From 6fd32068b70685c72a4c79296e6b47861a23a3e3 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Fri, 15 Mar 2013 19:09:56 -0400
Subject: [PATCH] Added the possibility to wrap an entity in a periodic cell on
a per-atom base instead of per-residue base in
mol::alg::structure_analysis::WrapEntityInPeriodicCell
---
modules/mol/alg/src/structure_analysis.cc | 32 ++++++++++++++---------
1 file changed, 19 insertions(+), 13 deletions(-)
diff --git a/modules/mol/alg/src/structure_analysis.cc b/modules/mol/alg/src/structure_analysis.cc
index de7a176b1..c2d02f0ad 100644
--- a/modules/mol/alg/src/structure_analysis.cc
+++ b/modules/mol/alg/src/structure_analysis.cc
@@ -63,10 +63,10 @@ Real CalculateAverageAgreementWithDensityMap(const geom::Vec3List& vl, img::MapH
#endif
void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 basis_vec, bool group_residues){
mol::XCSEditor edi=eh.EditXCS(mol::BUFFERED_EDIT);
- geom::Vec3 cm,wrapped_cm,shift;
- ResidueHandleList residues=eh.GetResidueList();
- unsigned int n_residues=eh.GetResidueCount();
if (group_residues) {
+ geom::Vec3 cm,wrapped_cm,shift;
+ ResidueHandleList residues=eh.GetResidueList();
+ unsigned int n_residues=eh.GetResidueCount();
for (unsigned int i=0; i<n_residues; ++i) {
ResidueHandle r=residues[i];
AtomHandleList atoms=r.GetAtomList();
@@ -75,17 +75,23 @@ void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom:
edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),ref_pos,basis_vec));
}
}
+ for (unsigned int i=0; i<n_residues; ++i) {
+ ResidueHandle r=residues[i];
+ cm=r.GetCenterOfMass();
+ wrapped_cm=geom::WrapVec3(cm,cell_center,basis_vec);
+ if (wrapped_cm==cm) continue;
+ AtomHandleList atoms=r.GetAtomList();
+ unsigned int n_atoms=r.GetAtomCount();
+ shift=wrapped_cm-cm;
+ for (unsigned int j=0; j<n_atoms; ++j) {
+ edi.SetAtomPos(atoms[j],atoms[j].GetPos()+shift);
+ }
+ }
}
- for (unsigned int i=0; i<n_residues; ++i) {
- ResidueHandle r=residues[i];
- cm=r.GetCenterOfMass();
- wrapped_cm=geom::WrapVec3(cm,cell_center,basis_vec);
- if (wrapped_cm==cm) continue;
- AtomHandleList atoms=r.GetAtomList();
- unsigned int n_atoms=r.GetAtomCount();
- shift=wrapped_cm-cm;
- for (unsigned int j=0; j<n_atoms; ++j) {
- edi.SetAtomPos(atoms[j],atoms[j].GetPos()+shift);
+ else {
+ AtomHandleList atoms=eh.GetAtomList();
+ for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+ edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),cell_center,basis_vec));
}
}
}
--
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