the states.
:type fragment: :class:`FragmentInfo`
+ :param coord_idx: Idx of entry from which to extract the dssp states
+ :type coord_idx: :class:`int`
+
: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
- connected stretches of residues in the database.
+ data or if fragment/ coord_idx is invalid. Fragment can be invalid
+ when it does not fully fit into one of the connected stretches of
+ residues in the database.
.. method:: GetDihedralAngles(fragment)
+ GetDihedralAngles(coord_idx)
:returns: The phi and psi dihedral angles of every residue of *fragment*
+ or full entry at *coord_idx*
:rtype: :class:`list` of pairs (:class:`tuple`)
:param fragment: Fragment definition from which to extract the dihedrals.
:type fragment: :class:`FragmentInfo`
+ :param coord_idx: Idx of entry from which to extract the dihedral angles
+ :type coord_idx: :class:`int`
+
: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
+ dihedral angle data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
.. method:: GetResidueDepths(fragment)
+ GetResidueDepths(coord_idx)
- :returns: Residue depth for each residue of *fragment*.
+ :returns: Residue depth for each residue of *fragment* or full entry
+ at *coord_idx*
:rtype: :class:`list` of :class:`float`
:param fragment: Fragment definition from which to extract the residue
depths
:type fragment: :class:`FragmentInfo`
+ :param coord_idx: Idx of entry from which to extract the residue depths
+ :type coord_idx: :class:`int`
+
: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
+ residue depth data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
.. method:: GetSolventAccessibilitites(fragment)
+ GetSolventAccessibilitites(coord_idx)
- :returns: Solvent accessibility for each residue of *fragment* in square A
- as calculated by :meth:`~ost.mol.alg.Accessibility` when adding
- the structure to the database.
+ :returns: Solvent accessibility for each residue of *fragment* or full entry
+ at *coord_idx* in square A as calculated by
+ :meth:`~ost.mol.alg.Accessibility` when adding the structure to
+ the database.
:rtype: :class:`list` of :class:`float`
:param fragment: Fragment definition from which to extract the solvent
accessibilities
:type fragment: :class:`FragmentInfo`
+ :param coord_idx: Idx of entry from which to extract the solvent
+ accessibilities
+ :type coord_idx: :class:`int`
+
: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
+ solvent accessibility data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
.. method:: GetSequenceProfile(fragment)
+ GetSequenceProfile(coord_idx)
- :returns: The sequence profile for the residues defined by *fragment* with
- the BLOSUM62 probabilities as NULL model.
+ :returns: The sequence profile for the residues defined by *fragment* or
+ full entry at *coord_idx* with the BLOSUM62 probabilities as NULL
+ model.
:rtype: :class:`ost.seq.ProfileHandle`
:param fragment: Fragment definition from which to extract the sequence
@@ -420,16 +457,21 @@ database, you might want to consider two things:
:type fragment: :class:`FragmentInfo`
- :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
+ :param coord_idx: Idx of entry from which to extract the sequence profile
+ :type coord_idx: :class:`int`
+
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ sequence profile data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
.. method:: GetStructureProfile(fragment)
+ GetStructureProfile(coord_idx)
- :returns: The structure profile for the residues defined by *fragment* with
- the BLOSUM62 probabilities as NULL model.
+ :returns: The structure profile for the residues defined by *fragment* or
+ full entry at *coord_idx* with the BLOSUM62 probabilities as NULL
+ model.
:rtype: :class:`ost.seq.ProfileHandle`
:param fragment: Fragment definition from which to extract the structure
@@ -437,9 +479,12 @@ database, you might want to consider two things:
:type fragment: :class:`FragmentInfo`
- :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
+ :param coord_idx: Idx of entry from which to extract the structure profile
+ :type coord_idx: :class:`int`
+
+ :raises: :exc:`~exceptions.RuntimeError` if database does not contain
+ structure profile data or if fragment/ coord_idx is invalid.
+ Fragment can be invalid when it does not fully fit into one of the
connected stretches of residues in the database.
@@ -461,7 +506,7 @@ database, you might want to consider two things:
:raises: :exc:`~exceptions.RuntimeError` if *bb_list* and
*residue_depths* differ in size, when their size is 0
- or when database does not contain aa frequencies struct data.
+ or when database does not contain residue depth data.
.. method:: SetStructureProfile(coord_idx, prof)
diff --git a/loop/pymod/export_backbone.cc b/loop/pymod/export_backbone.cc
index 61265152fa088f9c7a2b91c633b8485f32a93c4c..d7642b12167bf86db09f92b692b1fc471d8fcbca 100644
--- a/loop/pymod/export_backbone.cc
+++ b/loop/pymod/export_backbone.cc
@@ -28,7 +28,8 @@ using namespace boost::python;
// WRAPPERS
namespace {
-BackboneListPtr FullInitWrapper(const String& sequence, boost::python::list l) {
+BackboneListPtr FullInitWrapper(const String& sequence,
+ const boost::python::list& l) {
if (boost::python::len(l) == 0) return BackboneListPtr(new BackboneList);
@@ -75,8 +76,21 @@ BackboneListPtr FullInitWrapper(const String& sequence, boost::python::list l) {
}
}
-BackboneListPtr FullInitWrapperRHList(const String& sequence,
- ost::mol::ResidueHandleList l) {
+BackboneListPtr FullInitWrapperRHList(ost::mol::ResidueHandleList& l) {
+ if (l.size() == 0) return BackboneListPtr(new BackboneList);
+ BackboneListPtr p(new BackboneList(l));
+ return p;
+}
+
+BackboneListPtr FullInitWrapperList(list& l) {
+ ost::mol::ResidueHandleList residues;
+ core::ConvertListToVector(l, residues);
+ BackboneListPtr p(new BackboneList(residues));
+ return p;
+}
+
+BackboneListPtr FullInitWrapperSeqRHList(const String& sequence,
+ ost::mol::ResidueHandleList& l) {
if (l.size() == 0) return BackboneListPtr(new BackboneList);
BackboneListPtr p(new BackboneList(sequence,l));
return p;
@@ -176,7 +190,9 @@ void export_Backbone() {
.def(init<>())
.def(init<const String&>())
.def("__init__", make_constructor(&FullInitWrapper))
+ .def("__init__", make_constructor(&FullInitWrapperList))
.def("__init__", make_constructor(&FullInitWrapperRHList))
+ .def("__init__", make_constructor(&FullInitWrapperSeqRHList))
.def("Copy", &WrapCopy)
.def("ToDensity", &BackboneList::ToDensity,
diff --git a/loop/pymod/export_structure_db.cc b/loop/pymod/export_structure_db.cc
index a9f96d4629a10e8f32dbbc2915a63b94012f7c02..869efa2e60e2ee462e195a03b3a6ed1a8bbcdc6b 100644
--- a/loop/pymod/export_structure_db.cc
+++ b/loop/pymod/export_structure_db.cc
@@ -45,6 +45,24 @@ namespace {
return bb_list;
}
+ BackboneList wrap_get_bb_list_three(StructureDBPtr db,
+ uint coord_idx,
+ const String& sequence) {
+ BackboneList bb_list;
+ db->FillBackbone(bb_list, coord_idx, sequence);
+ return bb_list;
+ }
+
+ BackboneList wrap_get_bb_list_four(StructureDBPtr db,
+ const ost::mol::ResidueHandle& stem_one,
+ const ost::mol::ResidueHandle& stem_two,
+ uint coord_idx,
+ const String& sequence) {
+ BackboneList bb_list;
+ db->FillBackbone(bb_list, stem_one, stem_two, coord_idx, sequence);
+ return bb_list;
+ }
+
boost::python::list WrapGetCoordIdx(StructureDBPtr db,
const String& id,
const String& chain_name) {
@@ -55,8 +73,15 @@ namespace {
return return_list;
}
- boost::python::list WrapGetDihedralAngles(StructureDBPtr db, FragmentInfo& info){
+ String WrapGetSequence(StructureDBPtr db, FragmentInfo& info) {
+ return db->GetSequence(info);
+ }
+ String WrapGetDSSPStates(StructureDBPtr db, FragmentInfo& info) {
+ return db->GetDSSPStates(info);
+ }
+
+ boost::python::list WrapGetDihedralAngles(StructureDBPtr db, FragmentInfo& info){
std::vector<std::pair<Real,Real> > dihedrals = db->GetDihedralAngles(info);
boost::python::list return_list;
core::AppendVectorToList(dihedrals, return_list);
@@ -77,6 +102,51 @@ namespace {
return return_list;
}
+ ost::seq::ProfileHandlePtr WrapGetSequenceProfile(StructureDBPtr db, FragmentInfo& info) {
+ return db->GetSequenceProfile(info);
+ }
+
+ ost::seq::ProfileHandlePtr WrapGetStructureProfile(StructureDBPtr db, FragmentInfo& info) {
+ return db->GetStructureProfile(info);
+ }
+
+ String WrapGetFullSequence(StructureDBPtr db, int coord_idx) {
+ return db->GetSequence(coord_idx);
+ }
+
+ String WrapGetFullDSSPStates(StructureDBPtr db, int coord_idx) {
+ return db->GetDSSPStates(coord_idx);
+ }
+
+ boost::python::list WrapGetFullDihedralAngles(StructureDBPtr db, int coord_idx){
+ std::vector<std::pair<Real,Real> > dihedrals = db->GetDihedralAngles(coord_idx);
+ boost::python::list return_list;
+ core::AppendVectorToList(dihedrals, return_list);
+ return return_list;
+ }
+
+ boost::python::list WrapGetFullResidueDepths(StructureDBPtr db, int coord_idx){
+ std::vector<Real> depths = db->GetResidueDepths(coord_idx);
+ boost::python::list return_list;
+ core::AppendVectorToList(depths, return_list);
+ return return_list;
+ }
+
+ boost::python::list WrapGetFullSolventAccessibilities(StructureDBPtr db, int coord_idx){
+ std::vector<int> acc = db->GetSolventAccessibilities(coord_idx);
+ boost::python::list return_list;
+ core::AppendVectorToList(acc, return_list);
+ return return_list;
+ }
+
+ ost::seq::ProfileHandlePtr WrapGetFullSequenceProfile(StructureDBPtr db, int coord_idx) {
+ return db->GetSequenceProfile(coord_idx);
+ }
+
+ ost::seq::ProfileHandlePtr WrapGetFullStructureProfile(StructureDBPtr db, int coord_idx) {
+ return db->GetStructureProfile(coord_idx);
+ }
+
StructureDBPtr WrapGetSubDB(StructureDBPtr db,
const boost::python::list& indices){
std::vector<uint> v_indices;
@@ -92,6 +162,27 @@ namespace {
return db->GenerateStructureProfile(bb_list, v_residue_depths);
}
+ std::vector<int> WrapAddCoordinatesView(StructureDBPtr db,
+ const String& id,
+ const String& chain_name,
+ ost::mol::EntityView& ent,
+ ost::seq::SequenceHandle& seqres,
+ ost::seq::ProfileHandlePtr prof,
+ bool only_longest_stretch) {
+ return db->AddCoordinates(id, chain_name, ent, seqres, prof,
+ only_longest_stretch);
+ }
+
+ std::vector<int> WrapAddCoordinatesHandle(StructureDBPtr db,
+ const String& id,
+ const String& chain_name,
+ ost::mol::EntityHandle& ent,
+ ost::seq::SequenceHandle& seqres,
+ ost::seq::ProfileHandlePtr prof,
+ bool only_longest_stretch) {
+ return db->AddCoordinates(id, chain_name, ent, seqres, prof,
+ only_longest_stretch);
+ }
}
@@ -117,6 +208,7 @@ void export_StructureDB(){
enum_<StructureDB::DBDataType>("StructureDBDataType")
.value("All", StructureDB::All)
+ .value("Minimal", StructureDB::Minimal)
.value("Dihedrals", StructureDB::Dihedrals)
.value("SolventAccessibilities", StructureDB::SolventAccessibilities)
.value("ResidueDepths", StructureDB::ResidueDepths)
@@ -134,7 +226,12 @@ void export_StructureDB(){
.staticmethod("LoadPortable")
.def("SavePortable", &StructureDB::SavePortable, (arg("filename")))
.def("HasData", &StructureDB::HasData, (arg("structure_db_data_type")))
- .def("AddCoordinates", &StructureDB::AddCoordinates,
+ .def("AddCoordinates", &WrapAddCoordinatesView,
+ (arg("id"), arg("chain_name"),
+ arg("ent"), arg("seqres"),
+ arg("prof")=ost::seq::ProfileHandlePtr(),
+ arg("only_longest_stretch")=true))
+ .def("AddCoordinates", &WrapAddCoordinatesHandle,
(arg("id"), arg("chain_name"),
arg("ent"), arg("seqres"),
arg("prof")=ost::seq::ProfileHandlePtr(),
@@ -144,22 +241,36 @@ void export_StructureDB(){
.def("GetCoordIndex", &WrapGetCoordIdx,
(arg("pdb_id"), arg("chain_name")))
.def("GetBackboneList", &wrap_get_bb_list_one,
- (arg("fragment"), arg("sequence")))
+ (arg("fragment"), arg("sequence")=""))
.def("GetBackboneList", &wrap_get_bb_list_two,
- (arg("stem_one"), arg("stem_two"), arg("fragment"), arg("sequence")))
+ (arg("stem_one"), arg("stem_two"), arg("fragment"), arg("sequence")=""))
+ .def("GetBackboneList", &wrap_get_bb_list_three,
+ (arg("coord_idx"), arg("sequence")=""))
+ .def("GetBackboneList", &wrap_get_bb_list_four,
+ (arg("stem_one"), arg("stem_two"), arg("coord_idx"), arg("sequence")=""))
.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")))
- .def("GetDSSPStates", &StructureDB::GetDSSPStates, (arg("fragment")))
+ .def("GetSequence", &WrapGetSequence, (arg("fragment")))
+ .def("GetDSSPStates", &WrapGetDSSPStates, (arg("fragment")))
.def("GetDihedralAngles", &WrapGetDihedralAngles, (arg("fragment")))
.def("GetResidueDepths", &WrapGetResidueDepths, (arg("fragment")))
.def("GetSolventAccessibilities", &WrapGetSolventAccessibilities,
(arg("fragment")))
- .def("GetSequenceProfile", &StructureDB::GetSequenceProfile,
+ .def("GetSequenceProfile", &WrapGetSequenceProfile,
(arg("fragment")))
- .def("GetStructureProfile", &StructureDB::GetStructureProfile,
+ .def("GetStructureProfile", &WrapGetStructureProfile,
+ (arg("fragment")))
+ .def("GetSequence", &WrapGetFullSequence, (arg("coord_idx")))
+ .def("GetDSSPStates", &WrapGetFullDSSPStates, (arg("coord_idx")))
+ .def("GetDihedralAngles", &WrapGetFullDihedralAngles, (arg("coord_idx")))
+ .def("GetResidueDepths", &WrapGetFullResidueDepths, (arg("coord_idx")))
+ .def("GetSolventAccessibilities", &WrapGetFullSolventAccessibilities,
+ (arg("coord_idx")))
+ .def("GetSequenceProfile", &WrapGetFullSequenceProfile,
+ (arg("coord_idx")))
+ .def("GetStructureProfile", &WrapGetFullStructureProfile,
(arg("fragment")))
.def("GetStartResnum", &StructureDB::GetStartResnum, (arg("fragment")))
.def("GenerateStructureProfile", &WrapGenerateStructureProfile,
diff --git a/loop/src/backbone.cc b/loop/src/backbone.cc
index 35bc7e86a0de04cdf761e2fc71c3ec5057aea6d7..f3167d04c1da08262f2ccd5082497c95469234c7 100644
--- a/loop/src/backbone.cc
+++ b/loop/src/backbone.cc
@@ -144,6 +144,14 @@ BackboneList::BackboneList(const String& sequence){
ConstructBackboneList_(sequence, phi_angles, psi_angles, omega_angles);
}
+BackboneList::BackboneList(const ost::mol::ResidueHandleList& res_list) {
+
+ bb_list_.reserve(res_list.size());
+ for (uint i = 0; i < res_list.size(); ++i) {
+ bb_list_.push_back(Backbone(res_list[i]));
+ }
+}
+
BackboneList::BackboneList(const String& sequence,
const ost::mol::ResidueHandleList& res_list) {
diff --git a/loop/src/backbone.hh b/loop/src/backbone.hh
index 253bcd429305548c0c58b728921c43141eab658f..303fa80560b5742634727f3fcf0257025a0a00cc 100644
--- a/loop/src/backbone.hh
+++ b/loop/src/backbone.hh
@@ -173,6 +173,7 @@ public:
BackboneList(const String& sequence, const std::vector<Real>& phi_angles,
const std::vector<Real>& psi_angles,
const std::vector<Real>& omega_angles);
+ BackboneList(const ost::mol::ResidueHandleList& res_list);
BackboneList(const String& sequence,
const ost::mol::ResidueHandleList& res_list);
// NOTE: default copy and assignment used!
diff --git a/loop/src/dense_hash_table.hh b/loop/src/dense_hash_table.hh
index ec9f573a09688bcf7f69dcd5ee0e204f360e2bc6..1831bd3f700a6f1d7ffd71275637ecf2b3ad14de 100644
--- a/loop/src/dense_hash_table.hh
+++ b/loop/src/dense_hash_table.hh
@@ -19,6 +19,7 @@
#include <memory>
#include <fstream>
+#include <algorithm>
#include <ost/dllexport.hh>
#include <boost/type_traits/is_fundamental.hpp>
@@ -140,7 +141,9 @@ public:
this->DoInsert(*i);
}
} else {
- memcpy(table_, ht.table_, sizeof(ValueType)*num_buckets_);
+ // cannot use memcpy since ValueType may be non-trivial-copyable
+ // (e.g. std::pair is not!)
+ std::copy(ht.table_, ht.table_ + num_buckets_, table_);
}
this->ResetThresholds();
}
diff --git a/loop/src/structure_db.cc b/loop/src/structure_db.cc
index b78558c11193b8b0af934e3183c26c7ee7afa71a..9f909ab226f40d1ed0a6ed7f7fbb388cca7a7f94 100644
--- a/loop/src/structure_db.cc
+++ b/loop/src/structure_db.cc
@@ -891,6 +891,19 @@ std::vector<int> StructureDB::AddCoordinates(const String& id,
}
+std::vector<int> StructureDB::AddCoordinates(const String& id,
+ const String& chain_name,
+ ost::mol::EntityHandle& ent,
+ ost::seq::SequenceHandle& seqres,
+ ost::seq::ProfileHandlePtr prof,
+ bool only_longest_stretch) {
+
+ ost::mol::EntityView view = ent.CreateFullView();
+ return this->AddCoordinates(id, chain_name, view, seqres,
+ prof, only_longest_stretch);
+}
+
+
void StructureDB::RemoveCoordinates(uint coord_idx) {
if(coord_idx >= coord_toc_.size()) {
@@ -1058,11 +1071,17 @@ void StructureDB::FillBackbone(BackboneList& bb_list, const FragmentInfo& info,
const String& sequence) const {
this->CheckFragmentInfo(info);
- if (info.length != sequence.size()) {
+ if (!sequence.empty() && info.length != sequence.size()) {
throw promod3::Error("Inconsistent sequence size in FillBackbone!");
}
+ String bb_list_seq = sequence;
+ if(bb_list_seq.empty()) {
+ bb_list_seq = this->GetSequence(info);
+ }
+
bb_list.clear();
+
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
@@ -1070,7 +1089,7 @@ void StructureDB::FillBackbone(BackboneList& bb_list, const FragmentInfo& info,
coords_[coord_start+i].ca.ToVec3(),
coords_[coord_start+i].c.ToVec3(),
coords_[coord_start+i].o.ToVec3(),
- sequence[i]);
+ bb_list_seq[i]);
}
}
@@ -1135,146 +1154,44 @@ void StructureDB::FillBackbone(BackboneList& bb_list,
this->FillBackbone(bb_list, t, info, sequence);
}
-String StructureDB::GetSequence(const FragmentInfo& info) const{
-
- this->CheckFragmentInfo(info);
-
- std::string return_sequence(static_cast<uint>(info.length),'?');
- int start = GetStartIndex(info);
- int end = start+info.length;
- int pos = 0;
- for (; start < end; ++start, ++pos) {
- 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');
- int start = GetStartIndex(info);
- int end = start+info.length;
- int pos = 0;
- for (; start < end; ++start, ++pos) {
- return_states[pos] = dssp_[start];
- }
- return return_states;
-}
-
-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);
-
- std::vector<std::pair<Real,Real> > return_vec(info.length);
- int start = GetStartIndex(info);
- int end = start+info.length;
- int pos = 0;
- for (; start < end; ++start, ++pos) {
- 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;
- return_depths.reserve(info.length);
- int start = GetStartIndex(info);
- int end = start+info.length;
- for (; start < end; ++start) {
- return_depths.push_back(0.1 * res_depths_[start]);
- }
- return return_depths;
-}
-
-std::vector<int> StructureDB::GetSolventAccessibilities(const FragmentInfo& info) const{
+void StructureDB::FillBackbone(BackboneList& bb_list, uint coord_idx,
+ const String& sequence) const {
- if(!this->HasData(SolventAccessibilities)) {
- throw promod3::Error("StructureDB does not contain "
- "solvent accessibilities!");
+ if(coord_idx >= this->GetNumCoords()) {
+ throw promod3::Error("Provided invalid coord_idx!");
}
- this->CheckFragmentInfo(info);
-
- std::vector<int> return_accessibilities;
- return_accessibilities.reserve(info.length);
- int start = GetStartIndex(info);
- int end = start+info.length;
- for (; start < end; ++start) {
- return_accessibilities.push_back(solv_acc_[start]);
- }
- return return_accessibilities;
+ CoordInfo c_info = this->GetCoordInfo(coord_idx);
+ FragmentInfo f_info(coord_idx, 0, c_info.size);
+ this->FillBackbone(bb_list, f_info, sequence);
}
-ost::seq::ProfileHandlePtr
-StructureDB::GetSequenceProfile(const FragmentInfo& info) const {
+void StructureDB::FillBackbone(BackboneList& bb_list, const geom::Mat4& tf,
+ uint coord_idx,
+ const String& sequence) const {
- if(!this->HasData(AAFrequencies)) {
- throw promod3::Error("StructureDB does not contain amino acid "
- "frequencies!");
+ if(coord_idx >= this->GetNumCoords()) {
+ throw promod3::Error("Provided invalid coord_idx!");
}
- this->CheckFragmentInfo(info);
-
- ost::seq::ProfileHandlePtr prof(new ost::seq::ProfileHandle);
- prof->SetNullModel(ost::seq::ProfileColumn::HHblitsNullModel());
- int start = GetStartIndex(info);
- int end = start+info.length;
- for (; start < end; ++start) {
- const short* freqs = aa_frequencies_[start].data();
- ost::seq::ProfileColumn col;
- Real* col_data = col.freqs_begin();
- for (uint i = 0; i < 20; ++i) {
- col_data[i] = static_cast<Real>(0.0001 * freqs[i]);
- }
- prof->AddColumn(col, seq_[start]);
- }
- return prof;
+ CoordInfo c_info = this->GetCoordInfo(coord_idx);
+ FragmentInfo f_info(coord_idx, 0, c_info.size);
+ this->FillBackbone(bb_list, tf, f_info, sequence);
}
-ost::seq::ProfileHandlePtr
-StructureDB::GetStructureProfile(const FragmentInfo& info) const {
+void StructureDB::FillBackbone(BackboneList& bb_list,
+ const ost::mol::ResidueHandle& stem_one,
+ const ost::mol::ResidueHandle& stem_two,
+ uint coord_idx,
+ const String& sequence) const {
- if(!this->HasData(AAFrequenciesStruct)) {
- throw promod3::Error("StructureDB does not contain amino acid "
- "frequencies derived from structural information!");
+ if(coord_idx >= this->GetNumCoords()) {
+ throw promod3::Error("Provided invalid coord_idx!");
}
- this->CheckFragmentInfo(info);
-
- ost::seq::ProfileHandlePtr prof(new ost::seq::ProfileHandle);
- prof->SetNullModel(ost::seq::ProfileColumn::HHblitsNullModel());
- int start = GetStartIndex(info);
- int end = start+info.length;
- for (; start < end; ++start) {
- const short* freqs = aa_frequencies_struct_[start].data();
- ost::seq::ProfileColumn col;
- Real* col_data = col.freqs_begin();
- for (uint i = 0; i < 20; ++i) {
- col_data[i] = static_cast<Real>(0.0001 * freqs[i]);
- }
- prof->AddColumn(col, seq_[start]);
- }
- return prof;
+ CoordInfo c_info = this->GetCoordInfo(coord_idx);
+ FragmentInfo f_info(coord_idx, 0, c_info.size);
+ this->FillBackbone(bb_list, stem_one, stem_two, f_info, sequence);
}
int StructureDB::GetStartResnum(const FragmentInfo& info) const {
@@ -1558,6 +1475,228 @@ void StructureDB::SetStructureProfile(uint chain_idx,
}
}
+String StructureDB::GetSequence(const FragmentInfo& info) const{
+
+ this->CheckFragmentInfo(info);
+
+ std::string return_sequence(static_cast<uint>(info.length),'?');
+ int start = GetStartIndex(info);
+ int end = start+info.length;
+ int pos = 0;
+ for (; start < end; ++start, ++pos) {
+ 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');
+ int start = GetStartIndex(info);
+ int end = start+info.length;
+ int pos = 0;
+ for (; start < end; ++start, ++pos) {
+ return_states[pos] = dssp_[start];
+ }
+ return return_states;
+}
+
+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);
+
+ std::vector<std::pair<Real,Real> > return_vec(info.length);
+ int start = GetStartIndex(info);
+ int end = start+info.length;
+ int pos = 0;
+ for (; start < end; ++start, ++pos) {
+ 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;
+ return_depths.reserve(info.length);
+ int start = GetStartIndex(info);
+ int end = start+info.length;
+ for (; start < end; ++start) {
+ 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;
+ return_accessibilities.reserve(info.length);
+ int start = GetStartIndex(info);
+ int end = start+info.length;
+ for (; start < end; ++start) {
+ return_accessibilities.push_back(solv_acc_[start]);
+ }
+ return return_accessibilities;
+}
+
+ost::seq::ProfileHandlePtr
+StructureDB::GetSequenceProfile(const FragmentInfo& info) const {
+
+ if(!this->HasData(AAFrequencies)) {
+ throw promod3::Error("StructureDB does not contain amino acid "
+ "frequencies!");
+ }
+
+ this->CheckFragmentInfo(info);
+
+ ost::seq::ProfileHandlePtr prof(new ost::seq::ProfileHandle);
+ prof->SetNullModel(ost::seq::ProfileColumn::HHblitsNullModel());
+ int start = GetStartIndex(info);
+ int end = start+info.length;
+ for (; start < end; ++start) {
+ const short* freqs = aa_frequencies_[start].data();
+ ost::seq::ProfileColumn col;
+ Real* col_data = col.freqs_begin();
+ for (uint i = 0; i < 20; ++i) {
+ col_data[i] = static_cast<Real>(0.0001 * freqs[i]);
+ }
+ prof->AddColumn(col, seq_[start]);
+ }
+ return prof;
+}
+
+ost::seq::ProfileHandlePtr
+StructureDB::GetStructureProfile(const FragmentInfo& info) const {
+
+ if(!this->HasData(AAFrequenciesStruct)) {
+ throw promod3::Error("StructureDB does not contain amino acid "
+ "frequencies derived from structural information!");
+ }
+
+ this->CheckFragmentInfo(info);
+
+ ost::seq::ProfileHandlePtr prof(new ost::seq::ProfileHandle);
+ prof->SetNullModel(ost::seq::ProfileColumn::HHblitsNullModel());
+ int start = GetStartIndex(info);
+ int end = start+info.length;
+ for (; start < end; ++start) {
+ const short* freqs = aa_frequencies_struct_[start].data();
+ ost::seq::ProfileColumn col;
+ Real* col_data = col.freqs_begin();
+ for (uint i = 0; i < 20; ++i) {
+ col_data[i] = static_cast<Real>(0.0001 * freqs[i]);
+ }
+ prof->AddColumn(col, seq_[start]);
+ }
+ return prof;
+}
+
+String StructureDB::GetSequence(uint coord_idx) const{
+
+ if(coord_idx >= this->GetNumCoords()) {
+ throw promod3::Error("Provided invalid coord_idx!");
+ }
+
+ CoordInfo c_info = this->GetCoordInfo(coord_idx);
+ FragmentInfo f_info(coord_idx, 0, c_info.size);
+ return this->GetSequence(f_info);
+}
+
+String StructureDB::GetDSSPStates(uint coord_idx) const{
+
+ if(coord_idx >= this->GetNumCoords()) {
+ throw promod3::Error("Provided invalid coord_idx!");
+ }
+
+ CoordInfo c_info = this->GetCoordInfo(coord_idx);
+ FragmentInfo f_info(coord_idx, 0, c_info.size);
+ return this->GetDSSPStates(f_info);
+}
+
+std::vector<std::pair<Real,Real> >
+StructureDB::GetDihedralAngles(uint coord_idx) const{
+
+ if(coord_idx >= this->GetNumCoords()) {
+ throw promod3::Error("Provided invalid coord_idx!");
+ }
+
+ CoordInfo c_info = this->GetCoordInfo(coord_idx);
+ FragmentInfo f_info(coord_idx, 0, c_info.size);
+ return this->GetDihedralAngles(f_info);
+}
+
+std::vector<Real> StructureDB::GetResidueDepths(uint coord_idx) const{
+
+ if(coord_idx >= this->GetNumCoords()) {
+ throw promod3::Error("Provided invalid coord_idx!");
+ }
+
+ CoordInfo c_info = this->GetCoordInfo(coord_idx);
+ FragmentInfo f_info(coord_idx, 0, c_info.size);
+ return this->GetResidueDepths(f_info);
+}
+
+std::vector<int> StructureDB::GetSolventAccessibilities(uint coord_idx) const{
+
+ if(coord_idx >= this->GetNumCoords()) {
+ throw promod3::Error("Provided invalid coord_idx!");
+ }
+
+ CoordInfo c_info = this->GetCoordInfo(coord_idx);
+ FragmentInfo f_info(coord_idx, 0, c_info.size);
+ return this->GetSolventAccessibilities(f_info);
+}
+
+ost::seq::ProfileHandlePtr
+StructureDB::GetSequenceProfile(uint coord_idx) const {
+
+ if(coord_idx >= this->GetNumCoords()) {
+ throw promod3::Error("Provided invalid coord_idx!");
+ }
+
+ CoordInfo c_info = this->GetCoordInfo(coord_idx);
+ FragmentInfo f_info(coord_idx, 0, c_info.size);
+ return this->GetSequenceProfile(f_info);
+}
+
+ost::seq::ProfileHandlePtr
+StructureDB::GetStructureProfile(uint coord_idx) const {
+
+ if(coord_idx >= this->GetNumCoords()) {
+ throw promod3::Error("Provided invalid coord_idx!");
+ }
+
+ CoordInfo c_info = this->GetCoordInfo(coord_idx);
+ FragmentInfo f_info(coord_idx, 0, c_info.size);
+ return this->GetStructureProfile(f_info);
+}
+
void StructureDB::CheckFragmentInfo(const FragmentInfo& info) const {
if (info.chain_index >= coord_toc_.size()) {
throw promod3::Error("Provided Fragment info tries to access non existent "
diff --git a/loop/src/structure_db.hh b/loop/src/structure_db.hh
index 228785d6c19ab6084783272cd5f9fff86deffefd..c57110f84a8307e3259c70c7e470bb62576faafd 100644
--- a/loop/src/structure_db.hh
+++ b/loop/src/structure_db.hh
@@ -130,9 +130,9 @@ struct FragmentInfo {
class StructureDB {
public:
- enum DBDataType {All = -1, Dihedrals = 1, SolventAccessibilities = 2,
- ResidueDepths = 4, DSSP = 8, AAFrequencies = 16,
- AAFrequenciesStruct = 32};
+ enum DBDataType {All = -1, Minimal = 0, Dihedrals = 1,
+ SolventAccessibilities = 2, ResidueDepths = 4, DSSP = 8,
+ AAFrequencies = 16, AAFrequenciesStruct = 32};
StructureDB(int32_t stored_data = -1): stored_data_(stored_data) { }
@@ -160,6 +160,13 @@ public:
ost::seq::ProfileHandlePtr(),
bool only_longest_stretch = true);
+ std::vector<int> AddCoordinates(const String& id, const String& chain_name,
+ ost::mol::EntityHandle& ent,
+ ost::seq::SequenceHandle& seqres,
+ ost::seq::ProfileHandlePtr prof =
+ ost::seq::ProfileHandlePtr(),
+ bool only_longest_stretch = true);
+
void RemoveCoordinates(uint coord_idx);
std::vector<int> GetCoordIdx(const String& id,
@@ -174,16 +181,40 @@ public:
bool superpose_stems = true) const;
void FillBackbone(BackboneList& bb_list, const FragmentInfo& info,
- const String& sequence) const;
+ const String& sequence = "") const;
void FillBackbone(BackboneList& bb_list, const geom::Mat4& tf,
- const FragmentInfo& info, const String& sequence) const;
+ const FragmentInfo& info, const String& sequence = "") const;
void FillBackbone(BackboneList& bb_list,
const ost::mol::ResidueHandle& stem_one,
const ost::mol::ResidueHandle& stem_two,
- const FragmentInfo& info, const String& sequence) const;
+ const FragmentInfo& info, const String& sequence = "") const;
+
+ void FillBackbone(BackboneList& bb_list, uint coord_idx,
+ const String& sequence = "") const;
+
+ void FillBackbone(BackboneList& bb_list, const geom::Mat4& tf,
+ uint coord_idx, const String& sequence = "") const;
+
+ void FillBackbone(BackboneList& bb_list,
+ const ost::mol::ResidueHandle& stem_one,
+ const ost::mol::ResidueHandle& stem_two,
+ uint coord_idx, const String& sequence = "") const;
+
+ int GetStartResnum(const FragmentInfo& info) const;
+
+ StructureDBPtr GetSubDB(const std::vector<uint>& indices) const;
+ void PrintStatistics() const;
+
+ ost::seq::ProfileHandlePtr GenerateStructureProfile(
+ const BackboneList& other_db,
+ const std::vector<Real>& residue_depths) const;
+
+ void SetStructureProfile(uint chain_idx, ost::seq::ProfileHandlePtr prof);
+
+ // getters for FragmentInfo
String GetSequence(const FragmentInfo& info) const;
String GetDSSPStates(const FragmentInfo& info) const;
@@ -198,18 +229,20 @@ public:
ost::seq::ProfileHandlePtr GetStructureProfile(const FragmentInfo& info) const;
- int GetStartResnum(const FragmentInfo& info) const;
+ // getters for full coords
+ String GetSequence(uint coord_idx) const;
- StructureDBPtr GetSubDB(const std::vector<uint>& indices) const;
+ String GetDSSPStates(uint coord_idx) const;
- void PrintStatistics() const;
+ std::vector<std::pair<Real,Real> > GetDihedralAngles(uint coord_idx) const;
- ost::seq::ProfileHandlePtr GenerateStructureProfile(
- const BackboneList& other_db,
- const std::vector<Real>& residue_depths) const;
+ std::vector<Real> GetResidueDepths(uint coord_idx) const;
- void SetStructureProfile(uint chain_idx, ost::seq::ProfileHandlePtr prof);
+ std::vector<int> GetSolventAccessibilities(uint coord_idx) const;
+
+ ost::seq::ProfileHandlePtr GetSequenceProfile(uint coord_idx) const;
+ ost::seq::ProfileHandlePtr GetStructureProfile(uint coord_idx) const;
// functions to gain direct access to db internals, not intended for python
// export
diff --git a/loop/tests/test_all_atom_env.cc b/loop/tests/test_all_atom_env.cc
index 0c2a45d3c4c1a7f2fc1965c4aec7e0922dbacabe..9ef3fe0e62530a556013b073d63481e055c84657 100644
--- a/loop/tests/test_all_atom_env.cc
+++ b/loop/tests/test_all_atom_env.cc
@@ -19,7 +19,6 @@
#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>
diff --git a/loop/tests/test_all_atom_positions.cc b/loop/tests/test_all_atom_positions.cc
index f50d5c5b40ee476385049e66059eca9857a1d71d..24bdb4c39193ca7aecbfacd56d186f4f9de4c817 100644
--- a/loop/tests/test_all_atom_positions.cc
+++ b/loop/tests/test_all_atom_positions.cc
@@ -19,7 +19,6 @@
#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/mol/bond_handle.hh>
#include <ost/io/mol/pdb_reader.hh>
diff --git a/loop/tests/test_amino_acid_atoms.cc b/loop/tests/test_amino_acid_atoms.cc
index d4723925bbd0510426e36bf78a66ffea69145bf6..4bad4428695aa2b43577f47cdb6ec3cd1ea15277 100644
--- a/loop/tests/test_amino_acid_atoms.cc
+++ b/loop/tests/test_amino_acid_atoms.cc
@@ -19,7 +19,6 @@
#include <promod3/core/message.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
BOOST_AUTO_TEST_SUITE( loop );
diff --git a/loop/tests/test_backbone.cc b/loop/tests/test_backbone.cc
index 8b7e31c938c78d32ce1d9d336436776960f1661f..6bdd0bdf586eb38d13b550f130173b3055d9a7a9 100644
--- a/loop/tests/test_backbone.cc
+++ b/loop/tests/test_backbone.cc
@@ -19,7 +19,6 @@
#include <promod3/core/message.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
BOOST_AUTO_TEST_SUITE( loop );
diff --git a/loop/tests/test_forcefield.cc b/loop/tests/test_forcefield.cc
index 8c0722a397b01412f1413b52d43d3095836b25c2..7cca86ab81b5cb330c4d209ac55f3fec6ed465c5 100644
--- a/loop/tests/test_forcefield.cc
+++ b/loop/tests/test_forcefield.cc
@@ -19,7 +19,6 @@
#include <promod3/core/message.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
#include <promod3/loop/hydrogen_constructor.hh>
diff --git a/loop/tests/test_hydrogens.cc b/loop/tests/test_hydrogens.cc
index 523d10128b8df758752d9809dee468c4e2ffbeb9..78485056ca773d65fa53280b24d237f2d6131ba0 100644
--- a/loop/tests/test_hydrogens.cc
+++ b/loop/tests/test_hydrogens.cc
@@ -20,7 +20,6 @@
#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/mol/atom_view.hh>
#include <ost/mol/entity_view.hh>
diff --git a/loop/tests/test_idx_handler.cc b/loop/tests/test_idx_handler.cc
index a726fc2be0e34be231d4b60e6eed1b53d44121dd..4f1fb5561282d291b83bd2cd4fa506c3b580c804 100644
--- a/loop/tests/test_idx_handler.cc
+++ b/loop/tests/test_idx_handler.cc
@@ -20,7 +20,6 @@
#include <promod3/core/message.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
BOOST_AUTO_TEST_SUITE( loop );
diff --git a/loop/tests/test_mm_system_creator.cc b/loop/tests/test_mm_system_creator.cc
index 0077c2a900b6d35f51ed7ec7ee2c95acfcd99d38..c3b1b42ec2b2097bd0a0ae7b368c7f84abd1638d 100644
--- a/loop/tests/test_mm_system_creator.cc
+++ b/loop/tests/test_mm_system_creator.cc
@@ -19,7 +19,6 @@
#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>
diff --git a/loop/tests/test_psipred_prediction.cc b/loop/tests/test_psipred_prediction.cc
index 5dbc83c7ba8d5a08970886598342c328b733aa32..6bbf8d6d054d5432997b5a25a5284b4cfb52f76e 100644
--- a/loop/tests/test_psipred_prediction.cc
+++ b/loop/tests/test_psipred_prediction.cc
@@ -18,7 +18,6 @@
#include <promod3/core/message.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
BOOST_AUTO_TEST_SUITE( loop );
using namespace promod3::loop;
diff --git a/loop/tests/test_sidechain_construction.cc b/loop/tests/test_sidechain_construction.cc
index 2e65c53c7d40efce1db613e4d2836969429d6421..df28b8d5876124987326e551a5682184f338c013 100644
--- a/loop/tests/test_sidechain_construction.cc
+++ b/loop/tests/test_sidechain_construction.cc
@@ -21,7 +21,6 @@
#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/mol/bond_handle.hh>
#include <ost/io/mol/pdb_reader.hh>
diff --git a/loop/tests/test_structuredb.cc b/loop/tests/test_structuredb.cc
index 69715800d0b4bcbda3a3c70fef82a4d162cce1eb..c66d38b5223edf0c6fdf04487a955f3ee65c4843 100644
--- a/loop/tests/test_structuredb.cc
+++ b/loop/tests/test_structuredb.cc
@@ -19,7 +19,6 @@
#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>
diff --git a/loop/tests/test_torsion_sampler.cc b/loop/tests/test_torsion_sampler.cc
index af517a90beb8e9c6d989083895e71239757c4f6d..0734377129b67d618809f6cfaae90937ab1986e5 100644
--- a/loop/tests/test_torsion_sampler.cc
+++ b/loop/tests/test_torsion_sampler.cc
@@ -19,7 +19,6 @@
#include <promod3/loop/loop_object_loader.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>
diff --git a/loop/tests/tests.cc b/loop/tests/tests.cc
index 5757e0a2c6da50f5d690c41365dbb0913543503e..9e3aa9100b52fde848409fdc40999bb4d07e05b4 100644
--- a/loop/tests/tests.cc
+++ b/loop/tests/tests.cc
@@ -16,6 +16,4 @@
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_loop
-#define BOOST_AUTO_TEST_MAIN
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
diff --git a/modelling/doc/algorithms.rst b/modelling/doc/algorithms.rst
index 51357bc0615a49e58f2ef12f3efad67eeb3b003d..7c775b0a1ba537244c4f7e22bdff9a38cb5ef582 100644
--- a/modelling/doc/algorithms.rst
+++ b/modelling/doc/algorithms.rst
@@ -164,3 +164,165 @@ example pipeline.
.. autofunction:: GenerateDeNovoTrajectories
+Motif Finder
+--------------------------------------------------------------------------------
+
+Distinct spatial arrangements of atoms or functional groups are key for protein
+function. For their detection, ProMod3 implements the MotifFinder algorithm
+which is based on geometric hashing as described by Nussinov and Wolfson
+[nussinov1991]_. The algorithm consists of a learning stage, a detection stage
+and a refinement stage.
