From 7ef92de58c98739fbfec20662adf8b7290ded6fa Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Thu, 24 Oct 2013 12:38:15 -0400
Subject: [PATCH] Added function to extract the matrix of pairwise distances
between the atoms in two different views
---
modules/mol/alg/pymod/export_structure_analysis.cc | 1 +
modules/mol/alg/src/structure_analysis.cc | 13 +++++++++++++
modules/mol/alg/src/structure_analysis.hh | 1 +
3 files changed, 15 insertions(+)
diff --git a/modules/mol/alg/pymod/export_structure_analysis.cc b/modules/mol/alg/pymod/export_structure_analysis.cc
index 707006e3b..2a84fe027 100644
--- a/modules/mol/alg/pymod/export_structure_analysis.cc
+++ b/modules/mol/alg/pymod/export_structure_analysis.cc
@@ -32,4 +32,5 @@ void export_StructureAnalysis()
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("PariwiseDistanceMatrix",&PariwiseDistanceMatrix,(arg("EntityView1"),arg("EntityView2")));
}
diff --git a/modules/mol/alg/src/structure_analysis.cc b/modules/mol/alg/src/structure_analysis.cc
index 98d433339..b8c6f10ba 100644
--- a/modules/mol/alg/src/structure_analysis.cc
+++ b/modules/mol/alg/src/structure_analysis.cc
@@ -59,6 +59,19 @@ Real CalculateAverageAgreementWithDensityMap(const geom::Vec3List& vl, img::MapH
}
return sum/float(vl.size());
}
+
+std::vector< std::vector<Real> > PariwiseDistanceMatrix(const EntityView view1, const EntityView view2){
+ std::vector< std::vector<Real> > dist_mat;
+ unsigned int n1=view1.GetAtomCount(),n2=view2.GetAtomCount();
+ dist_mat.resize(n1,std::vector<Real>(n2,0));
+ AtomViewList atoms1=view1.GetAtomList(),atoms2=view2.GetAtomList();
+ for (unsigned int i=0; i!=n1; ++i){
+ for (unsigned int j=0; j!=n2; ++j) {
+ dist_mat[i][j]=geom::Distance(atoms1[i].GetPos(),atoms2[j].GetPos());
+ }
+ }
+ return dist_mat;
+}
#endif
void DLLEXPORT_OST_MOL_ALG WrapEntityInPeriodicCell(EntityHandle eh, const geom::Vec3 cell_center, const geom::Vec3 ucell_size, \
diff --git a/modules/mol/alg/src/structure_analysis.hh b/modules/mol/alg/src/structure_analysis.hh
index bafd70887..f7cb48540 100644
--- a/modules/mol/alg/src/structure_analysis.hh
+++ b/modules/mol/alg/src/structure_analysis.hh
@@ -38,5 +38,6 @@ namespace ost { namespace mol { namespace alg {
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);
+ std::vector< std::vector<Real> > DLLEXPORT_OST_MOL_ALG PariwiseDistanceMatrix(const EntityView view1, const EntityView view2);
}}}//ns
#endif
--
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