wrap_mol_alg.cc

//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
//------------------------------------------------------------------------------

#include <boost/python.hpp>
#include <boost/python/raw_function.hpp>
#include <boost/python/suite/indexing/map_indexing_suite.hpp>
#include <ost/log.hh>
#include <ost/config.hh>
#include <ost/mol/alg/local_dist_diff_test.hh>
#include <ost/mol/alg/distance_test_common.hh>
#include <ost/mol/alg/distance_rmsd_test.hh>
#include <ost/mol/alg/superpose_frames.hh>
#include <ost/mol/alg/filter_clashes.hh>
#include <ost/mol/alg/consistency_checks.hh>
#include <ost/mol/alg/pdbize.hh>
#include <ost/mol/alg/contact_overlap.hh>
#include <ost/mol/alg/construct_cbeta.hh>
#include <ost/export_helper/pair_to_tuple_conv.hh>
#include <ost/export_helper/vec_to_list_conv.hh>


using namespace boost::python;
using namespace ost;

void export_svdSuperPose();
void export_TrajectoryAnalysis();
void export_StructureAnalysis();
void export_Clash();
void export_NonStandard();
void export_Molck();
void export_contact_overlap();
void export_accessibility();
void export_sec_struct();
void export_sec_struct_segments();
void export_find_membrane();
void export_entity_to_density();
void export_biounit();

namespace {
  
std::pair<long int,long int> (*lddt_a)(const mol::EntityView&, const mol::alg::GlobalRDMap& , std::vector<Real>, int, const String&)=&mol::alg::LocalDistDiffTest;
Real (*lddt_c)(const mol::EntityView&, const mol::EntityView& , Real, Real, const String&)=&mol::alg::LocalDistDiffTest;
// Real (*lddt_d)(const mol::EntityView&, std::vector<mol::EntityView>&, const mol::alg::GlobalRDMap&, mol::alg::lDDTSettings&)=&mol::alg::LocalDistDiffTest;
Real (*lddt_b)(const seq::AlignmentHandle&,Real, Real, int, int)=&mol::alg::LocalDistDiffTest;
std::pair<mol::EntityView,mol::alg::ClashingInfo> (*fc_a)(const mol::EntityView&, const mol::alg::ClashingDistances&,bool)=&mol::alg::FilterClashes;
std::pair<mol::EntityView,mol::alg::ClashingInfo> (*fc_b)(const mol::EntityHandle&, const mol::alg::ClashingDistances&, bool)=&mol::alg::FilterClashes;
std::pair<mol::EntityView,mol::alg::StereoChemistryInfo> (*csc_a)(const mol::EntityView&, const mol::alg::StereoChemicalParams&, const mol::alg::StereoChemicalParams&, Real, Real, bool)=&mol::alg::CheckStereoChemistry;
std::pair<mol::EntityView,mol::alg::StereoChemistryInfo> (*csc_b)(const mol::EntityHandle&, const mol::alg::StereoChemicalParams&, const mol::alg::StereoChemicalParams&, Real, Real, bool)=&mol::alg::CheckStereoChemistry;
mol::CoordGroupHandle (*superpose_frames1)(mol::CoordGroupHandle&, mol::EntityView&, int, int, int)=&mol::alg::SuperposeFrames;
mol::CoordGroupHandle (*superpose_frames2)(mol::CoordGroupHandle&,  mol::EntityView&, mol::EntityView&, int, int)=&mol::alg::SuperposeFrames;


Real lddt_d(const mol::EntityView& model, list& reference_list, const mol::alg::GlobalRDMap& distance_list, mol::alg::lDDTSettings& settings){
  int reference_list_length = boost::python::extract<int>(reference_list.attr("__len__")());
  std::vector<ost::mol::EntityView> reference_list_vector(reference_list_length);
  
  for (int i=0; i<reference_list_length; i++) {
    reference_list_vector[i] = boost::python::extract<ost::mol::EntityView>(reference_list[i]);
  }

  return LocalDistDiffTest(model, reference_list_vector, distance_list, settings);
}

ost::mol::alg::StereoChemicalParams fill_stereochemical_params_wrapper (const String& header, const list& stereo_chemical_props_file)  
{
  int stereo_chemical_props_file_length = boost::python::extract<int>(stereo_chemical_props_file.attr("__len__")());
  std::vector<String> stereo_chemical_props_file_vector;
  