+
+Learning Stage: A motif (query) is represented by a set of coordinates. Triplets
+(p1, p2, p3) of coordinates are selected that define triangles. For each
+triangle one can define an orthogonal vector basis
+(in our case v1 = norm(p2-p1), v3 = norm(cross(v1,p3-p1),
+v2 = norm(cross(v1,v3)))). For each coordinate not in [p1,p2,p3], we add the
+identity of the query/triangle as value to a hash map.
+The corresponding key consists of discretized values describing the edge lengths
+of the triangle, as well as the coordinate transformed into the triangle
+specific orthogonal vector basis. That's 6 numbers in total.
+
+Detection Stage: The goal is to identify one or several subsets of target
+coordinates that resemble an input query.
+We first setup an accumulator containing a counter for each triangle observed
+in the input query. We then iterate over each possible triangle with vertices
+p1, p2 and p3 in the target coordinates. At the beginning of each iteration,
+all counters in the accumulator are set to zero. Again, we build a vector basis
+given that triangle and transform all coordinates not in [p1,p2,p3] into that
+vector space. For each transformed coordinate we obtain a key for the query hash
+map. If there is one or several values at that location in the hash map,
+we increment the corresponding locations in the accumulator.
+Once all coordinates are processed, we search for high counts in the
+accumulator. Given *N* query coordinates, we keep a solution for further
+refinement if count/(*N*-3) >= *hash_tresh*. This is repeated until all
+triangles in the target are processed. One key problem with this approach is
+the discretization of floating point numbers that give raise to the hash map
+keys. Two extremely close values might end up in different bins just because
+they are close to the bin boundaries. For each of the 6 relevant numbers
+we estimate the actual bin as well as the closest neighbouring bin. Processing
+all possible combinations results in 64 hash map lookups instead of only one.
+
+Refinement Stage: Every potential solution identified in the detection stage is
+further refined based on the *distance_thresh* and *refine_thresh* parameters.
+A potential solution found in the detection stage is a pair of triangles, one
+in the query and one in the target, for which we find many matching coordinates
+in their respective vector space. We start with a coordinate mapping based on
+the triangle vertices from the query and the target (3 pairs).
+This coordinate mapping is iteratively updated by estimating the minimum RMSD
+superposition of the mapped query coordinates onto the target, apply that
+superposition on the query, find the closest target coordinate for each
+coordinate in the query and redo the mapping by including all pairs with
+minimum distance < *distance_thresh*. Iteration stops if nothing changes
+anymore. The solution is returned to the user if the final fraction of mapped
+query coordinates is larger or equal *refine_thresh*.
+The larger the mapping, the more accurate the superposition. As we start with
+only the three triangle vertices, *distance_thresh* is doubled for the initial
+iteration.
+
+.. literalinclude:: ../../../tests/doc/scripts/modelling_motif_finder.py
+
+.. class:: MotifQuery(positions, identifier, min_triangle_edge_length, \
+ max_triangle_edge_length, bin_size)
+ MotifQuery(positions, identifier, min_triangle_edge_length, \
+ max_triangle_edge_length, bin_size, flags)
+ MotifQuery(query_list)
+
+ A single query or a container of queries.
+ The constructor performs the learning stage of a single query or combines
+ several queries, so they can be searched at once.
+
+ :param positions: Coordinates of the query
+ :param identifier: Descriptor of the query
+ :param min_triangle_edge_length: To avoid the full O(n^3) hell, triangles
+ with any edge length below *min_triangle_edge_length*
+ are skipped
+ :param max_triangle_edge_length: Same as *min_triangle_edge_length* but
+ upper bound
+ :param bin_size: Bin size in A, relevant to generate hash map keys
+ :param flags: Flag in range [0,63] for every coordinate in *positions*.
+ They're also added to the hash map keys (default: 0).
+ This means that additionally to having a matching
+ relative position, the coordinates must also have a
+ matching flag in the detection/refinement stage.
+ If not provided (in the query and in the search),
+ only coordinates matter.
+ :param query_list: E pluribus unum
+
+ :type positions: :class:`ost.geom.Vec3List`
+ :type identifier: :class:`str`
+ :type min_triangle_edge_length: :class:`float`
+ :type max_triangle_edge_length: :class:`float`
+ :type bin_size: :class:`float`
+ :type flags: :class:`list` of :class:`int`
+ :type query_list: :class:`list` of :class:`MotifQuery`
+
+
+ .. method:: Save(filename)
+
+ Saves the query down to disk
+
+ :param filename: filename
+ :type filename: :class:`str`
+
+ .. staticmethod:: Load(filename)
+
+ Load query from disk
+
+ :param filename: filename
+ :type filename: :class:`str`
+
+ .. method:: GetPositions(query_idx)
+
+ Returns coordinates of specified query
+
+ :param query_idx: Query from which you want the positions
+ :type query_idx: :class:`int`
+
+ .. method:: GetIdentifiers()
+
+ Returns a list of all query identifiers.
+
+ .. method:: GetN()
+
+ Returns the number of queries
+
+
+
+.. class:: MotifMatch
+
+ Object that holds information about a match found in :meth:`FindMotifs`
+
+ .. attribute:: query_idx
+
+ Index of matching query
+
+ .. attribute:: mat
+
+ Transformation matrix to superpose matching query onto target
+
+ .. attribute:: alignment
+
+ List of tuples which define matching pairs of query/target coordinates
+
+
+.. method:: FindMotifs(query, target_positions, hash_tresh=0.4, \
+ distance_thresh=1.0, refine_thresh=0.7, \
+ flags=list())
+
+ Performs the detection and refinement stages of the geometric hashing
+ algorithm.
+
+ :param query: Query to be searched
+ :param target_positions: Coordinates of the target
+ :param hash_thresh: Parameter relevant for detection stage
+ :param distance_thresh: Parameter relevant for refinement stage
+ :param refine_thresh: Parameter relevant for refinement stage
+ :param flags: Equivalent to *flags* in :class:`MotifQuery`
+ constructor. If you didn't provide anything there,
+ this can be ignored. Only the actual coordinates
+ matter in this case.
+
+ :returns: All found matches
+
+ :rtype: :class:`list` of :class:`MotifMatch`
diff --git a/modelling/pymod/CMakeLists.txt b/modelling/pymod/CMakeLists.txt
index 9d0648c9f8055a113dffc32e93a2cddae113c0c7..e75ef2691e15c3fbba1e4d6ca2d5566f49750634 100644
--- a/modelling/pymod/CMakeLists.txt
+++ b/modelling/pymod/CMakeLists.txt
@@ -10,6 +10,7 @@ set(MODELLING_CPP
export_score_container.cc
export_scoring_weights.cc
export_sidechain_reconstructor.cc
+ export_motif_finder.cc
wrap_modelling.cc
)
diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py
index 406bc8da948400a724e7ec4f3f031f698c2188d8..4fd329c70738a374ef25c890dfe81ec408745bb3 100644
--- a/modelling/pymod/_closegaps.py
+++ b/modelling/pymod/_closegaps.py
@@ -579,7 +579,7 @@ def MergeGapsByDistance(mhandle, distance, chain_idx = None,
break
def FillLoopsByDatabase(mhandle, fragment_db, structure_db,
- torsion_sampler, max_loops_to_search=40,
+ torsion_sampler=None, max_loops_to_search=40,
min_loops_required=4, max_res_extension=-1,
extended_search=True, use_scoring_extender=True,
use_full_extender=True, score_variant=0,
@@ -604,7 +604,9 @@ def FillLoopsByDatabase(mhandle, fragment_db, structure_db,
:param structure_db: Backbone/profile data.
:type structure_db: :class:`~promod3.loop.StructureDB`
- :param torsion_sampler: A sampler for torsion angles.
+ :param torsion_sampler: A sampler for torsion angles. A default one is
+ loaded if None.
+
:type torsion_sampler: :class:`~promod3.loop.TorsionSampler`
:param max_loops_to_search: Define how many candidates are 'enough' to be
@@ -695,6 +697,10 @@ def FillLoopsByDatabase(mhandle, fragment_db, structure_db,
prof_name = 'closegaps::FillLoopsByDatabase'
prof = core.StaticRuntimeProfiler.StartScoped(prof_name)
+ # load stuff if needed
+ if torsion_sampler is None:
+ torsion_sampler = loop.LoadTorsionSamplerCoil()
+
n_non_terminal_gaps = 0
for gap in mhandle.gaps:
if not gap.IsTerminal():
@@ -714,7 +720,16 @@ def FillLoopsByDatabase(mhandle, fragment_db, structure_db,
# some score variants cannot deal with multiple insertions in one "gap"
disallow_ins_merge = (score_variant == 0)
# do we want DB features?
- add_db_features = (len(mhandle.profiles) > 0)
+ add_db_features = False
+ if len(mhandle.profiles) > 0 and \
+ structure_db.HasData(loop.StructureDBDataType.AAFrequenciesStruct) and \
+ structure_db.HasData(loop.StructureDBDataType.AAFrequencies):
+ add_db_features = True
+ elif len(mhandle.profiles) > 0:
+ ost.LogWarning("Cannot make use of profiles attached to mhandle in " +\
+ "FillLoopsByDatabase as the provided StructureDB " +\
+ "does not contain profiles. This might lead to " +\
+ "suboptimal modelling results.")
# check min_loops_required
if min_loops_required < 0:
@@ -887,7 +902,7 @@ def FillLoopsByDatabase(mhandle, fragment_db, structure_db,
gap_idx = new_idx
-def FillLoopsByMonteCarlo(mhandle, torsion_sampler, max_loops_to_search=6,
+def FillLoopsByMonteCarlo(mhandle, torsion_sampler=None, max_loops_to_search=6,
max_extension=30, mc_num_loops=2, mc_steps=5000,
use_scoring_extender=True, use_full_extender=True,
score_variant=0, ring_punch_detection=1,
@@ -911,7 +926,8 @@ def FillLoopsByMonteCarlo(mhandle, torsion_sampler, max_loops_to_search=6,
:param mhandle: Modelling handle on which to apply change.
:type mhandle: :class:`ModellingHandle`
- :param torsion_sampler: A sampler for torsion angles.
+ :param torsion_sampler: A sampler for torsion angles. A default one is
+ loaded if None.
:type torsion_sampler: :class:`~promod3.loop.TorsionSampler`
:param max_loops_to_search: Define how many candidates are 'enough' to be
@@ -971,6 +987,10 @@ def FillLoopsByMonteCarlo(mhandle, torsion_sampler, max_loops_to_search=6,
prof_name = 'closegaps::FillLoopsByMonteCarlo'
prof = core.StaticRuntimeProfiler.StartScoped(prof_name)
+ # load stuff if needed
+ if torsion_sampler is None:
+ torsion_sampler = loop.LoadTorsionSamplerCoil()
+
n_non_terminal_gaps = 0
for gap in mhandle.gaps:
if not gap.IsTerminal():
@@ -1206,24 +1226,25 @@ def CloseGaps(mhandle, merge_distance=4, fragment_db=None, structure_db=None,
MergeGapsByDistance(mhandle, distance, chain_idx=chain_idx,
resnum_range=resnum_range)
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,
+ torsion_sampler=torsion_sampler,
+ min_loops_required=-1, max_res_extension=6,
+ chain_idx=chain_idx, 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,
+ torsion_sampler=torsion_sampler, min_loops_required=-1,
chain_idx=chain_idx, resnum_range=resnum_range,
clash_thresh=10,
length_dep_weights=length_dep_weights)
FillLoopsByDatabase(mhandle, fragment_db, structure_db,
- torsion_sampler, chain_idx=chain_idx,
+ torsion_sampler=torsion_sampler, chain_idx=chain_idx,
resnum_range=resnum_range,
length_dep_weights=length_dep_weights)
# close remaining gaps by Monte Carlo
- FillLoopsByMonteCarlo(mhandle, torsion_sampler,
+ FillLoopsByMonteCarlo(mhandle, torsion_sampler=torsion_sampler,
fragger_handles=fragger_handles,
chain_idx=chain_idx,
resnum_range=resnum_range,
diff --git a/modelling/pymod/_reconstruct_sidechains.py b/modelling/pymod/_reconstruct_sidechains.py
index 2586ac8f7199b1ba46784b0d6b71851f346a944d..9ae6bb43fcb930ca594efb9507cac79eeca67a45 100644
--- a/modelling/pymod/_reconstruct_sidechains.py
+++ b/modelling/pymod/_reconstruct_sidechains.py
@@ -471,8 +471,13 @@ def ReconstructSidechains(ent, keep_sidechains=False, build_disulfids=True,
if energy_function == "SCWRL4":
rotamer_constructor = sidechain.SCWRL4RotamerConstructor(False)
- if energy_function == "SCWRL3":
+ elif energy_function == "SCWRL3":
rotamer_constructor = sidechain.SCWRL3RotamerConstructor(False)
+ elif energy_function == "VINA":
+ rotamer_constructor = sidechain.VINARotamerConstructor(False)
+ else:
+ raise RuntimeError("Only \"SCWRL4\", \"SCWRL3\" and \"VINA\" allowed "\
+ "for energy_function")
if rotamer_constructor == None:
raise RuntimeError("Invalid Energy function to reconstruct sidechains!")
diff --git a/modelling/pymod/export_motif_finder.cc b/modelling/pymod/export_motif_finder.cc
new file mode 100644
index 0000000000000000000000000000000000000000..80a756193bd909abc7a2301229a0dc94835dd04d
--- /dev/null
+++ b/modelling/pymod/export_motif_finder.cc
@@ -0,0 +1,157 @@
+// Copyright (c) 2013-2019, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
+#include <boost/python.hpp>
+#include <boost/shared_ptr.hpp>
+#include <promod3/core/export_helper.hh>
+
+#include <promod3/modelling/motif_finder.hh>
+
+using namespace promod3;
+using namespace promod3::modelling;
+using namespace boost::python;
+
+
+boost::shared_ptr<MotifQuery> WrapInitPositions(const geom::Vec3List& positions,
+ const String& identifier,
+ Real min_triangle_edge_length,
+ Real max_triangle_edge_length,
+ Real bin_size) {
+
+ boost::shared_ptr<MotifQuery> ptr(new MotifQuery(positions, identifier,
+ min_triangle_edge_length,
+ max_triangle_edge_length,
+ bin_size));
+ return ptr;
+}
+
+boost::shared_ptr<MotifQuery> WrapInitPositionsFlags(const geom::Vec3List& positions,
+ const String& identifier,
+ Real min_triangle_edge_length,
+ Real max_triangle_edge_length,
+ Real bin_size,
+ const list& flags) {
+ std::vector<int> v_flags;
+ promod3::core::ConvertListToVector(flags, v_flags);
+ boost::shared_ptr<MotifQuery> ptr(new MotifQuery(positions, identifier,
+ min_triangle_edge_length,
+ max_triangle_edge_length,
+ bin_size, v_flags));
+ return ptr;
+}
+
+boost::shared_ptr<MotifQuery> WrapInitQueries(const list& queries) {
+
+ std::vector<MotifQuery> v_queries;
+ for(uint i = 0; i < len(queries); ++i) {
+ v_queries.push_back(extract<MotifQuery>(queries[i]));
+ }
+ boost::shared_ptr<MotifQuery> ptr(new MotifQuery(v_queries));
+ return ptr;
+}
+
+
+boost::python::list WrapFindMotifs(const MotifQuery& query,
+ const geom::Vec3List& positions,
+ Real hash_thresh,
+ Real distance_thresh,
+ Real refine_thresh,
+ const boost::python::list& flags) {
+
+ std::vector<int> v_flags;
+ promod3::core::ConvertListToVector(flags, v_flags);
+
+ std::vector<MotifMatch> v_result = FindMotifs(query, positions,
+ hash_thresh,
+ distance_thresh,
+ refine_thresh,
+ v_flags);
+ list return_list;
+ for(std::vector<MotifMatch>::iterator it = v_result.begin();
+ it != v_result.end(); ++it) {
+ return_list.append(*it);
+ }
+ return return_list;
+}
+
+
+boost::python::list WrapGetAlignment(const MotifMatch& match) {
+
+ std::vector<std::pair<int,int> > aln = match.aln;
+ list return_list;
+ for(std::vector<std::pair<int,int> >::iterator it = aln.begin();
+ it != aln.end(); ++it) {
+ return_list.append(boost::python::make_tuple(it->first, it->second));
+ }
+ return return_list;
+}
+
+
+size_t GetNTrianglesSingleQuery(const MotifQuery& query, uint idx) {
+ return query.GetNTriangles(idx);
+}
+
+
+size_t GetNTrianglesFull(const MotifQuery& query) {
+ return query.GetNTriangles();
+}
+
+
+void export_motif_finder() {
+
+ class_<Triangle>("Triangle", no_init)
+ .def_readonly("p1", &Triangle::p1)
+ .def_readonly("p2", &Triangle::p2)
+ .def_readonly("p3", &Triangle::p3)
+ ;
+
+
+ class_<MotifQuery>("MotifQuery", no_init)
+ .def("__init__", make_constructor(&WrapInitPositions))
+ .def("__init__", make_constructor(&WrapInitPositionsFlags))
+ .def("__init__", make_constructor(&WrapInitQueries))
+ .def("Load", &MotifQuery::Load, (arg("filename"))).staticmethod("Load")
+ .def("Save", &MotifQuery::Save, (arg("filename")))
+ .def("GetPositions", &MotifQuery::GetPositions,
+ return_value_policy<copy_const_reference>(), (arg("query_idx")))
+ .def("GetIdentifiers", &MotifQuery::GetIdentifiers,
+ return_value_policy<copy_const_reference>())
+ .def("GetN", &MotifQuery::GetN)
+ .def("GetQuerySize", &MotifQuery::GetQuerySize, (arg("query_idx")))
+ .def("GetNTriangles", &GetNTrianglesSingleQuery, (arg("query_idx")))
+ .def("GetNTriangles", &GetNTrianglesFull)
+ .def("GetMaxTriangleEdgeLength", &MotifQuery::GetMaxTriangleEdgeLength)
+ .def("GetTriangle", &MotifQuery::GetTriangle,(arg("query_idx"),
+ arg("triangle_idx")))
+ .def("Prune", &MotifQuery::Prune, (arg("factor")))
+ .def("PrintBinSizes", &MotifQuery::PrintBinSizes)
+ ;
+
+
+ class_<MotifMatch>("MotifMatch", no_init)
+ .def_readonly("query_idx", &MotifMatch::query_idx)
+ .def_readonly("triangle_idx", &MotifMatch::triangle_idx)
+ .def_readonly("mat", &MotifMatch::mat)
+ .add_property("alignment", &WrapGetAlignment)
+ ;
+
+
+ def("FindMotifs", &WrapFindMotifs, (arg("query"), arg("target_positions"),
+ arg("hash_thresh")=0.4,
+ arg("distance_thresh")=1.0,
+ arg("refine_thresh")=0.7,
+ arg("flags")=boost::python::list()));
+}
diff --git a/modelling/pymod/wrap_modelling.cc b/modelling/pymod/wrap_modelling.cc
index 7e4affa848f8deca25c2f428db14751cc328d533..3cd41a88958b61cd40d28f818fce934f058b4962 100644
--- a/modelling/pymod/wrap_modelling.cc
+++ b/modelling/pymod/wrap_modelling.cc
@@ -27,6 +27,7 @@ void export_rigid_blocks();
void export_score_container();
void export_scoring_weights();
void export_SidechainReconstructor();
+void export_motif_finder();
BOOST_PYTHON_MODULE(_modelling)
{
@@ -41,4 +42,5 @@ BOOST_PYTHON_MODULE(_modelling)
export_score_container();
export_scoring_weights();
export_SidechainReconstructor();
+ export_motif_finder();
}
diff --git a/modelling/src/CMakeLists.txt b/modelling/src/CMakeLists.txt
index d1a8740f55374585dcd21efdb9d36f8e764c7348..440e65e09b7ae505f125b7cd0088092b7557d4b5 100644
--- a/modelling/src/CMakeLists.txt
+++ b/modelling/src/CMakeLists.txt
@@ -18,6 +18,7 @@ set(MODELLING_SOURCES
scoring_weights.cc
sidechain_reconstructor.cc
sidechain_env_listener.cc
+ motif_finder.cc
)
set(MODELLING_HEADERS
@@ -40,6 +41,8 @@ set(MODELLING_HEADERS
scoring_weights.hh
sidechain_reconstructor.hh
sidechain_env_listener.hh
+ motif_finder.hh
+ robin_hood.h
)
module(NAME modelling
diff --git a/modelling/src/motif_finder.cc b/modelling/src/motif_finder.cc
new file mode 100644
index 0000000000000000000000000000000000000000..48ae0ce1d0c2d3e09d91c171d3ac5d8715427658
--- /dev/null
+++ b/modelling/src/motif_finder.cc
@@ -0,0 +1,1429 @@
+// Copyright (c) 2013-2019, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
+#include <promod3/modelling/motif_finder.hh>
+#include <promod3/core/runtime_profiling.hh>
+#include <promod3/modelling/robin_hood.h>
+#include <promod3/core/portable_binary_serializer.hh>
+#include <promod3/core/check_io.hh>
+
+#include <promod3/core/eigen_types.hh>
+#include <promod3/core/superpose.hh>
+
+#if PM3_ENABLE_SSE && OST_DOUBLE_PRECISION == 0
+#include <xmmintrin.h>
+#endif
+#include <limits>
+
+namespace {
+
+struct MotifHasherKey {
+
+ MotifHasherKey(): key(0) { }
+
+ inline void SetF(uint32_t f) {
+ key = (key & (~f_mask)) | (static_cast<uint64_t>(f) << 57);
+ }
+ inline void SetG(uint32_t g) {
+ key = (key & (~g_mask)) | (static_cast<uint64_t>(g) << 51);
+ }
+ inline void SetH(uint32_t h) {
+ key = (key & (~h_mask)) | (static_cast<uint64_t>(h) << 45);
+ }
+ inline void SetI(uint32_t i) {
+ key = (key & (~i_mask)) | (static_cast<uint64_t>(i) << 39);
+ }
+ inline void SetA(uint32_t a) {
+ key = (key & (~a_mask)) | (static_cast<uint64_t>(a) << 34);
+ }
+ inline void SetB(uint32_t b) {
+ key = (key & (~b_mask)) | (static_cast<uint64_t>(b) << 29);
+ }
+ inline void SetC(uint32_t c) {
+ key = (key & (~c_mask)) | (static_cast<uint64_t>(c) << 24);
+ }
+ inline void SetX(int32_t x) {
+ key = (key & (~x_mask)) | ((static_cast<uint64_t>(x+127)) << 16);
+ }
+ inline void SetY(int32_t y) {
+ key = (key & (~y_mask)) | ((static_cast<uint64_t>(y+127)) << 8);
+ }
+ inline void SetZ(int32_t z) {
+ key = (key & (~z_mask)) | (static_cast<uint64_t>(z+127));
+ }
+
+ bool operator==(const MotifHasherKey& other) const {
+ return key == other.key;
+ }
+
+ bool operator!=(const MotifHasherKey& other) const {
+ return key != other.key;
+ }
+
+ // data layout
+ // 0ffffffgggggghhhhhhiiiiiiaaaaabbbbbcccccxxxxxxxxyyyyyyyyzzzzzzzz
+ // f,g,h,i are flags that describe arbitrary properties of the positions
+ // building the reference triangle and the actually described position.
+ // a,b,c describe the edge lengths of the reference triangle and x,y,z
+ // describe the coordinates of the position relative the the reference
+ // triangle.
+ // f,g,h,i can represent values in [0,63]
+ // a,b,c can represent values in [0,31]
+ // x,y,z can represent values in [-127,127]
+ // THERE ARE NO CHECKS FOR OVERFLOWS!
+ static const uint64_t f_mask = 0x7E00000000000000;
+ static const uint64_t g_mask = 0x01F8000000000000;
+ static const uint64_t h_mask = 0x0007E00000000000;
+ static const uint64_t i_mask = 0x00001F8000000000;
+ static const uint64_t a_mask = 0x0000007C00000000;
+ static const uint64_t b_mask = 0x00000003E0000000;
+ static const uint64_t c_mask = 0x000000001F000000;
+ static const uint64_t x_mask = 0x0000000000FF0000;
+ static const uint64_t y_mask = 0x000000000000FF00;
+ static const uint64_t z_mask = 0x00000000000000FF;
+
+ uint64_t key;
+};
+
+
+struct MotifHasherKeyHasher {
+ std::size_t operator()(const MotifHasherKey& k) const {
+ static robin_hood::hash<uint64_t> hasher;
+ return hasher(k.key);
+ }
+};
+
+
+typedef uint32_t MotifHasherValueItem;
+
+typedef std::vector<MotifHasherValueItem> MotifHasherValue;
+typedef robin_hood::unordered_map<MotifHasherKey, MotifHasherValue,
+ MotifHasherKeyHasher> MotifHasherMap;
+
+
+struct InitialHit{
+ InitialHit(int triangle_idx, int target_p1, int target_p2,
+ int target_p3, int counts): triangle_idx(triangle_idx),
+ target_p1(target_p1),
+ target_p2(target_p2),
+ target_p3(target_p3),
+ counts(counts) { }
+
+ int triangle_idx;
+ int target_p1;
+ int target_p2;
+ int target_p3;
+ int counts;
+};
+
+
+struct InitialHits{
+
+ InitialHits(const promod3::modelling::MotifQuery& query,
+ uint max_hits): max_hits(max_hits) {
+ initial_hits.resize(query.GetN());
+ }
+
+ void AddHits(const std::vector<int>& query_indices,
+ const std::vector<int>& triangle_indices,
+ const std::vector<int>& counts,
+ int target_p1, int target_p2, int target_p3) {
+
+ for(uint hit_idx = 0; hit_idx < query_indices.size(); ++hit_idx) {
+
+ InitialHit hit(triangle_indices[hit_idx], target_p1, target_p2, target_p3,
+ counts[hit_idx]);
+ std::vector<InitialHit>& hits = initial_hits[query_indices[hit_idx]];
+ bool added = false;
+ for(auto it = hits.begin(); it != hits.end(); ++it) {
+ if(hit.counts > it->counts) {
+ hits.insert(it, hit);
+ added = true;
+ break;
+ }
+ }
+ if(!added) {
+ hits.push_back(hit);
+ }
+ while(hits.size() > max_hits) {
+ hits.pop_back();
+ }
+ }
+ }
+
+ uint max_hits;
+ std::vector<std::vector<InitialHit> > initial_hits;
+};
+
+
+struct Accumulator{
+
+ Accumulator(const promod3::modelling::MotifQuery& query,
+ Real coverage_thresh) {
+
+ int n = 0;
+ for(uint i = 0; i < query.GetN(); ++i) {
+ range_start.push_back(n);
+ uint32_t query_size = query.GetQuerySize(i);
+ uint32_t n_triangles = query.GetNTriangles(i);
+ uint16_t thresh = std::ceil((query_size-3) * coverage_thresh);
+ for(uint j = 0; j < n_triangles; ++j) {
+ thresholds.push_back(thresh);
+ }
+ n += n_triangles;
+ }
+ accumulator.assign(n, 0);
+ }
+
+
+ void Eval() {
+
+ std::vector<int> indices;
+
+ #if PM3_ENABLE_SSE && OST_DOUBLE_PRECISION == 0
+
+ uint pos = 0;
+ __m128i a,b;
+ int mask;
+ for(uint sse_loop = 0; sse_loop < accumulator.size() / 8;
+ ++sse_loop, pos += 8) {
+ a = _mm_load_si128(reinterpret_cast<const __m128i*>(&accumulator[pos]));
+ b = _mm_load_si128(reinterpret_cast<const __m128i*>(&thresholds[pos]));
+ // there is no comparison intrinsic dealing with unsigned integers
+ // we have to take some detour...
+ a = _mm_cmpeq_epi16(_mm_max_epu16(a, b), a);
+ // there is no movemask for 16 bit integers, we use the one for 8 bit
+ // instead. Every positive hit will be marked by two neighbouring bits.
+ mask = _mm_movemask_epi8(a);
+ if(mask != 0) {
+ for(int i = 0; i < 8; ++i) {
+ if(mask & 1) {
+ indices.push_back(pos + i);
+ }
+ mask = mask>>2;
+ }
+ }
+ }
+
+ // do the leftovers
+ for(; pos < accumulator.size(); ++pos) {
+ if(accumulator[pos] >= thresholds[pos]) {
+ indices.push_back(pos);
+ }
+ }
+
+ #else
+
+ for(uint i = 0; i < accumulator.size(); ++i) {
+ if(accumulator[i] >= thresholds[i]) {
+ indices.push_back(i);
+ }
+ }
+
+ #endif
+
+ query_indices.clear();
+ triangle_indices.clear();
+ counts.clear();
+ uint query_idx_plus_one = 1;
+ uint n_ranges = range_start.size();
+ for(uint i = 0; i < indices.size(); ++i) {
+ uint idx = indices[i];
+ while(query_idx_plus_one < n_ranges) {
+ if(range_start[query_idx_plus_one] > idx) {
+ break;
+ }
+ ++query_idx_plus_one;
+ }
+ query_indices.push_back(query_idx_plus_one-1);
+ triangle_indices.push_back(idx-range_start[query_indices.back()]);
+ counts.push_back(accumulator[idx]);
+ }
+ }
+
+ inline void AddCount(uint idx) {
+ ++accumulator[idx];
+ }
+
+ inline void SetZero() {
+ memset(&accumulator[0], 0, accumulator.size() * sizeof(uint16_t));
+ }
+
+ void Process(int p1, int p2, int p3, InitialHits& initial_hits) {
+ this->Eval();
+ initial_hits.AddHits(query_indices, triangle_indices, counts, p1, p2, p3);
+ this->SetZero();
+ }
+
+ // stuff that holds actual data for the accumulator
+ std::vector<uint32_t> range_start;
+ std::vector<uint16_t> accumulator;
+ std::vector<uint16_t> thresholds;
+ // That's mutable stuff to work on
+ std::vector<int> query_indices;
+ std::vector<int> triangle_indices;
+ std::vector<int> counts;
+};
+
+
+void BaseTransform(const promod3::core::EMat3X& pos, Real bin_size,
+ int p1, int p2, int p3,
+ promod3::core::EMat3X& transformed_pos) {
+
+ // translate to new origin
+ transformed_pos = pos.colwise() - pos.col(p1);
+
+ // define new coordinate system
+ promod3::core::EMat3 base;
+ base.col(0) = transformed_pos.col(p2);
+ base.col(2) = base.col(0).cross(transformed_pos.col(p3));
+ base.col(1) = base.col(0).cross(base.col(2));
+ base.colwise().normalize();
+
+ // apply bin size
+ base = bin_size * base;
+
+ // change base
+ transformed_pos = base.inverse() * transformed_pos;
+}
+
+
+void SetupEigenMatrices(const geom::Vec3List& positions,
+ promod3::core::EMat3X& eigen_positions,
+ promod3::core::EMatXX& eigen_distances) {
+
+ int n = positions.size();
+ eigen_positions = promod3::core::EMat3X::Zero(3,n);
+ for(int i = 0; i < n; ++i) {
+ promod3::core::EMatFillCol(eigen_positions, i, positions[i]);
+ }
+
+ eigen_distances = promod3::core::EMatXX::Zero(n, n);
+ for(int i = 0; i < n; ++i) {
+ for(int j = i+1; j < n; ++j) {
+ Real d = (eigen_positions.col(i) - eigen_positions.col(j)).norm();
+ eigen_distances(i,j) = d;
+ eigen_distances(j,i) = d;
+ }
+ }
+}
+
+
+#if 0 // more elaborate version to get an initial alignment...
+void GetInitialAlignment(const promod3::core::EMat3X& query_pos,
+ int query_p1, int query_p2, int query_p3,
+ const promod3::core::EMat3X& target_pos,
+ int target_p1, int target_p2, int target_p3,
+ std::vector<std::pair<int,int> >& alignment) {
+
+ // This function creates a hash map containing the query positions
+ // with the found hit-triangle as a base. Normally, one would store the
+ // according query and triangle index as a value in the hash map. However,
+ // we already know that. We store the index of the according position in
+ // the query instead.
+ // Having that map constructed, we iterate over the target positions
+ // that have also been transformed with the found hit-triangle as a base.
+ // By doing that, we can map the matching query and target positions.
+
+ // first add the triangle indices, they are considered as match anyway
+ alignment.clear();
+ alignment.push_back(std::make_pair(query_p1, target_p1));
+ alignment.push_back(std::make_pair(query_p2, target_p2));
+ alignment.push_back(std::make_pair(query_p3, target_p3));
+
+ promod3::core::EMat3X transformed_query_pos;
+ promod3::core::EMat3X transformed_target_pos;
+ BaseTransform(query_pos, query_p1, query_p2, query_p3,
+ transformed_query_pos);
+ BaseTransform(target_pos, target_p1, target_p2, target_p3,
+ transformed_target_pos);
+
+ MotifHasherMap map;
+ for(int i = 0; i < transformed_query_pos.cols(); ++i) {
+ if(i != query_p1 && i != query_p2 && i != query_p3) {
+ Real x = std::floor(transformed_query_pos(0,i));
+ Real y = std::floor(transformed_query_pos(1,i));
+ Real z = std::floor(transformed_query_pos(2,i));
+ if(x < 32 && y < 32 && z < 32 && x > -32 && y > -32 && z > -32) {
+ MotifHasherKey key;
+ // only set X,Y and Z component, leave A, B and C zero, as the two
+ // triangles match anyway at this stage
+ key.SetX(static_cast<int32_t>(transformed_query_pos(0,i)));
+ key.SetY(static_cast<int32_t>(transformed_query_pos(1,i)));
+ key.SetZ(static_cast<int32_t>(transformed_query_pos(2,i)));
+ MotifHasherMap::iterator it = map.find(key);
+ if(it == map.end()) {
+ map[key] = MotifHasherValue();
+ it = map.find(key);
+ }
+ it->second.push_back(i);
+ }
+ }
+ }
+
+ for(int i = 0; i < transformed_target_pos.cols(); ++i) {
+ if(i != target_p1 && i != target_p2 && i != target_p3) {
+ Real x = transformed_target_pos(0,i);
+ Real y = transformed_target_pos(1,i);
+ Real z = transformed_target_pos(2,i);
+ if(x > Real(-31.5) && x < Real(31.5) && y > Real(-31.5) &&
+ y < Real(31.5) && z > Real(-31.5) && z < Real(31.5)) {
+
+ int32_t x_min = std::floor(x);
+ int32_t y_min = std::floor(y);
+ int32_t z_min = std::floor(z);
+ if(x - x_min < Real(0.5)) --x_min;
+ if(y - y_min < Real(0.5)) --y_min;
+ if(z - z_min < Real(0.5)) --z_min;
+
+ MotifHasherKey key;
+ for(int32_t j = x_min; j <= x_min+1; ++j) {
+ key.SetX(j);
+ for(int32_t k = y_min; k <= y_min+1; ++k) {
+ key.SetY(k);
+ for(int32_t l = z_min; l <= z_min+1; ++l) {
+ key.SetZ(l);
+ MotifHasherMap::iterator it = map.find(key);
+ if(it != map.end()) {
+ for(MotifHasherValue::const_iterator v_it = it->second.begin();
+ v_it != it->second.end(); ++v_it) {
+ alignment.push_back(std::make_pair(*v_it, i));
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+}
+#endif
+
+
+bool RefineInitialHit(const promod3::modelling::MotifQuery& query,
+ const promod3::core::EMat3X& target_pos,
+ const std::vector<int>& target_flags,
+ Real dist_thresh, Real refine_thresh, int query_idx,
+ int query_triangle_idx, int target_p1, int target_p2,
+ int target_p3, geom::Mat4& mat,
+ std::vector<std::pair<int, int> >& alignment) {
+
+ // the query is only available as geom::Vec3List. This makes sense from a
+ // usability perspective, but we transfer the thing to an Eigen matrix
+ // for processing here...
+ int query_n = query.GetQuerySize(query_idx);
+ const geom::Vec3List& query_vec3_pos = query.GetPositions(query_idx);
+ promod3::core::EMat3X query_pos = promod3::core::EMat3X::Zero(3, query_n);
+ for(int i = 0; i < query_n; ++i) {
+ promod3::core::EMatFillCol(query_pos, i, query_vec3_pos[i]);
+ }
+
+ // we superpose iteratively, so we need to keep track of several
+ // transformations
+ std::vector<geom::Mat4> transformations;
+
+ // setup initial alignment to start iterative superposition
+ promod3::modelling::Triangle query_triangle =
+ query.GetTriangle(query_idx, query_triangle_idx);
+ alignment.clear();
+ alignment.push_back(std::make_pair(query_triangle.p1, target_p1));
+ alignment.push_back(std::make_pair(query_triangle.p2, target_p2));
+ alignment.push_back(std::make_pair(query_triangle.p3, target_p3));
+
+ // first iteration has relaxed distance threshold, as the initial
+ // superposition might be less accurate (only three positions from triangle)
+ Real squared_dist_thresh = dist_thresh * dist_thresh * 4;
+
+ for(int iteration = 0; iteration < 5; ++iteration) {
+
+ if(alignment.size() < 3) {
+ return false;
+ }
+
+ promod3::core::EMatX3 m1 = promod3::core::EMatX3::Zero(alignment.size(),3);
+ promod3::core::EMatX3 m2 = promod3::core::EMatX3::Zero(alignment.size(),3);
+
+ for(uint i = 0; i < alignment.size(); ++i) {
+ m1.row(i) = query_pos.col(alignment[i].first).transpose();
+ m2.row(i) = target_pos.col(alignment[i].second).transpose();
+ }
+
+ geom::Mat4 t = promod3::core::MinRMSDSuperposition(m1, m2);
+
+ // apply the transform to the query positions
+ promod3::core::EMat3 rot;
+ rot(0,0) = t(0,0); rot(0,1) = t(0,1); rot(0,2) = t(0,2);
+ rot(1,0) = t(1,0); rot(1,1) = t(1,1); rot(1,2) = t(1,2);
+ rot(2,0) = t(2,0); rot(2,1) = t(2,1); rot(2,2) = t(2,2);
+
+ promod3::core::EVec3 trans;
+ trans(0,0) = t(0,3);
+ trans(1,0) = t(1,3);
+ trans(2,0) = t(2,3);
+
+ query_pos = rot * query_pos;
+ query_pos = query_pos.colwise() + trans;
+
+ std::vector<std::pair<int,int> > new_alignment;
+
+ for(int i = 0; i < query_pos.cols(); ++i) {
+ promod3::core::ERVecX squared_distances =
+ (target_pos.colwise() - query_pos.col(i)).colwise().squaredNorm();
+
+ // in case of empty flags, we use the in built eigen function to
+ // find the minimum. We have to do the full iteration and check for
+ // matching flags otherwise
+ if(target_flags.empty()) {
+ Real min = squared_distances.minCoeff();
+ if(min <= squared_dist_thresh) {
+ int min_idx = -1;
+ for(int j = 0; j < squared_distances.cols(); ++j) {
+ if(squared_distances(0,j) == min) {
+ min_idx = j;
+ break;
+ }
+ }
+ new_alignment.push_back(std::make_pair(i,min_idx));
+ }
+ } else {
+ const std::vector<uint8_t>& query_flags = query.GetFlags(query_idx);
+ int query_flag = query_flags[i];
+ Real min = std::numeric_limits<Real>::max();
+ int min_idx = -1;
+ for(uint j = 0; j < squared_distances.cols(); ++j) {
+ if(squared_distances(0,j) < min && query_flag == target_flags[j]) {
+ min = squared_distances(0,j);
+ min_idx = j;
+ }
+ }
+ if(min <= squared_dist_thresh) {
+ new_alignment.push_back(std::make_pair(i,min_idx));
+ }
+ }
+ }
+
+ transformations.push_back(t);
+ if(new_alignment == alignment) {
+ break;
+ }
+ alignment = new_alignment;
+
+ if(iteration == 0) {
+ squared_dist_thresh = dist_thresh * dist_thresh;
+ }
+ }
+
+ // check whether enough positions are superposed
+ if(static_cast<Real>(alignment.size()) / query_n < refine_thresh) {
+ return false;
+ }
+
+ // chain together the final transformation matrix
+ int t_idx = transformations.size() - 1;
+ mat = transformations[t_idx];
+ while(t_idx > 0) {
+ mat = mat * transformations[--t_idx];
+ }
+
+ return true;
+}
+
+
+void RefineInitialHits(const InitialHits& initial_hits,
+ const promod3::modelling::MotifQuery& query,
+ const promod3::core::EMat3X& target_pos,
+ const std::vector<int>& flags, Real dist_thresh,
+ Real refine_thresh,
+ std::vector<promod3::modelling::MotifMatch>& results) {
+
+
+ promod3::core::ScopedTimerPtr prof = promod3::core::StaticRuntimeProfiler::StartScoped(
+ "FindMotifs::RefineInitialHits", 2);
+
+ geom::Mat4 mat;
+ std::vector<std::pair<int,int> > aln;
+
+ for(uint query_idx = 0; query_idx < query.GetN(); ++query_idx) {
+ std::vector<promod3::modelling::MotifMatch> query_results;
+
+ for(auto it = initial_hits.initial_hits[query_idx].begin();
+ it != initial_hits.initial_hits[query_idx].end(); ++it) {
+ if(RefineInitialHit(query, target_pos, flags, dist_thresh,
+ refine_thresh, query_idx, it->triangle_idx,
+ it->target_p1, it->target_p2, it->target_p3,
+ mat, aln)) {
+ // only add the result if its unique
+ bool already_there = false;
+ for(uint res_idx = 0; res_idx < query_results.size(); ++res_idx) {
+ // we do not check for the transformation matrix
+ // if the alignment is the same, the matrix will also be the same
+ if(query_results[res_idx].aln == aln) {
+ already_there = true;
+ break;
+ }
+ }
+ if(!already_there) {
+ query_results.push_back(promod3::modelling::MotifMatch(query_idx,
+ it->triangle_idx,
+ mat, aln));
+ }
+ }
+ }
+ results.insert(results.end(), query_results.begin(), query_results.end());
+ }
+}
+
+
+template<typename T>
+void WriteVec(std::ofstream& stream, const std::vector<T>& vec) {
+ uint32_t size = vec.size();
+ stream.write(reinterpret_cast<char*>(&size), sizeof(uint32_t));
+ if(size > 0) {
+ stream.write(reinterpret_cast<const char*>(&vec[0]), size*sizeof(T));
+ }
+}
+
+
+template<typename T>
+void ReadVec(std::ifstream& stream, std::vector<T>& vec) {
+ uint32_t size;
+ stream.read(reinterpret_cast<char*>(&size), sizeof(uint32_t));
+ if(size > 0) {
+ vec.resize(size);
+ stream.read(reinterpret_cast<char*>(&vec[0]), size*sizeof(T));
+ }
+}
+
+
+void Accumulate(const promod3::core::EMat3X& transformed_pos,
+ Real a, Real b, Real c, int p1, int p2, int p3,
+ Real min_pos_bound, Real max_pos_bound,
+ const std::vector<int>& flags,
+ const MotifHasherMap& map, Accumulator& acc) {
+
+ promod3::core::ScopedTimerPtr prof = promod3::core::StaticRuntimeProfiler::StartScoped(
+ "FindMotifs::Accumulate", 2);
+
+ int32_t x_min, y_min, z_min;
+ uint32_t a_min = static_cast<uint32_t>(a);
+ uint32_t b_min = static_cast<uint32_t>(b);
+ uint32_t c_min = static_cast<uint32_t>(c);
+ if(a - a_min < Real(0.5)) --a_min;
+ if(b - b_min < Real(0.5)) --b_min;
+ if(c - c_min < Real(0.5)) --c_min;
+
+ MotifHasherKey key;
+ if(!flags.empty()) {
+ key.SetF(flags[p1]);
+ key.SetG(flags[p2]);
+ key.SetH(flags[p3]);
+ }
+
+ Real x,y,z;
+ for(int p_idx = 0; p_idx < transformed_pos.cols(); ++p_idx) {
+ if(p_idx != p1 && p_idx != p2 && p_idx != p3) {
+ x = transformed_pos(0, p_idx);
+ y = transformed_pos(1, p_idx);
+ z = transformed_pos(2, p_idx);
+ if(x > min_pos_bound && x < max_pos_bound && y > min_pos_bound &&
+ y < max_pos_bound && z > min_pos_bound && z < max_pos_bound) {
+ x_min = std::floor(x);
+ y_min = std::floor(y);
+ z_min = std::floor(z);
+ if(x - x_min < Real(0.5)) --x_min;
+ if(y - y_min < Real(0.5)) --y_min;
+ if(z - z_min < Real(0.5)) --z_min;
+ if(!flags.empty()) {
+ key.SetI(flags[p_idx]);
+ }
+ for(uint32_t i = a_min; i <= a_min+1; ++i) {
+ key.SetA(i);
+ for(uint32_t j = b_min; j <= b_min+1; ++j) {
+ key.SetB(j);
+ for(uint32_t k = c_min; k <= c_min+1; ++k) {
+ key.SetC(k);
+ for(int32_t l = x_min; l <= x_min+1; ++l) {
+ key.SetX(l);
+ for(int32_t m = y_min; m <= y_min+1; ++m) {
+ key.SetY(m);
+ for(int32_t n = z_min; n <= z_min+1; ++n) {
+ key.SetZ(n);
+ MotifHasherMap::const_iterator it = map.find(key);
+ if(it != map.end()) {
+ for(auto v_it = it->second.begin();
+ v_it != it->second.end(); ++v_it) {
+ acc.AddCount(*v_it);
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+}
+
+
+void SortTriangleEdges(Real a, Real b, Real c, int p1, int p2, int p3,
+ Real& sorted_a, Real& sorted_b, Real& sorted_c,
+ int& sorted_p1, int& sorted_p2, int& sorted_p3) {
+
+ // reassigns a,b,c,p1,p2,p3 so that sorted_a<=sorted_b<=sorted_c.
