Correct wrapping for the cases when residues are not whole but split by the PBC

The residues first get wrapped and then the entity. The wrapping is per residue
and each residue gets wrapped according to the position of its center of mass

modules/mol/alg/pymod/export_structure_analysis.cc

@@ -31,5 +31,5 @@ void export_StructureAnalysis()
   def("CalculateAverageAgreementWithDensityMap",&CalculateAverageAgreementWithDensityMap,(arg("pos_list"),arg("density_map")));
   def("CalculateAgreementWithDensityMap",&CalculateAgreementWithDensityMap,(arg("pos_list"),arg("density_map")));
 #endif
-  def("WrapEntityInPeriodicCell",&WrapEntityInPeriodicCell,(arg("Entity"),arg("cell_center"),arg("nasis_vec")));
+  def("WrapEntityInPeriodicCell",&WrapEntityInPeriodicCell,(arg("Entity"),arg("cell_center"),arg("basis_vec"),arg("group_res")=true));
 }

modules/mol/alg/src/structure_analysis.cc

@@ -61,12 +61,21 @@ Real CalculateAverageAgreementWithDensityMap(const geom::Vec3List& vl, img::MapH
 }
 
 #endif
-void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 basis_vec){
+void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 basis_vec, bool group_residues){
   mol::XCSEditor edi=eh.EditXCS(mol::BUFFERED_EDIT);
   geom::Vec3 cm,wrapped_cm,shift;
-  edi=eh.EditXCS();
   ResidueHandleList residues=eh.GetResidueList();
   unsigned int n_residues=eh.GetResidueCount();
+  if (group_residues) {
+    for (unsigned int i=0; i<n_residues; ++i) {
+      ResidueHandle r=residues[i];
+      AtomHandleList atoms=r.GetAtomList();
+      geom::Vec3 ref_pos=atoms[0].GetPos();
+      for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+        edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),ref_pos,basis_vec));
+      }
+    }
+  }
   for (unsigned int i=0; i<n_residues; ++i) {
     ResidueHandle r=residues[i];
     cm=r.GetCenterOfMass();

modules/mol/alg/src/structure_analysis.hh

@@ -37,6 +37,6 @@ namespace ost { namespace mol { namespace alg {
   std::vector<Real> DLLEXPORT_OST_MOL_ALG CalculateAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map);
   Real DLLEXPORT_OST_MOL_ALG CalculateAverageAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map);
 #endif
-  void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 basis_vec);
+  void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 basis_vec, bool group_res=true);
 }}}//ns
 #endif