From 661b7cf3cdde38f8c46e853d905f6f21bd6b81b7 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Wed, 11 Apr 2012 12:06:32 -0400
Subject: [PATCH] Added the necessary functions to add frames with periodic
boundary conditions to a CoordGroup.
---
modules/mol/base/pymod/export_coord_group.cc | 5 ++++-
modules/mol/base/src/coord_group.cc | 12 +++++++++++-
modules/mol/base/src/coord_group.hh | 3 ++-
modules/mol/base/src/coord_source.hh | 1 +
modules/mol/base/src/in_mem_coord_source.cc | 6 ++++++
modules/mol/base/src/in_mem_coord_source.hh | 1 +
6 files changed, 25 insertions(+), 3 deletions(-)
diff --git a/modules/mol/base/pymod/export_coord_group.cc b/modules/mol/base/pymod/export_coord_group.cc
index fa3a06132..4ada5f884 100644
--- a/modules/mol/base/pymod/export_coord_group.cc
+++ b/modules/mol/base/pymod/export_coord_group.cc
@@ -38,6 +38,8 @@ namespace {
void (CoordGroupHandle::*capture1)()=&CoordGroupHandle::Capture;
void (CoordGroupHandle::*capture2)(uint)=&CoordGroupHandle::Capture;
+ void (CoordGroupHandle::*add_frame1)(const geom::Vec3List&)=&CoordGroupHandle::AddFrame;
+ void (CoordGroupHandle::*add_frame2)(const geom::Vec3List&,const geom::Vec3&,const geom::Vec3&)=&CoordGroupHandle::AddFrame;
}
void export_CoordGroup()
@@ -47,7 +49,8 @@ void export_CoordGroup()
.def("GetEntity",&CoordGroupHandle::GetEntity)
.def("GetAtomCount",&CoordGroupHandle::GetAtomCount)
.def("AddFrames", &CoordGroupHandle::AddFrames)
- .def("AddFrame", &CoordGroupHandle::AddFrame)
+ .def("AddFrame", add_frame1)
+ .def("AddFrame", add_frame2)
.def("GetFrameCount",&CoordGroupHandle::GetFrameCount)
.def("GetFramePositions",&CoordGroupHandle::GetFramePositions)
.def("SetFramePositions",&CoordGroupHandle::SetFramePositions)
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index 127c82463..949199240 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -103,6 +103,16 @@ CoordGroupHandle::operator bool() const
}
}
+ void CoordGroupHandle::AddFrame(const geom::Vec3List& clist, const geom::Vec3& cell_size, const geom::Vec3& cell_angles)
+{
+ this->CheckValidity();
+ if (source_->IsMutable()) {
+ source_->AddFrame(clist,cell_size,cell_angles);
+ } else {
+ throw IntegrityError("Can't add frame to immutable CoordGroup");
+ }
+}
+
void CoordGroupHandle::AddFrames(const CoordGroupHandle& cg)
{
this->CheckValidity();
@@ -142,7 +152,7 @@ CoordFramePtr CoordGroupHandle::GetFrame(uint frame) const
this->CheckValidity();
return source_->GetFrame(frame);
}
-
+
AtomHandleList CoordGroupHandle::GetAtomList() const
{
this->CheckValidity();
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index 22a829dd6..8aa907f4f 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -69,7 +69,8 @@ public:
/// \brief add frame
//void AddFrame(const std::vector<geom::Vec3>& clist);
void AddFrame(const geom::Vec3List& clist);
-
+ void AddFrame(const geom::Vec3List& clist,const geom::Vec3& cell_size,const geom::Vec3& cell_angles);
+
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);
diff --git a/modules/mol/base/src/coord_source.hh b/modules/mol/base/src/coord_source.hh
index 604817535..fec0d9946 100644
--- a/modules/mol/base/src/coord_source.hh
+++ b/modules/mol/base/src/coord_source.hh
@@ -70,6 +70,7 @@ public:
void Capture(uint f);
virtual void AddFrame(const std::vector<geom::Vec3>& coords) = 0;
+ virtual void AddFrame(const std::vector<geom::Vec3>& coords,const geom::Vec3& cell_size,const geom::Vec3& cell_angles) = 0;
virtual void InsertFrame(int pos, const std::vector<geom::Vec3>& coords) = 0;
protected:
void SetMutable(bool flag);
diff --git a/modules/mol/base/src/in_mem_coord_source.cc b/modules/mol/base/src/in_mem_coord_source.cc
index 1690c1104..ea01db894 100644
--- a/modules/mol/base/src/in_mem_coord_source.cc
+++ b/modules/mol/base/src/in_mem_coord_source.cc
@@ -30,6 +30,12 @@ void InMemCoordSource::AddFrame(const std::vector<geom::Vec3>& coords)
frames_.push_back(fp);
}
+void InMemCoordSource::AddFrame(const std::vector<geom::Vec3>& coords,const geom::Vec3& cell_size,const geom::Vec3& cell_angles)
+{
+ CoordFramePtr fp(new CoordFrame(coords,cell_size,cell_angles));
+ frames_.push_back(fp);
+}
+
void InMemCoordSource::InsertFrame(int pos, const std::vector<geom::Vec3>& coords)
{
CoordFrameList::iterator it = frames_.begin();
diff --git a/modules/mol/base/src/in_mem_coord_source.hh b/modules/mol/base/src/in_mem_coord_source.hh
index dc032ebbe..0984791aa 100644
--- a/modules/mol/base/src/in_mem_coord_source.hh
+++ b/modules/mol/base/src/in_mem_coord_source.hh
@@ -44,6 +44,7 @@ public:
void AddFrame(const CoordFramePtr& frame);
virtual void AddFrame(const std::vector<geom::Vec3>& coords);
+ virtual void AddFrame(const std::vector<geom::Vec3>& coords,const geom::Vec3& cell_size,const geom::Vec3& cell_angles);
virtual void InsertFrame(int pos, const std::vector<geom::Vec3>& coords);
private:
--
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