  for (int i=0; i<stereo_chemical_props_file_length; i++) {
    String extracted_string = boost::python::extract<String>(stereo_chemical_props_file[i]);
    stereo_chemical_props_file_vector.push_back(extracted_string);    
  }
  return ost::mol::alg::FillStereoChemicalParams(header,stereo_chemical_props_file_vector);
}

ost::mol::alg::ClashingDistances fill_clashing_distances_wrapper (const list& stereo_chemical_props_file)
{
  int stereo_chemical_props_file_length = boost::python::extract<int>(stereo_chemical_props_file.attr("__len__")());
  std::vector<String> stereo_chemical_props_file_vector(stereo_chemical_props_file_length);
  
  for (int i=0; i<stereo_chemical_props_file_length; i++) {
    stereo_chemical_props_file_vector[i] = boost::python::extract<char const*>(stereo_chemical_props_file[i]);
  }
 
 return ost::mol::alg::FillClashingDistances(stereo_chemical_props_file_vector);
}

ost::mol::alg::GlobalRDMap create_distance_list_from_multiple_references(const list& reference_list, const list& cutoff_list, int sequence_separation, Real max_dist)
{
  int reference_list_length = boost::python::extract<int>(reference_list.attr("__len__")());
  std::vector<ost::mol::EntityView> reference_list_vector(reference_list_length);
  
  for (int i=0; i<reference_list_length; i++) {
    reference_list_vector[i] = boost::python::extract<ost::mol::EntityView>(reference_list[i]);
  }

  int cutoff_list_length = boost::python::extract<int>(cutoff_list.attr("__len__")());
  std::vector<Real> cutoff_list_vector(cutoff_list_length);
  
  for (int i=0; i<cutoff_list_length; i++) {
    cutoff_list_vector[i] = boost::python::extract<Real>(cutoff_list[i]);
  }
  return ost::mol::alg::CreateDistanceListFromMultipleReferences(reference_list_vector, cutoff_list_vector, sequence_separation, max_dist);  	
}

object lDDTSettingsInitWrapper(tuple args, dict kwargs){

  object self = args[0];
  args = tuple(args.slice(1,_));

  Real radius = 15.0;
  if(kwargs.contains("radius")){
    radius = extract<Real>(kwargs["radius"]);
    kwargs["radius"].del();
  }

  int sequence_separation = 0;
  if(kwargs.contains("sequence_separation")){
    sequence_separation = extract<int>(kwargs["sequence_separation"]);
    kwargs["sequence_separation"].del();
  }

  std::vector<Real> cutoffs;
  if(kwargs.contains("cutoffs")){
    list cutoff_list = extract<list>(kwargs["cutoffs"]);
    int cutoff_list_length = boost::python::extract<int>(cutoff_list.attr("__len__")());
    for (int i=0; i<cutoff_list_length; i++) {
      cutoffs.push_back(boost::python::extract<Real>(cutoff_list[i]));
    }
    kwargs["cutoffs"].del();
  } else {
    cutoffs.push_back(0.5);
    cutoffs.push_back(1.0);
    cutoffs.push_back(2.0);
    cutoffs.push_back(4.0);
  }

  String label = "locallddt";
  if(kwargs.contains("label")){
    label = extract<String>(kwargs["label"]);
    kwargs["label"].del();
  }

  if(len(kwargs) > 0){
    std::stringstream ss;
    ss << "Invalid keywords observed when setting up lDDTSettings! ";
    ss << "Or did you pass the same keyword twice? ";
    ss << "Valid keywords are: radius, ";
    ss << "sequence_separation, parameter_file_path, ";
    ss << "cutoffs, label!";
    throw std::invalid_argument(ss.str());
  }

  return self.attr("__init__")(radius, 
                               sequence_separation,
                               cutoffs,
                               label);
}

object lDDTScorerInitWrapper(tuple args, dict kwargs){

  object self = args[0];
  args = tuple(args.slice(1, len(args)));

  std::vector<ost::mol::EntityView> reference_list_vector;
  if(kwargs.contains("references")){
    list reference_list = boost::python::extract<list>(kwargs["references"]);
    int reference_list_length = boost::python::extract<int>(reference_list.attr("__len__")());
    for (int i=0; i<reference_list_length; i++) {
      reference_list_vector.push_back(boost::python::extract<ost::mol::EntityView>(reference_list[i]));
    }
    kwargs["references"].del();
  } else {
    throw std::invalid_argument("'references' argument is required");
  }

