Refactored iinterface and export of ClashingDistance class

modules/mol/alg/doc/molalg.rst

@@ -276,7 +276,7 @@ The following function detects steric clashes in atomic structures. Two atoms ar
     :param clash_distance: minimum clashing distance (in Angstroms)
     :param tolerance: tolerance threshold (in Angstroms)
 
-  .. method GetClashingDistance()
+  .. method:: GetClashingDistance()
 
      Recovers a reference distance and a tolerance threshold from the list
 
@@ -285,6 +285,15 @@ The following function detects steric clashes in atomic structures. Two atoms ar
 
     :returns: a tuple containing the minimum clashing distance and the tolerance threshold
 
+  .. method:: GetAdjustedClashingDistance()
+
+     Recovers a reference distance from the list, already adjusted by the tolerance threshold
+
+    :param ele1: string containing the first element's name
+    :param ele2: string containing the second element's name
+
+    :returns: the adjusted minimum clashing distance
+
   .. method::  GetMaxAdjustedDistance()
  
     Returns the longest clashing distance in the list, after adjustment with tolerance threshold    

modules/mol/alg/pymod/__init__.py

@@ -6,11 +6,11 @@ import ost.mol.alg.structure_analysis
 import ost.mol.alg.helix_kinks
 
 # Fills a list of reference clashing distances from a file (requires a path to the file)
-def FillClashingDistancesFromFile(filename,default_clashing_distance,default_tolerance):
+def FillClashingDistancesFromFile(filename):
   fh=open(filename,'r')
   lines=fh.readlines()
   fh.close()
-  return FillClashingDistances(lines,default_clashing_distance,default_tolerance)
+  return FillClashingDistances(lines)
 
 # Fills a list of bond stereo-chemical statistics from a file (requires a path to the file)
 def FillBondStereoChemicalParamsFromFile(filename):

modules/mol/alg/pymod/wrap_mol_alg.cc

@@ -24,6 +24,7 @@
 #include <ost/mol/alg/superpose_frames.hh>
 #include <ost/mol/alg/filter_clashes.hh>
 #include <ost/mol/alg/consistency_checks.hh>
+#include <ost/export_helper/pair_to_tuple_conv.hh>
 
 using namespace boost::python;
 using namespace ost;
@@ -60,7 +61,7 @@ ost::mol::alg::StereoChemicalParams fill_stereochemical_params_wrapper (const St
   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, Real min_default_distance, Real min_distance_tolerance)  
+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);
@@ -103,6 +104,9 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
   export_entity_to_density();
   #endif
   
+  to_python_converter<std::pair<Real,Real>,
+                      PairToTupleConverter<Real, Real> >();
+
   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));
@@ -124,6 +128,7 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
   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)  
     

modules/mol/alg/src/filter_clashes.cc

@@ -108,6 +108,12 @@ std::pair<Real,Real> ClashingDistances::GetClashingDistance(const String& ele1,c
   return find_ci->second;
 }
 
+Real ClashingDistances::GetAdjustedClashingDistance(const String& ele1,const String& ele2) const
+{
+  std::pair <Real,Real> clash_dist = GetClashingDistance(ele1,ele2);
+  return clash_dist.first-clash_dist.second;
+}
+
 void ClashingDistances::PrintAllDistances() const
 {
    for (std::map <String,std::pair<float,float> >::const_iterator index = min_distance_.begin();index != min_distance_.end();++index) {

modules/mol/alg/src/filter_clashes.hh

@@ -40,6 +40,9 @@ public:
   /// \brief Recovers a reference distance and a tolerance threshold (respectively) from the list
   std::pair<Real,Real> GetClashingDistance(const String& ele1,const String& ele2) const;
 
+  /// \brief Recovers a reference distance already adjusted by the tolerance threshold from the list
+  Real GetAdjustedClashingDistance(const String& ele1,const String& ele2) const;
+
   /// \brief Recovers the longest distance in the list, corrected by tolerance
   Real GetMaxAdjustedDistance() const;