From f50455becc72a6125a4da6b07d7157cbc5a14437 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Fri, 27 May 2011 11:00:02 +0200
Subject: [PATCH] Local per reside LDT
Adds to the LDT function the option to save the local LDT in a floatProp. Mainly work by Pascal
---
modules/mol/alg/pymod/wrap_mol_alg.cc | 11 +++-----
modules/mol/alg/src/local_dist_test.cc | 35 ++++++++++++++++++++++----
modules/mol/alg/src/local_dist_test.hh | 5 +++-
3 files changed, 37 insertions(+), 14 deletions(-)
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 2d4098996..eb4811256 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -22,19 +22,18 @@
#include <ost/mol/alg/local_dist_test.hh>
#include <ost/mol/alg/superpose_frames.hh>
#include <ost/mol/alg/filter_clashes.hh>
-#include <ost/mol/alg/construct_cbeta.hh>
using namespace boost::python;
using namespace ost;
void export_svdSuperPose();
-void export_Clash();
+
#if OST_IMG_ENABLED
void export_entity_to_density();
#endif
namespace {
-Real (*ldt_a)(const mol::EntityView&, const mol::EntityView& ref, Real, Real)=&mol::alg::LocalDistTest;
+Real (*ldt_a)(const mol::EntityView&, const mol::EntityView& ref, Real, Real, const String&)=&mol::alg::LocalDistTest;
Real (*ldt_b)(const seq::AlignmentHandle&,Real, Real, int, int)=&mol::alg::LocalDistTest;
mol::EntityView (*fc_a)(const mol::EntityView&, Real,bool)=&mol::alg::FilterClashes;
mol::EntityView (*fc_b)(const mol::EntityHandle&, Real, bool)=&mol::alg::FilterClashes;
@@ -47,15 +46,11 @@ BOOST_PYTHON_MODULE(_mol_alg)
export_entity_to_density();
#endif
- def("LocalDistTest", ldt_a);
+ def("LocalDistTest", ldt_a, (arg("local_ldt_property_string")=""));
def("LocalDistTest", ldt_b, (arg("ref_index")=0, arg("mdl_index")=1));
def("FilterClashes", fc_a, (arg("ent"), arg("tolerance")=0.1, arg("always_remove_bb")=false));
def("FilterClashes", fc_b, (arg("ent"), arg("tolerance")=0.1, arg("always_remove_bb")=false));
def("SuperposeFrames", &ost::mol::alg::SuperposeFrames,
(arg("source"), arg("sel")=ost::mol::EntityView(), arg("begin")=0,
arg("end")=-1, arg("ref")=-1));
-// def("ConstructCBetas", one_arg, args("entity_handle"));
- def("ConstructCBetas", &ost::mol::alg::ConstructCBetas, (arg("entity_handle"), arg("include_gly")=false));
-
- export_Clash();
}
diff --git a/modules/mol/alg/src/local_dist_test.cc b/modules/mol/alg/src/local_dist_test.cc
index de78df711..5441f681b 100644
--- a/modules/mol/alg/src/local_dist_test.cc
+++ b/modules/mol/alg/src/local_dist_test.cc
@@ -53,7 +53,7 @@ std::pair<Real, Real> calc_overlap1(ResidueView ref_res,
EntityView ref,
ChainView mdl_chain,
Real tol, Real max_dist, bool only_fixed,
- bool swap)
+ bool swap,std::vector<std::pair<Real, Real> >& overlap_list )
{
std::pair<Real, Real> overlap(0.0, 0.0);
AtomViewList ref_atoms=ref_res.GetAtomList();
@@ -98,6 +98,8 @@ std::pair<Real, Real> calc_overlap1(ResidueView ref_res,
AtomView av2=mdl_chain.FindAtom(aj->GetResidue().GetNumber(),
aj->GetName());
overlap.second+=1.0;
+ overlap_list[ref_res.GetIndex()].second+=1.0;
+ overlap_list[aj->GetResidue().GetIndex()].second+=1.0;
