From 7e55657fce168fd6a030046fac5c62dd204aa45a Mon Sep 17 00:00:00 2001
From: ansgar <ansgar@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Sat, 27 Mar 2010 18:43:45 +0000
Subject: [PATCH] added atom pos access in CoordGroup
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@1895 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/mol/base/pymod/export_coord_group.cc | 2 ++
modules/mol/base/src/coord_group.cc | 12 +++++++
modules/mol/base/src/coord_group.hh | 8 ++++-
modules/mol/base/src/coord_source.cc | 33 +++++++++++++++++---
modules/mol/base/src/coord_source.hh | 8 ++++-
modules/mol/base/src/in_mem_coord_source.cc | 2 +-
modules/mol/base/src/in_mem_coord_source.hh | 2 +-
7 files changed, 59 insertions(+), 8 deletions(-)
diff --git a/modules/mol/base/pymod/export_coord_group.cc b/modules/mol/base/pymod/export_coord_group.cc
index 979fc5528..28059f82b 100644
--- a/modules/mol/base/pymod/export_coord_group.cc
+++ b/modules/mol/base/pymod/export_coord_group.cc
@@ -48,6 +48,8 @@ void export_CoordGroup()
.def("GetAtomCount",&CoordGroupHandle::GetAtomCount)
.def("GetFrameCount",&CoordGroupHandle::GetFrameCount)
.def("SetFramePositions",&CoordGroupHandle::SetFramePositions)
+ .def("SetAtomPos",&CoordGroupHandle::SetAtomPos)
+ .def("GetAtomPos",&CoordGroupHandle::GetAtomPos)
.def("CopyFrame",&CoordGroupHandle::CopyFrame)
.def("IsValid", &CoordGroupHandle::IsValid)
.def("Capture", capture1)
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index e6fbd4641..6675b5499 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -100,6 +100,18 @@ void CoordGroupHandle::CheckValidity() const
}
}
+void CoordGroupHandle::SetAtomPos(uint frame, AtomHandle atom, const geom::Vec3& pos)
+{
+ this->CheckValidity();
+ source_->SetAtomPos(frame,atom,pos);
+}
+
+geom::Vec3 CoordGroupHandle::GetAtomPos(uint frame, AtomHandle atom) const
+{
+ this->CheckValidity();
+ return source_->GetAtomPos(frame,atom);
+}
+
CoordFramePtr CoordGroupHandle::GetFrame(uint frame) const
{
this->CheckValidity();
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index 04bffc41a..3b038e37b 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -55,7 +55,7 @@ public:
/// \brief assign positions to the given frame - order and count must match
/// initial atomlist
void SetFramePositions(uint frame, const std::vector<geom::Vec3>& clist);
-
+
/// \brief copy atom positions of given frame to stored atoms in entity
void CopyFrame(uint frame);
@@ -68,6 +68,12 @@ public:
/// \brief add frame
void AddFrame(const std::vector<geom::Vec3>& clist);
+ /// \brief set an indidivial atom position in the given frame
+ void SetAtomPos(uint frame, AtomHandle atom, const geom::Vec3& pos);
+
+ /// \brief retrieve an indidivial atom position in the given frame
+ geom::Vec3 GetAtomPos(uint frame, AtomHandle atom) const;
+
/// \brief check for handle validity
bool IsValid() const;
diff --git a/modules/mol/base/src/coord_source.cc b/modules/mol/base/src/coord_source.cc
index b1e54ecee..a8d95ff1a 100644
--- a/modules/mol/base/src/coord_source.cc
+++ b/modules/mol/base/src/coord_source.cc
@@ -31,11 +31,17 @@ namespace ost { namespace mol {