+ if(a <= b && b <= c) {
+ sorted_a = a;
+ sorted_b = b;
+ sorted_c = c;
+ sorted_p1 = p1;
+ sorted_p2 = p2;
+ sorted_p3 = p3;
+ } else if(a <= c && c <= b) {
+ sorted_a = a;
+ sorted_b = c;
+ sorted_c = b;
+ sorted_p1 = p2;
+ sorted_p2 = p1;
+ sorted_p3 = p3;
+ } else if(b <= a && a <= c) {
+ sorted_a = b;
+ sorted_b = a;
+ sorted_c = c;
+ sorted_p1 = p3;
+ sorted_p2 = p2;
+ sorted_p3 = p1;
+ } else if(b <= c && c <= a) {
+ sorted_a = b;
+ sorted_b = c;
+ sorted_c = a;
+ sorted_p1 = p2;
+ sorted_p2 = p3;
+ sorted_p3 = p1;
+ } else if(c <= a && a <= b) {
+ sorted_a = c;
+ sorted_b = a;
+ sorted_c = b;
+ sorted_p1 = p3;
+ sorted_p2 = p1;
+ sorted_p3 = p2;
+ } else { //(c <= b && b <= a)
+ sorted_a = c;
+ sorted_b = b;
+ sorted_c = a;
+ sorted_p1 = p1;
+ sorted_p2 = p3;
+ sorted_p3 = p2;
+ }
+}
+
+} // anon ns
+
+
+namespace promod3 { namespace modelling {
+
+
+struct MotifQueryData {
+ MotifHasherMap map;
+ std::vector<geom::Vec3List> positions;
+ std::vector<String> identifiers;
+ std::vector<std::vector<Triangle> > triangles;
+ std::vector<std::vector<uint8_t> > flags;
+ Real min_triangle_edge_length;
+ Real max_triangle_edge_length;
+ Real min_pos_bound;
+ Real max_pos_bound;
+ Real bin_size;
+};
+
+
+MotifQuery::MotifQuery() { }
+
+
+MotifQuery::MotifQuery(const geom::Vec3List& positions,
+ const String& identifier,
+ Real min_triangle_edge_length,
+ Real max_triangle_edge_length,
+ Real bin_size,
+ const std::vector<int>& flags) {
+
+ promod3::core::ScopedTimerPtr prof = promod3::core::StaticRuntimeProfiler::StartScoped(
+ "MotifQuery::MotifQuery", 2);
+
+ if(positions.size() < 4) {
+ throw promod3::Error("Require at least 4 positions to construct "
+ "MotifQuery");
+ }
+
+ if(min_triangle_edge_length <= 0.0 || max_triangle_edge_length <= 0.0) {
+ throw promod3::Error("min/max triangle edge lengths must be positive!");
+ }
+
+ if(min_triangle_edge_length >= max_triangle_edge_length) {
+ throw promod3::Error("min_triangle_edge_length must be < "
+ "max_triangle_edge_length");
+ }
+
+ if(bin_size <= 0.0) {
+ throw promod3::Error("Bin size must be positive!");
+ }
+
+ // maximum triangle bin would be 31 but we allow one less...
+ // this avoids some range checks when Accumulating in FindMotifs
+ int max_triangle_bin = static_cast<uint32_t>(max_triangle_edge_length / bin_size);
+ if(max_triangle_bin > 30) {
+ throw promod3::Error("Cannot represent triangle in internal data structure. "
+ "Increase bin_size or decrease max_edge_length");
+ }
+
+ if(!flags.empty()) {
+ if(flags.size() != positions.size()) {
+ throw promod3::Error("Number of flags must be consistent with positions!");
+ }
+ for(auto it = flags.begin(); it != flags.end(); ++it) {
+ if(*it < 0 || *it > 63) {
+ throw promod3::Error("All flags must be in range [0, 63]!");
+ }
+ }
+ }
+
+ data_ = std::shared_ptr<MotifQueryData>(new MotifQueryData);
+ data_->positions.push_back(positions);
+ data_->identifiers.push_back(identifier);
+ data_->triangles.push_back(std::vector<Triangle>());
+ data_->min_triangle_edge_length = min_triangle_edge_length;
+ data_->max_triangle_edge_length = max_triangle_edge_length;
+ data_->bin_size = bin_size;
+
+ if(!flags.empty()) {
+ data_->flags.push_back(std::vector<uint8_t>(flags.begin(), flags.end()));
+ } else {
+ data_->flags.push_back(std::vector<uint8_t>(positions.size(), 0));
+ }
+
+ promod3::core::EMat3X eigen_positions;
+ promod3::core::EMatXX eigen_distances;
+ SetupEigenMatrices(positions, eigen_positions, eigen_distances);
+
+ MotifHasherKey key;
+ promod3::core::EMat3X transformed_pos;
+ Real a, b, c,sorted_a, sorted_b, sorted_c, diff_ab, diff_bc;
+ int sorted_p1, sorted_p2, sorted_p3;
+ int32_t d,e,f;
+ int n = eigen_positions.cols();
+ uint32_t triangle_idx = 0;
+ Real min_pos_bound = std::numeric_limits<Real>::max();
+ Real max_pos_bound = -std::numeric_limits<Real>::max();
+
+ for(int p1 = 0; p1 < n; ++p1) {
+ for(int p2 = p1+1; p2 < n; ++p2) {
+ a = eigen_distances(p1,p2);
+ if(a > max_triangle_edge_length || a < min_triangle_edge_length) {
+ continue;
+ }
+ for(int p3 = p2+1; p3 < n; ++p3) {
+ b = eigen_distances(p2,p3);
+ c = eigen_distances(p1,p3);
+ if(b > max_triangle_edge_length || c > max_triangle_edge_length ||
+ b < min_triangle_edge_length || c < min_triangle_edge_length) {
+ continue;
+ }
+
+ // we define a<=b<=c. a connects p1 and p2, c connects p1 and p3.
+ // This is not necessarily the case for the current values of
+ // a,b,c,p1,p2,p3, so let's do some shuffling.
+ SortTriangleEdges(a, b, c, p1, p2, p3, sorted_a, sorted_b, sorted_c,
+ sorted_p1, sorted_p2, sorted_p3);
+
+ // normalize the sorted edge_lengths
+ sorted_a /= bin_size;
+ sorted_b /= bin_size;
+ sorted_c /= bin_size;
+
+ diff_ab = sorted_b - sorted_a;
+ diff_bc = sorted_c - sorted_b;
+ if(diff_ab < Real(1.0) && diff_bc < (1.0)) {
+ // we sample the close neighbours in the hash map when performing
+ // a search. As soon as edges of the triangle are similar, we get
+ // ambiguities with the base. If this if-statement is true, those
+ // ambiguities become really bad. So let's just ignore this triangle
+ continue;
+ }
+
+ // transform all positions into the vector basis defined by the
+ // triangle with edges at p1, p2, p3 and add the stuff to the hash
+ // map
+ BaseTransform(eigen_positions, bin_size,
+ sorted_p1, sorted_p2, sorted_p3,
+ transformed_pos);
+ key.SetA(static_cast<uint32_t>(sorted_a));
+ key.SetB(static_cast<uint32_t>(sorted_b));
+ key.SetC(static_cast<uint32_t>(sorted_c));
+ key.SetF(static_cast<uint32_t>(data_->flags.back()[sorted_p1]));
+ key.SetG(static_cast<uint32_t>(data_->flags.back()[sorted_p2]));
+ key.SetH(static_cast<uint32_t>(data_->flags.back()[sorted_p3]));
+ for(int i = 0; i < n; ++i) {
+ if(i != sorted_p1 && i != sorted_p2 && i != sorted_p3) {
+ d = std::floor(transformed_pos(0,i));
+ e = std::floor(transformed_pos(1,i));
+ f = std::floor(transformed_pos(2,i));
+
+ // allowed range would be [-127, 127] but we decrease that range to
+ // [-126, 126] to avoid some checks when Accumulating in FindMotifs
+ if(d < 126 && e < 126 && f < 126 &&
+ d > -126 && e > -126 && f > -126) {
+ min_pos_bound = std::min(transformed_pos(0,i), min_pos_bound);
+ min_pos_bound = std::min(transformed_pos(1,i), min_pos_bound);
+ min_pos_bound = std::min(transformed_pos(2,i), min_pos_bound);
+ max_pos_bound = std::max(transformed_pos(0,i), max_pos_bound);
+ max_pos_bound = std::max(transformed_pos(1,i), max_pos_bound);
+ max_pos_bound = std::max(transformed_pos(2,i), max_pos_bound);
+ key.SetX(d);
+ key.SetY(e);
+ key.SetZ(f);
+ key.SetI(static_cast<uint32_t>(data_->flags.back()[i]));
+ MotifHasherMap::iterator it = data_->map.find(key);
+ if(it == data_->map.end()) {
+ data_->map[key] = MotifHasherValue();
+ it = data_->map.find(key);
+ }
+ it->second.push_back(triangle_idx);
+ }
+ }
+ }
+
+ data_->triangles.back().push_back(Triangle(sorted_p1, sorted_p2,
+ sorted_p3));
+ ++triangle_idx;
+ }
+ }
+ }
+
+ data_->min_pos_bound = min_pos_bound;
+ data_->max_pos_bound = max_pos_bound;
+}
+
+
+MotifQuery::MotifQuery(const std::vector<MotifQuery>& queries) {
+
+ promod3::core::ScopedTimerPtr prof = promod3::core::StaticRuntimeProfiler::StartScoped(
+ "MotifQuery::MotifQuery", 2);
+
+ if(queries.empty()) {
+ throw promod3::Error("Cannot initialize MotifQuery from empty list");
+ }
+
+
+ data_ = std::shared_ptr<MotifQueryData>(new MotifQueryData);
+ data_->min_triangle_edge_length = std::numeric_limits<Real>::max();
+ data_->max_triangle_edge_length = -std::numeric_limits<Real>::max();
+ data_->min_pos_bound = std::numeric_limits<Real>::max();
+ data_->max_pos_bound = -std::numeric_limits<Real>::max();
+ data_->bin_size = queries[0].GetBinSize();
+
+ MotifHasherMap& map = data_->map;
+
+ // iterate over all queries and update data_ along the way
+ uint32_t total_num_triangles = 0;
+ for(auto query_it = queries.begin(); query_it != queries.end(); ++query_it) {
+
+ if(std::numeric_limits<uint32_t>::max() - query_it->GetNTriangles() <=
+ total_num_triangles) {
+ std::stringstream ss;
+ ss << "Query can maximally contain ";
+ ss << std::numeric_limits<uint32_t>::max() << " triangles. ";
+ ss << "Reduce number of queries or size of single queries.";
+ throw promod3::Error(ss.str());
+ }
+
+ if(query_it->GetBinSize() != data_->bin_size) {
+ throw promod3::Error("All queries must have consistent bin sizes!");
+ }
+
+ // update the map in data_
+ for(auto other_map_it = query_it->data_->map.begin();
+ other_map_it != query_it->data_->map.end(); ++other_map_it) {
+ MotifHasherMap::iterator map_it = map.find(other_map_it->first);
+ if(map_it == map.end()) {
+ map[other_map_it->first] = MotifHasherValue();
+ map_it = map.find(other_map_it->first);
+ }
+ for(auto item_it = other_map_it->second.begin();
+ item_it != other_map_it->second.end(); ++item_it) {
+ map_it->second.push_back((*item_it) + total_num_triangles);
+ }
+ }
+
+ // update everything else in data_
+ data_->positions.insert(data_->positions.end(),
+ query_it->data_->positions.begin(),
+ query_it->data_->positions.end());
+ data_->identifiers.insert(data_->identifiers.end(),
+ query_it->data_->identifiers.begin(),
+ query_it->data_->identifiers.end());
+ data_->triangles.insert(data_->triangles.end(),
+ query_it->data_->triangles.begin(),
+ query_it->data_->triangles.end());
+ data_->flags.insert(data_->flags.end(),
+ query_it->data_->flags.begin(),
+ query_it->data_->flags.end());
+ data_->min_triangle_edge_length = std::min(data_->min_triangle_edge_length,
+ query_it->data_->min_triangle_edge_length);
+ data_->max_triangle_edge_length = std::max(data_->max_triangle_edge_length,
+ query_it->data_->max_triangle_edge_length);
+ data_->min_pos_bound = std::min(data_->min_pos_bound,
+ query_it->data_->min_pos_bound);
+ data_->max_pos_bound = std::max(data_->max_pos_bound,
+ query_it->data_->max_pos_bound);
+ total_num_triangles += query_it->GetNTriangles();
+ }
+}
+
+
+MotifQuery MotifQuery::Load(const String& filename) {
+
+ promod3::core::ScopedTimerPtr prof = promod3::core::StaticRuntimeProfiler::StartScoped(
+ "MotifQuery::Load", 2);
+
+ std::ifstream in_stream_(filename.c_str(), std::ios::binary);
+ if (!in_stream_) {
+ std::stringstream ss;
+ ss << "The file '" << filename << "' does not exist.";
+ throw promod3::Error(ss.str());
+ }
+
+ core::PortableBinaryDataSource in_stream(in_stream_);
+ core::CheckMagicNumber(in_stream);
+ uint32_t version = core::GetVersionNumber(in_stream_);
+ if(version != 1) {
+ std::stringstream ss;
+ ss << "Unsupported file version '" << version << "' in '" << filename;
+ throw promod3::Error(ss.str());
+ }
+ core::CheckTypeSize<uint64_t>(in_stream);
+ core::CheckTypeSize<uint32_t>(in_stream);
+ core::CheckTypeSize<uint16_t>(in_stream);
+ core::CheckTypeSize<uint8_t>(in_stream);
+ core::CheckTypeSize<float>(in_stream);
+
+ MotifQuery query;
+ query.data_ = std::shared_ptr<MotifQueryData>(new MotifQueryData);
+ std::vector<uint32_t> query_sizes;
+ std::vector<float> position_vec;
+ std::vector<uint64_t> keys;
+ std::vector<uint32_t> n_items;
+ std::vector<uint32_t> items;
+ std::vector<uint32_t> n_triangles;
+ std::vector<uint16_t> triangle_vec;
+ std::vector<uint8_t> flag_vec;
+
+ in_stream & query.data_->identifiers;
+ ReadVec(in_stream.Stream(), query_sizes);
+ ReadVec(in_stream.Stream(), position_vec);
+ ReadVec(in_stream.Stream(), keys);
+ ReadVec(in_stream.Stream(), n_items);
+ ReadVec(in_stream.Stream(), items);
+ ReadVec(in_stream.Stream(), n_triangles);
+ ReadVec(in_stream.Stream(), triangle_vec);
+ ReadVec(in_stream.Stream(), flag_vec);
+ in_stream & query.data_->min_triangle_edge_length;
+ in_stream & query.data_->max_triangle_edge_length;
+ in_stream & query.data_->min_pos_bound;
+ in_stream & query.data_->max_pos_bound;
+ in_stream & query.data_->bin_size;
+
+ int position_idx = 0;
+ int triangle_idx = 0;
+ int flag_idx = 0;
+ for(uint i = 0; i < query.data_->identifiers.size(); ++i) {
+ geom::Vec3List positions;
+ for(uint j = 0; j < query_sizes[i]; ++j) {
+ positions.push_back(geom::Vec3(position_vec[position_idx],
+ position_vec[position_idx+1],
+ position_vec[position_idx+2]));
+ position_idx += 3;
+ }
+ query.data_->positions.push_back(positions);
+
+ std::vector<Triangle> triangles;
+ for(uint j = 0; j < n_triangles[i]; ++j) {
+ triangles.push_back(Triangle(triangle_vec[triangle_idx],
+ triangle_vec[triangle_idx+1],
+ triangle_vec[triangle_idx+2]));
+ triangle_idx += 3;
+ }
+ query.data_->triangles.push_back(triangles);
+
+ std::vector<uint8_t> flags;
+ for(uint j = 0; j < query_sizes[i]; ++j) {
+ flags.push_back(flag_vec[flag_idx++]);
+ }
+ query.data_->flags.push_back(flags);
+ }
+
+ int item_idx = 0;
+ for(uint i = 0; i < keys.size(); ++i) {
+ MotifHasherKey key;
+ key.key = keys[i];
+ MotifHasherValue value;
+ for(uint j = 0; j < n_items[i]; ++j) {
+ value.push_back(items[item_idx++]);
+ }
+ query.data_->map[key] = value;
+ }
+
+ return query;
+}
+
+
+void MotifQuery::Save(const String& filename) const {
+
+ promod3::core::ScopedTimerPtr prof = promod3::core::StaticRuntimeProfiler::StartScoped(
+ "MotifQuery::Save", 2);
+
+ 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());
+ }
+
+ std::vector<uint32_t> query_sizes;
+ std::vector<float> position_vec;
+ std::vector<uint64_t> keys;
+ std::vector<uint32_t> n_items;
+ std::vector<uint32_t> items;
+ std::vector<uint32_t> n_triangles;
+ std::vector<uint16_t> triangle_vec;
+ std::vector<uint8_t> flag_vec;
+
+ for(uint i = 0; i < data_->positions.size(); ++i) {
+ int n = data_->positions[i].size();
+ query_sizes.push_back(n);
+ for(int j = 0; j < n; ++j) {
+ position_vec.push_back(data_->positions[i][j][0]);
+ position_vec.push_back(data_->positions[i][j][1]);
+ position_vec.push_back(data_->positions[i][j][2]);
+ }
+ for(int j = 0; j < n; ++j) {
+ flag_vec.push_back(data_->flags[i][j]);
+ }
+ n_triangles.push_back(data_->triangles[i].size());
+ for(uint j = 0; j < n_triangles.back(); ++j) {
+ triangle_vec.push_back(data_->triangles[i][j].p1);
+ triangle_vec.push_back(data_->triangles[i][j].p2);
+ triangle_vec.push_back(data_->triangles[i][j].p3);
+ }
+ }
+
+ for(MotifHasherMap::const_iterator it = data_->map.begin();
+ it != data_->map.end(); ++it) {
+ keys.push_back(it->first.key);
+ n_items.push_back(it->second.size());
+ for(uint i = 0; i < n_items.back(); ++i) {
+ items.push_back(it->second[i]);
+ }
+ }
+
+ core::PortableBinaryDataSink out_stream(out_stream_);
+ core::WriteMagicNumber(out_stream);
+ core::WriteVersionNumber(out_stream, 1);
+ core::WriteTypeSize<uint64_t>(out_stream);
+ core::WriteTypeSize<uint32_t>(out_stream);
+ core::WriteTypeSize<uint16_t>(out_stream);
+ core::WriteTypeSize<uint8_t>(out_stream);
+ core::WriteTypeSize<float>(out_stream);
+
+ out_stream & data_->identifiers;
+ WriteVec(out_stream.Stream(), query_sizes);
+ WriteVec(out_stream.Stream(), position_vec);
+ WriteVec(out_stream.Stream(), keys);
+ WriteVec(out_stream.Stream(), n_items);
+ WriteVec(out_stream.Stream(), items);
+ WriteVec(out_stream.Stream(), n_triangles);
+ WriteVec(out_stream.Stream(), triangle_vec);
+ WriteVec(out_stream.Stream(), flag_vec);
+ out_stream & data_->min_triangle_edge_length;
+ out_stream & data_->max_triangle_edge_length;
+ out_stream & data_->min_pos_bound;
+ out_stream & data_->max_pos_bound;
+ out_stream & data_->bin_size;
+}
+
+
+const geom::Vec3List& MotifQuery::GetPositions(uint idx) const{
+ return data_->positions[idx];
+}
+
+
+const std::vector<uint8_t>& MotifQuery::GetFlags(uint idx) const{
+ return data_->flags[idx];
+}
+
+
+const std::vector<String>& MotifQuery::GetIdentifiers() const{
+ return data_->identifiers;
+}
+
+
+size_t MotifQuery::GetN() const {
+ return data_->identifiers.size();
+}
+
+
+size_t MotifQuery::GetQuerySize(uint idx) const {
+ return data_->positions[idx].size();
+}
+
+
+size_t MotifQuery::GetNTriangles(uint idx) const {
+ return data_->triangles[idx].size();
+}
+
+
+size_t MotifQuery::GetNTriangles() const {
+ size_t s = 0;
+ for(auto it = data_->triangles.begin(); it != data_->triangles.end(); ++it) {
+ s += it->size();
+ }
+ return s;
+}
+
+
+Real MotifQuery::GetMinTriangleEdgeLength() const {
+ return data_->min_triangle_edge_length;
+}
+
+
+Real MotifQuery::GetMaxTriangleEdgeLength() const {
+ return data_->max_triangle_edge_length;
+}
+
+
+Real MotifQuery::GetMinPosBound() const {
+ return data_->min_pos_bound;
+}
+
+
+Real MotifQuery::GetMaxPosBound() const {
+ return data_->max_pos_bound;
+}
+
+
+Real MotifQuery::GetBinSize() const {
+ return data_->bin_size;
+}
+
+
+Triangle MotifQuery::GetTriangle(uint query_idx, uint triangle_idx) const {
+ return data_->triangles[query_idx][triangle_idx];
+}
+
+
+void MotifQuery::PrintBinSizes() const {
+
+ std::vector<size_t> bin_sizes;
+ size_t max_size = 0;
+
+ for(auto it = data_->map.begin(); it!=data_->map.end(); ++it) {
+ bin_sizes.push_back(it->second.size());
+ max_size = std::max(bin_sizes.back(), max_size);
+ }
+
+ std::vector<int> histogram(max_size+1, 0);
+ for(auto it = bin_sizes.begin(); it != bin_sizes.end(); ++it) {
+ histogram[*it]+=1;
+ }
+
+ for(uint idx = 0; idx < histogram.size(); ++idx) {
+ std::cout<<idx<<' '<<histogram[idx]<<std::endl;
+ }
+}
+
+
+void MotifQuery::Prune(Real factor) {
+
+ std::vector<int> counts_per_triangle(this->GetNTriangles(), 0);
+ std::vector<int> min_counts_per_triangle;
+ for(uint i = 0; i < this->GetN(); ++i) {
+ int thresh = std::ceil((this->GetQuerySize(i)-3) * factor);
+ for(uint j = 0; j < this->GetNTriangles(i); ++j) {
+ min_counts_per_triangle.push_back(thresh);
+ }
+ }
+
+ MotifHasherMap new_map;
+ const MotifHasherMap& map = data_->map;
+
+ std::set<size_t> bin_size_set;
+ for(auto it = map.begin(); it!=map.end(); ++it) {
+ bin_size_set.insert(it->second.size());
+ }
+ std::vector<size_t> bin_sizes(bin_size_set.begin(), bin_size_set.end());
+ std::sort(bin_sizes.begin(), bin_sizes.end());
+
+ for(auto bin_size = bin_sizes.begin(); bin_size != bin_sizes.end(); ++bin_size) {
+ for(auto map_it = map.begin(); map_it != map.end(); ++map_it) {
+ if(map_it->second.size() == *bin_size) {
+ const MotifHasherValue& triangle_indices = map_it->second;
+ MotifHasherValue new_triangle_indices;
+ for(auto triangle = triangle_indices.begin(); triangle != triangle_indices.end(); ++triangle) {
+ if(counts_per_triangle[*triangle] <= min_counts_per_triangle[*triangle]) {
+ ++counts_per_triangle[*triangle];
+ new_triangle_indices.push_back(*triangle);
+ }
+ }
+ if(!new_triangle_indices.empty()) {
+ new_map[map_it->first] = new_triangle_indices;
+ }
+ }
+ }
+ }
+
+ data_->map = new_map;
+}
+
+
+std::vector<MotifMatch> FindMotifs(const MotifQuery& query,
+ const geom::Vec3List& positions,
+ Real hash_thresh,
+ Real distance_thresh,
+ Real refine_thresh,
+ const std::vector<int>& flags) {
+
+ promod3::core::ScopedTimerPtr prof = promod3::core::StaticRuntimeProfiler::StartScoped(
+ "FindMotifs::FindMotifs", 2);
+
+ // initial and final hits
+ InitialHits initial_hits(query, 50);
+ std::vector<MotifMatch> results;
+
+ // general setup
+ promod3::core::EMat3X eigen_positions;
+ promod3::core::EMatXX eigen_distances;
+ promod3::core::EMat3X transformed_pos;
+ Real a,b,c,sorted_a,sorted_b,sorted_c, diff_ab, diff_bc;
+ int sorted_p1, sorted_p2, sorted_p3;
+ SetupEigenMatrices(positions, eigen_positions, eigen_distances);
+ int n_target = eigen_positions.cols();
+ Real bin_size = query.GetBinSize();
+ Real half_bin_size = bin_size / 2;
+
+ // check whether any flags for the single positions are set
+ // if yes, check their validity
+ if(!flags.empty()) {
+ if(flags.size() != positions.size()) {
+ throw promod3::Error("Number of flags must be consistent with positions!");
+ }
+ for(auto it = flags.begin(); it != flags.end(); ++it) {
+ if(*it < 0 || *it > 63) {
+ throw promod3::Error("All flags must be in range [0, 63]!");
+ }
+ }
+ }
+
+ // add/subtract constant to allow for some variation
+ // min/max edge lengths are absolute distances
+ Real min_edge_length = query.GetMinTriangleEdgeLength() - half_bin_size;
+ Real max_edge_length = query.GetMaxTriangleEdgeLength() + half_bin_size;
+ // pos bounds are already relative to bins, therefore +-0.5
+ Real min_pos_bound = query.GetMinPosBound() - 0.5;
+ Real max_pos_bound = query.GetMaxPosBound() + 0.5;
+
+ // fetch hash map and setup accumulator
+ const MotifHasherMap& map = query.data_->map;
+ Accumulator accumulator(query, hash_thresh);
+
+ for(int p1 = 0; p1 < n_target; ++p1) {
+ for(int p2 = p1+1; p2 < n_target; ++p2) {
+ a = eigen_distances(p1,p2);
+ if(a > max_edge_length || a < min_edge_length) {
+ continue;
+ }
+ for(int p3 = p2+1; p3 < n_target; ++p3) {
+ b = eigen_distances(p2,p3);
+ c = eigen_distances(p1,p3);
+ if(b > max_edge_length || c > max_edge_length ||
+ b < min_edge_length || c < min_edge_length) {
+ continue;
+ }
+
+ // we define a<=b<=c. a connects p1 and p2, c connects p1 and p3.
+ // This is not necessarily the case for the current values of
+ // a,b,c,p1,p2,p3, so let's do some shuffling.
+ SortTriangleEdges(a, b, c, p1, p2, p3, sorted_a, sorted_b, sorted_c,
+ sorted_p1, sorted_p2, sorted_p3);
+
+ // normalize the sorted edge_lengths
+ sorted_a /= bin_size;
+ sorted_b /= bin_size;
+ sorted_c /= bin_size;
+
+ diff_ab = sorted_b - sorted_a;
+ diff_bc = sorted_c - sorted_b;
+
+ if(diff_ab <= 1.0 && diff_bc <= 1.0) {
+ // Small changes in any of the edge lengths might lead to a flip in
+ // the basis. In total we have 6 possible bases...
+ //
+ // However: when constructing the query I introduced a hack that disallows
+ // triangles where all three edges are very similar. So we can skip...
+ // the case for only two edges being similar is treated below.
+ continue;
+ }
+
+ BaseTransform(eigen_positions, bin_size,
+ sorted_p1, sorted_p2, sorted_p3,
+ transformed_pos);
+ Accumulate(transformed_pos, sorted_a, sorted_b, sorted_c,
+ p1, p2, p3, min_pos_bound, max_pos_bound,
+ flags, map, accumulator);
+
+ if(diff_ab > bin_size && diff_bc < bin_size) {
+ // The edges b and c have similar length. We thus evaluate a second
+ // basis that represents b>c
+ BaseTransform(eigen_positions, bin_size,
+ sorted_p2, sorted_p1, sorted_p3,
+ transformed_pos);
+ Accumulate(transformed_pos, sorted_a, sorted_b, sorted_c, p1, p2, p3,
+ min_pos_bound, max_pos_bound, flags, map, accumulator);
+ }
+
+ if(diff_bc > bin_size && diff_ab < bin_size) {
+ // The edges a and b have similar length. We thus evaluate a second
+ // basis that represents a>b
+ BaseTransform(eigen_positions, bin_size,
+ sorted_p3, sorted_p2, sorted_p1,
+ transformed_pos);
+ Accumulate(transformed_pos, sorted_a, sorted_b, sorted_c, p1, p2, p3,
+ min_pos_bound, max_pos_bound, flags, map, accumulator);
+ }
+
+ // Iterate the accumulator and transfer initial solutions that fulfill
+ // the hashing thresholds. Once done, the accumulator is cleared and
+ // ready for another round of counting
+ accumulator.Process(sorted_p1, sorted_p2, sorted_p3, initial_hits);
+ }
+ }
+ }
+
+ RefineInitialHits(initial_hits, query, eigen_positions, flags,
+ distance_thresh, refine_thresh, results);
+
+ return results;
+}
+
+}} // ns
diff --git a/modelling/src/motif_finder.hh b/modelling/src/motif_finder.hh
new file mode 100644
index 0000000000000000000000000000000000000000..0bdf900860b65a5029266518c273134ae5a45079
--- /dev/null
+++ b/modelling/src/motif_finder.hh
@@ -0,0 +1,113 @@
+// Copyright (c) 2013-2019, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#ifndef PROMOD_MODELLING_MOTIF_FINDER_HH
+#define PROMOD_MODELLING_MOTIF_FINDER_HH
+
+#include <ost/mol/entity_view.hh>
+#include <ost/mol/residue_view.hh>
+#include <ost/geom/vec3.hh>
+#include <vector>
+
+namespace promod3 { namespace modelling {
+
+struct Triangle{
+
+ Triangle(uint16_t p1, uint16_t p2, uint16_t p3): p1(p1), p2(p2), p3(p3) { }
+
+ uint16_t p1;
+ uint16_t p2;
+ uint16_t p3;
+};
+
+
+// forward declaration to keep stuff in source file
+struct MotifQueryData;
+
+struct MotifQuery{
+
+ MotifQuery(const geom::Vec3List& positions, const String& identifier,
+ Real min_triangle_edge_length,
+ Real max_triangle_edge_length,
+ Real bin_size,
+ const std::vector<int>& flags = std::vector<int>());
+
+ MotifQuery(const std::vector<MotifQuery>& queries);
+
+ static MotifQuery Load(const String& filename);
+
+ void Save(const String& filename) const;
+
+ const geom::Vec3List& GetPositions(uint idx) const;
+
+ const std::vector<uint8_t>& GetFlags(uint idx) const;
+
+ const std::vector<String>& GetIdentifiers() const;
+
+ size_t GetN() const;
+
+ size_t GetQuerySize(uint idx) const;
+
+ size_t GetNTriangles(uint idx) const;
+
+ size_t GetNTriangles() const;
+
+ Real GetMinTriangleEdgeLength() const;
+
+ Real GetMaxTriangleEdgeLength() const;
+
+ Real GetMinPosBound() const;
+
+ Real GetMaxPosBound() const;
+
+ Real GetBinSize() const;
+
+ Triangle GetTriangle(uint idx, uint triangle_idx) const;
+
+ void PrintBinSizes() const;
+
+ void Prune(Real factor);
+
+ std::shared_ptr<MotifQueryData> data_;
+
+private:
+
+ MotifQuery();
+};
+
+
+struct MotifMatch{
+
+ MotifMatch(int q_idx, int t_idx, const geom::Mat4& m,
+ const std::vector<std::pair<int,int> >& a): query_idx(q_idx),
+ mat(m), aln(a) { }
+ int query_idx;
+ int triangle_idx;
+ geom::Mat4 mat;
+ std::vector<std::pair<int,int> > aln;
+};
+
+
+std::vector<MotifMatch> FindMotifs(const MotifQuery& query,
+ const geom::Vec3List& positions,
+ Real hash_thresh = 0.4,
+ Real distance_thresh = 1.0,
+ Real refine_thresh = 0.7,
+ const std::vector<int>& flags = std::vector<int>());
+
+
+}} // ns
+
+#endif
diff --git a/modelling/src/robin_hood.h b/modelling/src/robin_hood.h
new file mode 100644
index 0000000000000000000000000000000000000000..fe02f6b7b1e613d45654cc1f175741835c4f3fc9
--- /dev/null
+++ b/modelling/src/robin_hood.h
@@ -0,0 +1,2063 @@
+/////////////////////////////////////////////////////////////////
+// SOURCE: https://github.com/martinus/robin-hood-hashing.git //
+// COMMIT: c9d72bdf02c4289903544325b272eb9f4adb7b83 //
+// WE ASSUME THAT NO UPDATES ARE REQUIRED //
+/////////////////////////////////////////////////////////////////
+
+
+// ______ _____ ______ _________
+// ______________ ___ /_ ___(_)_______ ___ /_ ______ ______ ______ /
+// __ ___/_ __ \__ __ \__ / __ __ \ __ __ \_ __ \_ __ \_ __ /
+// _ / / /_/ /_ /_/ /_ / _ / / / _ / / // /_/ // /_/ // /_/ /
+// /_/ \____/ /_.___/ /_/ /_/ /_/ ________/_/ /_/ \____/ \____/ \__,_/
+// _/_____/
+//
+// Fast & memory efficient hashtable based on robin hood hashing for C++11/14/17/20
+// version 3.4.1
+// https://github.com/martinus/robin-hood-hashing
+//
+// Licensed under the MIT License <http://opensource.org/licenses/MIT>.
