From cc919347050afb8424a8f7dddd7d450ef0e45a2f Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Mon, 13 Feb 2012 14:56:55 -0500
Subject: [PATCH] CoordGroupHandle::GetFramePositions This function allows to
extract the list of positions of all the atoms in a given frame I also added
the export for it and for CoordGroupHandle::AddFrame
---
modules/mol/base/pymod/export_coord_group.cc | 2 ++
modules/mol/base/src/coord_group.cc | 8 ++++++++
modules/mol/base/src/coord_group.hh | 3 +++
3 files changed, 13 insertions(+)
diff --git a/modules/mol/base/pymod/export_coord_group.cc b/modules/mol/base/pymod/export_coord_group.cc
index c6f30e8f5..fa3a06132 100644
--- a/modules/mol/base/pymod/export_coord_group.cc
+++ b/modules/mol/base/pymod/export_coord_group.cc
@@ -47,7 +47,9 @@ void export_CoordGroup()
.def("GetEntity",&CoordGroupHandle::GetEntity)
.def("GetAtomCount",&CoordGroupHandle::GetAtomCount)
.def("AddFrames", &CoordGroupHandle::AddFrames)
+ .def("AddFrame", &CoordGroupHandle::AddFrame)
.def("GetFrameCount",&CoordGroupHandle::GetFrameCount)
+ .def("GetFramePositions",&CoordGroupHandle::GetFramePositions)
.def("SetFramePositions",&CoordGroupHandle::SetFramePositions)
.def("SetAtomPos",&CoordGroupHandle::SetAtomPos)
.def("GetAtomPos",&CoordGroupHandle::GetAtomPos)
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index 47622e901..127c82463 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -73,6 +73,14 @@ void CoordGroupHandle::SetFramePositions(uint frame,
//source_->SetFramePositions(frame, clist);
}
+
+geom::Vec3List CoordGroupHandle::GetFramePositions(uint frame)
+ {
+ this->CheckValidity();
+ return *(this->GetFrame(frame));
+ }
+
+
void CoordGroupHandle::CopyFrame(uint frame)
{
this->CheckValidity();
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index 57701931b..22a829dd6 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -52,6 +52,9 @@ public:
/// initial atomlist
void SetFramePositions(uint frame, const std::vector<geom::Vec3>& clist);
+ /// \brief get the positions of all the atoms in the given frame
+ geom::Vec3List GetFramePositions(uint frame);
+
/// \brief copy atom positions of given frame to stored atoms in entity
void CopyFrame(uint frame);
--
GitLab