Merge branch 'release-2.1.0'

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
 --------------------------------------------------------------------------------
 

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)

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" )

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"

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
 

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();
 

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

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

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

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>

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>

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>

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>

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|

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/

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

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|

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
 --------------------------------------------------------------------------------
 

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

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