+// SPDX-License-Identifier: MIT
+// Copyright (c) 2018-2019 Martin Ankerl <http://martin.ankerl.com>
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in all
+// copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
+#ifndef ROBIN_HOOD_H_INCLUDED
+#define ROBIN_HOOD_H_INCLUDED
+
+// see https://semver.org/
+#define ROBIN_HOOD_VERSION_MAJOR 3 // for incompatible API changes
+#define ROBIN_HOOD_VERSION_MINOR 4 // for adding functionality in a backwards-compatible manner
+#define ROBIN_HOOD_VERSION_PATCH 1 // for backwards-compatible bug fixes
+
+#include <algorithm>
+#include <cstdlib>
+#include <cstring>
+#include <functional>
+#include <stdexcept>
+#include <string>
+#include <type_traits>
+#include <utility>
+
+// #define ROBIN_HOOD_LOG_ENABLED
+#ifdef ROBIN_HOOD_LOG_ENABLED
+# include <iostream>
+# define ROBIN_HOOD_LOG(x) std::cout << __FUNCTION__ << "@" << __LINE__ << ": " << x << std::endl
+#else
+# define ROBIN_HOOD_LOG(x)
+#endif
+
+// #define ROBIN_HOOD_TRACE_ENABLED
+#ifdef ROBIN_HOOD_TRACE_ENABLED
+# include <iostream>
+# define ROBIN_HOOD_TRACE(x) \
+ std::cout << __FUNCTION__ << "@" << __LINE__ << ": " << x << std::endl
+#else
+# define ROBIN_HOOD_TRACE(x)
+#endif
+
+// all non-argument macros should use this facility. See
+// https://www.fluentcpp.com/2019/05/28/better-macros-better-flags/
+#define ROBIN_HOOD(x) ROBIN_HOOD_PRIVATE_DEFINITION_##x()
+
+// mark unused members with this macro
+#define ROBIN_HOOD_UNUSED(identifier)
+
+// bitness
+#if SIZE_MAX == UINT32_MAX
+# define ROBIN_HOOD_PRIVATE_DEFINITION_BITNESS() 32
+#elif SIZE_MAX == UINT64_MAX
+# define ROBIN_HOOD_PRIVATE_DEFINITION_BITNESS() 64
+#else
+# error Unsupported bitness
+#endif
+
+// endianess
+#ifdef _WIN32
+# define ROBIN_HOOD_PRIVATE_DEFINITION_LITTLE_ENDIAN() 1
+# define ROBIN_HOOD_PRIVATE_DEFINITION_BIG_ENDIAN() 0
+#else
+# define ROBIN_HOOD_PRIVATE_DEFINITION_LITTLE_ENDIAN() \
+ (__BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__)
+# define ROBIN_HOOD_PRIVATE_DEFINITION_BIG_ENDIAN() (__BYTE_ORDER__ == __ORDER_BIG_ENDIAN__)
+#endif
+
+// inline
+#ifdef _WIN32
+# define ROBIN_HOOD_PRIVATE_DEFINITION_NOINLINE() __declspec(noinline)
+#else
+# define ROBIN_HOOD_PRIVATE_DEFINITION_NOINLINE() __attribute__((noinline))
+#endif
+
+// exceptions
+#if !defined(__cpp_exceptions) && !defined(__EXCEPTIONS) && !defined(_CPPUNWIND)
+# define ROBIN_HOOD_PRIVATE_DEFINITION_HAS_EXCEPTIONS() 0
+#else
+# define ROBIN_HOOD_PRIVATE_DEFINITION_HAS_EXCEPTIONS() 1
+#endif
+
+// count leading/trailing bits
+#ifdef _WIN32
+# if ROBIN_HOOD(BITNESS) == 32
+# define ROBIN_HOOD_PRIVATE_DEFINITION_BITSCANFORWARD() _BitScanForward
+# else
+# define ROBIN_HOOD_PRIVATE_DEFINITION_BITSCANFORWARD() _BitScanForward64
+# endif
+# include <intrin.h>
+# pragma intrinsic(ROBIN_HOOD(BITSCANFORWARD))
+# define ROBIN_HOOD_COUNT_TRAILING_ZEROES(x) \
+ [](size_t mask) noexcept->int { \
+ unsigned long index; \
+ return ROBIN_HOOD(BITSCANFORWARD)(&index, mask) ? static_cast<int>(index) \
+ : ROBIN_HOOD(BITNESS); \
+ } \
+ (x)
+#else
+# if ROBIN_HOOD(BITNESS) == 32
+# define ROBIN_HOOD_PRIVATE_DEFINITION_CTZ() __builtin_ctzl
+# define ROBIN_HOOD_PRIVATE_DEFINITION_CLZ() __builtin_clzl
+# else
+# define ROBIN_HOOD_PRIVATE_DEFINITION_CTZ() __builtin_ctzll
+# define ROBIN_HOOD_PRIVATE_DEFINITION_CLZ() __builtin_clzll
+# endif
+# define ROBIN_HOOD_COUNT_LEADING_ZEROES(x) ((x) ? ROBIN_HOOD(CLZ)(x) : ROBIN_HOOD(BITNESS))
+# define ROBIN_HOOD_COUNT_TRAILING_ZEROES(x) ((x) ? ROBIN_HOOD(CTZ)(x) : ROBIN_HOOD(BITNESS))
+#endif
+
+// fallthrough
+#ifndef __has_cpp_attribute // For backwards compatibility
+# define __has_cpp_attribute(x) 0
+#endif
+#if __has_cpp_attribute(clang::fallthrough)
+# define ROBIN_HOOD_PRIVATE_DEFINITION_FALLTHROUGH() [[clang::fallthrough]]
+#elif __has_cpp_attribute(gnu::fallthrough)
+# define ROBIN_HOOD_PRIVATE_DEFINITION_FALLTHROUGH() [[gnu::fallthrough]]
+#else
+# define ROBIN_HOOD_PRIVATE_DEFINITION_FALLTHROUGH()
+#endif
+
+// likely/unlikely
+#if defined(_WIN32)
+# define ROBIN_HOOD_LIKELY(condition) condition
+# define ROBIN_HOOD_UNLIKELY(condition) condition
+#else
+# define ROBIN_HOOD_LIKELY(condition) __builtin_expect(condition, 1)
+# define ROBIN_HOOD_UNLIKELY(condition) __builtin_expect(condition, 0)
+#endif
+
+// workaround missing "is_trivially_copyable" in g++ < 5.0
+// See https://stackoverflow.com/a/31798726/48181
+#if defined(__GNUC__) && __GNUC__ < 5
+# define ROBIN_HOOD_IS_TRIVIALLY_COPYABLE(...) __has_trivial_copy(__VA_ARGS__)
+#else
+# define ROBIN_HOOD_IS_TRIVIALLY_COPYABLE(...) std::is_trivially_copyable<__VA_ARGS__>::value
+#endif
+
+// helpers for C++ versions, see https://gcc.gnu.org/onlinedocs/cpp/Standard-Predefined-Macros.html
+#define ROBIN_HOOD_PRIVATE_DEFINITION_CXX() __cplusplus
+#define ROBIN_HOOD_PRIVATE_DEFINITION_CXX98() 199711L
+#define ROBIN_HOOD_PRIVATE_DEFINITION_CXX11() 201103L
+#define ROBIN_HOOD_PRIVATE_DEFINITION_CXX14() 201402L
+#define ROBIN_HOOD_PRIVATE_DEFINITION_CXX17() 201703L
+
+#if ROBIN_HOOD(CXX) >= ROBIN_HOOD(CXX17)
+# define ROBIN_HOOD_PRIVATE_DEFINITION_NODISCARD() [[nodiscard]]
+#else
+# define ROBIN_HOOD_PRIVATE_DEFINITION_NODISCARD()
+#endif
+
+namespace robin_hood {
+
+#if ROBIN_HOOD(CXX) >= ROBIN_HOOD(CXX14)
+# define ROBIN_HOOD_STD std
+#else
+
+// c++11 compatibility layer
+namespace ROBIN_HOOD_STD {
+template <class T>
+struct alignment_of
+ : std::integral_constant<std::size_t, alignof(typename std::remove_all_extents<T>::type)> {};
+
+template <class T, T... Ints>
+class integer_sequence {
+public:
+ using value_type = T;
+ static_assert(std::is_integral<value_type>::value, "not integral type");
+ static constexpr std::size_t size() noexcept {
+ return sizeof...(Ints);
+ }
+};
+template <std::size_t... Inds>
+using index_sequence = integer_sequence<std::size_t, Inds...>;
+
+namespace detail_ {
+template <class T, T Begin, T End, bool>
+struct IntSeqImpl {
+ using TValue = T;
+ static_assert(std::is_integral<TValue>::value, "not integral type");
+ static_assert(Begin >= 0 && Begin < End, "unexpected argument (Begin<0 || Begin<=End)");
+
+ template <class, class>
+ struct IntSeqCombiner;
+
+ template <TValue... Inds0, TValue... Inds1>
+ struct IntSeqCombiner<integer_sequence<TValue, Inds0...>, integer_sequence<TValue, Inds1...>> {
+ using TResult = integer_sequence<TValue, Inds0..., Inds1...>;
+ };
+
+ using TResult =
+ typename IntSeqCombiner<typename IntSeqImpl<TValue, Begin, Begin + (End - Begin) / 2,
+ (End - Begin) / 2 == 1>::TResult,
+ typename IntSeqImpl<TValue, Begin + (End - Begin) / 2, End,
+ (End - Begin + 1) / 2 == 1>::TResult>::TResult;
+};
+
+template <class T, T Begin>
+struct IntSeqImpl<T, Begin, Begin, false> {
+ using TValue = T;
+ static_assert(std::is_integral<TValue>::value, "not integral type");
+ static_assert(Begin >= 0, "unexpected argument (Begin<0)");
+ using TResult = integer_sequence<TValue>;
+};
+
+template <class T, T Begin, T End>
+struct IntSeqImpl<T, Begin, End, true> {
+ using TValue = T;
+ static_assert(std::is_integral<TValue>::value, "not integral type");
+ static_assert(Begin >= 0, "unexpected argument (Begin<0)");
+ using TResult = integer_sequence<TValue, Begin>;
+};
+} // namespace detail_
+
+template <class T, T N>
+using make_integer_sequence = typename detail_::IntSeqImpl<T, 0, N, (N - 0) == 1>::TResult;
+
+template <std::size_t N>
+using make_index_sequence = make_integer_sequence<std::size_t, N>;
+
+template <class... T>
+using index_sequence_for = make_index_sequence<sizeof...(T)>;
+
+} // namespace ROBIN_HOOD_STD
+
+#endif
+
+namespace detail {
+
+// umul
+#if defined(__SIZEOF_INT128__)
+# define ROBIN_HOOD_PRIVATE_DEFINITION_HAS_UMUL128() 1
+# if defined(__GNUC__) || defined(__clang__)
+# pragma GCC diagnostic push
+# pragma GCC diagnostic ignored "-Wpedantic"
+using uint128_t = unsigned __int128;
+# pragma GCC diagnostic pop
+# endif
+inline uint64_t umul128(uint64_t a, uint64_t b, uint64_t* high) noexcept {
+ auto result = static_cast<uint128_t>(a) * static_cast<uint128_t>(b);
+ *high = static_cast<uint64_t>(result >> 64U);
+ return static_cast<uint64_t>(result);
+}
+#elif (defined(_WIN32) && ROBIN_HOOD(BITNESS) == 64)
+# define ROBIN_HOOD_PRIVATE_DEFINITION_HAS_UMUL128() 1
+# include <intrin.h> // for __umulh
+# pragma intrinsic(__umulh)
+# ifndef _M_ARM64
+# pragma intrinsic(_umul128)
+# endif
+inline uint64_t umul128(uint64_t a, uint64_t b, uint64_t* high) noexcept {
+# ifdef _M_ARM64
+ *high = __umulh(a, b);
+ return ((uint64_t)(a)) * (b);
+# else
+ return _umul128(a, b, high);
+# endif
+}
+#else
+# define ROBIN_HOOD_PRIVATE_DEFINITION_HAS_UMUL128() 0
+#endif
+
+// This cast gets rid of warnings like "cast from 'uint8_t*' {aka 'unsigned char*'} to
+// 'uint64_t*' {aka 'long unsigned int*'} increases required alignment of target type". Use with
+// care!
+template <typename T>
+inline T reinterpret_cast_no_cast_align_warning(void* ptr) noexcept {
+ return reinterpret_cast<T>(ptr);
+}
+
+template <typename T>
+inline T reinterpret_cast_no_cast_align_warning(void const* ptr) noexcept {
+ return reinterpret_cast<T>(ptr);
+}
+
+// make sure this is not inlined as it is slow and dramatically enlarges code, thus making other
+// inlinings more difficult. Throws are also generally the slow path.
+template <typename E, typename... Args>
+ROBIN_HOOD(NOINLINE)
+#if ROBIN_HOOD(HAS_EXCEPTIONS)
+void doThrow(Args&&... args) {
+ // NOLINTNEXTLINE(cppcoreguidelines-pro-bounds-array-to-pointer-decay)
+ throw E(std::forward<Args>(args)...);
+}
+#else
+void doThrow(Args&&... ROBIN_HOOD_UNUSED(args) /*unused*/) {
+ abort();
+}
+#endif
+
+template <typename E, typename T, typename... Args>
+T* assertNotNull(T* t, Args&&... args) {
+ if (ROBIN_HOOD_UNLIKELY(nullptr == t)) {
+ doThrow<E>(std::forward<Args>(args)...);
+ }
+ return t;
+}
+
+template <typename T>
+inline T unaligned_load(void const* ptr) noexcept {
+ // using memcpy so we don't get into unaligned load problems.
+ // compiler should optimize this very well anyways.
+ T t;
+ std::memcpy(&t, ptr, sizeof(T));
+ return t;
+}
+
+// Allocates bulks of memory for objects of type T. This deallocates the memory in the destructor,
+// and keeps a linked list of the allocated memory around. Overhead per allocation is the size of a
+// pointer.
+template <typename T, size_t MinNumAllocs = 4, size_t MaxNumAllocs = 256>
+class BulkPoolAllocator {
+public:
+ BulkPoolAllocator() noexcept = default;
+
+ // does not copy anything, just creates a new allocator.
+ BulkPoolAllocator(const BulkPoolAllocator& ROBIN_HOOD_UNUSED(o) /*unused*/) noexcept
+ : mHead(nullptr)
+ , mListForFree(nullptr) {}
+
+ BulkPoolAllocator(BulkPoolAllocator&& o) noexcept
+ : mHead(o.mHead)
+ , mListForFree(o.mListForFree) {
+ o.mListForFree = nullptr;
+ o.mHead = nullptr;
+ }
+
+ BulkPoolAllocator& operator=(BulkPoolAllocator&& o) noexcept {
+ reset();
+ mHead = o.mHead;
+ mListForFree = o.mListForFree;
+ o.mListForFree = nullptr;
+ o.mHead = nullptr;
+ return *this;
+ }
+
+ BulkPoolAllocator&
+ operator=(const BulkPoolAllocator& ROBIN_HOOD_UNUSED(o) /*unused*/) noexcept {
+ // does not do anything
+ return *this;
+ }
+
+ ~BulkPoolAllocator() noexcept {
+ reset();
+ }
+
+ // Deallocates all allocated memory.
+ void reset() noexcept {
+ while (mListForFree) {
+ T* tmp = *mListForFree;
+ free(mListForFree);
+ mListForFree = reinterpret_cast_no_cast_align_warning<T**>(tmp);
+ }
+ mHead = nullptr;
+ }
+
+ // allocates, but does NOT initialize. Use in-place new constructor, e.g.
+ // T* obj = pool.allocate();
+ // ::new (static_cast<void*>(obj)) T();
+ T* allocate() {
+ T* tmp = mHead;
+ if (!tmp) {
+ tmp = performAllocation();
+ }
+
+ mHead = *reinterpret_cast_no_cast_align_warning<T**>(tmp);
+ return tmp;
+ }
+
+ // does not actually deallocate but puts it in store.
+ // make sure you have already called the destructor! e.g. with
+ // obj->~T();
+ // pool.deallocate(obj);
+ void deallocate(T* obj) noexcept {
+ *reinterpret_cast_no_cast_align_warning<T**>(obj) = mHead;
+ mHead = obj;
+ }
+
+ // Adds an already allocated block of memory to the allocator. This allocator is from now on
+ // responsible for freeing the data (with free()). If the provided data is not large enough to
+ // make use of, it is immediately freed. Otherwise it is reused and freed in the destructor.
+ void addOrFree(void* ptr, const size_t numBytes) noexcept {
+ // calculate number of available elements in ptr
+ if (numBytes < ALIGNMENT + ALIGNED_SIZE) {
+ // not enough data for at least one element. Free and return.
+ free(ptr);
+ } else {
+ add(ptr, numBytes);
+ }
+ }
+
+ void swap(BulkPoolAllocator<T, MinNumAllocs, MaxNumAllocs>& other) noexcept {
+ using std::swap;
+ swap(mHead, other.mHead);
+ swap(mListForFree, other.mListForFree);
+ }
+
+private:
+ // iterates the list of allocated memory to calculate how many to alloc next.
+ // Recalculating this each time saves us a size_t member.
+ // This ignores the fact that memory blocks might have been added manually with addOrFree. In
+ // practice, this should not matter much.
+ ROBIN_HOOD(NODISCARD) size_t calcNumElementsToAlloc() const noexcept {
+ auto tmp = mListForFree;
+ size_t numAllocs = MinNumAllocs;
+
+ while (numAllocs * 2 <= MaxNumAllocs && tmp) {
+ auto x = reinterpret_cast<T***>(tmp);
+ tmp = *x;
+ numAllocs *= 2;
+ }
+
+ return numAllocs;
+ }
+
+ // WARNING: Underflow if numBytes < ALIGNMENT! This is guarded in addOrFree().
+ void add(void* ptr, const size_t numBytes) noexcept {
+ const size_t numElements = (numBytes - ALIGNMENT) / ALIGNED_SIZE;
+
+ auto data = reinterpret_cast<T**>(ptr);
+
+ // link free list
+ auto x = reinterpret_cast<T***>(data);
+ *x = mListForFree;
+ mListForFree = data;
+
+ // create linked list for newly allocated data
+ auto const headT =
+ reinterpret_cast_no_cast_align_warning<T*>(reinterpret_cast<char*>(ptr) + ALIGNMENT);
+
+ auto const head = reinterpret_cast<char*>(headT);
+
+ // Visual Studio compiler automatically unrolls this loop, which is pretty cool
+ for (size_t i = 0; i < numElements; ++i) {
+ *reinterpret_cast_no_cast_align_warning<char**>(head + i * ALIGNED_SIZE) =
+ head + (i + 1) * ALIGNED_SIZE;
+ }
+
+ // last one points to 0
+ *reinterpret_cast_no_cast_align_warning<T**>(head + (numElements - 1) * ALIGNED_SIZE) =
+ mHead;
+ mHead = headT;
+ }
+
+ // Called when no memory is available (mHead == 0).
+ // Don't inline this slow path.
+ ROBIN_HOOD(NOINLINE) T* performAllocation() {
+ size_t const numElementsToAlloc = calcNumElementsToAlloc();
+
+ // alloc new memory: [prev |T, T, ... T]
+ // std::cout << (sizeof(T*) + ALIGNED_SIZE * numElementsToAlloc) << " bytes" << std::endl;
+ size_t const bytes = ALIGNMENT + ALIGNED_SIZE * numElementsToAlloc;
+ add(assertNotNull<std::bad_alloc>(malloc(bytes)), bytes);
+ return mHead;
+ }
+
+ // enforce byte alignment of the T's
+#if ROBIN_HOOD(CXX) >= ROBIN_HOOD(CXX14)
+ static constexpr size_t ALIGNMENT =
+ (std::max)(std::alignment_of<T>::value, std::alignment_of<T*>::value);
+#else
+ static const size_t ALIGNMENT =
+ (ROBIN_HOOD_STD::alignment_of<T>::value > ROBIN_HOOD_STD::alignment_of<T*>::value)
+ ? ROBIN_HOOD_STD::alignment_of<T>::value
+ : +ROBIN_HOOD_STD::alignment_of<T*>::value; // the + is for walkarround
+#endif
+
+ static constexpr size_t ALIGNED_SIZE = ((sizeof(T) - 1) / ALIGNMENT + 1) * ALIGNMENT;
+
+ static_assert(MinNumAllocs >= 1, "MinNumAllocs");
+ static_assert(MaxNumAllocs >= MinNumAllocs, "MaxNumAllocs");
+ static_assert(ALIGNED_SIZE >= sizeof(T*), "ALIGNED_SIZE");
+ static_assert(0 == (ALIGNED_SIZE % sizeof(T*)), "ALIGNED_SIZE mod");
+ static_assert(ALIGNMENT >= sizeof(T*), "ALIGNMENT");
+
+ T* mHead{nullptr};
+ T** mListForFree{nullptr};
+};
+
+template <typename T, size_t MinSize, size_t MaxSize, bool IsFlatMap>
+struct NodeAllocator;
+
+// dummy allocator that does nothing
+template <typename T, size_t MinSize, size_t MaxSize>
+struct NodeAllocator<T, MinSize, MaxSize, true> {
+
+ // we are not using the data, so just free it.
+ void addOrFree(void* ptr, size_t ROBIN_HOOD_UNUSED(numBytes) /*unused*/) noexcept {
+ free(ptr);
+ }
+};
+
+template <typename T, size_t MinSize, size_t MaxSize>
+struct NodeAllocator<T, MinSize, MaxSize, false> : public BulkPoolAllocator<T, MinSize, MaxSize> {};
+
+// dummy hash, unsed as mixer when robin_hood::hash is already used
+template <typename T>
+struct identity_hash {
+ constexpr size_t operator()(T const& obj) const noexcept {
+ return static_cast<size_t>(obj);
+ }
+};
+
+// c++14 doesn't have is_nothrow_swappable, and clang++ 6.0.1 doesn't like it either, so I'm making
+// my own here.
+namespace swappable {
+using std::swap;
+template <typename T>
+struct nothrow {
+ static const bool value = noexcept(swap(std::declval<T&>(), std::declval<T&>()));
+};
+
+} // namespace swappable
+
+} // namespace detail
+
+struct is_transparent_tag {};
+
+// A custom pair implementation is used in the map because std::pair is not is_trivially_copyable,
+// which means it would not be allowed to be used in std::memcpy. This struct is copyable, which is
+// also tested.
+template <typename T1, typename T2>
+struct pair {
+ using first_type = T1;
+ using second_type = T2;
+
+ template <typename U1 = T1, typename U2 = T2,
+ typename = typename std::enable_if<std::is_default_constructible<U1>::value &&
+ std::is_default_constructible<U2>::value>::type>
+ constexpr pair() noexcept(noexcept(U1()) && noexcept(U2()))
+ : first()
+ , second() {}
+
+ // pair constructors are explicit so we don't accidentally call this ctor when we don't have to.
+ explicit constexpr pair(std::pair<T1, T2> const& o) noexcept(
+ noexcept(T1(std::declval<T1 const&>())) && noexcept(T2(std::declval<T2 const&>())))
+ : first(o.first)
+ , second(o.second) {}
+
+ // pair constructors are explicit so we don't accidentally call this ctor when we don't have to.
+ explicit constexpr pair(std::pair<T1, T2>&& o) noexcept(
+ noexcept(T1(std::move(std::declval<T1&&>()))) &&
+ noexcept(T2(std::move(std::declval<T2&&>()))))
+ : first(std::move(o.first))
+ , second(std::move(o.second)) {}
+
+ constexpr pair(T1&& a, T2&& b) noexcept(noexcept(T1(std::move(std::declval<T1&&>()))) &&
+ noexcept(T2(std::move(std::declval<T2&&>()))))
+ : first(std::move(a))
+ , second(std::move(b)) {}
+
+ template <typename U1, typename U2>
+ constexpr pair(U1&& a, U2&& b) noexcept(noexcept(T1(std::forward<U1>(std::declval<U1&&>()))) &&
+ noexcept(T2(std::forward<U2>(std::declval<U2&&>()))))
+ : first(std::forward<U1>(a))
+ , second(std::forward<U2>(b)) {}
+
+ template <typename... U1, typename... U2>
+ constexpr pair(
+ std::piecewise_construct_t /*unused*/, std::tuple<U1...> a,
+ std::tuple<U2...> b) noexcept(noexcept(pair(std::declval<std::tuple<U1...>&>(),
+ std::declval<std::tuple<U2...>&>(),
+ ROBIN_HOOD_STD::index_sequence_for<U1...>(),
+ ROBIN_HOOD_STD::index_sequence_for<U2...>())))
+ : pair(a, b, ROBIN_HOOD_STD::index_sequence_for<U1...>(),
+ ROBIN_HOOD_STD::index_sequence_for<U2...>()) {}
+
+ // constructor called from the std::piecewise_construct_t ctor
+ template <typename... U1, size_t... I1, typename... U2, size_t... I2>
+ pair(std::tuple<U1...>& a, std::tuple<U2...>& b,
+ ROBIN_HOOD_STD::index_sequence<I1...> /*unused*/,
+ ROBIN_HOOD_STD::index_sequence<
+ I2...> /*unused*/) noexcept(noexcept(T1(std::
+ forward<U1>(std::get<I1>(
+ std::declval<
+ std::tuple<U1...>&>()))...)) &&
+ noexcept(T2(std::forward<U2>(
+ std::get<I2>(std::declval<std::tuple<U2...>&>()))...)))
+ : first(std::forward<U1>(std::get<I1>(a))...)
+ , second(std::forward<U2>(std::get<I2>(b))...) {
+ // make visual studio compiler happy about warning about unused a & b.
+ // Visual studio's pair implementation disables warning 4100.
+ (void)a;
+ (void)b;
+ }
+
+ ROBIN_HOOD(NODISCARD) first_type& getFirst() noexcept {
+ return first;
+ }
+ ROBIN_HOOD(NODISCARD) first_type const& getFirst() const noexcept {
+ return first;
+ }
+ ROBIN_HOOD(NODISCARD) second_type& getSecond() noexcept {
+ return second;
+ }
+ ROBIN_HOOD(NODISCARD) second_type const& getSecond() const noexcept {
+ return second;
+ }
+
+ void swap(pair<T1, T2>& o) noexcept((detail::swappable::nothrow<T1>::value) &&
+ (detail::swappable::nothrow<T2>::value)) {
+ using std::swap;
+ swap(first, o.first);
+ swap(second, o.second);
+ }
+
+ T1 first; // NOLINT(misc-non-private-member-variables-in-classes)
+ T2 second; // NOLINT(misc-non-private-member-variables-in-classes)
+};
+
+template <typename A, typename B>
+void swap(pair<A, B>& a, pair<A, B>& b) noexcept(
+ noexcept(std::declval<pair<A, B>&>().swap(std::declval<pair<A, B>&>()))) {
+ a.swap(b);
+}
+
+// Hash an arbitrary amount of bytes. This is basically Murmur2 hash without caring about big
+// endianness. TODO(martinus) add a fallback for very large strings?
+static size_t hash_bytes(void const* ptr, size_t const len) noexcept {
+ static constexpr uint64_t m = UINT64_C(0xc6a4a7935bd1e995);
+ static constexpr uint64_t seed = UINT64_C(0xe17a1465);
+ static constexpr unsigned int r = 47;
+
+ auto const data64 = static_cast<uint64_t const*>(ptr);
+ uint64_t h = seed ^ (len * m);
+
+ size_t const n_blocks = len / 8;
+ for (size_t i = 0; i < n_blocks; ++i) {
+ auto k = detail::unaligned_load<uint64_t>(data64 + i);
+
+ k *= m;
+ k ^= k >> r;
+ k *= m;
+
+ h ^= k;
+ h *= m;
+ }
+
+ auto const data8 = reinterpret_cast<uint8_t const*>(data64 + n_blocks);
+ switch (len & 7U) {
+ case 7:
+ h ^= static_cast<uint64_t>(data8[6]) << 48U;
+ ROBIN_HOOD(FALLTHROUGH); // FALLTHROUGH
+ case 6:
+ h ^= static_cast<uint64_t>(data8[5]) << 40U;
+ ROBIN_HOOD(FALLTHROUGH); // FALLTHROUGH
+ case 5:
+ h ^= static_cast<uint64_t>(data8[4]) << 32U;
+ ROBIN_HOOD(FALLTHROUGH); // FALLTHROUGH
+ case 4:
+ h ^= static_cast<uint64_t>(data8[3]) << 24U;
+ ROBIN_HOOD(FALLTHROUGH); // FALLTHROUGH
+ case 3:
+ h ^= static_cast<uint64_t>(data8[2]) << 16U;
+ ROBIN_HOOD(FALLTHROUGH); // FALLTHROUGH
+ case 2:
+ h ^= static_cast<uint64_t>(data8[1]) << 8U;
+ ROBIN_HOOD(FALLTHROUGH); // FALLTHROUGH
+ case 1:
+ h ^= static_cast<uint64_t>(data8[0]);
+ h *= m;
+ ROBIN_HOOD(FALLTHROUGH); // FALLTHROUGH
+ default:
+ break;
+ }
+
+ h ^= h >> r;
+ h *= m;
+ h ^= h >> r;
+ return static_cast<size_t>(h);
+}
+
+inline size_t hash_int(uint64_t obj) noexcept {
+#if ROBIN_HOOD(HAS_UMUL128)
+ // 167079903232 masksum, 120428523 ops best: 0xde5fb9d2630458e9
+ static constexpr uint64_t k = UINT64_C(0xde5fb9d2630458e9);
+ uint64_t h;
+ uint64_t l = detail::umul128(obj, k, &h);
+ return h + l;
+#elif ROBIN_HOOD(BITNESS) == 32
+ uint64_t const r = obj * UINT64_C(0xca4bcaa75ec3f625);
+ auto h = static_cast<uint32_t>(r >> 32U);
+ auto l = static_cast<uint32_t>(r);
+ return h + l;
+#else
+ // murmurhash 3 finalizer
+ uint64_t h = obj;
+ h ^= h >> 33;
+ h *= 0xff51afd7ed558ccd;
+ h ^= h >> 33;
+ h *= 0xc4ceb9fe1a85ec53;
+ h ^= h >> 33;
+ return static_cast<size_t>(h);
+#endif
+}
+
+// A thin wrapper around std::hash, performing an additional simple mixing step of the result.
+template <typename T>
+struct hash : public std::hash<T> {
+ size_t operator()(T const& obj) const
+ noexcept(noexcept(std::declval<std::hash<T>>().operator()(std::declval<T const&>()))) {
+ // call base hash
+ auto result = std::hash<T>::operator()(obj);
+ // return mixed of that, to be save against identity has
+ return hash_int(static_cast<uint64_t>(result));
+ }
+};
+
+template <>
+struct hash<std::string> {
+ size_t operator()(std::string const& str) const noexcept {
+ return hash_bytes(str.data(), str.size());
+ }
+};
+
+template <class T>
+struct hash<T*> {
+ size_t operator()(T* ptr) const noexcept {
+ return hash_int(reinterpret_cast<size_t>(ptr));
+ }
+};
+
+#define ROBIN_HOOD_HASH_INT(T) \
+ template <> \
+ struct hash<T> { \
+ size_t operator()(T obj) const noexcept { \
+ return hash_int(static_cast<uint64_t>(obj)); \
+ } \
+ }
+
+#if defined(__GNUC__) && !defined(__clang__)
+# pragma GCC diagnostic push
+# pragma GCC diagnostic ignored "-Wuseless-cast"
+#endif
+// see https://en.cppreference.com/w/cpp/utility/hash
+ROBIN_HOOD_HASH_INT(bool);
+ROBIN_HOOD_HASH_INT(char);
+ROBIN_HOOD_HASH_INT(signed char);
+ROBIN_HOOD_HASH_INT(unsigned char);
+ROBIN_HOOD_HASH_INT(char16_t);
+ROBIN_HOOD_HASH_INT(char32_t);
+ROBIN_HOOD_HASH_INT(wchar_t);
+ROBIN_HOOD_HASH_INT(short);
+ROBIN_HOOD_HASH_INT(unsigned short);
+ROBIN_HOOD_HASH_INT(int);
+ROBIN_HOOD_HASH_INT(unsigned int);
+ROBIN_HOOD_HASH_INT(long);
+ROBIN_HOOD_HASH_INT(long long);
+ROBIN_HOOD_HASH_INT(unsigned long);
+ROBIN_HOOD_HASH_INT(unsigned long long);
+#if defined(__GNUC__) && !defined(__clang__)
+# pragma GCC diagnostic pop
+#endif
+namespace detail {
+
+// using wrapper classes for hash and key_equal prevents the diamond problem when the same type is
+// used. see https://stackoverflow.com/a/28771920/48181
+template <typename T>
+struct WrapHash : public T {
+ WrapHash() = default;
+ explicit WrapHash(T const& o) noexcept(noexcept(T(std::declval<T const&>())))
+ : T(o) {}
+};
+
+template <typename T>
+struct WrapKeyEqual : public T {
+ WrapKeyEqual() = default;
+ explicit WrapKeyEqual(T const& o) noexcept(noexcept(T(std::declval<T const&>())))
+ : T(o) {}
+};
+
+// A highly optimized hashmap implementation, using the Robin Hood algorithm.
+//
+// In most cases, this map should be usable as a drop-in replacement for std::unordered_map, but be
+// about 2x faster in most cases and require much less allocations.
+//
+// This implementation uses the following memory layout:
+//
+// [Node, Node, ... Node | info, info, ... infoSentinel ]
+//
+// * Node: either a DataNode that directly has the std::pair<key, val> as member,
+// or a DataNode with a pointer to std::pair<key,val>. Which DataNode representation to use
+// depends on how fast the swap() operation is. Heuristically, this is automatically choosen based
+// on sizeof(). there are always 2^n Nodes.
+//
+// * info: Each Node in the map has a corresponding info byte, so there are 2^n info bytes.
+// Each byte is initialized to 0, meaning the corresponding Node is empty. Set to 1 means the
+// corresponding node contains data. Set to 2 means the corresponding Node is filled, but it
+// actually belongs to the previous position and was pushed out because that place is already
+// taken.
+//
+// * infoSentinel: Sentinel byte set to 1, so that iterator's ++ can stop at end() without the need
+// for a idx
+// variable.
+//
+// According to STL, order of templates has effect on throughput. That's why I've moved the boolean
+// to the front.
+// https://www.reddit.com/r/cpp/comments/ahp6iu/compile_time_binary_size_reductions_and_cs_future/eeguck4/
+template <bool IsFlatMap, size_t MaxLoadFactor100, typename Key, typename T, typename Hash,
+ typename KeyEqual>
+class unordered_map
+ : public WrapHash<Hash>,
+ public WrapKeyEqual<KeyEqual>,
+ detail::NodeAllocator<
+ robin_hood::pair<typename std::conditional<IsFlatMap, Key, Key const>::type, T>, 4, 16384,
+ IsFlatMap> {
+public:
+ using key_type = Key;
+ using mapped_type = T;
+ using value_type =
+ robin_hood::pair<typename std::conditional<IsFlatMap, Key, Key const>::type, T>;
+ using size_type = size_t;
+ using hasher = Hash;
+ using key_equal = KeyEqual;
+ using Self =
+ unordered_map<IsFlatMap, MaxLoadFactor100, key_type, mapped_type, hasher, key_equal>;
+ static constexpr bool is_flat_map = IsFlatMap;
+
+private:
+ static_assert(MaxLoadFactor100 > 10 && MaxLoadFactor100 < 100,
+ "MaxLoadFactor100 needs to be >10 && < 100");
+
+ using WHash = WrapHash<Hash>;
+ using WKeyEqual = WrapKeyEqual<KeyEqual>;
+
+ // configuration defaults
+
+ // make sure we have 8 elements, needed to quickly rehash mInfo
+ static constexpr size_t InitialNumElements = sizeof(uint64_t);
+ static constexpr uint32_t InitialInfoNumBits = 5;
+ static constexpr uint8_t InitialInfoInc = 1U << InitialInfoNumBits;
+ static constexpr uint8_t InitialInfoHashShift = sizeof(size_t) * 8 - InitialInfoNumBits;
+ using DataPool = detail::NodeAllocator<value_type, 4, 16384, IsFlatMap>;
+
+ // type needs to be wider than uint8_t.
+ using InfoType = uint32_t;
+
+ // DataNode ////////////////////////////////////////////////////////
+
+ // Primary template for the data node. We have special implementations for small and big
+ // objects. For large objects it is assumed that swap() is fairly slow, so we allocate these on
+ // the heap so swap merely swaps a pointer.
+ template <typename M, bool>
+ class DataNode {};
+
+ // Small: just allocate on the stack.
+ template <typename M>
+ class DataNode<M, true> final {
+ public:
+ template <typename... Args>
+ explicit DataNode(M& ROBIN_HOOD_UNUSED(map) /*unused*/, Args&&... args) noexcept(
+ noexcept(value_type(std::forward<Args>(args)...)))
+ : mData(std::forward<Args>(args)...) {}
+
+ DataNode(M& ROBIN_HOOD_UNUSED(map) /*unused*/, DataNode<M, true>&& n) noexcept(
+ std::is_nothrow_move_constructible<value_type>::value)
+ : mData(std::move(n.mData)) {}
+
+ // doesn't do anything
+ void destroy(M& ROBIN_HOOD_UNUSED(map) /*unused*/) noexcept {}
+ void destroyDoNotDeallocate() noexcept {}
+
+ value_type const* operator->() const noexcept {
+ return &mData;
+ }
+ value_type* operator->() noexcept {
+ return &mData;
+ }
+
+ const value_type& operator*() const noexcept {
+ return mData;
+ }
+
+ value_type& operator*() noexcept {
+ return mData;
+ }
+
+ ROBIN_HOOD(NODISCARD) typename value_type::first_type& getFirst() noexcept {
+ return mData.first;
+ }
+
+ ROBIN_HOOD(NODISCARD) typename value_type::first_type const& getFirst() const noexcept {
+ return mData.first;
+ }
+
+ ROBIN_HOOD(NODISCARD) typename value_type::second_type& getSecond() noexcept {
+ return mData.second;
+ }
+
+ ROBIN_HOOD(NODISCARD) typename value_type::second_type const& getSecond() const noexcept {
+ return mData.second;
+ }
+
+ void swap(DataNode<M, true>& o) noexcept(
+ noexcept(std::declval<value_type>().swap(std::declval<value_type>()))) {
+ mData.swap(o.mData);
+ }
+
+ private:
+ value_type mData;
+ };
+
+ // big object: allocate on heap.
+ template <typename M>
+ class DataNode<M, false> {
+ public:
+ template <typename... Args>
+ explicit DataNode(M& map, Args&&... args)
+ : mData(map.allocate()) {
+ ::new (static_cast<void*>(mData)) value_type(std::forward<Args>(args)...);
+ }
+
+ DataNode(M& ROBIN_HOOD_UNUSED(map) /*unused*/, DataNode<M, false>&& n) noexcept
+ : mData(std::move(n.mData)) {}
+
+ void destroy(M& map) noexcept {
+ // don't deallocate, just put it into list of datapool.
+ mData->~value_type();
+ map.deallocate(mData);
+ }
+
+ void destroyDoNotDeallocate() noexcept {
+ mData->~value_type();
+ }
+
+ value_type const* operator->() const noexcept {
+ return mData;
+ }
+
+ value_type* operator->() noexcept {
+ return mData;
+ }
+
+ const value_type& operator*() const {
+ return *mData;
+ }
+
+ value_type& operator*() {
+ return *mData;
+ }
+
+ ROBIN_HOOD(NODISCARD) typename value_type::first_type& getFirst() {
+ return mData->first;
+ }
+
+ ROBIN_HOOD(NODISCARD) typename value_type::first_type const& getFirst() const {
+ return mData->first;
+ }
+
+ ROBIN_HOOD(NODISCARD) typename value_type::second_type& getSecond() {
+ return mData->second;
+ }
+
+ ROBIN_HOOD(NODISCARD) typename value_type::second_type const& getSecond() const {
+ return mData->second;
+ }
+
+ void swap(DataNode<M, false>& o) noexcept {
+ using std::swap;
+ swap(mData, o.mData);
+ }
+
+ private:
+ value_type* mData;
+ };
+
+ using Node = DataNode<Self, IsFlatMap>;
+
+ // Cloner //////////////////////////////////////////////////////////
+
+ template <typename M, bool UseMemcpy>
+ struct Cloner;
+
+ // fast path: Just copy data, without allocating anything.
+ template <typename M>
+ struct Cloner<M, true> {
+ void operator()(M const& source, M& target) const {
+ // std::memcpy(target.mKeyVals, source.mKeyVals,
+ // target.calcNumBytesTotal(target.mMask + 1));
+ auto src = reinterpret_cast<char const*>(source.mKeyVals);
+ auto tgt = reinterpret_cast<char*>(target.mKeyVals);
+ std::copy(src, src + target.calcNumBytesTotal(target.mMask + 1), tgt);
+ }
+ };
+
+ template <typename M>
+ struct Cloner<M, false> {
+ void operator()(M const& s, M& t) const {
+ std::copy(s.mInfo, s.mInfo + t.calcNumBytesInfo(t.mMask + 1), t.mInfo);
+
+ for (size_t i = 0; i < t.mMask + 1; ++i) {
+ if (t.mInfo[i]) {
+ ::new (static_cast<void*>(t.mKeyVals + i)) Node(t, *s.mKeyVals[i]);
+ }
+ }
+ }
+ };
+
+ // Destroyer ///////////////////////////////////////////////////////
+
+ template <typename M, bool IsFlatMapAndTrivial>
+ struct Destroyer {};
+
+ template <typename M>
+ struct Destroyer<M, true> {
+ void nodes(M& m) const noexcept {
+ m.mNumElements = 0;
+ }
+
+ void nodesDoNotDeallocate(M& m) const noexcept {
+ m.mNumElements = 0;
+ }
+ };
+
+ template <typename M>
+ struct Destroyer<M, false> {
+ void nodes(M& m) const noexcept {
+ m.mNumElements = 0;
+ // clear also resets mInfo to 0, that's sometimes not necessary.
+ for (size_t idx = 0; idx <= m.mMask; ++idx) {
+ if (0 != m.mInfo[idx]) {
+ Node& n = m.mKeyVals[idx];
+ n.destroy(m);
+ n.~Node();
+ }
+ }
+ }
+
+ void nodesDoNotDeallocate(M& m) const noexcept {
+ m.mNumElements = 0;
+ // clear also resets mInfo to 0, that's sometimes not necessary.
+ for (size_t idx = 0; idx <= m.mMask; ++idx) {
+ if (0 != m.mInfo[idx]) {
+ Node& n = m.mKeyVals[idx];
+ n.destroyDoNotDeallocate();
+ n.~Node();
+ }
+ }
+ }
+ };
+
+ // Iter ////////////////////////////////////////////////////////////
+
+ struct fast_forward_tag {};
+
+ // generic iterator for both const_iterator and iterator.
+ template <bool IsConst>
+ // NOLINTNEXTLINE(hicpp-special-member-functions,cppcoreguidelines-special-member-functions)
+ class Iter {
+ private:
+ using NodePtr = typename std::conditional<IsConst, Node const*, Node*>::type;
+
+ public:
+ using difference_type = std::ptrdiff_t;
+ using value_type = typename Self::value_type;
+ using reference = typename std::conditional<IsConst, value_type const&, value_type&>::type;
+ using pointer = typename std::conditional<IsConst, value_type const*, value_type*>::type;
+ using iterator_category = std::forward_iterator_tag;
+
+ // default constructed iterator can be compared to itself, but WON'T return true when
+ // compared to end().
+ Iter() = default;
+
+ // Rule of zero: nothing specified. The conversion constructor is only enabled for iterator
+ // to const_iterator, so it doesn't accidentally work as a copy ctor.
+
+ // Conversion constructor from iterator to const_iterator.
+ template <bool OtherIsConst,
+ typename = typename std::enable_if<IsConst && !OtherIsConst>::type>
+ // NOLINTNEXTLINE(hicpp-explicit-conversions)
+ Iter(Iter<OtherIsConst> const& other) noexcept
+ : mKeyVals(other.mKeyVals)
+ , mInfo(other.mInfo) {}
+
+ Iter(NodePtr valPtr, uint8_t const* infoPtr) noexcept
+ : mKeyVals(valPtr)
+ , mInfo(infoPtr) {}
+
+ Iter(NodePtr valPtr, uint8_t const* infoPtr,
+ fast_forward_tag ROBIN_HOOD_UNUSED(tag) /*unused*/) noexcept
+ : mKeyVals(valPtr)
+ , mInfo(infoPtr) {
+ fastForward();
+ }
+
+ template <bool OtherIsConst,
+ typename = typename std::enable_if<IsConst && !OtherIsConst>::type>
+ Iter& operator=(Iter<OtherIsConst> const& other) noexcept {
+ mKeyVals = other.mKeyVals;
+ mInfo = other.mInfo;
+ return *this;
+ }
+
+ // prefix increment. Undefined behavior if we are at end()!
+ Iter& operator++() noexcept {
+ mInfo++;
+ mKeyVals++;
+ fastForward();
+ return *this;
+ }
+
+ reference operator*() const {
+ return **mKeyVals;
+ }
+
+ pointer operator->() const {
+ return &**mKeyVals;
+ }
+
+ template <bool O>
+ bool operator==(Iter<O> const& o) const noexcept {
+ return mKeyVals == o.mKeyVals;
+ }
+
+ template <bool O>
+ bool operator!=(Iter<O> const& o) const noexcept {
+ return mKeyVals != o.mKeyVals;
+ }
+
+ private:
+ // fast forward to the next non-free info byte
+ void fastForward() noexcept {
+ int inc;
+ do {
+ auto const n = detail::unaligned_load<size_t>(mInfo);
+#if ROBIN_HOOD(LITTLE_ENDIAN)
+ inc = ROBIN_HOOD_COUNT_TRAILING_ZEROES(n) / 8;
+#else
+ inc = ROBIN_HOOD_COUNT_LEADING_ZEROES(n) / 8;
+#endif
+ mInfo += inc;
+ mKeyVals += inc;
+ } while (inc == static_cast<int>(sizeof(size_t)));
+ }
+
+ friend class unordered_map<IsFlatMap, MaxLoadFactor100, key_type, mapped_type, hasher,
+ key_equal>;
+ NodePtr mKeyVals{nullptr};
+ uint8_t const* mInfo{nullptr};
+ };
+
+ ////////////////////////////////////////////////////////////////////
+
+ // highly performance relevant code.
+ // Lower bits are used for indexing into the array (2^n size)
+ // The upper 1-5 bits need to be a reasonable good hash, to save comparisons.
+ template <typename HashKey>
+ void keyToIdx(HashKey&& key, size_t* idx, InfoType* info) const {
+ // for a user-specified hash that is *not* robin_hood::hash, apply robin_hood::hash as an
+ // additional mixing step. This serves as a bad hash prevention, if the given data is badly
+ // mixed.
+ using Mix =
+ typename std::conditional<std::is_same<::robin_hood::hash<key_type>, hasher>::value,
+ ::robin_hood::detail::identity_hash<size_t>,
+ ::robin_hood::hash<size_t>>::type;
+ *idx = Mix{}(WHash::operator()(key));
+
+ *info = mInfoInc + static_cast<InfoType>(*idx >> mInfoHashShift);
+ *idx &= mMask;
+ }
+
+ // forwards the index by one, wrapping around at the end
+ void next(InfoType* info, size_t* idx) const noexcept {
+ *idx = (*idx + 1) & mMask;
+ *info += mInfoInc;
+ }
+
+ void nextWhileLess(InfoType* info, size_t* idx) const noexcept {
+ // unrolling this by hand did not bring any speedups.