CoordSource::CoordSource(const AtomHandleList& atoms):
- atoms_(atoms), mutable_(false)
+ atoms_(atoms),
+ entity_(),
+ mutable_(false),
+ atom_dict_()
{
if (!atoms_.empty()) {
entity_=atoms_.front().GetEntity();
}
+ for(uint n=0;n<atoms_.size();++n) {
+ atom_dict_[atoms_[n].GetHashCode()]=n;
+ }
}
@@ -105,8 +111,6 @@ CoordSourcePtr CoordSource::Extract(int start, int stop, int step)
return in_mem_source;
}
-
-
EntityHandle CoordSource::GetEntity() const
{
return entity_;
@@ -132,4 +136,25 @@ const AtomHandleList& CoordSource::GetAtomList() const
return atoms_;
}
-}}
+void CoordSource::SetAtomPos(uint frame, AtomHandle atom, const geom::Vec3& pos)
+{
+ if(!atom.IsValid()) return;
+ std::map<long,uint>::iterator it = atom_dict_.find(atom.GetHashCode());
+ if(it!=atom_dict_.end()) {
+ CoordFrame& fp=*(GetFrame(frame));
+ fp[it->second]=pos;
+ }
+}
+
+geom::Vec3 CoordSource::GetAtomPos(uint frame, AtomHandle atom) const
+{
+ if(!atom.IsValid()) return geom::Vec3();
+ std::map<long,uint>::const_iterator it = atom_dict_.find(atom.GetHashCode());
+ if(it!=atom_dict_.end()) {
+ const CoordFrame& fp=*(GetFrame(frame));
+ return fp[it->second];
+ }
+ return geom::Vec3();
+}
+
+}} // ns
diff --git a/modules/mol/base/src/coord_source.hh b/modules/mol/base/src/coord_source.hh
index c9e84102e..bc54b88a7 100644
--- a/modules/mol/base/src/coord_source.hh
+++ b/modules/mol/base/src/coord_source.hh
@@ -49,13 +49,18 @@ public:
virtual uint GetFrameCount()=0;
- virtual CoordFramePtr GetFrame(uint frame_id)=0;
+ virtual CoordFramePtr GetFrame(uint frame_id) const = 0;
int GetAtomCount() const;
EntityHandle GetEntity() const;
const AtomHandleList& GetAtomList() const;
+
+ void SetAtomPos(uint frame, AtomHandle atom, const geom::Vec3& pos);
+
+ geom::Vec3 GetAtomPos(uint frame, AtomHandle atom) const;
+
/// \brief assign the coordinates in the given frame to the atoms
void CopyFrame(uint frame);
bool IsMutable() const;
@@ -70,6 +75,7 @@ private:
AtomHandleList atoms_;
EntityHandle entity_;
bool mutable_;
+ std::map<long,uint> atom_dict_;
};
}}
diff --git a/modules/mol/base/src/in_mem_coord_source.cc b/modules/mol/base/src/in_mem_coord_source.cc
index 48182f4eb..98417d159 100644
--- a/modules/mol/base/src/in_mem_coord_source.cc
+++ b/modules/mol/base/src/in_mem_coord_source.cc
@@ -14,7 +14,7 @@ uint InMemCoordSource::GetFrameCount()
return frames_.size();
}
-CoordFramePtr InMemCoordSource::GetFrame(uint frame_id)
+CoordFramePtr InMemCoordSource::GetFrame(uint frame_id) const
{
return frame_id>=frames_.size() ? CoordFramePtr() : frames_[frame_id];
diff --git a/modules/mol/base/src/in_mem_coord_source.hh b/modules/mol/base/src/in_mem_coord_source.hh
index ebae59274..08388f313 100644
--- a/modules/mol/base/src/in_mem_coord_source.hh
+++ b/modules/mol/base/src/in_mem_coord_source.hh
@@ -40,7 +40,7 @@ public:
virtual uint GetFrameCount();
- virtual CoordFramePtr GetFrame(uint frame_id);
+ virtual CoordFramePtr GetFrame(uint frame_id) const;
void AddFrame(const CoordFramePtr& frame);
virtual void AddFrame(const std::vector<geom::Vec3>& coords);
--
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