  ost::mol::EntityView model;
  if(kwargs.contains("model")){
    model = boost::python::extract<ost::mol::EntityView>(kwargs["model"]);
    kwargs["model"].del();
  } else {
    throw std::invalid_argument("'model' argument is required");
  }

  ost::mol::alg::lDDTSettings settings;
  if(kwargs.contains("settings")){
    settings = extract<ost::mol::alg::lDDTSettings>(kwargs["settings"]);
    kwargs["settings"].del();
  } else {
    throw std::invalid_argument("'settings' argument is required");
  }

  if(len(kwargs) > 0){
    std::stringstream ss;
    ss << "Invalid keywords observed when setting up lDDTScorer! ";
    ss << "Or did you pass the same keyword twice? ";
    ss << "Valid keywords are: references, model and settings!";
    throw std::invalid_argument(ss.str());
  }

  return self.attr("__init__")(reference_list_vector,
                               model,
                               settings);
}


void clean_lddt_references_wrapper(const list& reference_list)
{
  int reference_list_length = boost::python::extract<int>(reference_list.attr("__len__")());
  std::vector<ost::mol::EntityView> reference_list_vector(reference_list_length);
  
  for (int i=0; i<reference_list_length; i++) {
    reference_list_vector[i] = boost::python::extract<ost::mol::EntityView>(reference_list[i]);
  }
 
 return ost::mol::alg::CleanlDDTReferences(reference_list_vector);
}

ost::mol::alg::GlobalRDMap prepare_lddt_global_rdmap_wrapper(const list& reference_list,
                                                             list& cutoff_list,
                                                             int sequence_separation,
                                                             Real max_dist)
{
  int reference_list_length = boost::python::extract<int>(reference_list.attr("__len__")());
  std::vector<ost::mol::EntityView> reference_list_vector(reference_list_length);
  
  for (int i=0; i<reference_list_length; i++) {
    reference_list_vector[i] = boost::python::extract<ost::mol::EntityView>(reference_list[i]);
  }

  int cutoff_list_length = boost::python::extract<int>(cutoff_list.attr("__len__")());
  std::vector<Real> cutoff_list_vector(cutoff_list_length);
  
  for (int i=0; i<cutoff_list_length; i++) {
    cutoff_list_vector[i] = boost::python::extract<Real>(cutoff_list[i]);
  }
 
 return mol::alg::PreparelDDTGlobalRDMap(reference_list_vector, cutoff_list_vector, sequence_separation, max_dist);
}

list get_lddt_per_residue_stats_wrapper(mol::EntityView& model,
                                        ost::mol::alg::GlobalRDMap& distance_list,
                                        bool structural_checks,
                                        String label) {
  std::vector<mol::alg::lDDTLocalScore> scores = GetlDDTPerResidueStats(model, distance_list, structural_checks, label);
  list local_scores_list;
  for (std::vector<mol::alg::lDDTLocalScore>::const_iterator sit = scores.begin(); sit != scores.end(); ++sit) {
    local_scores_list.append(*sit);
  }
  return local_scores_list;
}

list get_local_scores_wrapper(mol::alg::lDDTScorer& scorer) {
  std::vector<mol::alg::lDDTLocalScore> scores = scorer.GetLocalScores();
  list local_scores_list;
  for (std::vector<mol::alg::lDDTLocalScore>::const_iterator sit = scores.begin(); sit != scores.end(); ++sit) {
    local_scores_list.append(*sit);
  }
  return local_scores_list;
}

list get_references_wrapper(mol::alg::lDDTScorer& scorer) {
  std::vector<mol::EntityView> references = scorer.GetReferences();
  list local_references_list;
  for (std::vector<mol::EntityView>::const_iterator sit = references.begin(); sit != references.end(); ++sit) {
    local_references_list.append(*sit);
  }
  return local_references_list;
}


void print_lddt_per_residue_stats_wrapper(list& scores, bool structural_checks, int cutoffs_size){
  int scores_length = boost::python::extract<int>(scores.attr("__len__")());
  std::vector<mol::alg::lDDTLocalScore> scores_vector(scores_length);
  