+ while (*info < mInfo[*idx]) {
+ next(info, idx);
+ }
+ }
+
+ // Shift everything up by one element. Tries to move stuff around.
+ // True if some shifting has occured (entry under idx is a constructed object)
+ // Fals if no shift has occured (entry under idx is unconstructed memory)
+ void
+ shiftUp(size_t idx,
+ size_t const insertion_idx) noexcept(std::is_nothrow_move_assignable<Node>::value) {
+ while (idx != insertion_idx) {
+ size_t prev_idx = (idx - 1) & mMask;
+ if (mInfo[idx]) {
+ mKeyVals[idx] = std::move(mKeyVals[prev_idx]);
+ } else {
+ ::new (static_cast<void*>(mKeyVals + idx)) Node(std::move(mKeyVals[prev_idx]));
+ }
+ mInfo[idx] = static_cast<uint8_t>(mInfo[prev_idx] + mInfoInc);
+ if (ROBIN_HOOD_UNLIKELY(mInfo[idx] + mInfoInc > 0xFF)) {
+ mMaxNumElementsAllowed = 0;
+ }
+ idx = prev_idx;
+ }
+ }
+
+ void shiftDown(size_t idx) noexcept(std::is_nothrow_move_assignable<Node>::value) {
+ // until we find one that is either empty or has zero offset.
+ // TODO(martinus) we don't need to move everything, just the last one for the same bucket.
+ mKeyVals[idx].destroy(*this);
+
+ // until we find one that is either empty or has zero offset.
+ size_t nextIdx = (idx + 1) & mMask;
+ while (mInfo[nextIdx] >= 2 * mInfoInc) {
+ mInfo[idx] = static_cast<uint8_t>(mInfo[nextIdx] - mInfoInc);
+ mKeyVals[idx] = std::move(mKeyVals[nextIdx]);
+ idx = nextIdx;
+ nextIdx = (idx + 1) & mMask;
+ }
+
+ mInfo[idx] = 0;
+ // don't destroy, we've moved it
+ // mKeyVals[idx].destroy(*this);
+ mKeyVals[idx].~Node();
+ }
+
+ // copy of find(), except that it returns iterator instead of const_iterator.
+ template <typename Other>
+ ROBIN_HOOD(NODISCARD)
+ size_t findIdx(Other const& key) const {
+ size_t idx;
+ InfoType info;
+ keyToIdx(key, &idx, &info);
+
+ do {
+ // unrolling this twice gives a bit of a speedup. More unrolling did not help.
+ if (info == mInfo[idx] && WKeyEqual::operator()(key, mKeyVals[idx].getFirst())) {
+ return idx;
+ }
+ next(&info, &idx);
+ if (info == mInfo[idx] && WKeyEqual::operator()(key, mKeyVals[idx].getFirst())) {
+ return idx;
+ }
+ next(&info, &idx);
+ } while (info <= mInfo[idx]);
+
+ // nothing found!
+ return mMask == 0 ? 0 : mMask + 1;
+ }
+
+ void cloneData(const unordered_map& o) {
+ Cloner<unordered_map, IsFlatMap && ROBIN_HOOD_IS_TRIVIALLY_COPYABLE(Node)>()(o, *this);
+ }
+
+ // inserts a keyval that is guaranteed to be new, e.g. when the hashmap is resized.
+ // @return index where the element was created
+ size_t insert_move(Node&& keyval) {
+ // we don't retry, fail if overflowing
+ // don't need to check max num elements
+ if (0 == mMaxNumElementsAllowed && !try_increase_info()) {
+ throwOverflowError();
+ }
+
+ size_t idx;
+ InfoType info;
+ keyToIdx(keyval.getFirst(), &idx, &info);
+
+ // skip forward. Use <= because we are certain that the element is not there.
+ while (info <= mInfo[idx]) {
+ idx = (idx + 1) & mMask;
+ info += mInfoInc;
+ }
+
+ // key not found, so we are now exactly where we want to insert it.
+ auto const insertion_idx = idx;
+ auto const insertion_info = static_cast<uint8_t>(info);
+ if (ROBIN_HOOD_UNLIKELY(insertion_info + mInfoInc > 0xFF)) {
+ mMaxNumElementsAllowed = 0;
+ }
+
+ // find an empty spot
+ while (0 != mInfo[idx]) {
+ next(&info, &idx);
+ }
+
+ auto& l = mKeyVals[insertion_idx];
+ if (idx == insertion_idx) {
+ ::new (static_cast<void*>(&l)) Node(std::move(keyval));
+ } else {
+ shiftUp(idx, insertion_idx);
+ l = std::move(keyval);
+ }
+
+ // put at empty spot
+ mInfo[insertion_idx] = insertion_info;
+
+ ++mNumElements;
+ return insertion_idx;
+ }
+
+public:
+ using iterator = Iter<false>;
+ using const_iterator = Iter<true>;
+
+ // Creates an empty hash map. Nothing is allocated yet, this happens at the first insert. This
+ // tremendously speeds up ctor & dtor of a map that never receives an element. The penalty is
+ // payed at the first insert, and not before. Lookup of this empty map works because everybody
+ // points to DummyInfoByte::b. parameter bucket_count is dictated by the standard, but we can
+ // ignore it.
+ explicit unordered_map(size_t ROBIN_HOOD_UNUSED(bucket_count) /*unused*/ = 0,
+ const Hash& h = Hash{},
+ const KeyEqual& equal = KeyEqual{}) noexcept(noexcept(Hash(h)) &&
+ noexcept(KeyEqual(equal)))
+ : WHash(h)
+ , WKeyEqual(equal) {
+ ROBIN_HOOD_TRACE(this);
+ }
+
+ template <typename Iter>
+ unordered_map(Iter first, Iter last, size_t ROBIN_HOOD_UNUSED(bucket_count) /*unused*/ = 0,
+ const Hash& h = Hash{}, const KeyEqual& equal = KeyEqual{})
+ : WHash(h)
+ , WKeyEqual(equal) {
+ ROBIN_HOOD_TRACE(this);
+ insert(first, last);
+ }
+
+ unordered_map(std::initializer_list<value_type> initlist,
+ size_t ROBIN_HOOD_UNUSED(bucket_count) /*unused*/ = 0, const Hash& h = Hash{},
+ const KeyEqual& equal = KeyEqual{})
+ : WHash(h)
+ , WKeyEqual(equal) {
+ ROBIN_HOOD_TRACE(this);
+ insert(initlist.begin(), initlist.end());
+ }
+
+ unordered_map(unordered_map&& o) noexcept
+ : WHash(std::move(static_cast<WHash&>(o)))
+ , WKeyEqual(std::move(static_cast<WKeyEqual&>(o)))
+ , DataPool(std::move(static_cast<DataPool&>(o))) {
+ ROBIN_HOOD_TRACE(this);
+ if (o.mMask) {
+ mKeyVals = std::move(o.mKeyVals);
+ mInfo = std::move(o.mInfo);
+ mNumElements = std::move(o.mNumElements);
+ mMask = std::move(o.mMask);
+ mMaxNumElementsAllowed = std::move(o.mMaxNumElementsAllowed);
+ mInfoInc = std::move(o.mInfoInc);
+ mInfoHashShift = std::move(o.mInfoHashShift);
+ // set other's mask to 0 so its destructor won't do anything
+ o.init();
+ }
+ }
+
+ unordered_map& operator=(unordered_map&& o) noexcept {
+ ROBIN_HOOD_TRACE(this);
+ if (&o != this) {
+ if (o.mMask) {
+ // only move stuff if the other map actually has some data
+ destroy();
+ mKeyVals = std::move(o.mKeyVals);
+ mInfo = std::move(o.mInfo);
+ mNumElements = std::move(o.mNumElements);
+ mMask = std::move(o.mMask);
+ mMaxNumElementsAllowed = std::move(o.mMaxNumElementsAllowed);
+ mInfoInc = std::move(o.mInfoInc);
+ mInfoHashShift = std::move(o.mInfoHashShift);
+ WHash::operator=(std::move(static_cast<WHash&>(o)));
+ WKeyEqual::operator=(std::move(static_cast<WKeyEqual&>(o)));
+ DataPool::operator=(std::move(static_cast<DataPool&>(o)));
+
+ o.init();
+
+ } else {
+ // nothing in the other map => just clear us.
+ clear();
+ }
+ }
+ return *this;
+ }
+
+ unordered_map(const unordered_map& o)
+ : WHash(static_cast<const WHash&>(o))
+ , WKeyEqual(static_cast<const WKeyEqual&>(o))
+ , DataPool(static_cast<const DataPool&>(o)) {
+ ROBIN_HOOD_TRACE(this);
+ if (!o.empty()) {
+ // not empty: create an exact copy. it is also possible to just iterate through all
+ // elements and insert them, but copying is probably faster.
+
+ mKeyVals = static_cast<Node*>(
+ detail::assertNotNull<std::bad_alloc>(malloc(calcNumBytesTotal(o.mMask + 1))));
+ // no need for calloc because clonData does memcpy
+ mInfo = reinterpret_cast<uint8_t*>(mKeyVals + o.mMask + 1);
+ mNumElements = o.mNumElements;
+ mMask = o.mMask;
+ mMaxNumElementsAllowed = o.mMaxNumElementsAllowed;
+ mInfoInc = o.mInfoInc;
+ mInfoHashShift = o.mInfoHashShift;
+ cloneData(o);
+ }
+ }
+
+ // Creates a copy of the given map. Copy constructor of each entry is used.
+ unordered_map& operator=(unordered_map const& o) {
+ ROBIN_HOOD_TRACE(this);
+ if (&o == this) {
+ // prevent assigning of itself
+ return *this;
+ }
+
+ // we keep using the old allocator and not assign the new one, because we want to keep the
+ // memory available. when it is the same size.
+ if (o.empty()) {
+ if (0 == mMask) {
+ // nothing to do, we are empty too
+ return *this;
+ }
+
+ // not empty: destroy what we have there
+ // clear also resets mInfo to 0, that's sometimes not necessary.
+ destroy();
+ init();
+ WHash::operator=(static_cast<const WHash&>(o));
+ WKeyEqual::operator=(static_cast<const WKeyEqual&>(o));
+ DataPool::operator=(static_cast<DataPool const&>(o));
+
+ return *this;
+ }
+
+ // clean up old stuff
+ Destroyer<Self, IsFlatMap && std::is_trivially_destructible<Node>::value>{}.nodes(*this);
+
+ if (mMask != o.mMask) {
+ // no luck: we don't have the same array size allocated, so we need to realloc.
+ if (0 != mMask) {
+ // only deallocate if we actually have data!
+ free(mKeyVals);
+ }
+
+ mKeyVals = static_cast<Node*>(
+ detail::assertNotNull<std::bad_alloc>(malloc(calcNumBytesTotal(o.mMask + 1))));
+
+ // no need for calloc here because cloneData performs a memcpy.
+ mInfo = reinterpret_cast<uint8_t*>(mKeyVals + o.mMask + 1);
+ // sentinel is set in cloneData
+ }
+ WHash::operator=(static_cast<const WHash&>(o));
+ WKeyEqual::operator=(static_cast<const WKeyEqual&>(o));
+ DataPool::operator=(static_cast<DataPool const&>(o));
+ mNumElements = o.mNumElements;
+ mMask = o.mMask;
+ mMaxNumElementsAllowed = o.mMaxNumElementsAllowed;
+ mInfoInc = o.mInfoInc;
+ mInfoHashShift = o.mInfoHashShift;
+ cloneData(o);
+
+ return *this;
+ }
+
+ // Swaps everything between the two maps.
+ void swap(unordered_map& o) {
+ ROBIN_HOOD_TRACE(this);
+ using std::swap;
+ swap(o, *this);
+ }
+
+ // Clears all data, without resizing.
+ void clear() {
+ ROBIN_HOOD_TRACE(this);
+ if (empty()) {
+ // don't do anything! also important because we don't want to write to DummyInfoByte::b,
+ // even though we would just write 0 to it.
+ return;
+ }
+
+ Destroyer<Self, IsFlatMap && std::is_trivially_destructible<Node>::value>{}.nodes(*this);
+
+ // clear everything except the sentinel
+ // std::memset(mInfo, 0, sizeof(uint8_t) * (mMask + 1));
+ uint8_t const z = 0;
+ std::fill(mInfo, mInfo + (sizeof(uint8_t) * (mMask + 1)), z);
+
+ mInfoInc = InitialInfoInc;
+ mInfoHashShift = InitialInfoHashShift;
+ }
+
+ // Destroys the map and all it's contents.
+ ~unordered_map() {
+ ROBIN_HOOD_TRACE(this);
+ destroy();
+ }
+
+ // Checks if both maps contain the same entries. Order is irrelevant.
+ bool operator==(const unordered_map& other) const {
+ ROBIN_HOOD_TRACE(this);
+ if (other.size() != size()) {
+ return false;
+ }
+ for (auto const& otherEntry : other) {
+ auto const myIt = find(otherEntry.first);
+ if (myIt == end() || !(myIt->second == otherEntry.second)) {
+ return false;
+ }
+ }
+
+ return true;
+ }
+
+ bool operator!=(const unordered_map& other) const {
+ ROBIN_HOOD_TRACE(this);
+ return !operator==(other);
+ }
+
+ mapped_type& operator[](const key_type& key) {
+ ROBIN_HOOD_TRACE(this);
+ return doCreateByKey(key);
+ }
+
+ mapped_type& operator[](key_type&& key) {
+ ROBIN_HOOD_TRACE(this);
+ return doCreateByKey(std::move(key));
+ }
+
+ template <typename Iter>
+ void insert(Iter first, Iter last) {
+ for (; first != last; ++first) {
+ // value_type ctor needed because this might be called with std::pair's
+ insert(value_type(*first));
+ }
+ }
+
+ template <typename... Args>
+ std::pair<iterator, bool> emplace(Args&&... args) {
+ ROBIN_HOOD_TRACE(this);
+ Node n{*this, std::forward<Args>(args)...};
+ auto r = doInsert(std::move(n));
+ if (!r.second) {
+ // insertion not possible: destroy node
+ // NOLINTNEXTLINE(bugprone-use-after-move)
+ n.destroy(*this);
+ }
+ return r;
+ }
+
+ std::pair<iterator, bool> insert(const value_type& keyval) {
+ ROBIN_HOOD_TRACE(this);
+ return doInsert(keyval);
+ }
+
+ std::pair<iterator, bool> insert(value_type&& keyval) {
+ return doInsert(std::move(keyval));
+ }
+
+ // Returns 1 if key is found, 0 otherwise.
+ size_t count(const key_type& key) const { // NOLINT(modernize-use-nodiscard)
+ ROBIN_HOOD_TRACE(this);
+ auto kv = mKeyVals + findIdx(key);
+ if (kv != reinterpret_cast_no_cast_align_warning<Node*>(mInfo)) {
+ return 1;
+ }
+ return 0;
+ }
+
+ // Returns a reference to the value found for key.
+ // Throws std::out_of_range if element cannot be found
+ mapped_type& at(key_type const& key) {
+ ROBIN_HOOD_TRACE(this);
+ auto kv = mKeyVals + findIdx(key);
+ if (kv == reinterpret_cast_no_cast_align_warning<Node*>(mInfo)) {
+ doThrow<std::out_of_range>("key not found");
+ }
+ return kv->getSecond();
+ }
+
+ // Returns a reference to the value found for key.
+ // Throws std::out_of_range if element cannot be found
+ mapped_type const& at(key_type const& key) const { // NOLINT(modernize-use-nodiscard)
+ ROBIN_HOOD_TRACE(this);
+ auto kv = mKeyVals + findIdx(key);
+ if (kv == reinterpret_cast_no_cast_align_warning<Node*>(mInfo)) {
+ doThrow<std::out_of_range>("key not found");
+ }
+ return kv->getSecond();
+ }
+
+ const_iterator find(const key_type& key) const { // NOLINT(modernize-use-nodiscard)
+ ROBIN_HOOD_TRACE(this);
+ const size_t idx = findIdx(key);
+ return const_iterator{mKeyVals + idx, mInfo + idx};
+ }
+
+ template <typename OtherKey>
+ const_iterator find(const OtherKey& key, is_transparent_tag /*unused*/) const {
+ ROBIN_HOOD_TRACE(this);
+ const size_t idx = findIdx(key);
+ return const_iterator{mKeyVals + idx, mInfo + idx};
+ }
+
+ iterator find(const key_type& key) {
+ ROBIN_HOOD_TRACE(this);
+ const size_t idx = findIdx(key);
+ return iterator{mKeyVals + idx, mInfo + idx};
+ }
+
+ template <typename OtherKey>
+ iterator find(const OtherKey& key, is_transparent_tag /*unused*/) {
+ ROBIN_HOOD_TRACE(this);
+ const size_t idx = findIdx(key);
+ return iterator{mKeyVals + idx, mInfo + idx};
+ }
+
+ iterator begin() {
+ ROBIN_HOOD_TRACE(this);
+ if (empty()) {
+ return end();
+ }
+ return iterator(mKeyVals, mInfo, fast_forward_tag{});
+ }
+ const_iterator begin() const { // NOLINT(modernize-use-nodiscard)
+ ROBIN_HOOD_TRACE(this);
+ return cbegin();
+ }
+ const_iterator cbegin() const { // NOLINT(modernize-use-nodiscard)
+ ROBIN_HOOD_TRACE(this);
+ if (empty()) {
+ return cend();
+ }
+ return const_iterator(mKeyVals, mInfo, fast_forward_tag{});
+ }
+
+ iterator end() {
+ ROBIN_HOOD_TRACE(this);
+ // no need to supply valid info pointer: end() must not be dereferenced, and only node
+ // pointer is compared.
+ return iterator{reinterpret_cast_no_cast_align_warning<Node*>(mInfo), nullptr};
+ }
+ const_iterator end() const { // NOLINT(modernize-use-nodiscard)
+ ROBIN_HOOD_TRACE(this);
+ return cend();
+ }
+ const_iterator cend() const { // NOLINT(modernize-use-nodiscard)
+ ROBIN_HOOD_TRACE(this);
+ return const_iterator{reinterpret_cast_no_cast_align_warning<Node*>(mInfo), nullptr};
+ }
+
+ iterator erase(const_iterator pos) {
+ ROBIN_HOOD_TRACE(this);
+ // its safe to perform const cast here
+ // NOLINTNEXTLINE(cppcoreguidelines-pro-type-const-cast)
+ return erase(iterator{const_cast<Node*>(pos.mKeyVals), const_cast<uint8_t*>(pos.mInfo)});
+ }
+
+ // Erases element at pos, returns iterator to the next element.
+ iterator erase(iterator pos) {
+ ROBIN_HOOD_TRACE(this);
+ // we assume that pos always points to a valid entry, and not end().
+ auto const idx = static_cast<size_t>(pos.mKeyVals - mKeyVals);
+
+ shiftDown(idx);
+ --mNumElements;
+
+ if (*pos.mInfo) {
+ // we've backward shifted, return this again
+ return pos;
+ }
+
+ // no backward shift, return next element
+ return ++pos;
+ }
+
+ size_t erase(const key_type& key) {
+ ROBIN_HOOD_TRACE(this);
+ size_t idx;
+ InfoType info;
+ keyToIdx(key, &idx, &info);
+
+ // check while info matches with the source idx
+ do {
+ if (info == mInfo[idx] && WKeyEqual::operator()(key, mKeyVals[idx].getFirst())) {
+ shiftDown(idx);
+ --mNumElements;
+ return 1;
+ }
+ next(&info, &idx);
+ } while (info <= mInfo[idx]);
+
+ // nothing found to delete
+ return 0;
+ }
+
+ // reserves space for the specified number of elements. Makes sure the old data fits.
+ // exactly the same as reserve(c).
+ void rehash(size_t c) {
+ reserve(c);
+ }
+
+ // reserves space for the specified number of elements. Makes sure the old data fits.
+ // Exactly the same as resize(c). Use resize(0) to shrink to fit.
+ void reserve(size_t c) {
+ ROBIN_HOOD_TRACE(this);
+ auto const minElementsAllowed = (std::max)(c, mNumElements);
+ auto newSize = InitialNumElements;
+ while (calcMaxNumElementsAllowed(newSize) < minElementsAllowed && newSize != 0) {
+ newSize *= 2;
+ }
+ if (ROBIN_HOOD_UNLIKELY(newSize == 0)) {
+ throwOverflowError();
+ }
+
+ rehashPowerOfTwo(newSize);
+ }
+
+ size_type size() const noexcept { // NOLINT(modernize-use-nodiscard)
+ ROBIN_HOOD_TRACE(this);
+ return mNumElements;
+ }
+
+ size_type max_size() const noexcept { // NOLINT(modernize-use-nodiscard)
+ ROBIN_HOOD_TRACE(this);
+ return static_cast<size_type>(-1);
+ }
+
+ ROBIN_HOOD(NODISCARD) bool empty() const noexcept {
+ ROBIN_HOOD_TRACE(this);
+ return 0 == mNumElements;
+ }
+
+ float max_load_factor() const noexcept { // NOLINT(modernize-use-nodiscard)
+ ROBIN_HOOD_TRACE(this);
+ return MaxLoadFactor100 / 100.0F;
+ }
+
+ // Average number of elements per bucket. Since we allow only 1 per bucket
+ float load_factor() const noexcept { // NOLINT(modernize-use-nodiscard)
+ ROBIN_HOOD_TRACE(this);
+ return static_cast<float>(size()) / static_cast<float>(mMask + 1);
+ }
+
+ ROBIN_HOOD(NODISCARD) size_t mask() const noexcept {
+ ROBIN_HOOD_TRACE(this);
+ return mMask;
+ }
+
+ ROBIN_HOOD(NODISCARD) size_t calcMaxNumElementsAllowed(size_t maxElements) const noexcept {
+ if (ROBIN_HOOD_LIKELY(maxElements <= (std::numeric_limits<size_t>::max)() / 100)) {
+ return maxElements * MaxLoadFactor100 / 100;
+ }
+
+ // we might be a bit inprecise, but since maxElements is quite large that doesn't matter
+ return (maxElements / 100) * MaxLoadFactor100;
+ }
+
+ ROBIN_HOOD(NODISCARD) size_t calcNumBytesInfo(size_t numElements) const {
+ return numElements + sizeof(uint64_t);
+ }
+
+ // calculation ony allowed for 2^n values
+ ROBIN_HOOD(NODISCARD) size_t calcNumBytesTotal(size_t numElements) const {
+#if ROBIN_HOOD(BITNESS) == 64
+ return numElements * sizeof(Node) + calcNumBytesInfo(numElements);
+#else
+ // make sure we're doing 64bit operations, so we are at least safe against 32bit overflows.
+ auto const ne = static_cast<uint64_t>(numElements);
+ auto const s = static_cast<uint64_t>(sizeof(Node));
+ auto const infos = static_cast<uint64_t>(calcNumBytesInfo(numElements));
+
+ auto const total64 = ne * s + infos;
+ auto const total = static_cast<size_t>(total64);
+
+ if (ROBIN_HOOD_UNLIKELY(static_cast<uint64_t>(total) != total64)) {
+ throwOverflowError();
+ }
+ return total;
+#endif
+ }
+
+private:
+ // reserves space for at least the specified number of elements.
+ // only works if numBuckets if power of two
+ void rehashPowerOfTwo(size_t numBuckets) {
+ ROBIN_HOOD_TRACE(this);
+
+ Node* const oldKeyVals = mKeyVals;
+ uint8_t const* const oldInfo = mInfo;
+
+ const size_t oldMaxElements = mMask + 1;
+
+ // resize operation: move stuff
+ init_data(numBuckets);
+ if (oldMaxElements > 1) {
+ for (size_t i = 0; i < oldMaxElements; ++i) {
+ if (oldInfo[i] != 0) {
+ insert_move(std::move(oldKeyVals[i]));
+ // destroy the node but DON'T destroy the data.
+ oldKeyVals[i].~Node();
+ }
+ }
+
+ // don't destroy old data: put it into the pool instead
+ DataPool::addOrFree(oldKeyVals, calcNumBytesTotal(oldMaxElements));
+ }
+ }
+
+ ROBIN_HOOD(NOINLINE) void throwOverflowError() const {
+#if ROBIN_HOOD(HAS_EXCEPTIONS)
+ throw std::overflow_error("robin_hood::map overflow");
+#else
+ abort();
+#endif
+ }
+
+ void init_data(size_t max_elements) {
+ mNumElements = 0;
+ mMask = max_elements - 1;
+ mMaxNumElementsAllowed = calcMaxNumElementsAllowed(max_elements);
+
+ // calloc also zeroes everything
+ mKeyVals = reinterpret_cast<Node*>(
+ detail::assertNotNull<std::bad_alloc>(calloc(1, calcNumBytesTotal(max_elements))));
+ mInfo = reinterpret_cast<uint8_t*>(mKeyVals + max_elements);
+
+ // set sentinel
+ mInfo[max_elements] = 1;
+
+ mInfoInc = InitialInfoInc;
+ mInfoHashShift = InitialInfoHashShift;
+ }
+
+ template <typename Arg>
+ mapped_type& doCreateByKey(Arg&& key) {
+ while (true) {
+ size_t idx;
+ InfoType info;
+ keyToIdx(key, &idx, &info);
+ nextWhileLess(&info, &idx);
+
+ // while we potentially have a match. Can't do a do-while here because when mInfo is 0
+ // we don't want to skip forward
+ while (info == mInfo[idx]) {
+ if (WKeyEqual::operator()(key, mKeyVals[idx].getFirst())) {
+ // key already exists, do not insert.
+ return mKeyVals[idx].getSecond();
+ }
+ next(&info, &idx);
+ }
+
+ // unlikely that this evaluates to true
+ if (ROBIN_HOOD_UNLIKELY(mNumElements >= mMaxNumElementsAllowed)) {
+ increase_size();
+ continue;
+ }
+
+ // key not found, so we are now exactly where we want to insert it.
+ auto const insertion_idx = idx;
+ auto const insertion_info = info;
+ if (ROBIN_HOOD_UNLIKELY(insertion_info + mInfoInc > 0xFF)) {
+ mMaxNumElementsAllowed = 0;
+ }
+
+ // find an empty spot
+ while (0 != mInfo[idx]) {
+ next(&info, &idx);
+ }
+
+ auto& l = mKeyVals[insertion_idx];
+ if (idx == insertion_idx) {
+ // put at empty spot. This forwards all arguments into the node where the object is
+ // constructed exactly where it is needed.
+ ::new (static_cast<void*>(&l))
+ Node(*this, std::piecewise_construct,
+ std::forward_as_tuple(std::forward<Arg>(key)), std::forward_as_tuple());
+ } else {
+ shiftUp(idx, insertion_idx);
+ l = Node(*this, std::piecewise_construct,
+ std::forward_as_tuple(std::forward<Arg>(key)), std::forward_as_tuple());
+ }
+
+ // mKeyVals[idx].getFirst() = std::move(key);
+ mInfo[insertion_idx] = static_cast<uint8_t>(insertion_info);
+
+ ++mNumElements;
+ return mKeyVals[insertion_idx].getSecond();
+ }
+ }
+
+ // This is exactly the same code as operator[], except for the return values
+ template <typename Arg>
+ std::pair<iterator, bool> doInsert(Arg&& keyval) {
+ while (true) {
+ size_t idx;
+ InfoType info;
+ keyToIdx(keyval.getFirst(), &idx, &info);
+ nextWhileLess(&info, &idx);
+
+ // while we potentially have a match
+ while (info == mInfo[idx]) {
+ if (WKeyEqual::operator()(keyval.getFirst(), mKeyVals[idx].getFirst())) {
+ // key already exists, do NOT insert.
+ // see http://en.cppreference.com/w/cpp/container/unordered_map/insert
+ return std::make_pair<iterator, bool>(iterator(mKeyVals + idx, mInfo + idx),
+ false);
+ }
+ next(&info, &idx);
+ }
+
+ // unlikely that this evaluates to true
+ if (ROBIN_HOOD_UNLIKELY(mNumElements >= mMaxNumElementsAllowed)) {
+ increase_size();
+ continue;
+ }
+
+ // key not found, so we are now exactly where we want to insert it.
+ auto const insertion_idx = idx;
+ auto const insertion_info = info;
+ if (ROBIN_HOOD_UNLIKELY(insertion_info + mInfoInc > 0xFF)) {
+ mMaxNumElementsAllowed = 0;
+ }
+
+ // find an empty spot
+ while (0 != mInfo[idx]) {
+ next(&info, &idx);
+ }
+
+ auto& l = mKeyVals[insertion_idx];
+ if (idx == insertion_idx) {
+ ::new (static_cast<void*>(&l)) Node(*this, std::forward<Arg>(keyval));
+ } else {
+ shiftUp(idx, insertion_idx);
+ l = Node(*this, std::forward<Arg>(keyval));
+ }
+
+ // put at empty spot
+ mInfo[insertion_idx] = static_cast<uint8_t>(insertion_info);
+
+ ++mNumElements;
+ return std::make_pair(iterator(mKeyVals + insertion_idx, mInfo + insertion_idx), true);
+ }
+ }
+
+ bool try_increase_info() {
+ ROBIN_HOOD_LOG("mInfoInc=" << mInfoInc << ", numElements=" << mNumElements
+ << ", maxNumElementsAllowed="
+ << calcMaxNumElementsAllowed(mMask + 1));
+ if (mInfoInc <= 2) {
+ // need to be > 2 so that shift works (otherwise undefined behavior!)
+ return false;
+ }
+ // we got space left, try to make info smaller
+ mInfoInc = static_cast<uint8_t>(mInfoInc >> 1U);
+
+ // remove one bit of the hash, leaving more space for the distance info.
+ // This is extremely fast because we can operate on 8 bytes at once.
+ ++mInfoHashShift;
+ auto const data = reinterpret_cast_no_cast_align_warning<uint64_t*>(mInfo);
+ auto const numEntries = (mMask + 1) / 8;
+
+ for (size_t i = 0; i < numEntries; ++i) {
+ data[i] = (data[i] >> 1U) & UINT64_C(0x7f7f7f7f7f7f7f7f);
+ }
+ mMaxNumElementsAllowed = calcMaxNumElementsAllowed(mMask + 1);
+ return true;
+ }
+
+ void increase_size() {
+ // nothing allocated yet? just allocate InitialNumElements
+ if (0 == mMask) {
+ init_data(InitialNumElements);
+ return;
+ }
+
+ auto const maxNumElementsAllowed = calcMaxNumElementsAllowed(mMask + 1);
+ if (mNumElements < maxNumElementsAllowed && try_increase_info()) {
+ return;
+ }
+
+ ROBIN_HOOD_LOG("mNumElements=" << mNumElements << ", maxNumElementsAllowed="
+ << maxNumElementsAllowed << ", load="
+ << (static_cast<double>(mNumElements) * 100.0 /
+ (static_cast<double>(mMask) + 1)));
+ // it seems we have a really bad hash function! don't try to resize again
+ if (mNumElements * 2 < calcMaxNumElementsAllowed(mMask + 1)) {
+ throwOverflowError();
+ }
+
+ rehashPowerOfTwo((mMask + 1) * 2);
+ }
+
+ void destroy() {
+ if (0 == mMask) {
+ // don't deallocate!
+ return;
+ }
+
+ Destroyer<Self, IsFlatMap && std::is_trivially_destructible<Node>::value>{}
+ .nodesDoNotDeallocate(*this);
+ free(mKeyVals);
+ }
+
+ void init() noexcept {
+ mKeyVals = reinterpret_cast<Node*>(&mMask);
+ mInfo = reinterpret_cast<uint8_t*>(&mMask);
+ mNumElements = 0;
+ mMask = 0;
+ mMaxNumElementsAllowed = 0;
+ mInfoInc = InitialInfoInc;
+ mInfoHashShift = InitialInfoHashShift;
+ }
+
+ // members are sorted so no padding occurs
+ Node* mKeyVals = reinterpret_cast<Node*>(&mMask); // 8 byte 8
+ uint8_t* mInfo = reinterpret_cast<uint8_t*>(&mMask); // 8 byte 16
+ size_t mNumElements = 0; // 8 byte 24
+ size_t mMask = 0; // 8 byte 32
+ size_t mMaxNumElementsAllowed = 0; // 8 byte 40
+ InfoType mInfoInc = InitialInfoInc; // 4 byte 44
+ InfoType mInfoHashShift = InitialInfoHashShift; // 4 byte 48
+ // 16 byte 56 if NodeAllocator
+};
+
+} // namespace detail
+
+template <typename Key, typename T, typename Hash = hash<Key>,
+ typename KeyEqual = std::equal_to<Key>, size_t MaxLoadFactor100 = 80>
+using unordered_flat_map = detail::unordered_map<true, MaxLoadFactor100, Key, T, Hash, KeyEqual>;
+
+template <typename Key, typename T, typename Hash = hash<Key>,
+ typename KeyEqual = std::equal_to<Key>, size_t MaxLoadFactor100 = 80>
+using unordered_node_map = detail::unordered_map<false, MaxLoadFactor100, Key, T, Hash, KeyEqual>;
+
+template <typename Key, typename T, typename Hash = hash<Key>,
+ typename KeyEqual = std::equal_to<Key>, size_t MaxLoadFactor100 = 80>
+using unordered_map =
+ detail::unordered_map<sizeof(robin_hood::pair<Key, T>) <= sizeof(size_t) * 6 &&
+ std::is_nothrow_move_constructible<robin_hood::pair<Key, T>>::value &&
+ std::is_nothrow_move_assignable<robin_hood::pair<Key, T>>::value,
+ MaxLoadFactor100, Key, T, Hash, KeyEqual>;
+
+} // namespace robin_hood
+
+#endif
diff --git a/modelling/tests/test_loop_candidates.cc b/modelling/tests/test_loop_candidates.cc
index f82acf29f4c931c589960898fa936d53c5fdf290..844bdabd00fb9a387f889823af965ea52f4fccf2 100644
--- a/modelling/tests/test_loop_candidates.cc
+++ b/modelling/tests/test_loop_candidates.cc
@@ -19,7 +19,6 @@
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
#include <ost/conop/heuristic.hh>
#include <ost/io/mol/pdb_reader.hh>
diff --git a/modelling/tests/test_loop_closing.cc b/modelling/tests/test_loop_closing.cc
index 7d1c163f405f0a512ced58284e38f92ba90858d5..588bbeeb2d64100b3f700f2d81315922cd158984 100644
--- a/modelling/tests/test_loop_closing.cc
+++ b/modelling/tests/test_loop_closing.cc
@@ -23,7 +23,6 @@
#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>
diff --git a/modelling/tests/test_pipeline.py b/modelling/tests/test_pipeline.py
index 90471ecb22a126438e90936dbe154d12f3466af8..3a08f74b40498939972ec30162cfa64eebb9dcc3 100644
--- a/modelling/tests/test_pipeline.py
+++ b/modelling/tests/test_pipeline.py
@@ -22,6 +22,7 @@ import unittest
import math
import ost
from ost import io, mol, seq, settings
+from ost.mol import mm
from promod3 import loop, modelling, core
################################################################
@@ -337,18 +338,27 @@ class PipelineTests(unittest.TestCase):
self.assertTrue(issue.is_major())
self.assertEqual(len(issue.residue_list), 0)
# catch atoms almost on top
- mhandle = self.getMockModel(io.LoadPDB('data/gly_almost_on_top.pdb'))
- log.messages['ERROR'] = list()
- modelling.MinimizeModelEnergy(mhandle)
- self.assertEqual(len(log.messages['ERROR']), 1)
- self.assertEqual(len(mhandle.modelling_issues), 1)
- exp_msg = "OpenMM could not minimize energy! Usually this is caused "\
- "by atoms which are almost on top of each other."
- self.assertTrue(log.messages['ERROR'][0].startswith(exp_msg))
- issue = mhandle.modelling_issues[0]
- self.assertTrue(issue.text.startswith(exp_msg))
- self.assertTrue(issue.is_major())
- self.assertEqual(len(issue.residue_list), 0)
+ # -> this is known to only fail with the CPU platform
+ # -> tested with OpenMM 7.1.1 (unknown for others)
+ mm_settings = mm.Settings()
+ mm_settings.platform = mm.Platform.CPU
+ if mm.Simulation.IsPlatformAvailable(mm_settings):
+ model = io.LoadPDB('data/gly_almost_on_top.pdb')
+ mhandle = self.getMockModel(model)
+ log.messages['ERROR'] = list()
+ modelling.MinimizeModelEnergy(mhandle)
+ self.assertEqual(len(log.messages['ERROR']), 1)
+ self.assertEqual(len(mhandle.modelling_issues), 1)
+ exp_msg = "OpenMM could not minimize energy! Usually this is "\
+ "caused by atoms which are almost on top of each other."
+ self.assertTrue(log.messages['ERROR'][0].startswith(exp_msg))
+ issue = mhandle.modelling_issues[0]
+ self.assertTrue(issue.text.startswith(exp_msg))
+ self.assertTrue(issue.is_major())
+ self.assertEqual(len(issue.residue_list), 0)
+ else:
+ print "OpenMM CPU platform not available. " \
+ "Skipping almost_on_top check."
def testBuildFromRawModel(self):
'''Check that BuildFromRawModel works.'''
diff --git a/modelling/tests/test_sidechain_reconstructor.cc b/modelling/tests/test_sidechain_reconstructor.cc
index 7e730c697d6401bc8170bac20f3bdea6f33cd573..7a88f281dd8a78cb0ea734f0b1cdc61629f84215 100644
--- a/modelling/tests/test_sidechain_reconstructor.cc
+++ b/modelling/tests/test_sidechain_reconstructor.cc
@@ -19,7 +19,6 @@
#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>
diff --git a/modelling/tests/tests.cc b/modelling/tests/tests.cc
index b497ab9838fe7aeeb97fcc164d0fa443164c0a06..01f5d05d7eb7bb18857f2811d28c2c2166051f84 100644
--- a/modelling/tests/tests.cc
+++ b/modelling/tests/tests.cc
@@ -16,6 +16,4 @@
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_modelling
-#define BOOST_AUTO_TEST_MAIN
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
diff --git a/scoring/tests/test_all_atom_scorer.cc b/scoring/tests/test_all_atom_scorer.cc
index cf5ac6c945ce52b05d5bd32dde2fef8865c4eb27..d845b453f96a87f2e98a39a9eedc9d6b67a1c97a 100644
--- a/scoring/tests/test_all_atom_scorer.cc
+++ b/scoring/tests/test_all_atom_scorer.cc
@@ -23,7 +23,6 @@
#include <promod3/scoring/all_atom_overall_scorer.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>
diff --git a/scoring/tests/test_backbone_score_base.cc b/scoring/tests/test_backbone_score_base.cc
index b9e5e1d2eb3138e1ff6d4c035270f56a61931867..73bf2fc6265856c401b4081a455dc5cf1a8a1395 100644
--- a/scoring/tests/test_backbone_score_base.cc
+++ b/scoring/tests/test_backbone_score_base.cc
@@ -18,7 +18,6 @@
#include <promod3/scoring/backbone_score_base.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>
diff --git a/scoring/tests/test_backbone_scorer.cc b/scoring/tests/test_backbone_scorer.cc
index fd8f1897d7e409dfce1222f1e157429cb357db08..f4bab973ec1507fd43f72f1cdd4531fedb197a7f 100644
--- a/scoring/tests/test_backbone_scorer.cc
+++ b/scoring/tests/test_backbone_scorer.cc
@@ -23,7 +23,6 @@
#include <promod3/scoring/density_score.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>
diff --git a/scoring/tests/tests.cc b/scoring/tests/tests.cc
index afe7f82308e8672d821fb286ec92f9c02481bc35..ae4529507acd29c0669c89ecd648701d85a63eb5 100644
--- a/scoring/tests/tests.cc
+++ b/scoring/tests/tests.cc
@@ -16,6 +16,4 @@
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_scoring
-#define BOOST_AUTO_TEST_MAIN
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
diff --git a/sidechain/doc/CMakeLists.txt b/sidechain/doc/CMakeLists.txt
index 4c1d117225741bb404070a93a0bd5be100acf99f..2aa7692ed1939f0fffb5d4512c18457eb3e472fd 100644
--- a/sidechain/doc/CMakeLists.txt
+++ b/sidechain/doc/CMakeLists.txt
@@ -1,10 +1,9 @@
set(SIDECHAIN_RST
index.rst
rotamer.rst
-rotamer_id.rst
frame.rst
-rotamer_lib.rst
rotamer_constructor.rst
+rotamer_lib.rst
graph.rst
disulfid.rst
loading.rst
diff --git a/sidechain/doc/frame.rst b/sidechain/doc/frame.rst
index d8365f4a5316d2efebaaaafb50a87238b1b3ac2d..94a3150d0361fa6fe2b468b35752f0f19d57cebb 100644
--- a/sidechain/doc/frame.rst
+++ b/sidechain/doc/frame.rst
@@ -14,7 +14,7 @@
.. limitations under the License.
-Frame
+Frame - The Rigid Part
================================================================================
.. currentmodule:: promod3.sidechain
diff --git a/sidechain/doc/index.rst b/sidechain/doc/index.rst
index aeac7212ce7a9232b81c95d2178cb32d07ff6595..192257b499d3826c3ed5891cadb39ede1f7a7291 100644
--- a/sidechain/doc/index.rst
+++ b/sidechain/doc/index.rst
@@ -42,11 +42,10 @@ Contents:
.. toctree::
:maxdepth: 2
- rotamer_id
rotamer
frame
- rotamer_lib
rotamer_constructor
+ rotamer_lib
graph
disulfid
loading
diff --git a/sidechain/doc/rotamer.rst b/sidechain/doc/rotamer.rst
index d3ae44ebe66b3f2139cd7a5ba04e29de80efc9ac..56b95301448e5a955ef38ee0105c9d60b9de291f 100644
--- a/sidechain/doc/rotamer.rst
+++ b/sidechain/doc/rotamer.rst
@@ -14,22 +14,96 @@
.. limitations under the License.
