Added a function to wrap an entity in a periodic cell

modules/mol/alg/pymod/export_structure_analysis.cc

@@ -28,4 +28,5 @@ void export_StructureAnalysis()
 {
   def("GetPosListFromView",&GetPosListFromView, (arg("view")));
   def("CalculateAgreementWithDensityMap",&CalculateAgreementWithDensityMap,(arg("pos_list"),arg("density_map")));
-}
+  def("WrapEntityInPeriodicCell",&WrapEntityInPeriodicCell,(arg("Entity"),arg("cell_center"),arg("nasis_vec")));
+}
\ No newline at end of file

modules/mol/alg/src/structure_analysis.cc

@@ -50,5 +50,25 @@ Real CalculateAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle&
   }
   return sum;
 }
-  
+ 
+void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 basis_vec){
+  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();
+  for (unsigned int i=0; i<n_residues; ++i) {
+    ResidueHandle r=residues[i];
+    cm=r.GetCenterOfMass();
+    wrapped_cm=geom::WrapVec3(cm,cell_center,basis_vec);
+    if (wrapped_cm==cm) continue;
+    AtomHandleList atoms=r.GetAtomList();
+    unsigned int n_atoms=r.GetAtomCount();
+    shift=wrapped_cm-cm;
+    for (unsigned int j=0; j<n_atoms; ++j) {
+      edi.SetAtomPos(atoms[j],atoms[j].GetPos()+shift);
+    }
+  }
+}
+
 }}} //ns

modules/mol/alg/src/structure_analysis.hh

@@ -26,11 +26,13 @@
 #include <ost/mol/alg/module_config.hh>
 
 #include <ost/mol/entity_view.hh>
+#include <ost/mol/entity_handle.hh>
 #include <ost/img/map.hh>
 
 
 namespace ost { namespace mol { namespace alg {
   geom::Vec3List DLLEXPORT_OST_MOL_ALG GetPosListFromView(const EntityView& view);
   Real DLLEXPORT_OST_MOL_ALG CalculateAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map);
+  void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 basis_vec);
 }}}//ns
 #endif