Added EntityHandle::GetAtomPosList

This function returns a geom::Vec3List containing the positions
of all the atoms in the entity.

modules/mol/base/pymod/export_entity.cc

@@ -147,6 +147,7 @@ void export_Entity()
     .def("GetMass", &EntityHandle::GetMass)
     .def("GetCenterOfMass", &EntityHandle::GetCenterOfMass)
     .def("GetCenterOfAtoms", &EntityHandle::GetCenterOfAtoms)
+    .def("GetAtomPosList", &EntityHandle::GetAtomPosList)
     .def("GetGeometricCenter", geom_center<EntityHandle>)
     .add_property("geometric_center", geom_center<EntityHandle>)
 

modules/mol/base/src/entity_handle.cc

@@ -362,6 +362,11 @@ AtomHandleList EntityHandle::GetAtomList() const
   return atoms;
 }
 
+geom::Vec3List EntityHandle::GetAtomPosList() const {
+  this->CheckValidity();
+  return Impl()->GetAtomPosList();
+}
+  
 EntityHandle EntityHandle::GetHandle() const
 {
   return *this;

modules/mol/base/src/entity_handle.hh

@@ -280,6 +280,9 @@ public:
   /// \sa #AtomsBegin, #AtomsEnd
   AtomHandleList GetAtomList() const;
   
+  /// \brief get complete list of atom positions
+  geom::Vec3List GetAtomPosList() const;
+  
   /// \brief Get editor for external coordinate system to manipulate atom 
   ///     positions
   /// \sa editors

modules/mol/base/src/impl/entity_impl.cc

@@ -307,6 +307,15 @@ geom::Vec3 EntityImpl::GetCenterOfMass() const {
   return center;
 }
 
+geom::Vec3List EntityImpl::GetAtomPosList() const {
+  geom::Vec3List atom_pos_list;
+  atom_pos_list.reserve(this->GetAtomCount());
+  for(AtomImplMap::const_iterator it = atom_map_.begin();it!=atom_map_.end();++it) {
+    atom_pos_list.push_back(it->second->TransformedPos());
+  }
+  return atom_pos_list;
+}
+  
 Real EntityImpl::GetMass() const {
   double mass=0.0;
   for (ChainImplList::const_iterator i=chain_list_.begin(), 

modules/mol/base/src/impl/entity_impl.hh

@@ -93,7 +93,7 @@ public:
   Real GetMass() const;
   geom::Vec3 GetCenterOfMass() const;
   geom::Vec3 GetCenterOfAtoms() const;
-  
+  geom::Vec3List GetAtomPosList() const;
   /// \brief returns the axis-aligned bounding box of the entity
   geom::AlignedCuboid GetBounds() const;