-Rotamers
+Representing Sidechains - Rotamers & Co.
================================================================================
.. currentmodule:: promod3.sidechain
-A rotamer represents an amino acid sidechain and is basically a set of
-:class:`Particle` objects. There exist two types. The :class:`RRMRotamer` and
-:class:`FRMRotamer`.
-To gather all possible rotamers for one particular sidechain position,
+A rotamer represents an amino acid sidechain identified by a :class:`RotamerID`
+and is a set of :class:`Particle` objects.
+Two types of rotamers exist. The :class:`RRMRotamer` and :class:`FRMRotamer`.
+To gather all possible rotamers for one location,
ProMod3 offers the :class:`RRMRotamerGroup` and :class:`FRMRotamerGroup`.
-Pairwise interactions between particles give raise to pairwise energies between
-rotamers. Nevertheless, the energy calculation itself happens on the level
-of RotamerGroups and is mostly hidden away in the construction of the
-the :class:`RotamerGraph`. If you're too lazy to build up your rotamers
-by hand, you might be interested in the :class:`RotamerConstructor`.
+All parts of the structure that are kept rigid can be represented by
+a :class:`Frame` object.
+
+RotamerID
+--------------------------------------------------------------------------------
+
+The sidechain module has its own definition of amino acids to satisfy custom
+requirements for the implemented sidechain construction algorithms.
+As an example there are histidine in two possible protonation states,
+that affect the hbond term or different versions of proline/cysteine.
+
+.. class:: RotamerID
+
+ Enumerates the amino acids. Possible values:
+
+ .. hlist::
+ :columns: 2
+
+ * ARG - Arginine
+ * ASN - Asparagine
+ * ASP - Aspartate
+ * GLN - Glutamine
+ * GLU - Glutamate
+ * LYS - Lysine
+ * SER - Serine
+ * CYS - Cystein
+ * CYH - "free" Cystein
+ * CYD - disulfid bonded Cystein
+ * MET - Methionine
+ * TRP - Tryptophane
+ * TYR - Tyrosine
+ * THR - Threonine
+ * VAL - Valine
+ * ILE - Isoleucine
+ * LEU - Leucine
+ * PRO - Proline
+ * CPR - cis-Proline
+ * TPR - trans-Proline
+ * HIS - Histidine
+ * HSD - d-protonated Histidine
+ * HSE - e-protonated Histidine
+ * PHE - Phenylalanine
+ * GLY - Glycine
+ * ALA - Alanine
+ * XXX - Invalid
+
+ The RotamerID enum can be accessed either directly as ``promod3.sidechain.ARG``
+ or as ``promod3.sidechain.RotamerID.ARG``.
+
+
+How can I get an ID?
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The RotamerID enum can directly be accessed from Python. Two convenient
+functions exist to get RotamerIDs from the :class:`ost.conop.AminoAcid` enum
+or from amino acid three letter codes.
+
+.. method:: TLCToRotID(tlc)
+
+ Directly translates the three letter code into a RotamerID. Following
+ exactly the naming convention defined above.
+
+ :param tlc: Three letter code of amino acid
+ :type tlc: :class:`str`
+
+ :returns: :class:`RotamerID`, XXX if **tlc** cannot be recoginzed.
+
+
+.. method:: AAToRotID(aa)
+
+ Directly translates **aa** 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 :class:`ost.conop.AminoAcid`
+
+ :param aa: AA enum of amino acid
+ :type aa: :class:`ost.conop.AminoAcid`
+
+ :returns: :class:`RotamerID`, XXX if **aa** is invalid.
The Smallest Building Block - The Particle
@@ -44,7 +118,9 @@ function.
The available scoring functions between :class:`Particle` objects
- * SCWRL4
+ * SCWRL4 - :ref:`scwrl4-scoring-function`
+ * SCWRL3 - :ref:`scwrl3-scoring-function`
+ * VINA - :ref:`vina-scoring-function`
.. class:: Particle
@@ -93,13 +169,19 @@ function.
+.. _scwrl4-scoring-function:
The SCWRL4 scoring function
---------------------------------------------------------------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The SCWRL4 scoring function combines a Lennard-Jones style term with
+a hydrogen bond term. Details can be found in the relevant publication
+[krivov2009]_.
.. class:: SCWRL4ParticleType
The SCWRL4 energy function differentiates between following particle types
+ that define the behaviour of the Lennard-Jones style term:
* HParticle - represents hydrogen
* CParticle - default representation of a carbon
@@ -123,9 +205,17 @@ The SCWRL4 scoring function
:param charge: The charge of the particle, relevant for the hydrogen
bond term
:param lone_pairs: Direction of all possible lone pairs of the particle,
- relevant for the hydrogen bond term
+ relevant for the hydrogen bond term. If set, the
+ particle is a potential hydrogen bond acceptor.
+ An example would be the Serine OG atom, where you can
+ represent the two lone pairs with vectors pointing
+ from the OG position towards the lone pair centers.
:param polar_direction: The polar direction of the particle,
- relevant for the hdrogen bond term
+ relevant for the hydrogen bond term. If set, the
+ particle is a potential hydrogen bond donor. An
+ example would be the Serine HG hydrogen. The
+ *polar_direction* would be a vector
+ estimated as follows: hg_pos-og_pos.
:type name: :class:`str`
:type particle_type: :class:`SCWRL4ParticleType`
@@ -135,6 +225,82 @@ The SCWRL4 scoring function
:type polar_direction: :class:`ost.geom.Vec3`
+.. _scwrl3-scoring-function:
+
+The SCWRL3 scoring function
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The SCWRL3 scoring function implements a simple repulsion term that depends on
+the hard-sphere radius of the involved particles.
+Details can be found in the relevant publication [canutescu2003]_.
+
+.. method:: CreateSCWRL3Particle(name, radius, pos)
+
+ Creates and returns a :class:`Particle` that can evaluate the SCWRL3 scoring
+ function
+
+ :param name: The name of the particle
+ :param radius: The hard-sphere radius of the particle, relevant for the
+ repulsion term.
+ :param pos: The position of the particle
+
+ :type name: :class:`str`
+ :type radius: :class:`float`
+ :type pos: :class:`ost.geom.Vec3`
+
+
+.. _vina-scoring-function:
+
+The VINA scoring function
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The VINA scoring function is a combination of scores that are named
+gaussian1, gaussian2, repulsion, hydrophobic and hbond in the Autodock Vina
+software [trott2010]_. VINA only evaluates heavy atoms. Gaussian1, gaussian2
+and repulsion are evaluated for all pairs of particles. Hydrophobic is only
+evaluated between C_VINAParticle :class:`VINAParticleType` and hbond is
+evaluated between hydrogen bond donor/acceptor pairs. While SCWRL3 and SCWRL4
+are intended to evaluate sidechain-sidechain interactions in proteins,
+VINA is mainly targeted at interactions between sidechains and ligands.
+
+The VINA scoring function differentiates between the following particle types:
+
+.. class:: VINAParticleType
+
+ * O_D_VINAParticle - Oxygen that can be a hydrogen bond donor
+ * N_D_VINAParticle - Nitrogen that can be a hydrogen bond donor
+ * O_A_VINAParticle - Oxygen that can be a hydrogen bond acceptor
+ * N_A_VINAParticle - Nitrogen that can be a hydrogen bond acceptor
+ * O_AD_VINAParticle - Oxygen that can be a hydrogen bond donor and acceptor
+ * N_AD_VINAParticle - Nitrogen that can be a hydrogen bond donor and acceptor
+ * O_VINAParticle - Oxygen
+ * N_VINAParticle - Nitrogen
+ * S_VINAParticle - Sulfur
+ * P_VINAParticle - Phosphorus
+ * C_P_VINAParticle - Polar carbon that is covalently bound to a charged atom
+ * C_VINAParticle - Hydrophobic carbon that is only bound to other carbons or hydrogens
+ * F_VINAParticle - Fluorine
+ * Cl_VINAParticle - Chlorine
+ * Br_VINAParticle - Bromine
+ * I_VINAParticle - Iodine
+ * M_VINAParticle - Metals
+ * INVALID_VINAParticle - Invalid particle...
+
+
+.. method:: CreateVINAParticle(name, particle_type, pos)
+
+ Creates and returns a :class:`Particle` that can evaluate the VINA scoring
+ function
+
+ :param name: The name of the particle
+ :param radius: The type of the particle
+ :param pos: The position of the particle
+
+ :type name: :class:`str`
+ :type radius: :class:`VINAParticleType`
+ :type pos: :class:`ost.geom.Vec3`
+
+
Rotamers
--------------------------------------------------------------------------------
@@ -692,3 +858,4 @@ Rotamer Groups
Searches rotamer with lowest self energy *l_e* and deletes all
rotamers with *self_energy* > *l_e* + *thresh*
+
diff --git a/sidechain/doc/rotamer_constructor.rst b/sidechain/doc/rotamer_constructor.rst
index 3a297d5d0846dd0808cad22419dad15add0bf11b..c8cca8deb12f3b56c889c32e9c9bcc954d38599f 100644
--- a/sidechain/doc/rotamer_constructor.rst
+++ b/sidechain/doc/rotamer_constructor.rst
@@ -19,18 +19,18 @@ Rotamer Constructor
.. currentmodule:: promod3.sidechain
-Instead of creating rotamers by yourself, you can simply use the convenient
-functionality provided by ProMod3.
+Instead of creating rotamers or frame residues by yourself, you can use the
+convenient functionality provided by ProMod3.
-Constructing Rotamers and Frame Residues
+The RotamerConstructor Baseclass
--------------------------------------------------------------------------------
.. class:: RotamerConstructor
Abstract base class that cannot be initialized from Python. It builds
- an interface implemented by energy function specific constructors
+ an interface implemented by scoring function specific constructors
(e.g. :class:`SCWRL4RotamerConstructor`).
.. method:: ConstructRRMRotamerGroup(res, id, residue_index, rot_lib,\
@@ -213,6 +213,10 @@ Constructing Rotamers and Frame Residues
+Scoring Function Specific RotamerConstructors
+--------------------------------------------------------------------------------
+
+
.. class:: SCWRL4RotamerConstructor(cb_in_sidechain)
This object implements the full interface defined in
@@ -306,3 +310,180 @@ Constructing Rotamers and Frame Residues
:type psi: :class:`float`
:type n_ter: :class:`bool`
:type c_ter: :class:`bool`
+
+
+
+
+.. class:: SCWRL3RotamerConstructor(cb_in_sidechain)
+
+ This object implements the full interface defined in
+ :class:`RotamerConstructor` and constructs rotamers and frame residues that
+ are parametrized according to the SCWRL3 method. They contain only heavy atoms.
+
+ :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:: AssignInternalEnergies(rot_group, id, residue_index, \
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False])
+
+ Overrides the method defined in :class:`RotamerConstructor`.
+ Takes the rotamer group and assigns every single rotamer its internal
+ energy based on the probabilistic approach used by SCWRL3.
+ => -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
+ rotamer specific and max_p is the maximum probablity of any of the rotamers
+ in **rot_group**. If you construct a rotamer group by the
+ ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
+ is already called at construction and the energies are properly assigned.
+
+ :param rot_group: containing all rotamers for which internal energies have
+ to be assigned
+ :param id: Identifies the sidechain
+ :param residue_index: The index of the residue which is represented by
+ *rot_group*
+ :param phi: The dihedral angle of the current residue
+ :param psi: The dihedral angle of the current residue
+ :param n_ter: Whether the residue is n-terminal
+ :param c_ter: Whether the residue is c-terminal
+
+ :type rot_group: :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
+ :type id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+ :type n_ter: :class:`bool`
+ :type c_ter: :class:`bool`
+
+
+.. class:: VINARotamerConstructor(cb_in_sidechain)
+
+ This object implements the full interface defined in
+ :class:`RotamerConstructor` and constructs rotamers and frame residues that
+ are parametrized according to the VINA method. They contain only heavy atoms.
+
+ :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:: AssignInternalEnergies(rot_group, id, residue_index, \
+ [phi = -1.0472, psi = -0.7854, \
+ n_ter = False, c_ter = False])
+
+ Overrides the method defined in :class:`RotamerConstructor`.
+ Takes the rotamer group and assigns every single rotamer its internal
+ energy based on the probabilistic approach used by SCWRL3/SCWRL4.
+ => -internal_e_prefac*log(p/max_p), where internal_e_prefac and p are
+ rotamer specific and max_p is the maximum probablity of any of the rotamers
+ in **rot_group**. If you construct a rotamer group by the
+ ConstructRRMRotamerGroup/ConstructFRMRotamerGroup functions, this function
+ is already called at construction and the energies are properly assigned.
+
+ :param rot_group: containing all rotamers for which internal energies have
+ to be assigned
+ :param id: Identifies the sidechain
+ :param residue_index: The index of the residue which is represented by
+ *rot_group*
+ :param phi: The dihedral angle of the current residue
+ :param psi: The dihedral angle of the current residue
+ :param n_ter: Whether the residue is n-terminal
+ :param c_ter: Whether the residue is c-terminal
+
+ :type rot_group: :class:`RRMRotamerGroup` / :class:`FRMRotamerGroup`
+ :type id: :class:`RotamerID`
+ :type residue_index: :class:`int`
+ :type phi: :class:`float`
+ :type psi: :class:`float`
+ :type n_ter: :class:`bool`
+ :type c_ter: :class:`bool`
+
+
+ .. method:: ConstructFrameResidueHeuristic(res, res_idx)
+
+ Constructs a :class:`FrameResidue` from a :class:`ost.mol.ResidueHandle` using
+ a heuristic treatment of the atoms. It is important that the residue has
+ proper bonds assigned, as they influence the atom typing procedure.
+ Furthermore, you need hydrogens to automatically estimate the correct
+ atom type for oxygens and nitrogens (hydrogen bond donor/acceptor).
+ Alternatively you can assign generic properties to oxygens and nitrogens
+ to circumvent the requirement of hydrogens. This is further described for
+ the case of oxygen.
+
+ * Carbon is assigned C_VINAParticle :class:`VINAParticleType` if its only
+ bound to other carbons or hydrogens (and deuterium). All other carbons are
+ assigned C_P_VINAParticle :class:`VINAParticleType`.
+ * In case of oxygen, the heuristic first checks for set generic properties.
+ If the atom has the bool properties "is_hbond_acceptor" AND
+ "is_hbond_donor" set, it decides between the according oxygen types
+ in :class:`VINAParticleType`. If the generic properties are not set,
+ every oxygen is assumed to be an hbond acceptor. But only an hbond donor
+ if its bound to a hydrogen (or deuterium). You can set the generic
+ properties for an :class:`ost.mol.AtomHandle` by calling
+ at.SetBoolProp("is_hbond_donor", False) and
+ at.SetBoolProp("is_hbond_acceptor", True). An oxygen with those
+ generic properties is assigned O_A_VINAParticle :class:`VINAParticleType`.
+ * In case of nitrogen, the heuristic again first checks for set generic
+ properties.
+ If the atom has the bool properties "is_hbond_acceptor" AND
+ "is_hbond_donor" set, it decides between the according nitrogen types
+ in :class:`VINAParticleType`. If not, nitrogen is expected to be an
+ hbond donor if it is bound to a hydrogen (or deuterium) and
+ an hbond acceptor if it is bound to less than 3 other atoms (sounds
+ horrible but works surprisingly well).
+ * Atoms of elements ["MG", "MN", "ZN", "CA", "FE"] are assigned
+ M_VINAParticle :class:`VINAParticleType`.
+ * Atoms of elements ["S", "P", "F", "CL", "BR", "I"] are assigned their
+ corresponding :class:`VINAParticleType`.
+ * All other atoms are neglected and not added to the returned
+ :class:`FrameResidue`.
+
+ :param res: Residue from which to create the
+ :class:`FrameResidue`
+ :param res_idx: Index that is set in :class:`FrameResidue`
+ :type res: :class:`ost.mol.ResidueHandle`
+ :type res_idx: :class:`int`
+ :rtype: :class:`FrameResidue`
+
+
+ .. method:: ConstructRRMRotamerHeuristic(res)
+
+ Construct a :class:`RRMRotamer` with the atom typing heuristic
+ as in the :meth:`ConstructFrameResidueHeuristic` method.
+
+ :param res: Residue from which to create the
+ :class:`RRMRotamer`
+ :type res: :class:`ost.mol.ResidueHandle`
+ :rtype: :class:`RRMRotamer`
+
+
+ .. method:: ConstructFRMRotamerHeuristic(res)
+
+ Construct a :class:`FRMRotamer` with the atom typing heuristic
+ as in the :meth:`ConstructFrameResidueHeuristic` method. The
+ constructed :class:`FRMRotamer` only contains one subrotamer that
+ contains the atoms from *residue*.
+
+ :param res: Residue from which to create the
+ :class:`FRMRotamer`
+ :type res: :class:`ost.mol.ResidueHandle`
+ :rtype: :class:`FRMRotamer`
diff --git a/sidechain/doc/rotamer_id.rst b/sidechain/doc/rotamer_id.rst
deleted file mode 100644
index 746a51641352c7295152567a742eda8befedc803..0000000000000000000000000000000000000000
--- a/sidechain/doc/rotamer_id.rst
+++ /dev/null
@@ -1,108 +0,0 @@
-.. Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
-.. Biozentrum - University of Basel
-..
-.. Licensed under the Apache License, Version 2.0 (the "License");
-.. you may not use this file except in compliance with the License.
-.. You may obtain a copy of the License at
-..
-.. http://www.apache.org/licenses/LICENSE-2.0
-..
-.. Unless required by applicable law or agreed to in writing, software
-.. distributed under the License is distributed on an "AS IS" BASIS,
-.. WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-.. See the License for the specific language governing permissions and
-.. limitations under the License.
-
-
-RotamerID
-================================================================================
-
-.. currentmodule:: promod3.sidechain
-
-The sidechain module has its own definition of amino acids to satisfy custom
-requirements for the implemented sidechain construction algorithms.
-As an example there are histidine in two possible protonation states,
-that affect the hbond term or different versions of proline/cysteine.
-
-
-The RotamerID
---------------------------------------------------------------------------------
-
-.. class:: RotamerID
-
- Enumerates the amino acids. Possible values:
-
- .. hlist::
- :columns: 2
-
- * ARG - Arginine
- * ASN - Asparagine
- * ASP - Aspartate
- * GLN - Glutamine
- * GLU - Glutamate
- * LYS - Lysine
- * SER - Serine
- * CYS - Cystein
- * CYH - "free" Cystein
- * CYD - disulfid bonded Cystein
- * MET - Methionine
- * TRP - Tryptophane
- * TYR - Tyrosine
- * THR - Threonine
- * VAL - Valine
- * ILE - Isoleucine
- * LEU - Leucine
- * PRO - Proline
- * CPR - cis-Proline
- * TPR - trans-Proline
- * HIS - Histidine
- * HSD - d-protonated Histidine
- * HSE - e-protonated Histidine
- * PHE - Phenylalanine
- * GLY - Glycine
- * ALA - Alanine
- * XXX - Invalid
-
- The RotamerID enum can be accessed either directly as ``promod3.sidechain.ARG``
- or as ``promod3.sidechain.RotamerID.ARG``.
-
-
-How can I get an ID?
---------------------------------------------------------------------------------
-The RotamerID enum can directly be accessed from Python. Two convenient
-functions exist to get RotamerIDs from the :class:`ost.conop.AminoAcid` enum
-or from amino acid three letter codes.
-
-.. method:: TLCToRotID(tlc)
-
- Directly translates the three letter code into a RotamerID. Following
- exactly the naming convention defined above.
-
- :param tlc: Three letter code of amino acid
- :type tlc: :class:`str`
-
- :returns: :class:`RotamerID`, XXX if **tlc** cannot be recoginzed.
-
-
-.. method:: AAToRotID(aa)
-
- Directly translates **aa** 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 :class:`ost.conop.AminoAcid`
-
- :param aa: AA enum of amino acid
- :type aa: :class:`ost.conop.AminoAcid`
-
- :returns: :class:`RotamerID`, XXX if **aa** is invalid.
-
-
-
-
-
-
-
-
-
-
-
diff --git a/sidechain/pymod/export_particle.cc b/sidechain/pymod/export_particle.cc
index 7d0d472fe650daacff93f13669fa7476c0ed318f..d15e7157595016c1c40caf26e70d86be551c5da4 100644
--- a/sidechain/pymod/export_particle.cc
+++ b/sidechain/pymod/export_particle.cc
@@ -17,6 +17,8 @@
#include <boost/python.hpp>
#include <promod3/sidechain/particle.hh>
#include <promod3/sidechain/scwrl4_particle_scoring.hh>
+#include <promod3/sidechain/scwrl3_particle_scoring.hh>
+#include <promod3/sidechain/vina_particle_scoring.hh>
using namespace boost::python;
using namespace promod3::sidechain;
@@ -40,6 +42,22 @@ ParticlePtr WrapCreateSCWRL4Particle(const String& name,
return return_ptr;
}
+ParticlePtr WrapCreateSCWRL3Particle(const String& name,
+ Real radius,
+ const geom::Vec3& pos) {
+ SCWRL3Param* p = new SCWRL3Param(pos, radius);
+ ParticlePtr return_ptr(new Particle(name, p));
+ return return_ptr;
+}
+
+ParticlePtr WrapCreateVINAParticle(const String& name,
+ VINAParticleType particle_type,
+ const geom::Vec3& pos) {
+ VINAParam* p = new VINAParam(particle_type, pos);
+ ParticlePtr return_ptr(new Particle(name, p));
+ return return_ptr;
+}
+
}
@@ -47,6 +65,8 @@ void export_Particle() {
enum_<PScoringFunction>("PScoringFunction")
.value("SCWRL4", SCWRL4)
+ .value("SCWRL3", SCWRL3)
+ .value("VINA", VINA)
;
class_<Particle, ParticlePtr>("Particle", no_init)
@@ -81,4 +101,37 @@ void export_Particle() {
arg("lone_pairs") = geom::Vec3List(),
arg("polar_direction") = geom::Vec3()));
+
+ // SCWRL3 specific stuff
+ def("CreateSCWRL3Particle",
+ &WrapCreateSCWRL3Particle, (arg("name"),
+ arg("radius"),
+ arg("pos")));
+
+ // VINA specific stuff
+ enum_<VINAParticleType>("VINAParticleType")
+ .value("O_D_VINAParticle",O_D_VINAParticle)
+ .value("N_D_VINAParticle",N_D_VINAParticle)
+ .value("O_A_VINAParticle",O_A_VINAParticle)
+ .value("N_A_VINAParticle",N_A_VINAParticle)
+ .value("O_AD_VINAParticle",O_AD_VINAParticle)
+ .value("N_AD_VINAParticle",N_AD_VINAParticle)
+ .value("O_VINAParticle",O_VINAParticle)
+ .value("N_VINAParticle",N_VINAParticle)
+ .value("S_VINAParticle",S_VINAParticle)
+ .value("P_VINAParticle",P_VINAParticle)
+ .value("C_P_VINAParticle", C_P_VINAParticle)
+ .value("C_VINAParticle",C_VINAParticle)
+ .value("F_VINAParticle",F_VINAParticle)
+ .value("Cl_VINAParticle",Cl_VINAParticle)
+ .value("Br_VINAParticle",Br_VINAParticle)
+ .value("I_VINAParticle",I_VINAParticle)
+ .value("M_VINAParticle",M_VINAParticle)
+ .value("INVALID_VINAParticle",INVALID_VINAParticle)
+ ;
+
+ def("CreateVINAParticle",
+ &WrapCreateVINAParticle, (arg("name"),
+ arg("particle_type"),
+ arg("pos")));
}
diff --git a/sidechain/pymod/export_rotamer.cc b/sidechain/pymod/export_rotamer.cc
index 80468074311b622982c4326c50f579d8293ecf23..2a1a1fc4e35074672b6c17a548a05a9cfd75d650 100644
--- a/sidechain/pymod/export_rotamer.cc
+++ b/sidechain/pymod/export_rotamer.cc
@@ -241,6 +241,7 @@ void export_Rotamer()
.def("AddFrameEnergy",&RRMRotamerGroup::AddFrameEnergy,(arg("frame")))
.def("ApplySelfEnergyThresh", &RRMRotamerGroup::ApplySelfEnergyThresh,
(arg("thresh")=30))
+ .def("GetResidueIndex", &RRMRotamerGroup::GetResidueIndex)
;
register_ptr_to_python<RRMRotamerGroupPtr>();
@@ -260,6 +261,7 @@ void export_Rotamer()
.def("AddFrameEnergy",&FRMRotamerGroup::AddFrameEnergy,(arg("frame")))
.def("ApplySelfEnergyThresh", &FRMRotamerGroup::ApplySelfEnergyThresh,
(arg("thresh")=30))
+ .def("GetResidueIndex", &FRMRotamerGroup::GetResidueIndex)
;
register_ptr_to_python<FRMRotamerGroupPtr>();
diff --git a/sidechain/pymod/export_rotamer_constructor.cc b/sidechain/pymod/export_rotamer_constructor.cc
index fdb91bb4ac3a745b6027141ff4c974e781c9ccf4..b0253738d294b6fd3885a32f73c55bb8d707e91f 100644
--- a/sidechain/pymod/export_rotamer_constructor.cc
+++ b/sidechain/pymod/export_rotamer_constructor.cc
@@ -22,6 +22,7 @@
#include <promod3/sidechain/rotamer_group.hh>
#include <promod3/sidechain/scwrl4_rotamer_constructor.hh>
#include <promod3/sidechain/scwrl3_rotamer_constructor.hh>
+#include <promod3/sidechain/vina_rotamer_constructor.hh>
using namespace boost::python;
using namespace promod3::sidechain;
@@ -40,6 +41,11 @@ SCWRL3RotamerConstructorPtr WrapSCWRL3RotamerConstructorInit(bool cb_in_sidechai
return p;
}
+VINARotamerConstructorPtr WrapVINARotamerConstructorInit(bool cb_in_sidechain) {
+ VINARotamerConstructorPtr p(new VINARotamerConstructor(cb_in_sidechain));
+ return p;
+}
+
RRMRotamerGroupPtr WrapRRMGroup_res(RotamerConstructorPtr constructor,
const ost::mol::ResidueHandle& res,
RotamerID id,
@@ -456,4 +462,17 @@ void export_RotamerConstructor(){
.def("__init__", boost::python::make_constructor(&WrapSCWRL3RotamerConstructorInit))
;
+
+ class_<VINARotamerConstructor, VINARotamerConstructorPtr,
+ bases<RotamerConstructor> >("VINARotamerConstructor", no_init)
+ .def("__init__", boost::python::make_constructor(&WrapVINARotamerConstructorInit))
+ .def("ConstructFrameResidueHeuristic",
+ &VINARotamerConstructor::ConstructFrameResidueHeuristic, (arg("res"),
+ arg("residue_index")))
+ .def("ConstructRRMRotamerHeuristic",
+ &VINARotamerConstructor::ConstructRRMRotamerHeuristic, (arg("res")))
+ .def("ConstructFRMRotamerHeuristic",
+ &VINARotamerConstructor::ConstructFRMRotamerHeuristic, (arg("res")))
+ ;
+
}
diff --git a/sidechain/src/CMakeLists.txt b/sidechain/src/CMakeLists.txt
index 1c142e51635c10fc9c47042dd65b0bf78639a1e4..5930ffeefb030342cb8f59804134760db7cd06dc 100644
--- a/sidechain/src/CMakeLists.txt
+++ b/sidechain/src/CMakeLists.txt
@@ -8,6 +8,7 @@ set(SIDECHAIN_HEADERS
particle_scoring.hh
scwrl4_particle_scoring.hh
scwrl3_particle_scoring.hh
+ vina_particle_scoring.hh
rotamer.hh
rotamer_cruncher.hh
rotamer_density.hh
@@ -22,6 +23,7 @@ set(SIDECHAIN_HEADERS
rotamer_lookup.hh
scwrl4_rotamer_constructor.hh
scwrl3_rotamer_constructor.hh
+ vina_rotamer_constructor.hh
subrotamer_optimizer.hh
)
@@ -32,6 +34,7 @@ set(SIDECHAIN_SOURCES
particle_scoring.cc
scwrl4_particle_scoring.cc
scwrl3_particle_scoring.cc
+ vina_particle_scoring.cc
rotamer.cc
rotamer_cruncher.cc
rotamer_density.cc
@@ -46,6 +49,7 @@ set(SIDECHAIN_SOURCES
rotamer_lookup.cc
scwrl4_rotamer_constructor.cc
scwrl3_rotamer_constructor.cc
+ vina_rotamer_constructor.cc
subrotamer_optimizer.cc
)
diff --git a/sidechain/src/particle_scoring.cc b/sidechain/src/particle_scoring.cc
index de558f3f89248257b506561b5e4ad329b9ea9a21..be3c9b0d8cbd772c685600a75b007df8bab80bb6 100644
--- a/sidechain/src/particle_scoring.cc
+++ b/sidechain/src/particle_scoring.cc
@@ -17,6 +17,7 @@
#include <promod3/sidechain/particle_scoring.hh>
#include <promod3/sidechain/scwrl4_particle_scoring.hh>
#include <promod3/sidechain/scwrl3_particle_scoring.hh>
+#include <promod3/sidechain/vina_particle_scoring.hh>
namespace promod3{ namespace sidechain{
@@ -36,6 +37,10 @@ Real PairwiseParticleScore(PScoringParam* p_one, PScoringParam* p_two) {
return SCWRL3PairwiseScore(reinterpret_cast<SCWRL3Param*>(p_one),
reinterpret_cast<SCWRL3Param*>(p_two));
}
+ case VINA: {
+ return VINAPairwiseScore(reinterpret_cast<VINAParam*>(p_one),
+ reinterpret_cast<VINAParam*>(p_two));
+ }
default: {
throw promod3::Error("Don't know what scoring function to call between "
"particles... maybe a lazy developer forgot to "
@@ -98,7 +103,15 @@ void PScoringParamContainer::PairwiseScores(const PScoringParamContainer& other,
reinterpret_cast<SCWRL3Param*>(other.params_[idx[i].second]));
}
break;
-
+ }
+ case VINA: {
+ scores.resize(idx.size());
+ for(uint i = 0; i < idx.size(); ++i) {
+ scores[i] =
+ VINAPairwiseScore(reinterpret_cast<VINAParam*>(params_[idx[i].first]),
+ reinterpret_cast<VINAParam*>(other.params_[idx[i].second]));
+ }
+ break;
}
default: {
throw promod3::Error("Don't know what scoring function to call between "
diff --git a/sidechain/src/particle_scoring_base.hh b/sidechain/src/particle_scoring_base.hh
index e5cbdd167589f0a72df43d01dd9abd27ff8f9926..2200e55391cfe5c42d1fc65784fe53aa60a98bbc 100644
--- a/sidechain/src/particle_scoring_base.hh
+++ b/sidechain/src/particle_scoring_base.hh
@@ -26,6 +26,7 @@ namespace promod3{ namespace sidechain{
enum PScoringFunction{
SCWRL4,
SCWRL3,
+VINA,
INVALID_PSCORING_FUNCTION
};
diff --git a/sidechain/src/rotamer_constructor.cc b/sidechain/src/rotamer_constructor.cc
index 48c5189a85750eddfd820e5a35e4bdda645383ce..716b20293de3cb6d1d00eecdb97c98ec876eed79 100644
--- a/sidechain/src/rotamer_constructor.cc
+++ b/sidechain/src/rotamer_constructor.cc
@@ -23,10 +23,8 @@
namespace promod3 { namespace sidechain{
RotamerConstructor::RotamerConstructor(bool cb_in_sidechain,
- RotamerLookupMode mode,
const RotamerLookupParam& param):
- rotamer_lookup_(cb_in_sidechain, mode, param),
- mode_(mode) {
+ rotamer_lookup_(cb_in_sidechain, param) {
String s(XXX,'X');
for(uint i = 0; i < XXX; ++i){
@@ -437,7 +435,7 @@ FrameResiduePtr RotamerConstructor::ConstructSidechainFrameResidue(
}
promod3::loop::ConstructHydrogens(*pos_buffer_, id, *hydrogen_buffer_,
- mode_ == POLAR_HYDROGEN_MODE,
+ rotamer_lookup_.GetMode() == POLAR_HYDROGEN_MODE,
promod3::loop::PROT_STATE_HISH);
}
@@ -507,7 +505,7 @@ FrameResiduePtr RotamerConstructor::ConstructSidechainFrameResidue(
}
promod3::loop::ConstructHydrogens(*pos_buffer_, id, *hydrogen_buffer_,
- mode_ == POLAR_HYDROGEN_MODE,
+ rotamer_lookup_.GetMode() == POLAR_HYDROGEN_MODE,
promod3::loop::PROT_STATE_HISH);
}
@@ -561,7 +559,7 @@ RRMRotamerGroupPtr RotamerConstructor::ConstructRRMGroup(
// in case of his, we have to move the backbone positions in the buffer
// to the locations defining his in the different protonation states
- if(id_ == HIS && mode_ != HEAVY_ATOM_MODE){
+ if(id_ == HIS && rotamer_lookup_.SampleHISProtonationStates()){
MVBBPosBuffer(HIS, HSD);
MVBBPosBuffer(HIS, HSE);
}
@@ -590,50 +588,33 @@ RRMRotamerGroupPtr RotamerConstructor::ConstructRRMGroup(
chi_angles_[2] = lib_entries.first[i].chi3;
chi_angles_[3] = lib_entries.first[i].chi4;
- if(mode_ == HEAVY_ATOM_MODE) {
+ if(id_ == HIS && rotamer_lookup_.SampleHISProtonationStates()) {
+ id_ = HSE;
+ rotamers.push_back(ConstructRRM());
+ id_ = HSD;
+ rotamers.push_back(ConstructRRM());
+ id_ = HIS;
+ } else if(id_ == SER && rotamer_lookup_.GetMode() != HEAVY_ATOM_MODE) {
+ chi_angles_[1] = Real(M_PI);
+ rotamers.push_back(ConstructRRM());
+ chi_angles_[1] = Real(M_PI) / 3.0;
+ rotamers.push_back(ConstructRRM());
+ chi_angles_[1] = -Real(M_PI) / 3.0;
+ rotamers.push_back(ConstructRRM());
+ } else if(id_ == THR && rotamer_lookup_.GetMode() != HEAVY_ATOM_MODE) {
+ chi_angles_[1] = Real(M_PI);
+ rotamers.push_back(ConstructRRM());
+ chi_angles_[1] = Real(M_PI) / 3.0;
+ rotamers.push_back(ConstructRRM());
+ chi_angles_[1] = -Real(M_PI) / 3.0;
+ rotamers.push_back(ConstructRRM());
+ } else if(id_ == TYR && rotamer_lookup_.GetMode() != HEAVY_ATOM_MODE) {
+ chi_angles_[2] = Real(M_PI);
+ rotamers.push_back(ConstructRRM());
+ chi_angles_[2] = Real(0.0);
rotamers.push_back(ConstructRRM());
} else {
- // in POLAR_HYDROGEN_MODE or FULL_ATOMIC_MODE we're sampling
- // polar hydrogens of SER/THR/TYR and construct different
- // rotamers for HIS
- switch(id_){
- case HIS:{
- id_ = HSE;
- rotamers.push_back(ConstructRRM());
- id_ = HSD;
- rotamers.push_back(ConstructRRM());
- id_ = HIS;
- break;
- }
- case SER:{
- chi_angles_[1] = Real(M_PI);
- rotamers.push_back(ConstructRRM());
- chi_angles_[1] = Real(M_PI) / 3.0;
- rotamers.push_back(ConstructRRM());
- chi_angles_[1] = -Real(M_PI) / 3.0;
- rotamers.push_back(ConstructRRM());
- break;
- }
- case THR:{
- chi_angles_[1] = Real(M_PI);
- rotamers.push_back(ConstructRRM());
- chi_angles_[1] = Real(M_PI) / 3.0;
- rotamers.push_back(ConstructRRM());
- chi_angles_[1] = -Real(M_PI) / 3.0;
- rotamers.push_back(ConstructRRM());
- break;
- }
- case TYR:{
- chi_angles_[2] = Real(M_PI);
- rotamers.push_back(ConstructRRM());
- chi_angles_[2] = Real(0.0);
- rotamers.push_back(ConstructRRM());
- break;
- }
- default:{
- rotamers.push_back(ConstructRRM());
- }
- }
+ rotamers.push_back(ConstructRRM());
}
if(summed_prob >= probability_cutoff && !rotamers.empty()) break;
@@ -658,7 +639,7 @@ FRMRotamerGroupPtr RotamerConstructor::ConstructFRMGroup(
// in case of his, we have to move the backbone positions in the buffer
// to the locations defining his in the different protonation states
- if(id_ == HIS && mode_ != HEAVY_ATOM_MODE){
+ if(id_ == HIS && rotamer_lookup_.SampleHISProtonationStates()){
MVBBPosBuffer(HIS, HSD);
MVBBPosBuffer(HIS, HSE);
}
@@ -689,48 +670,37 @@ FRMRotamerGroupPtr RotamerConstructor::ConstructFRMGroup(
chi_dev_[1] = lib_entries.first[i].sig2;
chi_dev_[2] = lib_entries.first[i].sig3;
chi_dev_[3] = lib_entries.first[i].sig4;
- if(mode_ == HEAVY_ATOM_MODE) {
+
+ if(id_ == HIS && rotamer_lookup_.SampleHISProtonationStates()) {
+ id_ = HSE;
+ rotamers.push_back(ConstructFRM());
+ id_ = HSD;
+ rotamers.push_back(ConstructFRM());
+ id_ = HIS;
+ } else if(id_ == SER && rotamer_lookup_.GetMode() != HEAVY_ATOM_MODE) {
+ chi_dev_[1] = Real(0.17453);
+ chi_angles_[1] = Real(M_PI);
+ rotamers.push_back(ConstructFRM());
+ chi_angles_[1] = Real(M_PI) / 3.0;
+ rotamers.push_back(ConstructFRM());
+ chi_angles_[1] = -Real(M_PI) / 3.0;
+ rotamers.push_back(ConstructFRM());
+ } else if(id_ == THR && rotamer_lookup_.GetMode() != HEAVY_ATOM_MODE) {
+ chi_dev_[1] = Real(0.17453);
+ chi_angles_[1] = Real(M_PI);
+ rotamers.push_back(ConstructFRM());
+ chi_angles_[1] = Real(M_PI) / 3.0;
+ rotamers.push_back(ConstructFRM());
+ chi_angles_[1] = -Real(M_PI) / 3.0;
+ rotamers.push_back(ConstructFRM());
+ } else if(id_ == TYR && rotamer_lookup_.GetMode() != HEAVY_ATOM_MODE) {
+ chi_dev_[2] = Real(0.17453);
+ chi_angles_[2] = Real(M_PI);
+ rotamers.push_back(ConstructFRM());
+ chi_angles_[2] = Real(0.0);
rotamers.push_back(ConstructFRM());
} else {
- switch(id_){
- case HIS:{
- id_ = HSE;
- rotamers.push_back(ConstructFRM());
- id_ = HSD;
- rotamers.push_back(ConstructFRM());
- id_ = HIS;
- break;
- }
- case SER:{
- chi_dev_[1] = Real(0.17453);
- chi_angles_[1] = Real(M_PI);
- rotamers.push_back(ConstructFRM());
- chi_angles_[1] = Real(M_PI) / Real(3.0);
- rotamers.push_back(ConstructFRM());
- chi_angles_[1] = -Real(M_PI) / Real(3.0);
- rotamers.push_back(ConstructFRM());
- break;
- }
- case THR:{
- chi_dev_[1] = Real(0.17453);
- chi_angles_[1] = Real(M_PI);
- rotamers.push_back(ConstructFRM());
- chi_angles_[1] = Real(M_PI) / Real(3.0);
- rotamers.push_back(ConstructFRM());
- chi_angles_[1] = -Real(M_PI) / Real(3.0);
- rotamers.push_back(ConstructFRM());
- break;
- }
- case TYR:{
- chi_dev_[2] = Real(0.17453);
- chi_angles_[2] = Real(M_PI);
- rotamers.push_back(ConstructFRM());
- chi_angles_[2] = Real(0.0);
- rotamers.push_back(ConstructFRM());
- break;
- }
- default: rotamers.push_back(ConstructFRM());
- }
+ rotamers.push_back(ConstructFRM());
}
if(summed_prob >= probability_cutoff && !rotamers.empty()) break;
@@ -759,7 +729,7 @@ RRMRotamerPtr RotamerConstructor::ConstructRRM() {
if(info.has_hydrogens){
promod3::loop::ConstructHydrogens(*pos_buffer_, id_, *hydrogen_buffer_,
- mode_ == POLAR_HYDROGEN_MODE,
+ rotamer_lookup_.GetMode() == POLAR_HYDROGEN_MODE,
promod3::loop::PROT_STATE_HISH);
// If there are any custom rules, we apply them now and overrule the
@@ -808,7 +778,7 @@ FRMRotamerPtr RotamerConstructor::ConstructFRM() {
chi_angles_[3]);
if(info.has_hydrogens){
promod3::loop::ConstructHydrogens(*pos_buffer_, id_, *hydrogen_buffer_,
- mode_ == POLAR_HYDROGEN_MODE,
+ rotamer_lookup_.GetMode() == POLAR_HYDROGEN_MODE,
promod3::loop::PROT_STATE_HISH);
// If there are any custom rules, we apply them now an overrule the
// default hydrogen construction
@@ -914,10 +884,10 @@ FrameResiduePtr RotamerConstructor::ConstructBackboneFrameResidue() {
// set hydrogens (also enter if its an n_ter because proline would have no
// hydrogen)
- if((info.has_hydrogens || n_ter_) && mode_ != HEAVY_ATOM_MODE) {
- if(mode_ == FULL_ATOMIC_MODE) {
+ if((info.has_hydrogens || n_ter_) && rotamer_lookup_.GetMode() != HEAVY_ATOM_MODE) {
+ if(rotamer_lookup_.GetMode() == FULL_ATOMIC_MODE) {
promod3::loop::ConstructHydrogens(*pos_buffer_, id_, *hydrogen_buffer_,
- mode_ == POLAR_HYDROGEN_MODE,
+ rotamer_lookup_.GetMode() == POLAR_HYDROGEN_MODE,
promod3::loop::PROT_STATE_HISH);
}
if(n_ter_) {
diff --git a/sidechain/src/rotamer_constructor.hh b/sidechain/src/rotamer_constructor.hh
index 759d49d41cbd7cf04b424a2dba72fc02cc0af396..63f4933d0930082231dfba5ee3c993c18e94558b 100644
--- a/sidechain/src/rotamer_constructor.hh
+++ b/sidechain/src/rotamer_constructor.hh
@@ -41,7 +41,7 @@ class RotamerConstructor {
public:
- RotamerConstructor(bool cb_in_sidechain, RotamerLookupMode mode,
+ RotamerConstructor(bool cb_in_sidechain,
const RotamerLookupParam& param = RotamerLookupParam());
virtual ~RotamerConstructor() { }
@@ -267,7 +267,6 @@ private:
void MVBBPosBuffer(RotamerID from, RotamerID to);
RotamerLookup rotamer_lookup_;
- RotamerLookupMode mode_;
Real chi_angles_[4];
Real chi_dev_[4];
Real probability_;
diff --git a/sidechain/src/rotamer_lookup.cc b/sidechain/src/rotamer_lookup.cc
index 6ca63be5dfd0a20ee08bfb680355243911f15140..a7e4185673da48cf1329582dd84043e6f9d34fd0 100644
--- a/sidechain/src/rotamer_lookup.cc
+++ b/sidechain/src/rotamer_lookup.cc
@@ -18,15 +18,18 @@
namespace promod3 { namespace sidechain{
-RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
- const RotamerLookupParam& param): mode_(mode) {
+RotamerLookup::RotamerLookup(bool cb_in_sidechain,
+ const RotamerLookupParam& param) {
core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
"RotamerLookup::RotamerLookup", 2);
+ mode_ = param.mode;
+ sample_his_protonation_states_ = param.sample_his_protonation_states;
+
// ARG
- sidechain_infos_[ARG].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[ARG].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[ARG].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::ARG];
sidechain_infos_[ARG].frm_t = param.frm_t[ost::conop::ARG];
@@ -38,7 +41,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(ARG, "NH1", promod3::loop::ARG_NH1_INDEX, false);
AddInfo(ARG, "NH2", promod3::loop::ARG_NH2_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddInfo(ARG, "HE", promod3::loop::ARG_HE_INDEX, true);
AddInfo(ARG, "HH11", promod3::loop::ARG_HH11_INDEX, true);
AddInfo(ARG, "HH12", promod3::loop::ARG_HH12_INDEX, true);
@@ -46,7 +49,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(ARG, "HH22", promod3::loop::ARG_HH22_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(ARG, "HB2", promod3::loop::ARG_HB2_INDEX, true);
AddInfo(ARG, "HB3", promod3::loop::ARG_HB3_INDEX, true);
AddInfo(ARG, "HG2", promod3::loop::ARG_HG2_INDEX, true);
@@ -68,7 +71,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(ARG, 0, 4); // NH1
AddFRMRotatingParticle(ARG, 0, 5); // NH2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(ARG, 0, 6); // HE
AddFRMRotatingParticle(ARG, 0, 7); // HH11
AddFRMRotatingParticle(ARG, 0, 8); // HH12
@@ -76,7 +79,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(ARG, 0, 10); // HH22
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(ARG, 0, 11); // HB2
AddFRMRotatingParticle(ARG, 0, 12); // HB3
AddFRMRotatingParticle(ARG, 0, 13); // HG2
@@ -94,7 +97,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(ARG, 1, 4); // NH1
AddFRMRotatingParticle(ARG, 1, 5); // NH2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(ARG, 1, 6); // HE
AddFRMRotatingParticle(ARG, 1, 7); // HH11
AddFRMRotatingParticle(ARG, 1, 8); // HH12
@@ -102,7 +105,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(ARG, 1, 10); // HH22
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(ARG, 1, 11); // HB2
AddFRMFixParticle(ARG, 1, 12); // HB3
AddFRMRotatingParticle(ARG, 1, 13); // HG2
@@ -120,7 +123,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(ARG, 2, 4); // NH1
AddFRMRotatingParticle(ARG, 2, 5); // NH2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(ARG, 2, 6); // HE
AddFRMRotatingParticle(ARG, 2, 7); // HH11
AddFRMRotatingParticle(ARG, 2, 8); // HH12
@@ -128,7 +131,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(ARG, 2, 10); // HH22
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(ARG, 2, 11); // HB2
AddFRMFixParticle(ARG, 2, 12); // HB3
AddFRMFixParticle(ARG, 2, 13); // HG2
@@ -147,7 +150,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(ARG, 3, 4); // NH1
AddFRMRotatingParticle(ARG, 3, 5); // NH2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(ARG, 3, 6); // HE
AddFRMRotatingParticle(ARG, 3, 7); // HH11
AddFRMRotatingParticle(ARG, 3, 8); // HH12
@@ -155,7 +158,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(ARG, 3, 10); // HH22
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(ARG, 3, 11); // HB2
AddFRMFixParticle(ARG, 3, 12); // HB3
AddFRMFixParticle(ARG, 3, 13); // HG2
@@ -167,10 +170,10 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 6;
- if(mode == POLAR_HYDROGEN_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE) {
cb_idx = 11;
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 17;
}
AddFRMFixParticle(ARG, 0, cb_idx);
@@ -179,18 +182,18 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMFixParticle(ARG, 3, cb_idx);
}
- backbone_infos_[ARG].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[ARG].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(ARG, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(ARG, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(ARG, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(ARG, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(ARG, "H", promod3::loop::ARG_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(ARG, "HA", promod3::loop::ARG_HA_INDEX, true);
}
@@ -200,8 +203,8 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// ASN
- sidechain_infos_[ASN].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[ASN].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[ASN].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::ASN];
sidechain_infos_[ASN].frm_t = param.frm_t[ost::conop::ASN];
@@ -210,12 +213,12 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(ASN, "OD1", promod3::loop::ASN_OD1_INDEX, false);
AddInfo(ASN, "ND2", promod3::loop::ASN_ND2_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddInfo(ASN, "HD21", promod3::loop::ASN_HD21_INDEX, true);
AddInfo(ASN, "HD22", promod3::loop::ASN_HD22_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(ASN, "HB2", promod3::loop::ASN_HB2_INDEX, true);
AddInfo(ASN, "HB3", promod3::loop::ASN_HB3_INDEX, true);
}
@@ -230,12 +233,12 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(ASN, 0, 1); // OD1
AddFRMRotatingParticle(ASN, 0, 2); // ND2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(ASN, 0, 3); // HD21
AddFRMRotatingParticle(ASN, 0, 4); // HD22
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(ASN, 0, 5); // HB2
AddFRMRotatingParticle(ASN, 0, 6); // HB3
}
@@ -246,22 +249,22 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(ASN, 1, 1); // OD1
