From 1fbbb52d9becbe235037a08e52bb1c75c686e9d4 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Tue, 25 Mar 2014 16:37:24 -0400
Subject: [PATCH] Use bonds in entity to correctly group the atoms in a residue
when wrapping in periodic cell.
---
.../alg/pymod/export_structure_analysis.cc | 2 +-
modules/mol/alg/src/structure_analysis.cc | 41 +++++++++++++++----
modules/mol/alg/src/structure_analysis.hh | 2 +-
3 files changed, 34 insertions(+), 11 deletions(-)
diff --git a/modules/mol/alg/pymod/export_structure_analysis.cc b/modules/mol/alg/pymod/export_structure_analysis.cc
index 2016cb305..2714f5847 100644
--- a/modules/mol/alg/pymod/export_structure_analysis.cc
+++ b/modules/mol/alg/pymod/export_structure_analysis.cc
@@ -34,7 +34,7 @@ void export_StructureAnalysis()
def("CalculateAverageAgreementWithDensityMap",&CalculateAverageAgreementWithDensityMap,(arg("pos_list"),arg("density_map")));
def("CalculateAgreementWithDensityMap",&CalculateAgreementWithDensityMap,(arg("pos_list"),arg("density_map")));
#endif
- def("WrapEntityInPeriodicCell",&WrapEntityInPeriodicCell,(arg("Entity"),arg("cell_center"),arg("ucell_size"),arg("ucell_angles")=geom::Vec3(),arg("group_res")=true));
+ def("WrapEntityInPeriodicCell",&WrapEntityInPeriodicCell,(arg("Entity"),arg("cell_center"),arg("ucell_size"),arg("ucell_angles")=geom::Vec3(),arg("group_res")=true,arg("follow_bonds")=false));
def("PariwiseDistanceMatrix",pair_dist2,(arg("EntityView1"),arg("EntityView2")));
diff --git a/modules/mol/alg/src/structure_analysis.cc b/modules/mol/alg/src/structure_analysis.cc
index 960acf471..b561b0a7f 100644
--- a/modules/mol/alg/src/structure_analysis.cc
+++ b/modules/mol/alg/src/structure_analysis.cc
@@ -90,7 +90,7 @@ std::vector< std::vector<Real> > PariwiseDistanceMatrix(const EntityView& view){
#endif
void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 ucell_size, \
- const geom::Vec3 ucell_angles, bool group_residues){
+ const geom::Vec3 ucell_angles, bool group_residues,bool follow_bonds){
mol::XCSEditor edi=eh.EditXCS(mol::BUFFERED_EDIT);
bool orthogonal;
if (ucell_angles==geom::Vec3()){ orthogonal=true; }
@@ -103,14 +103,37 @@ void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom:
ResidueHandle r=residues[i];
AtomHandleList atoms=r.GetAtomList();
geom::Vec3 ref_pos=atoms[0].GetPos();
- if (orthogonal) {
- for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
- edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),ref_pos,ucell_size));
- }}
- else {
- for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
- edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),ref_pos,ucell_size,ucell_angles));
- }}
+ if (follow_bonds) {
+ int natoms=r.GetAtomCount(),n=1,cycles=1;
+ AtomHandle a=atoms[0];
+ AtomHandleList wrapped_atoms;
+ wrapped_atoms.reserve(natoms);
+ wrapped_atoms.push_back(a);
+ while (n<natoms and cycles<natoms) {
+ ++cycles;
+ for (AtomHandleList::iterator a=wrapped_atoms.begin(), e=wrapped_atoms.end(); a!=e; ++a) {
+ AtomHandleList al=(*a).GetBondPartners();
+ ref_pos=(*a).GetPos();
+ for (AtomHandleList::iterator a2=al.begin(), e2=al.end(); a2!=e2; ++a2) {
+ if (std::find(wrapped_atoms.begin(),wrapped_atoms.end(), *a2) !=wrapped_atoms.end()){
+ continue;
+ } else {
+ ++n;
+ wrapped_atoms.push_back(*a2);
+ if (orthogonal) {
+ edi.SetAtomPos((*a2),geom::WrapVec3((*a2).GetPos(),ref_pos,ucell_size));
+ } else {
+ edi.SetAtomPos((*a2),geom::WrapVec3((*a2).GetPos(),ref_pos,ucell_size,ucell_angles));
+ }}}}}
+ } else {
+ if (orthogonal) {
+ for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+ edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),ref_pos,ucell_size));
+ }}
+ else {
+ for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+ edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),ref_pos,ucell_size,ucell_angles));
+ }}}
}
for (unsigned int i=0; i<n_residues; ++i) {
ResidueHandle r=residues[i];
diff --git a/modules/mol/alg/src/structure_analysis.hh b/modules/mol/alg/src/structure_analysis.hh
index 9cdfa01f5..2f450f692 100644
--- a/modules/mol/alg/src/structure_analysis.hh
+++ b/modules/mol/alg/src/structure_analysis.hh
@@ -37,7 +37,7 @@ namespace ost { namespace mol { namespace alg {
std::vector<Real> DLLEXPORT_OST_MOL_ALG CalculateAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map);
Real DLLEXPORT_OST_MOL_ALG CalculateAverageAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map);
#endif
- void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 ucell_size, const geom::Vec3 ucell_angles=geom::Vec3(), bool group_res=true);
+ void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 ucell_size, const geom::Vec3 ucell_angles=geom::Vec3(), bool group_res=true, bool follow_bond=true);
std::vector< std::vector<Real> > DLLEXPORT_OST_MOL_ALG PariwiseDistanceMatrix(const EntityView& view1, const EntityView& view2);
std::vector< std::vector<Real> > DLLEXPORT_OST_MOL_ALG PariwiseDistanceMatrix(const EntityView& view);
}}}//ns
--
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