From 28e62d110a9aa3f080fa23992c061c0c77b07a14 Mon Sep 17 00:00:00 2001
From: Ansgar Philippsen <ansgar.philippsen@gmail.com>
Date: Tue, 26 Jun 2012 11:57:03 -0400
Subject: [PATCH] added frame delta and start time properties to coord group
---
modules/io/src/mol/dcd_io.cc | 2 +-
modules/mol/base/pymod/export_coord_group.cc | 12 ++++++++--
modules/mol/base/src/coord_group.cc | 24 ++++++++++++++++++++
modules/mol/base/src/coord_group.hh | 15 +++++++++++-
modules/mol/base/src/coord_source.cc | 10 +++-----
modules/mol/base/src/coord_source.hh | 17 ++++++++++----
modules/mol/base/src/in_mem_coord_source.cc | 2 +-
modules/mol/base/src/in_mem_coord_source.hh | 2 +-
8 files changed, 67 insertions(+), 17 deletions(-)
diff --git a/modules/io/src/mol/dcd_io.cc b/modules/io/src/mol/dcd_io.cc
index 7ec81f5ed..39255d366 100644
--- a/modules/io/src/mol/dcd_io.cc
+++ b/modules/io/src/mol/dcd_io.cc
@@ -306,7 +306,7 @@ public:
}
- virtual uint GetFrameCount()
+ virtual uint GetFrameCount() const
{
if (!frame_count_)
const_cast<DCDCoordSource*>(this)->FetchFrame(0);
diff --git a/modules/mol/base/pymod/export_coord_group.cc b/modules/mol/base/pymod/export_coord_group.cc
index 6bdeb1d69..a445e74c0 100644
--- a/modules/mol/base/pymod/export_coord_group.cc
+++ b/modules/mol/base/pymod/export_coord_group.cc
@@ -47,24 +47,32 @@ void export_CoordGroup()
class_<CoordGroupHandle>("CoordGroupHandle",no_init)
.def("IsValid",&CoordGroupHandle::IsValid)
.def("GetEntity",&CoordGroupHandle::GetEntity)
+ .add_property("entity",&CoordGroupHandle::GetEntity)
.def("GetAtomCount",&CoordGroupHandle::GetAtomCount)
+ .add_property("atom_count",&CoordGroupHandle::GetAtomCount)
.def("GetFrame",&CoordGroupHandle::GetFrame2)
.def("AddFrames", &CoordGroupHandle::AddFrames)
.def("AddFrame", add_frame1)
.def("AddFrame", add_frame2)
.def("GetFrameCount",&CoordGroupHandle::GetFrameCount)
+ .add_property("frame_count",&CoordGroupHandle::GetFrameCount)
.def("GetFramePositions",&CoordGroupHandle::GetFramePositions)
.def("SetFramePositions",&CoordGroupHandle::SetFramePositions)
.def("SetAtomPos",&CoordGroupHandle::SetAtomPos)
.def("GetAtomPos",&CoordGroupHandle::GetAtomPos)
.def("CopyFrame",&CoordGroupHandle::CopyFrame)
- .add_property("atoms", &CoordGroupHandle::GetAtomList)
- .add_property("entity", &CoordGroupHandle::GetEntity)
.def("IsValid", &CoordGroupHandle::IsValid)
.def("Capture", capture1)
.def("Capture", capture2)
.def("CaptureInto",&CoordGroupHandle::CaptureInto)
.def("GetAtomList",&CoordGroupHandle::GetAtomList)
+ .add_property("atoms", &CoordGroupHandle::GetAtomList)
+ .def("GetDelta",&CoordGroupHandle::GetDelta)
+ .def("SetDelta",&CoordGroupHandle::SetDelta)
+ .add_property("delta",&CoordGroupHandle::GetDelta,&CoordGroupHandle::SetDelta)
+ .def("GetStartTime",&CoordGroupHandle::GetStartTime)
+ .def("SetStartTime",&CoordGroupHandle::SetStartTime)
+ .add_property("start_time",&CoordGroupHandle::GetStartTime,&CoordGroupHandle::SetStartTime)
.def("__getitem__",cg_getitem)
.def("__setitem__",cg_setitem)
.def("Filter", &CoordGroupHandle::Filter, (arg("selected"),arg("first")=0,arg("last")=-1))
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index db3fd341c..bd56a4e00 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -66,6 +66,30 @@ uint CoordGroupHandle::GetFrameCount() const
return source_->GetFrameCount();
}
+float CoordGroupHandle::GetDelta() const
+{
+ this->CheckValidity();
+ return source_->GetFrameDelta();
+}
+
+void CoordGroupHandle::SetDelta(float d)
+{
+ this->CheckValidity();
+ source_->SetFrameDelta(d);
+}
+
+float CoordGroupHandle::GetStartTime() const
+{
+ this->CheckValidity();
+ return source_->GetStartTime();
+}
+
+void CoordGroupHandle::SetStartTime(float t)
+{
+ this->CheckValidity();
+ source_->SetStartTime(t);
+}
+
void CoordGroupHandle::SetFramePositions(uint frame,
const std::vector<geom::Vec3>& clist)