AddFRMRotatingParticle(ASN, 1, 2); // ND2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(ASN, 1, 3); // HD21
AddFRMRotatingParticle(ASN, 1, 4); // HD22
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(ASN, 1, 5); // HB2
AddFRMFixParticle(ASN, 1, 6); // HB3
}
if(cb_in_sidechain) {
int cb_idx = 3;
- if(mode == POLAR_HYDROGEN_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE) {
cb_idx = 5;
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 7;
}
AddFRMFixParticle(ASN, 0, cb_idx);
@@ -269,18 +272,18 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
}
- backbone_infos_[ASN].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[ASN].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(ASN, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(ASN, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(ASN, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(ASN, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(ASN, "H", promod3::loop::ASN_H_INDEX,true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(ASN, "HA", promod3::loop::ASN_HA_INDEX, true);
}
@@ -290,7 +293,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// ASP
- sidechain_infos_[ASP].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[ASP].has_hydrogens = (mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[ASP].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::ASP];
sidechain_infos_[ASP].frm_t = param.frm_t[ost::conop::ASP];
@@ -299,7 +302,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(ASP, "OD1", promod3::loop::ASP_OD1_INDEX, false);
AddInfo(ASP, "OD2", promod3::loop::ASP_OD2_INDEX, false);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(ASP, "HB2", promod3::loop::ASP_HB2_INDEX, true);
AddInfo(ASP, "HB3", promod3::loop::ASP_HB3_INDEX, true);
}
@@ -314,7 +317,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(ASP, 0, 1); // OD1
AddFRMRotatingParticle(ASP, 0, 2); // OD2
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(ASP, 0, 3); // HB2
AddFRMRotatingParticle(ASP, 0, 4); // HB3
}
@@ -325,32 +328,32 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(ASP, 1, 1); // OD1
AddFRMRotatingParticle(ASP, 1, 2); // OD2
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(ASP, 1, 3); // HB2
AddFRMFixParticle(ASP, 1, 4); // HB3
}
if(cb_in_sidechain) {
int cb_idx = 3;
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 5;
}
AddFRMFixParticle(ASP, 0, cb_idx);
AddFRMFixParticle(ASP, 1, cb_idx);
}
- backbone_infos_[ASP].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[ASP].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(ASP, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(ASP, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(ASP, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(ASP, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(ASP, "H", promod3::loop::ASP_H_INDEX,true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(ASP, "HA", promod3::loop::ASP_HA_INDEX, true);
}
@@ -360,8 +363,8 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// GLN
- sidechain_infos_[GLN].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[GLN].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[GLN].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::GLN];
sidechain_infos_[GLN].frm_t = param.frm_t[ost::conop::GLN];
@@ -371,12 +374,12 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(GLN, "OE1", promod3::loop::GLN_OE1_INDEX, false);
AddInfo(GLN, "NE2", promod3::loop::GLN_NE2_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddInfo(GLN, "HE21", promod3::loop::GLN_HE21_INDEX, true);
AddInfo(GLN, "HE22", promod3::loop::GLN_HE22_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(GLN, "HB2", promod3::loop::GLN_HB2_INDEX, true);
AddInfo(GLN, "HB3", promod3::loop::GLN_HB3_INDEX, true);
AddInfo(GLN, "HG2", promod3::loop::GLN_HG2_INDEX, true);
@@ -394,12 +397,12 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(GLN, 0, 2); // OE1
AddFRMRotatingParticle(GLN, 0, 3); // NE2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(GLN, 0, 4); // HE21
AddFRMRotatingParticle(GLN, 0, 5); // HE22
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(GLN, 0, 6); // HB2
AddFRMRotatingParticle(GLN, 0, 7); // HB3
AddFRMRotatingParticle(GLN, 0, 8); // HG2
@@ -413,12 +416,12 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(GLN, 1, 2); // OE1
AddFRMRotatingParticle(GLN, 1, 3); // NE2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(GLN, 1, 4); // HE21
AddFRMRotatingParticle(GLN, 1, 5); // HE22
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(GLN, 1, 6); // HB2
AddFRMFixParticle(GLN, 1, 7); // HB3
AddFRMRotatingParticle(GLN, 1, 8); // HG2
@@ -432,12 +435,12 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(GLN, 2, 2); // OE1
AddFRMRotatingParticle(GLN, 2, 3); // NE2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(GLN, 2, 4); // HE21
AddFRMRotatingParticle(GLN, 2, 5); // HE22
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(GLN, 2, 6); // HB2
AddFRMFixParticle(GLN, 2, 7); // HB3
AddFRMFixParticle(GLN, 2, 8); // HG2
@@ -446,10 +449,10 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 4;
- if(mode == POLAR_HYDROGEN_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE) {
cb_idx = 6;
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 10;
}
AddFRMFixParticle(GLN, 0, cb_idx);
@@ -458,8 +461,8 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
}
- backbone_infos_[GLN].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[GLN].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(GLN, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(GLN, "CA", promod3::loop::BB_CA_INDEX, false);
@@ -467,11 +470,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddBBInfo(GLN, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(GLN, "H", promod3::loop::GLN_H_INDEX,true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(GLN, "HA", promod3::loop::GLN_HA_INDEX, true);
}
@@ -481,7 +484,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// GLU
- sidechain_infos_[GLU].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[GLU].has_hydrogens = (mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[GLU].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::GLU];
sidechain_infos_[GLU].frm_t = param.frm_t[ost::conop::GLU];
@@ -492,7 +495,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(GLU, "OE2", promod3::loop::GLU_OE2_INDEX, false);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(GLU, "HB2", promod3::loop::GLU_HB2_INDEX, true);
AddInfo(GLU, "HB3", promod3::loop::GLU_HB3_INDEX, true);
AddInfo(GLU, "HG2", promod3::loop::GLU_HG2_INDEX, true);
@@ -510,7 +513,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(GLU, 0, 2); // OE1
AddFRMRotatingParticle(GLU, 0, 3); // OE2
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(GLU, 0, 4); // HB2
AddFRMRotatingParticle(GLU, 0, 5); // HB3
AddFRMRotatingParticle(GLU, 0, 6); // HG2
@@ -524,7 +527,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(GLU, 1, 2); // OE1
AddFRMRotatingParticle(GLU, 1, 3); // OE2
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(GLU, 1, 4); // HB2
AddFRMFixParticle(GLU, 1, 5); // HB3
AddFRMRotatingParticle(GLU, 1, 6); // HG2
@@ -538,7 +541,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(GLU, 2, 2); // OE1
AddFRMRotatingParticle(GLU, 2, 3); // OE2
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(GLU, 2, 4); // HB2
AddFRMFixParticle(GLU, 2, 5); // HB3
AddFRMFixParticle(GLU, 2, 6); // HG2
@@ -547,7 +550,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 4;
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 8;
}
AddFRMFixParticle(GLU, 0, cb_idx);
@@ -556,8 +559,8 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
}
- backbone_infos_[GLU].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[GLU].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(GLU, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(GLU, "CA", promod3::loop::BB_CA_INDEX, false);
@@ -565,11 +568,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddBBInfo(GLU, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(GLU, "H", promod3::loop::GLU_H_INDEX,true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(GLU, "HA", promod3::loop::GLU_HA_INDEX, true);
}
@@ -579,8 +582,8 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// LYS
- sidechain_infos_[LYS].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[LYS].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[LYS].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::LYS];
sidechain_infos_[LYS].frm_t = param.frm_t[ost::conop::LYS];
@@ -590,13 +593,13 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(LYS, "CE", promod3::loop::LYS_CE_INDEX,false);
AddInfo(LYS, "NZ", promod3::loop::LYS_NZ_INDEX,false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddInfo(LYS, "HZ1", promod3::loop::LYS_HZ1_INDEX,true);
AddInfo(LYS, "HZ2", promod3::loop::LYS_HZ2_INDEX,true);
AddInfo(LYS, "HZ3", promod3::loop::LYS_HZ3_INDEX,true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(LYS, "HB2", promod3::loop::LYS_HB2_INDEX, true);
AddInfo(LYS, "HB3", promod3::loop::LYS_HB3_INDEX, true);
AddInfo(LYS, "HG2", promod3::loop::LYS_HG2_INDEX, true);
@@ -618,13 +621,13 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(LYS, 0, 2); // CE
AddFRMRotatingParticle(LYS, 0, 3); // NZ
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(LYS, 0, 4); // HZ1
AddFRMRotatingParticle(LYS, 0, 5); // HZ2
AddFRMRotatingParticle(LYS, 0, 6); // HZ3
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(LYS, 0, 7); // HB2
AddFRMRotatingParticle(LYS, 0, 8); // HB3
AddFRMRotatingParticle(LYS, 0, 9); // HG2
@@ -642,13 +645,13 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(LYS, 1, 2); // CE
AddFRMRotatingParticle(LYS, 1, 3); // NZ
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(LYS, 1, 4); // HZ1
AddFRMRotatingParticle(LYS, 1, 5); // HZ2
AddFRMRotatingParticle(LYS, 1, 6); // HZ3
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(LYS, 1, 7); // HB2
AddFRMFixParticle(LYS, 1, 8); // HB3
AddFRMRotatingParticle(LYS, 1, 9); // HG2
@@ -666,13 +669,13 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(LYS, 2, 2); // CE
AddFRMRotatingParticle(LYS, 2, 3); // NZ
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(LYS, 2, 4); // HZ1
AddFRMRotatingParticle(LYS, 2, 5); // HZ2
AddFRMRotatingParticle(LYS, 2, 6); // HZ3
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(LYS, 2, 7); // HB2
AddFRMFixParticle(LYS, 2, 8); // HB3
AddFRMFixParticle(LYS, 2, 9); // HG2
@@ -690,13 +693,13 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMFixParticle(LYS, 3, 2); // CE
AddFRMRotatingParticle(LYS, 3, 3); // NZ
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(LYS, 3, 4); // HZ1
AddFRMRotatingParticle(LYS, 3, 5); // HZ2
AddFRMRotatingParticle(LYS, 3, 6); // HZ3
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(LYS, 3, 7); // HB2
AddFRMFixParticle(LYS, 3, 8); // HB3
AddFRMFixParticle(LYS, 3, 9); // HG2
@@ -709,10 +712,10 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 4;
- if(mode == POLAR_HYDROGEN_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE) {
cb_idx = 7;
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 15;
}
AddFRMFixParticle(LYS, 0, cb_idx);
@@ -721,18 +724,18 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMFixParticle(LYS, 3, cb_idx);
}
- backbone_infos_[LYS].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[LYS].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(LYS, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(LYS, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(LYS, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(LYS, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(LYS, "H", promod3::loop::LYS_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(LYS, "HA", promod3::loop::LYS_HA_INDEX, true);
}
@@ -742,19 +745,19 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// SER
- sidechain_infos_[SER].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[SER].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[SER].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::SER];
sidechain_infos_[SER].frm_t = param.frm_t[ost::conop::SER];
AddInfo(SER, "OG", promod3::loop::SER_OG_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddInfo(SER, "HG", promod3::loop::SER_HG_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(SER, "HB2", promod3::loop::SER_HB2_INDEX, true);
AddInfo(SER, "HB3", promod3::loop::SER_HB3_INDEX, true);
}
@@ -763,7 +766,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(SER, "CB", promod3::loop::BB_CB_INDEX, false);
}
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddCustomHydrogenInfo(SER, promod3::loop::SER_HG_INDEX,
promod3::loop::BB_CA_INDEX,
promod3::loop::BB_CB_INDEX,
@@ -775,22 +778,22 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
param.SER_CA_CB_prefactors);
AddFRMRotatingParticle(SER, 0, 0); // OG
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(SER, 0, 1); // HG
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(SER, 0, 2); // HB2
AddFRMRotatingParticle(SER, 0, 3); // HB3
}
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRule(SER, promod3::loop::BB_CB_INDEX, promod3::loop::SER_OG_INDEX,
param.SER_CB_OG_prefactors);
AddFRMFixParticle(SER, 1, 0); // OG
AddFRMRotatingParticle(SER, 1, 1); // HG
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(SER, 1, 2); // HB2
AddFRMFixParticle(SER, 1, 3); // HB3
}
@@ -798,30 +801,30 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 1;
- if(mode == POLAR_HYDROGEN_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE) {
cb_idx = 2;
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 4;
}
AddFRMFixParticle(SER, 0, cb_idx);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(SER, 1, cb_idx);
}
}
- backbone_infos_[SER].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[SER].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(SER, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(SER, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(SER, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(SER, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(SER, "H", promod3::loop::SER_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(SER, "HA", promod3::loop::SER_HA_INDEX, true);
}
@@ -831,14 +834,14 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// CYS
- sidechain_infos_[CYS].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[CYS].has_hydrogens = (mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[CYS].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::CYS];
sidechain_infos_[CYS].frm_t = param.frm_t[ost::conop::CYS];
AddInfo(CYS, "SG", promod3::loop::CYS_SG_INDEX, false);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(CYS, "HB2", promod3::loop::CYS_HB2_INDEX, true);
AddInfo(CYS, "HB3", promod3::loop::CYS_HB3_INDEX, true);
AddInfo(CYS, "HG", promod3::loop::CYS_HG_INDEX, true);
@@ -852,7 +855,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
param.CYS_CA_CB_prefactors);
AddFRMRotatingParticle(CYS, 0, 0); // SG
- if(FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(CYS, 0, 1); // HB2
AddFRMRotatingParticle(CYS, 0, 2); // HB3
AddFRMRotatingParticle(CYS, 0, 3); // HG
@@ -860,24 +863,24 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 1;
- if(FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 4;
}
AddFRMFixParticle(CYS, 0, cb_idx);
}
- backbone_infos_[CYS].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[CYS].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(CYS, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(CYS, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(CYS, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(CYS, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(CYS, "H", promod3::loop::CYS_H_INDEX,true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(CYS, "HA", promod3::loop::CYS_HA_INDEX,true);
}
@@ -893,14 +896,14 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// CYD
- sidechain_infos_[CYD].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[CYD].has_hydrogens = (mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[CYD].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::CYS];
sidechain_infos_[CYD].frm_t = param.frm_t[ost::conop::CYS];
AddInfo(CYD, "SG", promod3::loop::CYS_SG_INDEX, false);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(CYD, "HB2", promod3::loop::CYS_HB2_INDEX, true);
AddInfo(CYD, "HB3", promod3::loop::CYS_HB3_INDEX, true);
}
@@ -913,31 +916,31 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
param.CYS_CA_CB_prefactors);
AddFRMRotatingParticle(CYD, 0, 0); // SG
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(CYD, 0, 1); // HB2
AddFRMRotatingParticle(CYD, 0, 2); // HB3
}
if(cb_in_sidechain) {
int cb_idx = 1;
- if(FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 3;
}
AddFRMFixParticle(CYD, 0, cb_idx);
}
- backbone_infos_[CYD].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[CYD].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(CYD, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(CYD, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(CYD, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(CYD, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(CYD, "H", promod3::loop::CYS_H_INDEX,true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(CYD, "HA", promod3::loop::CYS_HA_INDEX,true);
}
@@ -947,7 +950,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// MET
- sidechain_infos_[MET].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[MET].has_hydrogens = (mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[MET].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::MET];
sidechain_infos_[MET].frm_t = param.frm_t[ost::conop::MET];
@@ -956,7 +959,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(MET, "SD", promod3::loop::MET_SD_INDEX,false);
AddInfo(MET, "CE", promod3::loop::MET_CE_INDEX,false);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(MET, "HB2", promod3::loop::MET_HB2_INDEX, true);
AddInfo(MET, "HB3", promod3::loop::MET_HB3_INDEX, true);
AddInfo(MET, "HG2", promod3::loop::MET_HG2_INDEX, true);
@@ -976,7 +979,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(MET, 0, 1); // SD
AddFRMRotatingParticle(MET, 0, 2); // CE
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(MET, 0, 3); // HB2
AddFRMRotatingParticle(MET, 0, 4); // HB3
AddFRMRotatingParticle(MET, 0, 5); // HG2
@@ -992,7 +995,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(MET, 1, 1); // SD
AddFRMRotatingParticle(MET, 1, 2); // CE
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(MET, 1, 3); // HB2
AddFRMFixParticle(MET, 1, 4); // HB3
AddFRMRotatingParticle(MET, 1, 5); // HG2
@@ -1008,7 +1011,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMFixParticle(MET, 2, 1);
AddFRMRotatingParticle(MET, 2, 2);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(MET, 2, 3); // HB2
AddFRMFixParticle(MET, 2, 4); // HB3
AddFRMFixParticle(MET, 2, 5); // HG2
@@ -1020,7 +1023,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 3;
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 10;
}
AddFRMFixParticle(MET, 0, cb_idx);
@@ -1028,18 +1031,18 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMFixParticle(MET, 2, cb_idx);
}
- backbone_infos_[MET].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[MET].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(MET, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(MET, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(MET, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(MET, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(MET, "H", promod3::loop::MET_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(MET, "H", promod3::loop::MET_H_INDEX, true);
}
@@ -1049,8 +1052,8 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// TRP
- sidechain_infos_[TRP].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[TRP].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[TRP].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::TRP];
sidechain_infos_[TRP].frm_t = param.frm_t[ost::conop::TRP];
@@ -1065,11 +1068,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(TRP, "CH2", promod3::loop::TRP_CH2_INDEX,false);
AddInfo(TRP, "CZ2", promod3::loop::TRP_CZ2_INDEX,false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddInfo(TRP, "HE1", promod3::loop::TRP_HE1_INDEX,true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(TRP, "HB2", promod3::loop::TRP_HB2_INDEX, true);
AddInfo(TRP, "HB3", promod3::loop::TRP_HB3_INDEX, true);
AddInfo(TRP, "HD1", promod3::loop::TRP_HD1_INDEX, true);
@@ -1095,11 +1098,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(TRP, 0, 7); // CH2
AddFRMRotatingParticle(TRP, 0, 8); // CZ2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(TRP, 0, 9); // HE1
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(TRP, 0, 10); // HB2
AddFRMRotatingParticle(TRP, 0, 11); // HB3
AddFRMRotatingParticle(TRP, 0, 12); // HD1
@@ -1121,11 +1124,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(TRP, 1, 7); // CH2
AddFRMRotatingParticle(TRP, 1, 8); // CZ2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(TRP, 1, 9);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(TRP, 1, 10); // HB2
AddFRMFixParticle(TRP, 1, 11); // HB3
AddFRMRotatingParticle(TRP, 1, 12); // HD1
@@ -1137,28 +1140,28 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 9;
- if(mode == POLAR_HYDROGEN_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE) {
cb_idx = 10;
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 17;
}
AddFRMFixParticle(TRP, 0, cb_idx);
AddFRMFixParticle(TRP, 1, cb_idx);
}
- backbone_infos_[TRP].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[TRP].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(TRP, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(TRP, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(TRP, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(TRP, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(TRP, "H", promod3::loop::TRP_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(TRP, "HA", promod3::loop::TRP_HA_INDEX, true);
}
@@ -1168,8 +1171,8 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// TYR
- sidechain_infos_[TYR].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[TYR].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[TYR].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::TYR];
sidechain_infos_[TYR].frm_t = param.frm_t[ost::conop::TYR];
@@ -1182,11 +1185,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(TYR, "CZ", promod3::loop::TYR_CZ_INDEX, false);
AddInfo(TYR, "OH", promod3::loop::TYR_OH_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddInfo(TYR, "HH", promod3::loop::TYR_HH_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(TYR, "HB2", promod3::loop::TYR_HB2_INDEX, true);
AddInfo(TYR, "HB3", promod3::loop::TYR_HB3_INDEX, true);
AddInfo(TYR, "HD1", promod3::loop::TYR_HD1_INDEX, true);
@@ -1199,7 +1202,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(TYR, "CB", promod3::loop::BB_CB_INDEX, false);
}
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddCustomHydrogenInfo(TYR, promod3::loop::TYR_HH_INDEX,
promod3::loop::TYR_CE1_INDEX,
promod3::loop::TYR_CZ_INDEX,
@@ -1217,11 +1220,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(TYR, 0, 5); // CZ
AddFRMRotatingParticle(TYR, 0, 6); // OH
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(TYR, 0, 7); // HH
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(TYR, 0, 8); // HB2
AddFRMRotatingParticle(TYR, 0, 9); // HB3
AddFRMRotatingParticle(TYR, 0, 10); // HD1
@@ -1240,11 +1243,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(TYR, 1, 5); // CZ
AddFRMRotatingParticle(TYR, 1, 6); // OH
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(TYR, 1, 7); // HH
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(TYR, 1, 8); // HB2
AddFRMFixParticle(TYR, 1, 9); // HB3
AddFRMRotatingParticle(TYR, 1, 10); // HD1
@@ -1254,7 +1257,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
}
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRule(TYR, promod3::loop::TYR_CZ_INDEX, promod3::loop::TYR_OH_INDEX,
param.TYR_CZ_OH_prefactors);
AddFRMFixParticle(TYR, 2, 0); // CG
@@ -1267,7 +1270,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(TYR, 2, 7);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(TYR, 2, 8); // HB2
AddFRMFixParticle(TYR, 2, 9); // HB3
AddFRMFixParticle(TYR, 2, 10); // HD1
@@ -1280,31 +1283,31 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 7;
- if(mode == POLAR_HYDROGEN_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE) {
cb_idx = 8;
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 14;
}
AddFRMFixParticle(TYR, 0, cb_idx);
AddFRMFixParticle(TYR, 1, cb_idx);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(TYR, 2, cb_idx);
}
}
- backbone_infos_[TYR].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[TYR].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(TYR, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(TYR, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(TYR, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(TYR, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(TYR, "H", promod3::loop::TYR_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(TYR, "HA", promod3::loop::TYR_HA_INDEX, true);
}
@@ -1314,8 +1317,8 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// THR
- sidechain_infos_[THR].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[THR].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[THR].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::THR];
sidechain_infos_[THR].frm_t = param.frm_t[ost::conop::THR];
@@ -1323,14 +1326,14 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(THR, "OG1", promod3::loop::THR_OG1_INDEX, false);
AddInfo(THR, "CG2", promod3::loop::THR_CG2_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddInfo(THR, "HG1", promod3::loop::THR_HG1_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(THR, "HB", promod3::loop::THR_HB_INDEX, true);
- AddInfo(THR, "HG21", promod3::loop::THR_HG22_INDEX, true);
- AddInfo(THR, "HG22", promod3::loop::THR_HG23_INDEX, true);
+ AddInfo(THR, "HG21", promod3::loop::THR_HG21_INDEX, true);
+ AddInfo(THR, "HG22", promod3::loop::THR_HG22_INDEX, true);
AddInfo(THR, "HG23", promod3::loop::THR_HG23_INDEX, true);
}
@@ -1338,7 +1341,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(THR, "CB", promod3::loop::BB_CB_INDEX, false);
}
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddCustomHydrogenInfo(THR, promod3::loop::THR_HG1_INDEX,
promod3::loop::BB_CA_INDEX, promod3::loop::BB_CB_INDEX,
promod3::loop::THR_OG1_INDEX,
@@ -1350,25 +1353,25 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(THR, 0, 0); // OG1
AddFRMRotatingParticle(THR, 0, 1); // CG2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(THR, 0, 2); // HG1
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(THR, 0, 3); // HB
AddFRMRotatingParticle(THR, 0, 4); // HG21
AddFRMRotatingParticle(THR, 0, 5); // HG22
AddFRMRotatingParticle(THR, 0, 6); // HG23
}
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRule(THR, promod3::loop::BB_CB_INDEX, promod3::loop::THR_OG1_INDEX,
param.THR_CB_OG1_prefactors);
AddFRMFixParticle(THR, 1, 0); // OG1
AddFRMFixParticle(THR, 1, 1); //CG2
AddFRMRotatingParticle(THR, 1, 2); // HG1
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(THR, 1, 3); // HB
AddFRMFixParticle(THR, 1, 4); // HG21
AddFRMFixParticle(THR, 1, 5); // HG22
@@ -1378,30 +1381,30 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 2;
- if(mode == POLAR_HYDROGEN_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE) {
cb_idx = 3;
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 7;
}
AddFRMFixParticle(THR, 0, cb_idx);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(THR, 1, cb_idx);
}
}
- backbone_infos_[THR].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[THR].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(THR, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(THR, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(THR, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(THR, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(THR, "H", promod3::loop::THR_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(THR, "HA", promod3::loop::THR_HA_INDEX, true);
}
@@ -1411,7 +1414,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// VAL
- sidechain_infos_[VAL].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[VAL].has_hydrogens = (mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[VAL].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::VAL];
sidechain_infos_[VAL].frm_t = param.frm_t[ost::conop::VAL];
@@ -1419,7 +1422,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(VAL, "CG1", promod3::loop::VAL_CG1_INDEX, false);
AddInfo(VAL, "CG2", promod3::loop::VAL_CG2_INDEX, false);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(VAL, "HB", promod3::loop::VAL_HB_INDEX, true);
AddInfo(VAL, "HG11", promod3::loop::VAL_HG11_INDEX, true);
AddInfo(VAL, "HG12", promod3::loop::VAL_HG12_INDEX, true);
@@ -1438,7 +1441,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(VAL, 0, 0); // CG1
AddFRMRotatingParticle(VAL, 0, 1); // CG2
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(VAL, 0, 2); // HB
AddFRMRotatingParticle(VAL, 0, 3); // HG11
AddFRMRotatingParticle(VAL, 0, 4); // HG12
@@ -1450,23 +1453,23 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 2;
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 9;
}
AddFRMFixParticle(VAL, 0, cb_idx);
}
- backbone_infos_[VAL].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[VAL].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(VAL, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(VAL, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(VAL, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(VAL, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(VAL, "H", promod3::loop::VAL_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(VAL, "HA", promod3::loop::VAL_HA_INDEX, true);
}
@@ -1476,7 +1479,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// ILE
- sidechain_infos_[ILE].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[ILE].has_hydrogens = (mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[ILE].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::ILE];
sidechain_infos_[ILE].frm_t = param.frm_t[ost::conop::ILE];
@@ -1485,7 +1488,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(ILE, "CG2", promod3::loop::ILE_CG2_INDEX, false);
AddInfo(ILE, "CD1", promod3::loop::ILE_CD1_INDEX, false);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(ILE, "HB", promod3::loop::ILE_HB_INDEX, true);
AddInfo(ILE, "HG12", promod3::loop::ILE_HG12_INDEX, true);
AddInfo(ILE, "HG13", promod3::loop::ILE_HG13_INDEX, true);
@@ -1507,7 +1510,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(ILE, 0, 1); // CG2
AddFRMRotatingParticle(ILE, 0, 2); // CD1
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(ILE, 0, 3); // HB
AddFRMRotatingParticle(ILE, 0, 4); // HG12
AddFRMRotatingParticle(ILE, 0, 5); // HG13
@@ -1526,7 +1529,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMFixParticle(ILE, 1, 1); // CG2
AddFRMRotatingParticle(ILE, 1, 2); // CD1
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(ILE, 1, 3); // HB
AddFRMRotatingParticle(ILE, 1, 4); // HG12
AddFRMRotatingParticle(ILE, 1, 5); // HG13
@@ -1540,25 +1543,25 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 3;
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 12;
}
AddFRMFixParticle(ILE, 0, cb_idx);
AddFRMFixParticle(ILE, 1, cb_idx);
}
- backbone_infos_[ILE].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[ILE].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(ILE, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(ILE, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(ILE, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(ILE, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(ILE, "H", promod3::loop::ILE_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(ILE, "HA", promod3::loop::ILE_HA_INDEX, true);
}
@@ -1568,7 +1571,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// LEU
- sidechain_infos_[LEU].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[LEU].has_hydrogens = (mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[LEU].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::LEU];
sidechain_infos_[LEU].frm_t = param.frm_t[ost::conop::LEU];
@@ -1577,7 +1580,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(LEU, "CD1", promod3::loop::LEU_CD1_INDEX, false);
AddInfo(LEU, "CD2", promod3::loop::LEU_CD2_INDEX, false);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(LEU, "HB2", promod3::loop::LEU_HB2_INDEX, true);
AddInfo(LEU, "HB3", promod3::loop::LEU_HB3_INDEX, true);
AddInfo(LEU, "HG", promod3::loop::LEU_HG_INDEX, true);
@@ -1600,7 +1603,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(LEU, 0, 1); // CD1
AddFRMRotatingParticle(LEU, 0, 2); // CD2
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(LEU, 0, 3); // HB2
AddFRMRotatingParticle(LEU, 0, 4); // HB3
AddFRMRotatingParticle(LEU, 0, 5); // HG
@@ -1618,7 +1621,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(LEU, 1, 1); // CG1
AddFRMRotatingParticle(LEU, 1, 2); // CG2
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(LEU, 1, 3); // HB2
AddFRMFixParticle(LEU, 1, 4); // HB3
AddFRMRotatingParticle(LEU, 1, 5); // HG
@@ -1632,25 +1635,25 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 3;
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 12;
}
AddFRMFixParticle(LEU, 0, cb_idx);
AddFRMFixParticle(LEU, 1, cb_idx);
}
- backbone_infos_[LEU].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[LEU].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(LEU, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(LEU, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(LEU, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(LEU, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(LEU, "H", promod3::loop::LEU_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(LEU, "HA", promod3::loop::LEU_HA_INDEX, true);
}
@@ -1665,7 +1668,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// subrotamer...
// PRO
- sidechain_infos_[PRO].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[PRO].has_hydrogens = (mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[PRO].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::PRO];
sidechain_infos_[PRO].frm_t = param.frm_t[ost::conop::PRO];
@@ -1673,7 +1676,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(PRO, "CG", promod3::loop::PRO_CG_INDEX, false);
AddInfo(PRO, "CD", promod3::loop::PRO_CD_INDEX, false);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(PRO, "HB2", promod3::loop::PRO_HB2_INDEX, true);
AddInfo(PRO, "HB3", promod3::loop::PRO_HB3_INDEX, true);
AddInfo(PRO, "HG2", promod3::loop::PRO_HG2_INDEX, true);
@@ -1686,13 +1689,13 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(PRO, "CB", promod3::loop::BB_CB_INDEX, false);
}
- backbone_infos_[PRO].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ backbone_infos_[PRO].has_hydrogens = (mode_ == FULL_ATOMIC_MODE);
AddBBInfo(PRO, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(PRO, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(PRO, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(PRO, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(PRO, "HA", promod3::loop::PRO_HA_INDEX, true);
}
@@ -1714,8 +1717,8 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// HSD
- sidechain_infos_[HSD].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[HSD].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[HSD].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::HIS];
sidechain_infos_[HSD].frm_t = param.frm_t[ost::conop::HIS];
@@ -1726,11 +1729,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(HSD, "CE1", promod3::loop::HIS_CE1_INDEX, false);
AddInfo(HSD, "NE2", promod3::loop::HIS_NE2_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddInfo(HSD, "HD1", promod3::loop::HIS_HD1_INDEX,true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(HSD, "HB2", promod3::loop::HIS_HB2_INDEX, true);
AddInfo(HSD, "HB3", promod3::loop::HIS_HB3_INDEX, true);
AddInfo(HSD, "HD2", promod3::loop::HIS_HD2_INDEX, true);
@@ -1749,11 +1752,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(HSD, 0, 3); // CE1
AddFRMRotatingParticle(HSD, 0, 4); // NE2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(HSD, 0, 5); // HD1
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(HSD, 0, 6); // HB2
AddFRMRotatingParticle(HSD, 0, 7); // HB3
AddFRMRotatingParticle(HSD, 0, 8); // HD2
@@ -1768,11 +1771,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(HSD, 1, 3); // CE1
AddFRMRotatingParticle(HSD, 1, 4); // NE2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(HSD, 1, 5); // HD1
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(HSD, 1, 6); // HB2
AddFRMRotatingParticle(HSD, 1, 7); // HB3
AddFRMRotatingParticle(HSD, 1, 8); // HD2
@@ -1781,28 +1784,28 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 5;
- if(mode == POLAR_HYDROGEN_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE) {
cb_idx = 6;
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 10;
}
AddFRMFixParticle(HSD, 0, cb_idx);
AddFRMFixParticle(HSD, 1, cb_idx);
}
- backbone_infos_[HSD].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[HSD].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(HSD, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(HSD, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(HSD, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(HSD, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(HSD, "H", promod3::loop::HIS_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(HSD, "HA", promod3::loop::HIS_HA_INDEX, true);
}
@@ -1812,8 +1815,8 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// HSE
- sidechain_infos_[HSE].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[HSE].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[HSE].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::HIS];
sidechain_infos_[HSE].frm_t = param.frm_t[ost::conop::HIS];
@@ -1824,11 +1827,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(HSE, "CE1", promod3::loop::HIS_CE1_INDEX, false);
AddInfo(HSE, "NE2", promod3::loop::HIS_NE2_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddInfo(HSE, "HE2", promod3::loop::HIS_HE2_INDEX,true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(HSE, "HB2", promod3::loop::HIS_HB2_INDEX, true);
AddInfo(HSE, "HB3", promod3::loop::HIS_HB3_INDEX, true);
AddInfo(HSE, "HD2", promod3::loop::HIS_HD2_INDEX, true);
@@ -1847,11 +1850,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(HSE, 0, 3); // CE1
AddFRMRotatingParticle(HSE, 0, 4); // NE2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(HSE, 0, 5); // HE2
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(HSE, 0, 6); // HB2
AddFRMRotatingParticle(HSE, 0, 7); // HB3
AddFRMRotatingParticle(HSE, 0, 8); // HD2
@@ -1866,11 +1869,11 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(HSE, 1, 3); // CE1
AddFRMRotatingParticle(HSE, 1, 4); // NE2
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(HSE, 1, 5); // HE2
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(HSE, 1, 6); // HB2
AddFRMRotatingParticle(HSE, 1, 7); // HB3
AddFRMRotatingParticle(HSE, 1, 8); // HD2
@@ -1879,28 +1882,28 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 5;
- if(mode == POLAR_HYDROGEN_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE) {
cb_idx = 6;
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 10;
}
AddFRMFixParticle(HSE, 0, cb_idx);
AddFRMFixParticle(HSE, 1, cb_idx);
}
- backbone_infos_[HSE].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[HSE].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(HSE, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(HSE, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(HSE, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(HSE, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(HSE, "H", promod3::loop::HIS_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(HSE, "HA", promod3::loop::HIS_HA_INDEX, true);
}
@@ -1917,7 +1920,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// PHE
- sidechain_infos_[PHE].has_hydrogens = (mode == FULL_ATOMIC_MODE);
+ sidechain_infos_[PHE].has_hydrogens = (mode_ == FULL_ATOMIC_MODE);
sidechain_infos_[PHE].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::PHE];
sidechain_infos_[PHE].frm_t = param.frm_t[ost::conop::PHE];
@@ -1929,7 +1932,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddInfo(PHE, "CE2", promod3::loop::PHE_CE2_INDEX, false);
AddInfo(PHE, "CZ", promod3::loop::PHE_CZ_INDEX, false);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(PHE, "HB2", promod3::loop::PHE_HB2_INDEX, true);
AddInfo(PHE, "HB3", promod3::loop::PHE_HB3_INDEX, true);
AddInfo(PHE, "HD1", promod3::loop::PHE_HD1_INDEX, true);
@@ -1952,7 +1955,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(PHE, 0, 4); // CE2
AddFRMRotatingParticle(PHE, 0, 5); // CZ
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMRotatingParticle(PHE, 0, 6); // HB2
AddFRMRotatingParticle(PHE, 0, 7); // HB3
AddFRMRotatingParticle(PHE, 0, 8); // HD1
@@ -1971,7 +1974,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
AddFRMRotatingParticle(PHE, 1, 4); // CE2
AddFRMRotatingParticle(PHE, 1, 5); // CZ
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddFRMFixParticle(PHE, 1, 6); // HB2
AddFRMFixParticle(PHE, 1, 7); // HB2
AddFRMRotatingParticle(PHE, 1, 8); // CD1
@@ -1983,25 +1986,25 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
int cb_idx = 6;
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
cb_idx = 13;
}
AddFRMFixParticle(PHE, 0, cb_idx);
AddFRMFixParticle(PHE, 1, cb_idx);
}
- backbone_infos_[PHE].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[PHE].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(PHE, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(PHE, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(PHE, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(PHE, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(PHE, "H", promod3::loop::PHE_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(PHE, "HA", promod3::loop::PHE_HA_INDEX, true);
}
@@ -2016,7 +2019,7 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
// If its full atomic, we only put the hydrogens in the sidechains
// if the CBeta is also there. Otherwise, everything goes into the
// backbone.
