From bfc47bd7ce9f54bdc6ace1d7db55f9a178dde73c Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Mon, 7 Feb 2011 20:36:54 +0100
Subject: [PATCH] added MergeCoordGroup function
---
modules/mol/base/pymod/__init__.py | 16 +++++++++++++++-
modules/mol/base/pymod/export_coord_group.cc | 2 ++
modules/mol/base/src/coord_group.cc | 15 +++++++++++++++
modules/mol/base/src/coord_group.hh | 1 +
4 files changed, 33 insertions(+), 1 deletion(-)
diff --git a/modules/mol/base/pymod/__init__.py b/modules/mol/base/pymod/__init__.py
index 6431ae0ce..a473f7ae4 100644
--- a/modules/mol/base/pymod/__init__.py
+++ b/modules/mol/base/pymod/__init__.py
@@ -18,4 +18,18 @@
#------------------------------------------------------------------------------
from _mol import *
import ost.geom as _geom
-from ost.mol import alg
\ No newline at end of file
+from ost.mol import alg
+
+
+def MergeCoordGroups(*coord_groups):
+ """
+ Merge several separate coord groups into one. The coord groups must have the
+ same number of atoms. In case no coord group is supplied, None will be
+ returned.
+ """
+ if len(coord_groups)==0:
+ return None
+ cg=CreateCoordGroup(coord_groups[0].atoms)
+ for coord_group in coord_groups:
+ cg.AddFrames(coord_group)
+ return cg
\ No newline at end of file
diff --git a/modules/mol/base/pymod/export_coord_group.cc b/modules/mol/base/pymod/export_coord_group.cc
index 5589268af..bed54377e 100644
--- a/modules/mol/base/pymod/export_coord_group.cc
+++ b/modules/mol/base/pymod/export_coord_group.cc
@@ -46,11 +46,13 @@ void export_CoordGroup()
.def("IsValid",&CoordGroupHandle::IsValid)
.def("GetEntity",&CoordGroupHandle::GetEntity)
.def("GetAtomCount",&CoordGroupHandle::GetAtomCount)
+ .def("AddFrames", &CoordGroupHandle::AddFrames)
.def("GetFrameCount",&CoordGroupHandle::GetFrameCount)
.def("SetFramePositions",&CoordGroupHandle::SetFramePositions)
.def("SetAtomPos",&CoordGroupHandle::SetAtomPos)
.def("GetAtomPos",&CoordGroupHandle::GetAtomPos)
.def("CopyFrame",&CoordGroupHandle::CopyFrame)
+ .add_property("atoms", &CoordGroupHandle::GetAtomList)
.def("IsValid", &CoordGroupHandle::IsValid)
.def("Capture", capture1)
.def("Capture", capture2)
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index 4dcabf68b..b4bea4c8e 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -93,6 +93,21 @@ void CoordGroupHandle::AddFrame(const std::vector<geom::Vec3>& clist)
}
}
+void CoordGroupHandle::AddFrames(const CoordGroupHandle& cg)
+{
+ this->CheckValidity();
+ if (source_->IsMutable()) {
+ if (cg.GetAtomCount()!=this->GetAtomCount()) {
+ throw IntegrityError("Atom number don't match");
+ }
+ for (size_t i=0; i<cg.GetFrameCount(); ++i) {
+ source_->AddFrame(*cg.GetFrame(i));
+ }
+ } else {
+ throw IntegrityError("Can't add frame to immutable CoordGroup");
+ }
+}
+
void CoordGroupHandle::CheckValidity() const
{
if (!source_) {
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index dfa3c8530..8f7f78c9e 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -67,6 +67,7 @@ public:
/// \brief add frame
void AddFrame(const std::vector<geom::Vec3>& clist);
+ void AddFrames(const CoordGroupHandle& cg);
/// \brief set an indidivial atom position in the given frame
void SetAtomPos(uint frame, AtomHandle atom, const geom::Vec3& pos);
--
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