From eef9f076acaa72f58f4e88c2048bd7ebc348b4e5 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Wed, 20 Feb 2013 15:39:18 -0500
Subject: [PATCH] Fixed the atom indices in the entity generated in the
CoordGroup::Filter function
---
modules/mol/base/src/atom_base.cc | 7 +++++++
modules/mol/base/src/atom_base.hh | 1 +
modules/mol/base/src/coord_group.cc | 6 +++++-
3 files changed, 13 insertions(+), 1 deletion(-)
diff --git a/modules/mol/base/src/atom_base.cc b/modules/mol/base/src/atom_base.cc
index c818fbc1c..a24ca3abb 100644
--- a/modules/mol/base/src/atom_base.cc
+++ b/modules/mol/base/src/atom_base.cc
@@ -240,5 +240,12 @@ unsigned long AtomBase::GetIndex() const
return Impl()->GetIndex();
}
+void AtomBase::SetIndex(const unsigned long index)
+{
+ this->CheckValidity();
+ return impl_->SetIndex(index);
+}
+
+
}} // ns
diff --git a/modules/mol/base/src/atom_base.hh b/modules/mol/base/src/atom_base.hh
index 137953115..4ddc13f2f 100644
--- a/modules/mol/base/src/atom_base.hh
+++ b/modules/mol/base/src/atom_base.hh
@@ -141,6 +141,7 @@ public:
void SetRadius(Real radius);
+ void SetIndex (const unsigned long index);
const geom::Mat3& GetAnisou() const;
diff --git a/modules/mol/base/src/coord_group.cc b/modules/mol/base/src/coord_group.cc
index 5af231a55..d02eecc27 100644
--- a/modules/mol/base/src/coord_group.cc
+++ b/modules/mol/base/src/coord_group.cc
@@ -239,8 +239,12 @@ CoordGroupHandle CoordGroupHandle::Filter(const EntityView& selected, int first,
indices.push_back(i->GetIndex());
}
new_ent=CreateEntityFromView(selected, false);
+ //we have to correct the atom indices in the new entity
+ AtomHandleList new_atoms=new_ent.GetAtomList();
+ for (int i=0,e=atoms.size();i!=e;++i){
+ new_atoms[i].SetIndex(i);
+ }
}
-
CoordGroupHandle filtered_cg=CreateCoordGroup(new_ent.GetAtomList());
std::vector<geom::Vec3> vecs(indices.size());
if (last==-1) last=this->GetFrameCount();
--
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