added fix transform interface to entity and xcs editor

modules/mol/base/pymod/export_entity.cc

@@ -197,6 +197,7 @@ void export_Entity()
     .add_property("transform",&EntityHandle::GetTransform,&EntityHandle::SetTransform)
     .def("HasTransform",&EntityHandle::HasTransform)
     .def("ClearTransform",&EntityHandle::ClearTransform)
+    .def("FixTransform",&EntityHandle::FixTransform)
     .def("EditXCS", &EntityHandle::EditXCS, arg("mode")=UNBUFFERED_EDIT)
     .def("EditICS", &EntityHandle::EditICS, arg("mode")=UNBUFFERED_EDIT)
     .def("RequestXCSEditor", &depr_request_xcs_editor, arg("mode")=UNBUFFERED_EDIT)

modules/mol/base/src/entity_handle.cc

@@ -295,6 +295,12 @@ void EntityHandle::ClearTransform()
   Impl()->ClearTransform();  
 }
 
+void EntityHandle::FixTransform()
+{
+  this->CheckValidity();
+  Impl()->FixTransform();  
+}
+
 ResidueHandle EntityHandle::FindResidue(const String& chain_name,
                                         const ResNum& residue) const {
   this->CheckValidity();

modules/mol/base/src/entity_handle.hh

@@ -279,6 +279,8 @@ public:
   bool HasTransform() const;
   /// \brief remove transform
   void ClearTransform();
+  /// \brief write transformed pos to orig, and the clear tf
+  void FixTransform();
 
   /// \brief get complete list of residues
   /// \sa #ResiduesBegin, #ResiduesEnd

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

@@ -748,8 +748,20 @@ void EntityImpl::SetTransform(const geom::Transform& tf)
 
 void EntityImpl::ClearTransform()
 {
-  has_transform_=false;
   SetTransform(geom::Transform());
+  has_transform_=false;
+}
+
+void EntityImpl::FixTransform()
+{
+  if(!has_transform_) return;
+  for(AtomImplMap::iterator it = atom_map_.begin();it!=atom_map_.end();++it) {
+    it->second->OriginalPos()=it->second->TransformedPos();
+  }
+  transform_=geom::Transform();
+  has_transform_=false;
+  this->UpdateTransformedPos();
+  this->MarkOrganizerDirty();
 }
 
 void EntityImpl::AttachObserver(const EntityObserverPtr& o)

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

@@ -151,6 +151,7 @@ public:
   const geom::Transform& GetTransform() const {return transform_;}
   bool HasTransform() const {return has_transform_;}
   void ClearTransform();
+  void FixTransform();
 
   void AttachObserver(const EntityObserverPtr& o);
   void DetachObserver(const EntityObserverPtr& o);

modules/mol/base/src/xcs_editor.cc

@@ -205,6 +205,11 @@ void XCSEditor::SetTransform(const geom::Transform& transform)
   this->Update();
 }
 
+void XCSEditor::FixTransform()
+{
+  ent_.Impl()->FixTransform();
+}
+
 void XCSEditor::Update()
 {
   if (GetMode()==UNBUFFERED_EDIT) {

modules/mol/base/src/xcs_editor.hh

@@ -104,6 +104,9 @@ public:
   void SetTransform(const geom::Mat4& transform);
   void SetTransform(const geom::Transform& transform);
 
+  /// \brief set transformed pos to new original pos
+  void FixTransform();
+
   /// \brief immediately update internal coordinate system
   void UpdateICS();