  for (int i=0; i<scores_length; i++) {
    scores_vector[i] = boost::python::extract<mol::alg::lDDTLocalScore>(scores[i]);
  }
 
 return mol::alg::PrintlDDTPerResidueStats(scores_vector, structural_checks, cutoffs_size);
}

geom::Vec3 cbeta_vectors(const geom::Vec3& n_pos, const geom::Vec3& ca_pos, 
                         const geom::Vec3& c_pos, Real l) {
  return mol::alg::CBetaPosition(n_pos, ca_pos, c_pos, l);
}

geom::Vec3 cbeta_residue(const ost::mol::ResidueHandle& r, Real l) {
  return mol::alg::CBetaPosition(r, l);
}
  
}


BOOST_PYTHON_MODULE(_ost_mol_alg)
{
  export_svdSuperPose();
  export_TrajectoryAnalysis();
  export_StructureAnalysis();
  export_Clash();
  export_NonStandard();
  export_Molck();
  export_contact_overlap();
  export_accessibility();
  export_sec_struct();
  export_sec_struct_segments();
  export_find_membrane();
  export_entity_to_density();
  export_biounit();
  
  def("LocalDistDiffTest", lddt_a, (arg("sequence_separation")=0,arg("local_lddt_property_string")=""));
  def("LocalDistDiffTest", lddt_c, (arg("local_lddt_property_string")=""));
  def("LocalDistDiffTest", lddt_b, (arg("ref_index")=0, arg("mdl_index")=1));
  def("LocalDistDiffTest", &lddt_d, (arg("model"), arg("reference_list"), ("distance_list"), arg("settings")));
  def("FilterClashes", fc_a, (arg("ent"), arg("clashing_distances"), arg("always_remove_bb")=false));
  def("FilterClashes", fc_b, (arg("ent"), arg("clashing_distances"), arg("always_remove_bb")=false));
  def("CheckStereoChemistry", csc_a, (arg("ent"), arg("bonds"), arg("angles"), arg("bond_tolerance"), arg("angle_tolerance"), arg("always_remove_bb")=false));
  def("CheckStereoChemistry", csc_b, (arg("ent"), arg("bonds"), arg("angles"), arg("bond_tolerance"), arg("angle_tolerance"), arg("always_remove_bb")=false));
  def("LDDTHA",&mol::alg::LDDTHA, (arg("sequence_separation")=0));
  def("CreateDistanceList",&mol::alg::CreateDistanceList);
  def("CreateDistanceListFromMultipleReferences",&create_distance_list_from_multiple_references);

  def("SuperposeFrames", superpose_frames1, 
      (arg("source"), arg("sel")=ost::mol::EntityView(), arg("begin")=0, 
       arg("end")=-1, arg("ref")=-1));
  def("SuperposeFrames", superpose_frames2, 
  (arg("source"), arg("sel"), arg("ref_view"),arg("begin")=0, arg("end")=-1));

  
  class_<mol::alg::ClashingDistances> ("ClashingDistances",init<>())
    .def("SetClashingDistance",&mol::alg::ClashingDistances::SetClashingDistance)
    .def("GetClashingDistance",&mol::alg::ClashingDistances::GetClashingDistance)
    .def("GetAdjustedClashingDistance",&mol::alg::ClashingDistances::GetAdjustedClashingDistance)
    .def("GetMaxAdjustedDistance",&mol::alg::ClashingDistances::GetMaxAdjustedDistance)    
    .def("IsEmpty",&mol::alg::ClashingDistances::IsEmpty)  
    
    .def("PrintAllDistances",&mol::alg::ClashingDistances::PrintAllDistances)  
  ;

  class_<mol::alg::StereoChemicalParams> ("StereoChemicalParams" ,init<>())
    .def("SetParam",&mol::alg::StereoChemicalParams::SetParam)
    .def("GetParam",&mol::alg::StereoChemicalParams::GetParam)
    .def("ContainsParam",&mol::alg::StereoChemicalParams::ContainsParam)    
    .def("IsEmpty",&mol::alg::StereoChemicalParams::IsEmpty)  
    
    .def("PrintAllParameters",&mol::alg::StereoChemicalParams::PrintAllParameters)  