{
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index 652fe3463..bf049aadd 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -35,6 +35,8 @@ class DLLEXPORT_OST_MOL CoordGroupHandle {
public:
/// \brief create empty, invalid handle
CoordGroupHandle();
+ /// \brief used internally
+ CoordGroupHandle(CoordSourcePtr source);
/// \brief return trajectories entity handle
EntityHandle GetEntity() const;
@@ -48,6 +50,18 @@ public:
/// \brief number of frames
uint GetFrameCount() const;
+ /// \brief time in ps between frames, default 0.0
+ float GetDelta() const;
+
+ /// \brief set time between each frame in ps
+ void SetDelta(float d);
+
+ /// \brief start time in ps, default 0.0
+ float GetStartTime() const;
+
+ /// \rbrief set start time in ps
+ void SetStartTime(float t);
+
/// \brief assign positions to the given frame - order and count must match
/// initial atomlist
void SetFramePositions(uint frame, const std::vector<geom::Vec3>& clist);
@@ -92,7 +106,6 @@ public:
/// view
CoordGroupHandle Filter(const EntityView& selected,int first=0,int last=-1) const;
- CoordGroupHandle(CoordSourcePtr source);
private:
diff --git a/modules/mol/base/src/coord_source.cc b/modules/mol/base/src/coord_source.cc
index 5f0e42a63..335117423 100644
--- a/modules/mol/base/src/coord_source.cc
+++ b/modules/mol/base/src/coord_source.cc
@@ -35,7 +35,9 @@ CoordSource::CoordSource(const AtomHandleList& atoms):
atoms_(atoms),
entity_(),
mutable_(false),
- atom_dict_()
+ atom_dict_(),
+ delta_(1.0),
+ start_time_(0.0)
{
if (!atoms_.empty()) {
entity_=atoms_.front().GetEntity();
@@ -45,12 +47,6 @@ CoordSource::CoordSource(const AtomHandleList& atoms):
}
}
-
-CoordSource::~CoordSource()
-{
-
-}
-
void CoordSource::CopyFrame(uint frame_id)
{
if (atoms_.empty()) {
diff --git a/modules/mol/base/src/coord_source.hh b/modules/mol/base/src/coord_source.hh
index fec0d9946..a50f256a1 100644
--- a/modules/mol/base/src/coord_source.hh
+++ b/modules/mol/base/src/coord_source.hh
@@ -43,14 +43,22 @@ class DLLEXPORT_OST_MOL CoordSource {
public:
CoordSource(const AtomHandleList& atoms);
- virtual ~CoordSource();
+ virtual ~CoordSource() {}
+ virtual uint GetFrameCount() const =0;
+
+ virtual CoordFramePtr GetFrame(uint frame_id) const = 0;
+
CoordSourcePtr Extract(int start=0, int stop=-1, int step=1);
- virtual uint GetFrameCount()=0;
+ // time in ps between frames
+ float GetFrameDelta() const {return delta_;}
+ void SetFrameDelta(float d) {delta_=d;}
+
+ // start time in ps
+ float GetStartTime() const {return start_time_;}
+ void SetStartTime(float t) {start_time_=t;}
- virtual CoordFramePtr GetFrame(uint frame_id) const = 0;
-
int GetAtomCount() const;
EntityHandle GetEntity() const;
@@ -79,6 +87,7 @@ private:
EntityHandle entity_;
bool mutable_;
std::map<long,uint> atom_dict_;
+ float delta_,start_time_;
};
}}
diff --git a/modules/mol/base/src/in_mem_coord_source.cc b/modules/mol/base/src/in_mem_coord_source.cc
index ea01db894..a8d985c25 100644
--- a/modules/mol/base/src/in_mem_coord_source.cc
+++ b/modules/mol/base/src/in_mem_coord_source.cc
@@ -9,7 +9,7 @@ InMemCoordSource::InMemCoordSource(const AtomHandleList& atoms):
this->SetMutable(true);
}
-uint InMemCoordSource::GetFrameCount()
+uint InMemCoordSource::GetFrameCount() const
{
return frames_.size();
}
diff --git a/modules/mol/base/src/in_mem_coord_source.hh b/modules/mol/base/src/in_mem_coord_source.hh
index 0984791aa..6b6d15f6a 100644
--- a/modules/mol/base/src/in_mem_coord_source.hh
+++ b/modules/mol/base/src/in_mem_coord_source.hh
@@ -38,7 +38,7 @@ class DLLEXPORT_OST_MOL InMemCoordSource : public CoordSource {
public:
InMemCoordSource(const AtomHandleList& atoms);
- virtual uint GetFrameCount();
+ virtual uint GetFrameCount() const;
virtual CoordFramePtr GetFrame(uint frame_id) const;
--
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