From 4e41b55e4aeab494ed38ac9479a3f02a346b31f8 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Wed, 13 Oct 2010 18:41:09 +0200
Subject: [PATCH] added CoordGroupHandle.Filter(sel)
The method filters a trajectory by only keeping the positions of atoms
present in "sel".
---
modules/mol/base/pymod/export_coord_group.cc | 1 +
modules/mol/base/src/coord_group.cc | 41 ++++++++++++++++++--
modules/mol/base/src/coord_group.hh | 4 ++
3 files changed, 43 insertions(+), 3 deletions(-)
diff --git a/modules/mol/base/pymod/export_coord_group.cc b/modules/mol/base/pymod/export_coord_group.cc
index 90efa24de..5589268af 100644
--- a/modules/mol/base/pymod/export_coord_group.cc
+++ b/modules/mol/base/pymod/export_coord_group.cc
@@ -58,6 +58,7 @@ void export_CoordGroup()
.def("GetAtomList",&CoordGroupHandle::GetAtomList)
.def("__getitem__",cg_getitem)
.def("__setitem__",cg_setitem)
+ .def("Filter", &CoordGroupHandle::Filter)
;
def("CreateCoordGroup",CreateCoordGroup);
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index df0b1a5de..4dcabf68b 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -18,10 +18,10 @@
//------------------------------------------------------------------------------
#include <ost/invalid_handle.hh>
#include <ost/integrity_error.hh>
-
+#include <ost/log.hh>
#include <ost/mol/in_mem_coord_source.hh>
-#include <ost/mol/entity_handle.hh>
-
+#include <ost/mol/view_op.hh>
+#include <ost/mol/mol.hh>
#include "coord_group.hh"
namespace ost { namespace mol {
@@ -154,4 +154,39 @@ void CoordGroupHandle::Capture(uint frame)
}
}
+CoordGroupHandle CoordGroupHandle::Filter(const EntityView& selected) const
+{
+ this->CheckValidity();
+ std::vector<unsigned long> indices;
+ EntityHandle new_ent;
+ if (!selected.IsValid()) {
+ indices.reserve(this->GetAtomCount());
+ for (size_t i=0;i<this->GetAtomCount(); ++i) {
+ indices.push_back(i);
+ }
+ new_ent=this->GetEntity().Copy();
+ } else {
+ AtomViewList atoms=selected.GetAtomList();
+ indices.reserve(atoms.size());
+ for (AtomViewList::const_iterator i=atoms.begin(),
+ e=atoms.end(); i!=e; ++i) {
+ indices.push_back(i->GetIndex());
+ }
+ new_ent=CreateEntityFromView(selected, false);
+ }
+
+ CoordGroupHandle filtered_cg=CreateCoordGroup(new_ent.GetAtomList());
+ std::vector<geom::Vec3> vecs(indices.size());
+ for (size_t i=0; i<this->GetFrameCount(); ++i) {
+ LOG_INFO("Filtering frame " << i << "/" << this->GetFrameCount());
+ CoordFramePtr frame=this->GetFrame(i);
+ for (std::vector<unsigned long>::const_iterator
+ j=indices.begin(), e2=indices.end(); j!=e2; ++j) {
+ vecs[j-indices.begin()]=(*frame)[*j];
+ }
+ filtered_cg.AddFrame(vecs);
+ }
+ return filtered_cg;
+}
+
}} // ns
diff --git a/modules/mol/base/src/coord_group.hh b/modules/mol/base/src/coord_group.hh
index 70844a26b..dfa3c8530 100644
--- a/modules/mol/base/src/coord_group.hh
+++ b/modules/mol/base/src/coord_group.hh
@@ -82,6 +82,10 @@ public:
AtomHandleList GetAtomList() const;
CoordFramePtr GetFrame(uint frame) const;
+ /// \brief return a filtered coord group, containing only the atoms in the
+ /// view
+ CoordGroupHandle Filter(const EntityView& selected) const;
+
CoordGroupHandle(CoordSourcePtr source);
private:
void CheckValidity() const;
--
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