  ;

  class_<mol::alg::UniqueAtomIdentifier> ("UniqueAtomIdentifier" ,init <const String&, const mol::ResNum&, const String&, const String&>())
    .def("GetChainName",&mol::alg::UniqueAtomIdentifier::GetChainName)
    .def("GetResNum",&mol::alg::UniqueAtomIdentifier::GetResNum)
    .def("GetResidueName",&mol::alg::UniqueAtomIdentifier::GetResidueName)
    .def("GetAtomName",&mol::alg::UniqueAtomIdentifier::GetAtomName)
    .def("GetQualifiedAtomName",&mol::alg::UniqueAtomIdentifier::GetQualifiedAtomName)
  ;

  class_<mol::alg::lDDTSettings>("lDDTSettings", no_init)
    .def("__init__", raw_function(lDDTSettingsInitWrapper))
    .def(init<Real, int, std::vector<Real>&, String>())
    .def("ToString", &mol::alg::lDDTSettings::ToString)
    .def("PrintParameters", &mol::alg::lDDTSettings::PrintParameters)
    .def("__repr__", &mol::alg::lDDTSettings::ToString)
    .def("__str__", &mol::alg::lDDTSettings::ToString)
    .def_readwrite("radius", &mol::alg::lDDTSettings::radius)
    .def_readwrite("sequence_separation", &mol::alg::lDDTSettings::sequence_separation)
    .def_readwrite("cutoffs", &mol::alg::lDDTSettings::cutoffs)
    .def_readwrite("label", &mol::alg::lDDTSettings::label);

  class_<mol::alg::lDDTLocalScore>("lDDTLocalScore", init<String, String, int, String, String, Real, int, int>())
    .def("ToString", &mol::alg::lDDTLocalScore::ToString)
    .def("GetHeader", &mol::alg::lDDTLocalScore::GetHeader)
    .def("__str__", &mol::alg::lDDTLocalScore::Repr)
    .def("__repr__", &mol::alg::lDDTLocalScore::Repr)
    .def_readwrite("cname", &mol::alg::lDDTLocalScore::cname)
    .def_readwrite("rname", &mol::alg::lDDTLocalScore::rname)
    .def_readwrite("rnum", &mol::alg::lDDTLocalScore::rnum)
    .def_readwrite("is_assessed", &mol::alg::lDDTLocalScore::is_assessed)
    .def_readwrite("quality_problems", &mol::alg::lDDTLocalScore::quality_problems)
    .def_readwrite("local_lddt", &mol::alg::lDDTLocalScore::local_lddt)
    .def_readwrite("conserved_dist", &mol::alg::lDDTLocalScore::conserved_dist)
    .def_readwrite("total_dist", &mol::alg::lDDTLocalScore::total_dist);

  class_<mol::alg::lDDTScorer>("lDDTScorer", no_init)
      .def("__init__", raw_function(lDDTScorerInitWrapper))
      .def(init<std::vector<mol::EntityView>&, mol::EntityView&, mol::alg::lDDTSettings&>())
      .add_property("global_score", &mol::alg::lDDTScorer::GetGlobalScore)
      .add_property("conserved_contacts", &mol::alg::lDDTScorer::GetNumConservedContacts)
      .add_property("total_contacts", &mol::alg::lDDTScorer::GetNumTotalContacts)
      .def("PrintPerResidueStats", &mol::alg::lDDTScorer::PrintPerResidueStats)
      .add_property("local_scores", &get_local_scores_wrapper)
      .def_readonly("model", &mol::alg::lDDTScorer::model_view)
      .add_property("references", &get_references_wrapper)
      .add_property("is_valid", &mol::alg::lDDTScorer::IsValid);

  class_<mol::alg::StereoChemicalProps>("StereoChemicalProps",
                           init<mol::alg::StereoChemicalParams&,
                           mol::alg::StereoChemicalParams&,
                           mol::alg::ClashingDistances&>())
    .def_readwrite("bond_table", &mol::alg::StereoChemicalProps::bond_table)
    .def_readwrite("angle_table", &mol::alg::StereoChemicalProps::angle_table)
    .def_readwrite("nonbonded_table", &mol::alg::StereoChemicalProps::nonbonded_table);
  