- sidechain_infos_[ALA].has_hydrogens = (mode == FULL_ATOMIC_MODE &&
+ sidechain_infos_[ALA].has_hydrogens = (mode_ == FULL_ATOMIC_MODE &&
cb_in_sidechain);
sidechain_infos_[ALA].internal_e_prefactor =
param.internal_e_prefactor[ost::conop::ALA];
@@ -2024,31 +2027,31 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
if(cb_in_sidechain) {
AddInfo(ALA, "CB", promod3::loop::BB_CB_INDEX, false);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddInfo(ALA, "HB1", promod3::loop::ALA_HB1_INDEX, true);
AddInfo(ALA, "HB2", promod3::loop::ALA_HB2_INDEX, true);
AddInfo(ALA, "HB3", promod3::loop::ALA_HB3_INDEX, true);
}
}
- backbone_infos_[ALA].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[ALA].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(ALA, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(ALA, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(ALA, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(ALA, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(ALA, "H", promod3::loop::ALA_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(ALA, "HA", promod3::loop::ALA_HA_INDEX, true);
}
if(!cb_in_sidechain) {
AddBBInfo(ALA, "CB", promod3::loop::BB_CB_INDEX, false);
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(ALA, "HB1", promod3::loop::ALA_HB1_INDEX, true);
AddBBInfo(ALA, "HB2", promod3::loop::ALA_HB2_INDEX, true);
AddBBInfo(ALA, "HB3", promod3::loop::ALA_HB3_INDEX, true);
@@ -2062,18 +2065,18 @@ RotamerLookup::RotamerLookup(bool cb_in_sidechain, RotamerLookupMode mode,
param.internal_e_prefactor[ost::conop::GLY];
sidechain_infos_[GLY].frm_t = param.frm_t[ost::conop::GLY];
- backbone_infos_[GLY].has_hydrogens = (mode == POLAR_HYDROGEN_MODE ||
- mode == FULL_ATOMIC_MODE);
+ backbone_infos_[GLY].has_hydrogens = (mode_ == POLAR_HYDROGEN_MODE ||
+ mode_ == FULL_ATOMIC_MODE);
AddBBInfo(GLY, "N", promod3::loop::BB_N_INDEX, false);
AddBBInfo(GLY, "CA", promod3::loop::BB_CA_INDEX, false);
AddBBInfo(GLY, "C", promod3::loop::BB_C_INDEX, false);
AddBBInfo(GLY, "O", promod3::loop::BB_O_INDEX, false);
- if(mode == POLAR_HYDROGEN_MODE || mode == FULL_ATOMIC_MODE) {
+ if(mode_ == POLAR_HYDROGEN_MODE || mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(GLY, "H", promod3::loop::GLY_H_INDEX, true);
}
- if(mode == FULL_ATOMIC_MODE) {
+ if(mode_ == FULL_ATOMIC_MODE) {
AddBBInfo(GLY, "HA2", promod3::loop::GLY_HA2_INDEX, true);
AddBBInfo(GLY, "HA3", promod3::loop::GLY_HA3_INDEX, true);
}
diff --git a/sidechain/src/rotamer_lookup.hh b/sidechain/src/rotamer_lookup.hh
index 50215ce8954beb932f97085d228702e26ddec380..9e804388b534918c138287be9c35bacab2765250 100644
--- a/sidechain/src/rotamer_lookup.hh
+++ b/sidechain/src/rotamer_lookup.hh
@@ -39,6 +39,10 @@ struct RotamerLookupParam {
RotamerLookupParam(bool default_parametrization = true) {
if(default_parametrization) {
+
+ mode = HEAVY_ATOM_MODE;
+ sample_his_protonation_states = false;
+
for(int i = 0; i < ost::conop::XXX + 1; ++i) {
frm_t[i] = 1.0;
internal_e_prefactor[i] = 1.0;
@@ -89,6 +93,15 @@ struct RotamerLookupParam {
}
}
+ // controls what atoms are defined in the rotamer lookup
+ RotamerLookupMode mode;
+
+ // if set to true, RotamerGroups will have two rotamers for each HIS rotamer.
+ // One with RotamerID HSE and one with RotamerID HSD. If your
+ // RotamerConstructor does not consider those different protonation states,
+ // you can set that to false...
+ bool sample_his_protonation_states;
+
// the internal energy prefactor of the constructed rotamers
Real internal_e_prefactor[ost::conop::XXX + 1];
@@ -196,6 +209,14 @@ struct CustomHydrogenInfo {
struct FRMRule {
FRMRule() { }
+
+ FRMRule(int idx_one, int idx_two): anchor_idx_one(idx_one),
+ anchor_idx_two(idx_two) { }
+
+ FRMRule(int idx_one, int idx_two,
+ const std::vector<Real>& prefactors): anchor_idx_one(idx_one),
+ anchor_idx_two(idx_two),
+ prefactors(prefactors) { }
int anchor_idx_one; // idx of heavy atom in RotamerConstructor::pos_buffer_
int anchor_idx_two; // idx of heavy atom in RotamerConstructor::pos_buffer_
@@ -224,7 +245,6 @@ class RotamerLookup{
public:
RotamerLookup(bool cb_in_sidechain,
- RotamerLookupMode mode,
const RotamerLookupParam& param = RotamerLookupParam());
// Data access
@@ -251,6 +271,14 @@ public:
return num_frm_particles_[id];
}
+ RotamerLookupMode GetMode() const {
+ return mode_;
+ }
+
+ bool SampleHISProtonationStates() const {
+ return sample_his_protonation_states_;
+ }
+
private:
void AddInfo(RotamerID id, const String& name, int idx, bool is_h) {
@@ -272,10 +300,7 @@ private:
void AddFRMRule(RotamerID id, int idx_one, int idx_two,
const std::vector<Real>& prefactors){
- frm_rules_[id].push_back(FRMRule());
- frm_rules_[id].back().anchor_idx_one = idx_one;
- frm_rules_[id].back().anchor_idx_two = idx_two;
- frm_rules_[id].back().prefactors = prefactors;
+ frm_rules_[id].push_back(FRMRule(idx_one, idx_two, prefactors));
}
void AddFRMFixParticle(RotamerID id, int rule_idx, int p_idx){
@@ -299,6 +324,7 @@ private:
int num_frm_particles_[XXX + 1];
RotamerLookupMode mode_;
+ bool sample_his_protonation_states_;
};
diff --git a/sidechain/src/scwrl3_rotamer_constructor.cc b/sidechain/src/scwrl3_rotamer_constructor.cc
index d5f9048bbb5cbcf1b220bff635983cdbfe94c694..06e9fadc1a725170b4ea817d074298eb9341f198 100644
--- a/sidechain/src/scwrl3_rotamer_constructor.cc
+++ b/sidechain/src/scwrl3_rotamer_constructor.cc
@@ -27,6 +27,9 @@ struct SCWRL3RotamerParam : public RotamerLookupParam {
SCWRL3RotamerParam() {
+ mode = HEAVY_ATOM_MODE;
+ sample_his_protonation_states = false;
+
// overwrite default internal_e_prefactor from base class
internal_e_prefactor[ost::conop::ARG] = 3.0;
internal_e_prefactor[ost::conop::ASN] = 3.0;
@@ -56,7 +59,7 @@ struct SCWRL3RotamerParam : public RotamerLookupParam {
SCWRL3RotamerConstructor::SCWRL3RotamerConstructor(bool cb_in_sidechain):
- RotamerConstructor(cb_in_sidechain, HEAVY_ATOM_MODE,
+ RotamerConstructor(cb_in_sidechain,
SCWRL3RotamerParam::Instance()) { }
void SCWRL3RotamerConstructor::AssignInternalEnergies(RRMRotamerGroupPtr group,
diff --git a/sidechain/src/scwrl4_rotamer_constructor.cc b/sidechain/src/scwrl4_rotamer_constructor.cc
index 687063f6cb9b59cdd9d9b3068f348b84a5f5a3af..7092e09dc48043dab72f00070b414f42d3afc0a3 100644
--- a/sidechain/src/scwrl4_rotamer_constructor.cc
+++ b/sidechain/src/scwrl4_rotamer_constructor.cc
@@ -220,6 +220,9 @@ struct SCWRL4RotamerParam : public RotamerLookupParam {
SCWRL4RotamerParam() {
+ mode = POLAR_HYDROGEN_MODE;
+ sample_his_protonation_states = true;
+
// overwrite default FRM prefactors from base class
ARG_CA_CB_prefactors[0] = -0.87;
ARG_CB_CG_prefactors[0] = -1.62;
@@ -823,7 +826,7 @@ struct SCWRL4RotamerParam : public RotamerLookupParam {
SCWRL4RotamerConstructor::SCWRL4RotamerConstructor(bool cb_in_sidechain):
- RotamerConstructor(cb_in_sidechain, POLAR_HYDROGEN_MODE,
+ RotamerConstructor(cb_in_sidechain,
SCWRL4RotamerParam::Instance()) { }
diff --git a/sidechain/src/vina_particle_scoring.cc b/sidechain/src/vina_particle_scoring.cc
new file mode 100644
index 0000000000000000000000000000000000000000..3701646958c3e9f099cf7be8cd5a1ec0fe2ccfef
--- /dev/null
+++ b/sidechain/src/vina_particle_scoring.cc
@@ -0,0 +1,132 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
+#include <promod3/sidechain/vina_particle_scoring.hh>
+#include <promod3/core/message.hh>
+
+
+namespace promod3 { namespace sidechain {
+
+VINAParam::VINAParam(VINAParticleType t,
+ const geom::Vec3& pos): pos_(pos),
+ radius_(VINAVDWRadii[t]),
+ collision_distance_(4.0) {
+
+ if(t==INVALID_VINAParticle) {
+ throw promod3::Error("Cannot initialize VINAParam with particle_type "
+ "INVALID_VINAParticle!");
+ }
+
+ hydrophobic_ = (t == C_VINAParticle || t == F_VINAParticle ||
+ t == Cl_VINAParticle || t == Br_VINAParticle ||
+ t == I_VINAParticle);
+
+ hbond_acceptor_ = (t == O_A_VINAParticle || t == N_A_VINAParticle ||
+ t == O_AD_VINAParticle || t == N_AD_VINAParticle);
+
+ hbond_donor_ = (t == O_D_VINAParticle || t == N_D_VINAParticle ||
+ t == O_AD_VINAParticle || t == N_AD_VINAParticle);
+}
+
+
+void VINAParam::ApplyTransform(const geom::Mat4& t) {
+
+ // get transformed pos
+ 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);
+ pos_ = geom::Vec3(a, b, c);
+}
+
+
+VINAParam* VINAParam::Copy() const {
+
+ VINAParam* return_ptr = new VINAParam(pos_, radius_,
+ collision_distance_,
+ hydrophobic_, hbond_acceptor_,
+ hbond_donor_);
+ return return_ptr;
+}
+
+
+bool VINAParam::EqualTo(PScoringParam* other) const {
+
+ if(other == NULL) return false;
+ if(other->GetScoringFunction() != VINA) return false;
+
+ // as the other scoring function is also VINA, we can assume that
+ // the following dynamic cast is fine...
+ VINAParam* p = dynamic_cast<VINAParam*>(other);
+
+ return pos_ == p->pos_ &&
+ radius_ == p->radius_ &&
+ collision_distance_ == p->collision_distance_ &&
+ hydrophobic_ == p->hydrophobic_ &&
+ hbond_acceptor_ == p->hbond_acceptor_ &&
+ hbond_donor_ == p->hbond_donor_;
+}
+
+
+Real VINAPairwiseScore(VINAParam* p_one, VINAParam* p_two) {
+
+ // linear weights of the different terms
+ const Real w_gaussian1 = -0.035579;
+ const Real w_gaussian2 = -0.005156;
+ const Real w_repulsion = 0.840245;
+ const Real w_hydrophobic = -0.035069;
+ const Real w_hbond = -0.587439;
+
+ Real r = geom::Distance(p_one->pos_, p_two->pos_);
+ Real d = r - (p_one->radius_ + p_two->radius_);
+
+ if(r > 8.0) {
+ return 0.0;
+ }
+
+ // do gaussian1
+ Real exp_one = d*Real(2.0);
+ Real e_gaussian1 = std::exp(-exp_one*exp_one);
+
+ // do gaussian2
+ Real exp_two = (d-Real(3.0))*Real(0.5);
+ Real e_gaussian2 = std::exp(-exp_two*exp_two);
+
+ // do repulsion
+ Real e_repulsion = (d < Real(0.0) ? d*d : 0.0);
+
+ // do hydrophobic
+ Real e_hydrophobic = 0.0;
+ if(p_one->hydrophobic_ && p_two->hydrophobic_ && d < Real(1.5)) {
+ e_hydrophobic = (d < Real(0.5) ? 1.0 : (Real(1.5) - d));
+ }
+
+ // do hbond
+ Real e_hbond = 0.0;
+ if(((p_one->hbond_acceptor_ && p_two->hbond_donor_) ||
+ (p_one->hbond_donor_ && p_two->hbond_acceptor_)) && d < Real(0.0)) {
+ e_hbond = (d < Real(-0.7) ? 1.0 : (d/Real(-0.7)));
+ }
+
+ Real e = w_gaussian1 * e_gaussian1 +
+ w_gaussian2 * e_gaussian2 +
+ w_repulsion * e_repulsion +
+ w_hydrophobic * e_hydrophobic +
+ w_hbond * e_hbond;
+
+ return e;
+}
+
+}}//ns
diff --git a/sidechain/src/vina_particle_scoring.hh b/sidechain/src/vina_particle_scoring.hh
new file mode 100644
index 0000000000000000000000000000000000000000..f001fffc398cb5ad30bbdadf0906ac3875efb2fa
--- /dev/null
+++ b/sidechain/src/vina_particle_scoring.hh
@@ -0,0 +1,104 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+#ifndef PROMOD3_VINA_PARTICLE_SCORING_HH
+#define PROMOD3_VINA_PARTICLE_SCORING_HH
+
+#include <ost/geom/mat4.hh>
+#include <ost/geom/vecmat3_op.hh>
+#include <promod3/sidechain/particle_scoring_base.hh>
+
+namespace promod3{ namespace sidechain{
+
+enum VINAParticleType {
+ O_D_VINAParticle, // oxygen hydrogen bond donor
+ N_D_VINAParticle, // nitrogen hydrogen bond donor
+ O_A_VINAParticle, // oxygen hydrogen bond acceptor
+ N_A_VINAParticle, // nitrogen hydrogen bond acceptor
+ O_AD_VINAParticle, // oxygen hydrogen bond acceptor and donor
+ N_AD_VINAParticle, // nitrogen hydrogen bond acceptor and donor
+ O_VINAParticle, // oxygen, neither hydrogen bond donor nor acceptor
+ N_VINAParticle, // nitrogen, neither hydrogen bond donor nor acceptor
+ S_VINAParticle, // sulfur
+ P_VINAParticle, // posphorus
+ C_P_VINAParticle, // polar carbon
+ C_VINAParticle, // hydrophobic carbon
+ F_VINAParticle, // fluorine
+ Cl_VINAParticle, // chlorine
+ Br_VINAParticle, // bromine
+ I_VINAParticle, // iodine
+ M_VINAParticle, // metals
+ INVALID_VINAParticle
+};
+
+const Real VINAVDWRadii[18] = {
+ 1.7, // O_D_VINAParticle
+ 1.8, // N_D_VINAParticle
+ 1.7, // O_A_VINAParticle
+ 1.8, // N_A_VINAParticle
+ 1.7, // O_AD_VINAParticle
+ 1.8, // N_AD_VINAParticle
+ 1.7, // O_VINAParticle
+ 1.8, // N_VINAParticle
+ 2.0, // S_VINAParticle
+ 2.1, // P_VINAParticle
+ 1.9, // C_P_VINAParticle
+ 1.9, // C_VINAParticle
+ 1.5, // F_VINAParticle
+ 1.8, // Cl_VINAParticle
+ 2.0, // Br_VINAParticle
+ 2.2, // I_VINAParticle
+ 1.2, // M_VINAParticle
+ 0.0 // INVALID
+};
+
+struct VINAParam : public PScoringParam {
+
+ VINAParam(VINAParticleType t, const geom::Vec3& pos);
+
+ VINAParam(const geom::Vec3& pos, Real r, Real c,
+ bool hydrophobic, bool hbond_acceptor,
+ bool hbond_donor): pos_(pos), radius_(r), collision_distance_(c),
+ hydrophobic_(hydrophobic),
+ hbond_acceptor_(hbond_acceptor),
+ hbond_donor_(hbond_donor) { }
+
+ virtual ~VINAParam() { }
+
+ virtual const geom::Vec3& GetPos() const { return pos_; }
+
+ virtual Real GetCollisionDistance() const { return collision_distance_; }
+
+ virtual void ApplyTransform(const geom::Mat4& t);
+
+ virtual VINAParam* Copy() const;
+
+ virtual bool EqualTo(PScoringParam* other) const;
+
+ virtual PScoringFunction GetScoringFunction() const { return VINA; }
+
+ geom::Vec3 pos_;
+ Real radius_;
+ Real collision_distance_;
+ bool hydrophobic_;
+ bool hbond_acceptor_;
+ bool hbond_donor_;
+};
+
+Real VINAPairwiseScore(VINAParam* p_one, VINAParam* p_two);
+
+}} //ns
+
+#endif
diff --git a/sidechain/src/vina_rotamer_constructor.cc b/sidechain/src/vina_rotamer_constructor.cc
new file mode 100644
index 0000000000000000000000000000000000000000..e5a170f39acc0ecd72c9b32d7094f04b93892a9c
--- /dev/null
+++ b/sidechain/src/vina_rotamer_constructor.cc
@@ -0,0 +1,521 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
+#include <algorithm>
+#include <promod3/sidechain/vina_rotamer_constructor.hh>
+#include <promod3/sidechain/vina_particle_scoring.hh>
+#include <promod3/core/runtime_profiling.hh>
+#include <promod3/core/message.hh>
+#include <promod3/core/runtime_profiling.hh>
+#include <ost/conop/conop.hh>
+
+
+namespace promod3 { namespace sidechain {
+
+struct VINARotamerParam : public RotamerLookupParam {
+
+ VINARotamerParam() {
+
+ mode = HEAVY_ATOM_MODE;
+ sample_his_protonation_states = true;
+
+ // overwrite default internal_e_prefactor from base class
+ // for now it's actually exactly the same...
+ // still needs some thinking/optimization
+ internal_e_prefactor[ost::conop::ARG] = 1.0;
+ internal_e_prefactor[ost::conop::ASN] = 1.0;
+ internal_e_prefactor[ost::conop::ASP] = 1.0;
+ internal_e_prefactor[ost::conop::GLN] = 1.0;
+ internal_e_prefactor[ost::conop::GLU] = 1.0;
+ internal_e_prefactor[ost::conop::LYS] = 1.0;
+ internal_e_prefactor[ost::conop::SER] = 1.0;
+ internal_e_prefactor[ost::conop::CYS] = 1.0;
+ internal_e_prefactor[ost::conop::MET] = 1.0;
+ internal_e_prefactor[ost::conop::TRP] = 1.0;
+ internal_e_prefactor[ost::conop::TYR] = 1.0;
+ internal_e_prefactor[ost::conop::THR] = 1.0;
+ internal_e_prefactor[ost::conop::VAL] = 1.0;
+ internal_e_prefactor[ost::conop::ILE] = 1.0;
+ internal_e_prefactor[ost::conop::LEU] = 1.0;
+ internal_e_prefactor[ost::conop::PRO] = 1.0;
+ internal_e_prefactor[ost::conop::HIS] = 1.0;
+ internal_e_prefactor[ost::conop::PHE] = 1.0;
+
+ particle_types_[promod3::loop::ALA_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::ALA_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ALA_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ALA_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::ALA_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::ARG_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::ARG_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ARG_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ARG_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::ARG_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::ARG_CG] = C_VINAParticle;
+ particle_types_[promod3::loop::ARG_CD] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ARG_NE] = N_D_VINAParticle;
+ particle_types_[promod3::loop::ARG_CZ] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ARG_NH1] = N_D_VINAParticle;
+ particle_types_[promod3::loop::ARG_NH2] = N_D_VINAParticle;
+ particle_types_[promod3::loop::ASN_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::ASN_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ASN_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ASN_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::ASN_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::ASN_CG] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ASN_OD1] = O_A_VINAParticle;
+ particle_types_[promod3::loop::ASN_ND2] = N_D_VINAParticle;
+ particle_types_[promod3::loop::ASP_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::ASP_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ASP_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ASP_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::ASP_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::ASP_CG] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ASP_OD1] = O_A_VINAParticle;
+ particle_types_[promod3::loop::ASP_OD2] = O_A_VINAParticle;
+ particle_types_[promod3::loop::GLN_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::GLN_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::GLN_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::GLN_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::GLN_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::GLN_CG] = C_VINAParticle;
+ particle_types_[promod3::loop::GLN_CD] = C_P_VINAParticle;
+ particle_types_[promod3::loop::GLN_OE1] = O_A_VINAParticle;
+ particle_types_[promod3::loop::GLN_NE2] = N_D_VINAParticle;
+ particle_types_[promod3::loop::GLU_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::GLU_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::GLU_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::GLU_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::GLU_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::GLU_CG] = C_VINAParticle;
+ particle_types_[promod3::loop::GLU_CD] = C_P_VINAParticle;
+ particle_types_[promod3::loop::GLU_OE1] = O_A_VINAParticle;
+ particle_types_[promod3::loop::GLU_OE2] = O_A_VINAParticle;
+ particle_types_[promod3::loop::LYS_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::LYS_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::LYS_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::LYS_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::LYS_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::LYS_CG] = C_VINAParticle;
+ particle_types_[promod3::loop::LYS_CD] = C_VINAParticle;
+ particle_types_[promod3::loop::LYS_CE] = C_P_VINAParticle;
+ particle_types_[promod3::loop::LYS_NZ] = N_D_VINAParticle;
+ particle_types_[promod3::loop::SER_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::SER_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::SER_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::SER_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::SER_CB] = C_P_VINAParticle;
+ particle_types_[promod3::loop::SER_OG] = O_AD_VINAParticle;
+ particle_types_[promod3::loop::CYS_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::CYS_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::CYS_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::CYS_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::CYS_CB] = C_P_VINAParticle;
+ particle_types_[promod3::loop::CYS_SG] = S_VINAParticle;
+ particle_types_[promod3::loop::MET_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::MET_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::MET_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::MET_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::MET_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::MET_CG] = C_P_VINAParticle;
+ particle_types_[promod3::loop::MET_SD] = S_VINAParticle;
+ particle_types_[promod3::loop::MET_CE] = C_P_VINAParticle;
+ particle_types_[promod3::loop::TRP_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::TRP_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::TRP_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::TRP_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::TRP_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::TRP_CG] = C_VINAParticle;
+ particle_types_[promod3::loop::TRP_CD1] = C_P_VINAParticle;
+ particle_types_[promod3::loop::TRP_CD2] = C_VINAParticle;
+ particle_types_[promod3::loop::TRP_CE2] = C_P_VINAParticle;
+ particle_types_[promod3::loop::TRP_NE1] = N_D_VINAParticle;
+ particle_types_[promod3::loop::TRP_CE3] = C_VINAParticle;
+ particle_types_[promod3::loop::TRP_CZ3] = C_VINAParticle;
+ particle_types_[promod3::loop::TRP_CH2] = C_VINAParticle;
+ particle_types_[promod3::loop::TRP_CZ2] = C_VINAParticle;
+ particle_types_[promod3::loop::TYR_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::TYR_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::TYR_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::TYR_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::TYR_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::TYR_CG] = C_VINAParticle;
+ particle_types_[promod3::loop::TYR_CD1] = C_VINAParticle;
+ particle_types_[promod3::loop::TYR_CD2] = C_VINAParticle;
+ particle_types_[promod3::loop::TYR_CE1] = C_VINAParticle;
+ particle_types_[promod3::loop::TYR_CE2] = C_VINAParticle;
+ particle_types_[promod3::loop::TYR_CZ] = C_P_VINAParticle;
+ particle_types_[promod3::loop::TYR_OH] = O_AD_VINAParticle;
+ particle_types_[promod3::loop::THR_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::THR_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::THR_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::THR_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::THR_CB] = C_P_VINAParticle;
+ particle_types_[promod3::loop::THR_OG1] = O_AD_VINAParticle;
+ particle_types_[promod3::loop::THR_CG2]= C_VINAParticle;
+ particle_types_[promod3::loop::VAL_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::VAL_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::VAL_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::VAL_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::VAL_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::VAL_CG1] = C_VINAParticle;
+ particle_types_[promod3::loop::VAL_CG2] = C_VINAParticle;
+ particle_types_[promod3::loop::ILE_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::ILE_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ILE_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::ILE_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::ILE_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::ILE_CG1] = C_VINAParticle;
+ particle_types_[promod3::loop::ILE_CG2] = C_VINAParticle;
+ particle_types_[promod3::loop::ILE_CD1] = C_VINAParticle;
+ particle_types_[promod3::loop::LEU_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::LEU_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::LEU_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::LEU_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::LEU_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::LEU_CG] = C_VINAParticle;
+ particle_types_[promod3::loop::LEU_CD1] = C_VINAParticle;
+ particle_types_[promod3::loop::LEU_CD2] = C_VINAParticle;
+ particle_types_[promod3::loop::GLY_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::GLY_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::GLY_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::GLY_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::PRO_N] = N_VINAParticle;
+ particle_types_[promod3::loop::PRO_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::PRO_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::PRO_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::PRO_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::PRO_CG] = C_VINAParticle;
+ particle_types_[promod3::loop::PRO_CD] = C_P_VINAParticle;
+ particle_types_[promod3::loop::PHE_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::PHE_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::PHE_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::PHE_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::PHE_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::PHE_CG] = C_VINAParticle;
+ particle_types_[promod3::loop::PHE_CD1] = C_VINAParticle;
+ particle_types_[promod3::loop::PHE_CD2] = C_VINAParticle;
+ particle_types_[promod3::loop::PHE_CE1] = C_VINAParticle;
+ particle_types_[promod3::loop::PHE_CE2] = C_VINAParticle;
+ particle_types_[promod3::loop::PHE_CZ] = C_VINAParticle;
+
+ // hack for histidine... let's just use HSD as default...
+ // explicit requests for HSD and HSE will be handled by the
+ // GetParticleType function
+ particle_types_[promod3::loop::HIS_N] = N_D_VINAParticle;
+ particle_types_[promod3::loop::HIS_CA] = C_P_VINAParticle;
+ particle_types_[promod3::loop::HIS_C] = C_P_VINAParticle;
+ particle_types_[promod3::loop::HIS_O] = O_A_VINAParticle;
+ particle_types_[promod3::loop::HIS_CB] = C_VINAParticle;
+ particle_types_[promod3::loop::HIS_CG] = C_P_VINAParticle;
+ particle_types_[promod3::loop::HIS_ND1] = N_D_VINAParticle;
+ particle_types_[promod3::loop::HIS_CD2] = C_P_VINAParticle;
+ particle_types_[promod3::loop::HIS_CE1] = C_P_VINAParticle;
+ particle_types_[promod3::loop::HIS_NE2] = N_A_VINAParticle;
+ }
+
+ static const VINARotamerParam& Instance() {
+ static VINARotamerParam vina_param;
+ return vina_param;
+ }
+
+ VINAParticleType GetParticleType(RotamerID rot_id, int atom_idx,
+ bool n_ter) const {
+
+ // all backbone nitrogens are hydrogen bond donors for n-termini
+ // (also proline)
+ if(n_ter && atom_idx == promod3::loop::BB_N_INDEX) {
+ return N_D_VINAParticle;
+ }
+
+ // this is an ugly hack for histidine
+ if(rot_id == HSD && atom_idx == promod3::loop::HIS_ND1_INDEX) {
+ return N_D_VINAParticle;
+ }
+ if(rot_id == HSD && atom_idx == promod3::loop::HIS_NE2_INDEX) {
+ return N_A_VINAParticle;
+ }
+
+ if(rot_id == HSE && atom_idx == promod3::loop::HIS_ND1_INDEX) {
+ return N_A_VINAParticle;
+ }
+ if(rot_id == HSE && atom_idx == promod3::loop::HIS_NE2_INDEX) {
+ return N_D_VINAParticle;
+ }
+
+ ost::conop::AminoAcid aa = RotIDToAA(rot_id);
+ promod3::loop::AminoAcidAtom aaa =
+ promod3::loop::AminoAcidLookup::GetInstance().GetAAA(aa, atom_idx);
+ return particle_types_[aaa];
+ }
+
+ VINAParticleType GetParticleType(const ost::mol::AtomHandle& at) const {
+
+ String ele = at.GetElement();
+ std::transform(ele.begin(), ele.end(), ele.begin(), ::toupper);
+
+ if(ele == "H" || ele == "D") {
+ return INVALID_VINAParticle;
+ }
+
+ if(ele == "C") {
+ ost::mol::AtomHandleList bound_to = at.GetBondPartners();
+ for(ost::mol::AtomHandleList::const_iterator it = bound_to.begin();
+ it != bound_to.end(); ++it) {
+ String it_ele = it->GetElement();
+ std::transform(it_ele.begin(), it_ele.end(), it_ele.begin(), ::toupper);
+ if(!(it_ele == "C" || it_ele == "H" || it_ele == "D")) {
+ return C_P_VINAParticle;
+ }
+ }
+ return C_VINAParticle;
+ }
+
+ if(ele == "N") {
+
+ bool is_hbond_donor = false;
+ bool is_hbond_acceptor = false;
+
+ // check if user defined protonation states
+ if(at.HasProp("is_hbond_acceptor") && at.HasProp("is_hbond_donor")) {
+ is_hbond_donor = at.GetBoolProp("is_hbond_donor");
+ is_hbond_acceptor = at.GetBoolProp("is_hbond_acceptor");
+ } else {
+ ost::mol::AtomHandleList bound_to = at.GetBondPartners();
+ for(ost::mol::AtomHandleList::const_iterator it = bound_to.begin();
+ it != bound_to.end(); ++it) {
+ String it_ele = it->GetElement();
+ std::transform(it_ele.begin(), it_ele.end(), it_ele.begin(), ::toupper);
+ if(it_ele == "H" || it_ele == "D") {
+ is_hbond_donor = true;
+ break;
+ }
+ }
+ // THIS IS WRONG (but works most of the time)
+ // needs better logic
+ if(at.GetBondCount() < 3) {
+ is_hbond_acceptor = true;
+ }
+ }
+
+ if(is_hbond_acceptor && is_hbond_donor) {
+ return N_AD_VINAParticle;
+ }
+ if(is_hbond_acceptor) {
+ return N_A_VINAParticle;
+ }
+ if(is_hbond_donor) {
+ return N_D_VINAParticle;
+ }
+ return N_VINAParticle;
+ }
+
+ if(ele == "O") {
+
+ bool is_hbond_donor = false;
+ bool is_hbond_acceptor = false;
+
+ // check if user defined protonation states
+ if(at.HasProp("is_hbond_acceptor") && at.HasProp("is_hbond_donor")) {
+ is_hbond_donor = at.GetBoolProp("is_hbond_donor");
+ is_hbond_acceptor = at.GetBoolProp("is_hbond_acceptor");
+ } else {
+ ost::mol::AtomHandleList bound_to = at.GetBondPartners();
+ for(ost::mol::AtomHandleList::const_iterator it = bound_to.begin();
+ it != bound_to.end(); ++it) {
+ String it_ele = it->GetElement();
+ std::transform(it_ele.begin(), it_ele.end(), it_ele.begin(), ::toupper);
+ if(it_ele == "H" || it_ele == "D") {
+ is_hbond_donor = true;
+ break;
+ }
+ }
+ // let's just assume that every oxygen can be an acceptor
+ is_hbond_acceptor = true;
+ }
+
+ if(is_hbond_acceptor && is_hbond_donor) {
+ return O_AD_VINAParticle;
+ }
+ if(is_hbond_acceptor) {
+ return O_A_VINAParticle;
+ }
+ if(is_hbond_donor) {
+ return O_D_VINAParticle;
+ }
+ return O_VINAParticle;
+ }
+
+ if(ele == "S") {
+ return S_VINAParticle;
+ }
+
+ if(ele == "P") {
+ return P_VINAParticle;
+ }
+
+ if(ele == "F") {
+ return F_VINAParticle;
+ }
+
+ if(ele == "CL") {
+ return Cl_VINAParticle;
+ }
+
+ if(ele == "BR") {
+ return Br_VINAParticle;
+ }
+
+ if(ele == "I") {
+ return I_VINAParticle;
+ }
+
+ if(ele == "MG" || ele == "MN" || ele == "ZN" ||
+ ele == "CA" || ele == "FE") {
+ return M_VINAParticle;
+ }
+
+ return INVALID_VINAParticle;
+ }
+
+ VINAParticleType particle_types_[promod3::loop::XXX_NUM_ATOMS];
+};
+
+
+VINARotamerConstructor::VINARotamerConstructor(bool cb_in_sidechain):
+ RotamerConstructor(cb_in_sidechain,
+ VINARotamerParam::Instance()) { }
+
+void VINARotamerConstructor::AssignInternalEnergies(RRMRotamerGroupPtr group,
+ RotamerID id,
+ uint residue_index,
+ Real phi, Real psi,
+ bool n_ter, bool c_ter) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "VINARotamerConstructor::AssignInternalEnergies", 2);
+
+ Real max_p = group->GetMaxP();
+ for(uint i = 0; i < group->size(); ++i){
+ RRMRotamerPtr r = (*group)[i];
+ Real internal_e_prefactor = r->GetInternalEnergyPrefactor();
+ Real probability = r->GetProbability();
+ Real e = -internal_e_prefactor * std::log(probability/max_p);
+ r->SetInternalEnergy(e);
+ }
+}
+
+
+void VINARotamerConstructor::AssignInternalEnergies(FRMRotamerGroupPtr group,
+ RotamerID id,
+ uint residue_index,
+ Real phi, Real psi,
+ bool n_ter, bool c_ter) {
+
+ core::ScopedTimerPtr prof = core::StaticRuntimeProfiler::StartScoped(
+ "VINARotamerConstructor::AssignInternalEnergies", 2);
+
+ Real max_p = group->GetMaxP();
+ for(uint i = 0; i < group->size(); ++i){
+ FRMRotamerPtr r = (*group)[i];
+ Real internal_e_prefactor = r->GetInternalEnergyPrefactor();
+ Real probability = r->GetProbability();
+ Real e = -internal_e_prefactor * std::log(probability/max_p);
+ r->SetInternalEnergy(e);
+ }
+}
+
+
+FrameResiduePtr VINARotamerConstructor::ConstructFrameResidueHeuristic(
+ const ost::mol::ResidueHandle& res,
+ uint residue_index) {
+
+ std::vector<Particle> particle_vec;
+ this->GenerateParticleVec(res, particle_vec);
+ FrameResiduePtr ptr(new FrameResidue(particle_vec, residue_index));
+ return ptr;
+}
+
+RRMRotamerPtr VINARotamerConstructor::ConstructRRMRotamerHeuristic(
+ const ost::mol::ResidueHandle& res) {
+
+ std::vector<Particle> particle_vec;
+ this->GenerateParticleVec(res, particle_vec);
+ RRMRotamerPtr ptr(new RRMRotamer(particle_vec));
+ return ptr;
+}
+
+FRMRotamerPtr VINARotamerConstructor::ConstructFRMRotamerHeuristic(
+ const ost::mol::ResidueHandle& res) {
+
+ std::vector<Particle> particle_vec;
+ this->GenerateParticleVec(res, particle_vec);
+ FRMRotamerPtr ptr(new FRMRotamer(particle_vec, 1.0));
+ std::vector<int> subrotamer_definition;
+ for(uint i = 0; i < particle_vec.size(); ++i) {
+ subrotamer_definition.push_back(i);
+ }
+ ptr->AddSubrotamerDefinition(subrotamer_definition);
+ return ptr;
+}
+
+
+void VINARotamerConstructor::ParametrizeParticle(int at_idx,
+ bool is_hydrogen,
+ Particle& particle) {
+
+ if(is_hydrogen) {
+ throw promod3::Error("Expect no hydrogen in VINARotamerConstructor!");
+ }
+
+ VINAParticleType t;
+ geom::Vec3 pos;
+
+ // let's say terminal oxygens can be both, hydrogen bond donors
+ // and acceptors
+ if(at_idx == -2) {
+ t = O_AD_VINAParticle;
+ pos = terminal_o_pos_;
+ } else if (at_idx == -1){
+ t = O_AD_VINAParticle;
+ pos = terminal_oxt_pos_;
+ } else {
+ t = VINARotamerParam::Instance().GetParticleType(id_, at_idx, n_ter_);
+ pos = pos_buffer_->GetPos(id_, at_idx);
+ }
+
+ VINAParam* p = new VINAParam(t, pos);
+ particle.SetSParam(p);
+}
+
+void VINARotamerConstructor::GenerateParticleVec(const ost::mol::ResidueHandle& res,
+ std::vector<Particle>& particle_vec) const {
+
+ particle_vec.clear();
+ ost::mol::AtomHandleList at_list = res.GetAtomList();
+ for(ost::mol::AtomHandleList::const_iterator at_it = at_list.begin();
+ at_it != at_list.end(); ++at_it) {
+ VINAParticleType t = VINARotamerParam::Instance().GetParticleType(*at_it);
+ if(t==INVALID_VINAParticle) {
+ continue; // hydrogens...
+ }
+ geom::Vec3 pos = at_it->GetPos();
+ VINAParam* p = new VINAParam(t, pos);
+ particle_vec.push_back(Particle(at_it->GetName(), p));
+ }
+}
+
+}} //ns
diff --git a/sidechain/src/vina_rotamer_constructor.hh b/sidechain/src/vina_rotamer_constructor.hh
new file mode 100644
index 0000000000000000000000000000000000000000..6841a596c217a20c9b3e96f7e0b332108d0208f5
--- /dev/null
+++ b/sidechain/src/vina_rotamer_constructor.hh
@@ -0,0 +1,70 @@
+// Copyright (c) 2013-2018, SIB - Swiss Institute of Bioinformatics and
+// Biozentrum - University of Basel
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+
+#ifndef PROMOD3_VINA_ROTAMER_CONSTRUCTOR_HH
+#define PROMOD3_VINA_ROTAMER_CONSTRUCTOR_HH
+
+#include <promod3/sidechain/rotamer_constructor.hh>
+
+namespace promod3 { namespace sidechain {
+
+class VINARotamerConstructor;
+typedef boost::shared_ptr<VINARotamerConstructor> VINARotamerConstructorPtr;
+
+class VINARotamerConstructor : public RotamerConstructor{
+
+public:
+
+ VINARotamerConstructor(bool cb_in_sidechain = false);
+
+ virtual ~VINARotamerConstructor() { }
+
+ // Assign internal energies to rotamer groups
+ virtual void AssignInternalEnergies(RRMRotamerGroupPtr group,
+ RotamerID id,
+ uint residue_index,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false);
+
+ virtual void AssignInternalEnergies(FRMRotamerGroupPtr group,
+ RotamerID id,
+ uint residue_index,
+ Real phi = -1.0472,
+ Real psi = -0.7854,
+ bool n_ter = false,
+ bool c_ter = false);
+
+ FrameResiduePtr ConstructFrameResidueHeuristic(
+ const ost::mol::ResidueHandle& res, uint residue_index);
+
+ RRMRotamerPtr ConstructRRMRotamerHeuristic(const ost::mol::ResidueHandle& res);
+
+ FRMRotamerPtr ConstructFRMRotamerHeuristic(const ost::mol::ResidueHandle& res);
+
+private:
+
+ virtual void ParametrizeParticle(int atom_idx, bool is_hydrogen,
+ Particle& p);
+
+ void GenerateParticleVec(const ost::mol::ResidueHandle& res,
+ std::vector<Particle>& particle_vec) const;
+};
+
+}} // ns
+
+#endif
diff --git a/sidechain/tests/test_frame_construction.cc b/sidechain/tests/test_frame_construction.cc
index 893b1f130db866c4120b140e17f79e841ead705d..dff01780772f5a617a61ed784c70f90ca130c83d 100644
--- a/sidechain/tests/test_frame_construction.cc
+++ b/sidechain/tests/test_frame_construction.cc
@@ -19,7 +19,6 @@
#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>
diff --git a/sidechain/tests/test_rotamers.cc b/sidechain/tests/test_rotamers.cc
index 7524af71093b8d86dd8270d475bc94b4e13a3543..8369c5dddbb4b3af820cbbe00508de29323c36ac 100644
--- a/sidechain/tests/test_rotamers.cc
+++ b/sidechain/tests/test_rotamers.cc
@@ -19,7 +19,6 @@
#include <promod3/core/message.hh>
#define BOOST_TEST_DYN_LINK
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>
#include <promod3/sidechain/sidechain_object_loader.hh>
#include <promod3/loop/all_atom_positions.hh>
diff --git a/sidechain/tests/tests.cc b/sidechain/tests/tests.cc
index bfcbfd198384cb41889ca820c948fa813c243dc6..91b6e2f7710389ef503812eae2ab8a65a134f5cb 100644
--- a/sidechain/tests/tests.cc
+++ b/sidechain/tests/tests.cc
@@ -16,6 +16,4 @@
#define BOOST_TEST_DYN_LINK
#define BOOST_TEST_MODULE promod3_sidechain
-#define BOOST_AUTO_TEST_MAIN
#include <boost/test/unit_test.hpp>
-#include <boost/test/auto_unit_test.hpp>