From 501e9f065acef4c83313d01c3241e1ddd5a72e60 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Wed, 20 Feb 2013 16:42:25 -0500
Subject: [PATCH] Fixed atom ordering in the GetFrameFromEntity() function in
the structure_analysis.py module.
This is used to make functions written at the CoordFrame level
accesible to analyze both entities and trajectories.
---
modules/mol/alg/pymod/structure_analysis.py | 2 +-
modules/mol/base/pymod/export_entity.cc | 2 +-
modules/mol/base/src/entity_handle.cc | 11 +++++++++--
modules/mol/base/src/entity_handle.hh | 2 +-
4 files changed, 12 insertions(+), 5 deletions(-)
diff --git a/modules/mol/alg/pymod/structure_analysis.py b/modules/mol/alg/pymod/structure_analysis.py
index 7cbd0dd4b..1ad301618 100644
--- a/modules/mol/alg/pymod/structure_analysis.py
+++ b/modules/mol/alg/pymod/structure_analysis.py
@@ -13,7 +13,7 @@ def GetFrameFromEntity(eh):
Input:
eh : EntityHandle
"""
- return ost.mol.CreateCoordFrame(eh.GetAtomPosList())
+ return ost.mol.CreateCoordFrame(eh.GetAtomPosList(ordered_by_index=True))
def GetDistanceBetwCenterOfMass(sele1,sele2):
"""
diff --git a/modules/mol/base/pymod/export_entity.cc b/modules/mol/base/pymod/export_entity.cc
index bb55d9bd6..280024f0a 100644
--- a/modules/mol/base/pymod/export_entity.cc
+++ b/modules/mol/base/pymod/export_entity.cc
@@ -155,7 +155,7 @@ void export_Entity()
.def("GetMass", &EntityHandle::GetMass)
.def("GetCenterOfMass", &EntityHandle::GetCenterOfMass)
.def("GetCenterOfAtoms", &EntityHandle::GetCenterOfAtoms)
- .def("GetAtomPosList", &EntityHandle::GetAtomPosList)
+ .def("GetAtomPosList", &EntityHandle::GetAtomPosList, arg("ordered_by_index")=false)
.def("GetGeometricCenter", geom_center<EntityHandle>)
.add_property("geometric_center", geom_center<EntityHandle>)
diff --git a/modules/mol/base/src/entity_handle.cc b/modules/mol/base/src/entity_handle.cc
index e34e11d2e..7bf3ed349 100644
--- a/modules/mol/base/src/entity_handle.cc
+++ b/modules/mol/base/src/entity_handle.cc
@@ -402,16 +402,23 @@ AtomHandleList EntityHandle::GetAtomList() const
return atoms;
}
-geom::Vec3List EntityHandle::GetAtomPosList() const {
+bool less_index(const mol::AtomHandle& a1, const mol::AtomHandle& a2)
+{
+ return a1.GetIndex()<a2.GetIndex();
+}
+
+geom::Vec3List EntityHandle::GetAtomPosList(bool ordered_by_index) const {
this->CheckValidity();
geom::Vec3List atom_pos_list;
atom_pos_list.reserve(this->GetAtomCount());
AtomHandleList atom_list=this->GetAtomList();
+ if (ordered_by_index){
+ std::sort(atom_list.begin(),atom_list.end(),less_index);
+ }
for (AtomHandleList::const_iterator a=atom_list.begin(), e=atom_list.end(); a!=e; ++a) {
atom_pos_list.push_back(a->GetPos());
}
return atom_pos_list;
- //return Impl()->GetAtomPosList();
}
EntityHandle EntityHandle::GetHandle() const
diff --git a/modules/mol/base/src/entity_handle.hh b/modules/mol/base/src/entity_handle.hh
index fe2a43913..c2888c9e2 100644
--- a/modules/mol/base/src/entity_handle.hh
+++ b/modules/mol/base/src/entity_handle.hh
@@ -289,7 +289,7 @@ public:
AtomHandleList GetAtomList() const;
/// \brief get complete list of atom positions
- geom::Vec3List GetAtomPosList() const;
+ geom::Vec3List GetAtomPosList(bool ordered_by_index = false) const;
/// \brief Get editor for external coordinate system to manipulate atom
/// positions
--
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