  def("FillClashingDistances",&fill_clashing_distances_wrapper);
  def("FillStereoChemicalParams",&fill_stereochemical_params_wrapper);
  def("IsStandardResidue",&mol::alg::IsStandardResidue);
  def("PrintGlobalRDMap",&mol::alg::PrintGlobalRDMap);
  def("PrintResidueRDMap",&mol::alg::PrintResidueRDMap);
  def("CleanlDDTReferences", &clean_lddt_references_wrapper);
  def("PreparelDDTGlobalRDMap",
      &prepare_lddt_global_rdmap_wrapper,
      (arg("reference_list"), arg("cutoffs"), arg("sequence_separation"), arg("radius")));
  def("CheckStructure",
      &mol::alg::CheckStructure,
      (arg("ent"), arg("bond_table"), arg("angle_table"), arg("nonbonded_table"),
       arg("bond_tolerance"), arg("angle_tolerance")));
  def("GetlDDTPerResidueStats",
      &get_lddt_per_residue_stats_wrapper,
      (arg("model"), arg("distance_list"), arg("structural_checks"), arg("label")));
  def("PrintlDDTPerResidueStats",
      &print_lddt_per_residue_stats_wrapper,
      (arg("scores"), arg("structural_checks"), arg("cutoff_list_length")));

 
  class_<mol::alg::PDBize>("PDBize",
                           init<int,int,int>((arg("peptide_min_size"),
                                              arg("nucleicacid_min_size"),
                                              arg("saccharide_min_size"))))
    .def(init<int>(arg("min_polymer_size")=10))
    .def("Add", &mol::alg::PDBize::Add, 
         (arg("asu"), arg("transformations"), arg("seqres")))
    .def("Finish", &mol::alg::PDBize::Finish, arg("shift_to_fit")=true)
  ;

  def("ResidueNamesMatch",&mol::alg::ResidueNamesMatch,
      (arg("probe"), arg("reference"), arg("log_as_error")=false));

  class_<mol::alg::BondLengthInfo> ("BondLengthInfo" ,init <>())
    .def(init<Real,Real,int>())
    .def("GetAvgLength",&mol::alg::BondLengthInfo::GetAvgLength)
    .def("GetAvgZscore",&mol::alg::BondLengthInfo::GetAvgZscore)
    .def("GetCount",&mol::alg::BondLengthInfo::GetCount)
  ;

  class_<mol::alg::ClashEvent> ("ClashEvent" ,init <>())
      .def(init<const mol::alg::UniqueAtomIdentifier&,const mol::alg::UniqueAtomIdentifier&, Real, Real>())
      .def("GetFirstAtom",&mol::alg::ClashEvent::GetFirstAtom)
      .def("GetSecondAtom",&mol::alg::ClashEvent::GetSecondAtom)
      .def("GetModelDistance",&mol::alg::ClashEvent::GetModelDistance)
      .def("GetAdjustedReferenceDistance",&mol::alg::ClashEvent::GetAdjustedReferenceDistance)
  ;

  class_<mol::alg::StereoChemicalBondViolation> ("StereoChemicalBondViolation" ,init <>())
      .def(init<const mol::alg::UniqueAtomIdentifier&,const mol::alg::UniqueAtomIdentifier&,
           Real, const std::pair<Real, Real>& >())
      .def("GetFirstAtom",&mol::alg::StereoChemicalBondViolation::GetFirstAtom)
      .def("GetSecondAtom",&mol::alg::StereoChemicalBondViolation::GetSecondAtom)
      .def("GetBondLength",&mol::alg::StereoChemicalBondViolation::GetBondLength)
      .def("GetAllowedRange",&mol::alg::StereoChemicalBondViolation::GetAllowedRange)
  ;

  class_<mol::alg::StereoChemicalAngleViolation> ("StereoChemicalAngleViolation" ,init <>())
      .def(init<const mol::alg::UniqueAtomIdentifier&,const mol::alg::UniqueAtomIdentifier&,
          const mol::alg::UniqueAtomIdentifier&, Real, const std::pair<Real, Real>& >())
      .def("GetFirstAtom",&mol::alg::StereoChemicalAngleViolation::GetFirstAtom)
      .def("GetSecondAtom",&mol::alg::StereoChemicalAngleViolation::GetSecondAtom)
      .def("GetThirdAtom",&mol::alg::StereoChemicalAngleViolation::GetThirdAtom)
      .def("GetAngleWidth",&mol::alg::StereoChemicalAngleViolation::GetAngleWidth)
      .def("GetAllowedRange",&mol::alg::StereoChemicalAngleViolation::GetAllowedRange)
  ;

