From 9060e0fc6213523c99a68d196e21f4cd330c5880 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Wed, 23 Oct 2013 10:35:46 -0400
Subject: [PATCH] Added support for non-orthogonal cells for the
WrapEntityInPeriodicCell function.
---
.../alg/pymod/export_structure_analysis.cc | 2 +-
modules/mol/alg/src/structure_analysis.cc | 31 ++++++++++++++-----
modules/mol/alg/src/structure_analysis.hh | 2 +-
3 files changed, 25 insertions(+), 10 deletions(-)
diff --git a/modules/mol/alg/pymod/export_structure_analysis.cc b/modules/mol/alg/pymod/export_structure_analysis.cc
index f9f58347d..707006e3b 100644
--- a/modules/mol/alg/pymod/export_structure_analysis.cc
+++ b/modules/mol/alg/pymod/export_structure_analysis.cc
@@ -31,5 +31,5 @@ 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("basis_vec"),arg("group_res")=true));
+ def("WrapEntityInPeriodicCell",&WrapEntityInPeriodicCell,(arg("Entity"),arg("cell_center"),arg("ucell_size"),arg("ucell_angles")=geom::Vec3(),arg("group_res")=true));
}
diff --git a/modules/mol/alg/src/structure_analysis.cc b/modules/mol/alg/src/structure_analysis.cc
index c2d02f0ad..98d433339 100644
--- a/modules/mol/alg/src/structure_analysis.cc
+++ b/modules/mol/alg/src/structure_analysis.cc
@@ -61,8 +61,12 @@ 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){
+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){
mol::XCSEditor edi=eh.EditXCS(mol::BUFFERED_EDIT);
+ bool orthogonal;
+ if (ucell_angles==geom::Vec3()){ orthogonal=true; }
+ else { orthogonal=false; }
if (group_residues) {
geom::Vec3 cm,wrapped_cm,shift;
ResidueHandleList residues=eh.GetResidueList();
@@ -71,14 +75,20 @@ 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();
- for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
- edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),ref_pos,basis_vec));
- }
+ 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];
cm=r.GetCenterOfMass();
- wrapped_cm=geom::WrapVec3(cm,cell_center,basis_vec);
+ if (orthogonal) {wrapped_cm=geom::WrapVec3(cm,cell_center,ucell_size);}
+ else {wrapped_cm=geom::WrapVec3(cm,cell_center,ucell_size,ucell_angles);}
if (wrapped_cm==cm) continue;
AtomHandleList atoms=r.GetAtomList();
unsigned int n_atoms=r.GetAtomCount();
@@ -90,9 +100,14 @@ void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom:
}
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));
- }
+ if (orthogonal){
+ for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+ edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),cell_center,ucell_size));
+ }}
+ else {
+ for (AtomHandleList::iterator a=atoms.begin(), e=atoms.end(); a!=e; ++a) {
+ edi.SetAtomPos((*a),geom::WrapVec3((*a).GetPos(),cell_center,ucell_size,ucell_angles));
+ }}
}
}
diff --git a/modules/mol/alg/src/structure_analysis.hh b/modules/mol/alg/src/structure_analysis.hh
index 7ad8ad575..bafd70887 100644
--- a/modules/mol/alg/src/structure_analysis.hh
+++ b/modules/mol/alg/src/structure_analysis.hh
@@ -37,6 +37,6 @@ 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 basis_vec, 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);
}}}//ns
#endif
--
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