From b3be5ccac71ddca7b79ba86bdbce460c5d6c5dbc Mon Sep 17 00:00:00 2001
From: Ansgar Philippsen <ansgar.philippsen@gmail.com>
Date: Wed, 7 Nov 2012 10:20:48 -0500
Subject: [PATCH] added fix transform interface to entity and xcs editor
---
modules/mol/base/pymod/export_entity.cc | 1 +
modules/mol/base/src/entity_handle.cc | 6 ++++++
modules/mol/base/src/entity_handle.hh | 2 ++
modules/mol/base/src/impl/entity_impl.cc | 14 +++++++++++++-
modules/mol/base/src/impl/entity_impl.hh | 1 +
modules/mol/base/src/xcs_editor.cc | 5 +++++
modules/mol/base/src/xcs_editor.hh | 3 +++
7 files changed, 31 insertions(+), 1 deletion(-)
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index bb55d9bd6..0373b2590 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/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)
diff --git a/modules/mol/base/src/entity_handle.cc b/modules/mol/base/src/entity_handle.cc
index e34e11d2e..eaa348914 100644
--- a/modules/mol/base/src/entity_handle.cc
+++ b/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();
diff --git a/modules/mol/base/src/entity_handle.hh b/modules/mol/base/src/entity_handle.hh
index fe2a43913..63a2bc6be 100644
--- a/modules/mol/base/src/entity_handle.hh
+++ b/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
diff --git a/modules/mol/base/src/impl/entity_impl.cc b/modules/mol/base/src/impl/entity_impl.cc
index f8fa19e32..852b9bebb 100644
--- a/modules/mol/base/src/impl/entity_impl.cc
+++ b/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)
diff --git a/modules/mol/base/src/impl/entity_impl.hh b/modules/mol/base/src/impl/entity_impl.hh
index 74d8ded33..6862e5e27 100644
--- a/modules/mol/base/src/impl/entity_impl.hh
+++ b/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);
diff --git a/modules/mol/base/src/xcs_editor.cc b/modules/mol/base/src/xcs_editor.cc
index 5596e3962..7bf68701d 100644
--- a/modules/mol/base/src/xcs_editor.cc
+++ b/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) {
diff --git a/modules/mol/base/src/xcs_editor.hh b/modules/mol/base/src/xcs_editor.hh
index a7cc317b2..e52d9e4c5 100644
--- a/modules/mol/base/src/xcs_editor.hh
+++ b/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();
--
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