  class_<mol::alg::ClashingInfo> ("ClashingInfo" ,init <>())
    .def(init<int,Real,const std::vector<mol::alg::ClashEvent> >())
    .def("GetClashCount",&mol::alg::ClashingInfo::GetClashCount)
    .def("GetAverageOffset",&mol::alg::ClashingInfo::GetAverageOffset)
    .def("GetClashList",&mol::alg::ClashingInfo::GetClashList)
  ;

  class_<mol::alg::StereoChemistryInfo> ("StereoChemistryInfo" ,init <>())
      .def(init<Real,int,int,Real,int,int, const std::map<String,mol::alg::BondLengthInfo>&,
               const std::vector<mol::alg::StereoChemicalBondViolation>&,
               const std::vector<mol::alg::StereoChemicalAngleViolation>& >())
      .def("GetAvgZscoreBonds",&mol::alg::StereoChemistryInfo::GetAvgZscoreBonds)
      .def("GetBadBondCount",&mol::alg::StereoChemistryInfo::GetBadBondCount)
      .def("GetBondCount",&mol::alg::StereoChemistryInfo::GetBondCount)
      .def("GetAvgZscoreAngles",&mol::alg::StereoChemistryInfo::GetAvgZscoreAngles)
      .def("GetBadAngleCount",&mol::alg::StereoChemistryInfo::GetBadAngleCount)
      .def("GetAngleCount",&mol::alg::StereoChemistryInfo::GetAngleCount)
      .def("GetAvgBondLengthInfo",&mol::alg::StereoChemistryInfo::GetAvgBondLengthInfo)
      .def("GetBondViolationList",&mol::alg::StereoChemistryInfo::GetBondViolationList)
      .def("GetAngleViolationList",&mol::alg::StereoChemistryInfo::GetAngleViolationList)
    ;

  to_python_converter<std::pair<ost::mol::alg::UniqueAtomIdentifier,ost::mol::alg::UniqueAtomIdentifier>,
                      PairToTupleConverter<ost::mol::alg::UniqueAtomIdentifier, ost::mol::alg::UniqueAtomIdentifier> >();

  to_python_converter<std::pair<Real,Real>,
                      PairToTupleConverter<Real, Real> >();

  to_python_converter<std::pair<Real,long int>,
                      PairToTupleConverter<Real, long int> >();

  to_python_converter<std::pair<mol::EntityView,mol::alg::StereoChemistryInfo>,
                      PairToTupleConverter<mol::EntityView, mol::alg::StereoChemistryInfo> >();

  to_python_converter<std::pair<mol::EntityView,mol::alg::ClashingInfo>,
                      PairToTupleConverter<mol::EntityView, mol::alg::ClashingInfo> >();

  to_python_converter<std::vector<mol::alg::ClashEvent>,
                      VectorToListConverter<mol::alg::ClashEvent> >();

  to_python_converter<std::vector<mol::alg::StereoChemicalBondViolation>,
                      VectorToListConverter<mol::alg::StereoChemicalBondViolation> >();

  to_python_converter<std::vector<mol::alg::StereoChemicalAngleViolation>,
                      VectorToListConverter<mol::alg::StereoChemicalAngleViolation> >();

  class_<mol::alg::ResidueRDMap>("ResidueRDMap")
    .def(map_indexing_suite<mol::alg::ResidueRDMap,true>())
  ;

  class_<mol::alg::GlobalRDMap>("GlobalRDMap")
    .def(map_indexing_suite<mol::alg::GlobalRDMap,true>())
  ;

  def("DRMSD",&mol::alg::DRMSD,(arg("view"),arg("distance_list"),
                                arg("cap_distance")=5.0,arg("sequence_separation")=0));

  def("CBetaPosition", &cbeta_vectors, (arg("n_pos"), arg("ca_pos"), 
                                        arg("c_pos"), arg("l")=1.5));
  def("CBetaPosition", &cbeta_residue, (arg("r"), arg("l") = 1.5));

  def("ConstructCBetas", &mol::alg::ConstructCBetas, (arg("ent"), 
                                                      arg("include_gly")=false));
}