Fixed atom ordering in the GetFrameFromEntity() function

in the structure_analysis.py module.

This is used to make functions written at the CoordFrame level
accesible to analyze both entities and trajectories.

modules/mol/alg/pymod/structure_analysis.py

@@ -13,7 +13,7 @@ def GetFrameFromEntity(eh):
   Input:
     eh : EntityHandle
   """
-  return ost.mol.CreateCoordFrame(eh.GetAtomPosList())
+  return ost.mol.CreateCoordFrame(eh.GetAtomPosList(ordered_by_index=True))
   
 def GetDistanceBetwCenterOfMass(sele1,sele2):
   """

modules/mol/base/pymod/export_entity.cc

@@ -155,7 +155,7 @@ void export_Entity()
     .def("GetMass", &EntityHandle::GetMass)
     .def("GetCenterOfMass", &EntityHandle::GetCenterOfMass)
     .def("GetCenterOfAtoms", &EntityHandle::GetCenterOfAtoms)
-    .def("GetAtomPosList", &EntityHandle::GetAtomPosList)
+    .def("GetAtomPosList", &EntityHandle::GetAtomPosList, arg("ordered_by_index")=false)
     .def("GetGeometricCenter", geom_center<EntityHandle>)
     .add_property("geometric_center", geom_center<EntityHandle>)
 

modules/mol/base/src/entity_handle.cc

@@ -402,16 +402,23 @@ AtomHandleList EntityHandle::GetAtomList() const
   return atoms;
 }
 
-geom::Vec3List EntityHandle::GetAtomPosList() const {
+bool less_index(const mol::AtomHandle& a1, const mol::AtomHandle& a2)
+{
+  return a1.GetIndex()<a2.GetIndex();
+}
+
+geom::Vec3List EntityHandle::GetAtomPosList(bool ordered_by_index) const {
   this->CheckValidity();
   geom::Vec3List atom_pos_list;
   atom_pos_list.reserve(this->GetAtomCount());
   AtomHandleList atom_list=this->GetAtomList();
+  if (ordered_by_index){
+    std::sort(atom_list.begin(),atom_list.end(),less_index);
+  }
   for (AtomHandleList::const_iterator a=atom_list.begin(), e=atom_list.end(); a!=e; ++a) {
     atom_pos_list.push_back(a->GetPos());
   }
   return atom_pos_list;
-  //return Impl()->GetAtomPosList();
 }
   
 EntityHandle EntityHandle::GetHandle() const

modules/mol/base/src/entity_handle.hh

@@ -289,7 +289,7 @@ public:
   AtomHandleList GetAtomList() const;
   
   /// \brief get complete list of atom positions
-  geom::Vec3List GetAtomPosList() const;
+  geom::Vec3List GetAtomPosList(bool ordered_by_index = false) const;
   
   /// \brief Get editor for external coordinate system to manipulate atom 
   ///     positions