if (!(av1 && av2)) {
continue;
}
@@ -105,6 +107,8 @@ std::pair<Real, Real> calc_overlap1(ResidueView ref_res,
Real ref_dist=geom::Length(ai->GetPos()-aj->GetPos());
if (std::abs(mdl_dist-ref_dist)<tol) {
overlap.first+=1;
+ overlap_list[ref_res.GetIndex()].first+=1.0;
+ overlap_list[aj->GetResidue().GetIndex()].first+=1.0;
}
}
}
@@ -195,8 +199,9 @@ std::pair<Real, Real> calc_overlap2(const seq::ConstSequenceHandle& ref_seq,
}
Real LocalDistTest(const EntityView& mdl, const EntityView& ref,
- Real cutoff, Real max_dist)
+ Real cutoff, Real max_dist, const String& local_ldt_property_string)
{
+
if (!mdl.GetResidueCount()) {
LOG_WARNING("model structures doesn't contain any residues");
return 0.0;
@@ -207,6 +212,7 @@ Real LocalDistTest(const EntityView& mdl, const EntityView& ref,
return 0.0;
}
ResidueViewList ref_residues=ref.GetResidueList();
+ std::vector<std::pair<Real, Real> > overlap_list(ref_residues.size(), std::pair<Real, Real>(0.0, 0.0));
ChainView mdl_chain=mdl.GetChainList()[0];
// Residues with symmetric side-chains require special treatment as there are
// two possible ways to name the atoms. We calculate the overlap with the
@@ -226,10 +232,10 @@ Real LocalDistTest(const EntityView& mdl, const EntityView& ref,
std::pair<Real, Real> ov1=calc_overlap1(*i, ref, mdl_chain,
cutoff, max_dist, true,
- false);
+ false, overlap_list);
std::pair<Real, Real> ov2=calc_overlap1(*i, ref, mdl_chain,
cutoff, max_dist, true,
- true);
+ true, overlap_list);
if (ov1.first/ov1.second<ov2.first/ov2.second) {
AtomViewList atoms=mdl_res.GetAtomList();
for (AtomViewList::iterator j=atoms.begin(),
@@ -244,10 +250,29 @@ Real LocalDistTest(const EntityView& mdl, const EntityView& ref,
for (ResidueViewList::iterator
i=ref_residues.begin(), e=ref_residues.end(); i!=e; ++i) {
std::pair<Real, Real> ov1=calc_overlap1(*i, ref, mdl_chain, cutoff,
- max_dist, false, false);
+ max_dist, false, false, overlap_list);
total_ov.first+=ov1.first;
total_ov.second+=ov1.second;
}
+
+ // attach local per-residue LDT as property:
+ if(local_ldt_property_string!="") {
+ for (ResidueViewList::iterator
+ i=ref_residues.begin(), e=ref_residues.end(); i!=e; ++i) {
+ std::pair<Real, Real> ov1=calc_overlap1(*i, ref, mdl_chain, cutoff,
+ max_dist, false, false, overlap_list);
+ total_ov.first+=ov1.first;
+ total_ov.second+=ov1.second;
+ Real local_ldt=overlap_list[(*i).GetIndex()].first/(overlap_list[(*i).GetIndex()].second ? overlap_list[(*i).GetIndex()].second : 1);
+ if (mdl_chain.FindResidue((*i).GetNumber()).IsValid()) {
+ ResidueView mdl_res=mdl_chain.FindResidue((*i).GetNumber());
+ mdl_res.SetFloatProp(local_ldt_property_string, local_ldt);
+ }
+ }
+ mdl_chain.SetFloatProp(local_ldt_property_string, total_ov.first/(total_ov.second ? total_ov.second : 1));
+ }
+ overlap_list.clear();
+
return total_ov.first/(total_ov.second ? total_ov.second : 1);
}
diff --git a/modules/mol/alg/src/local_dist_test.hh b/modules/mol/alg/src/local_dist_test.hh
index 06c87c322..76ef23803 100644
--- a/modules/mol/alg/src/local_dist_test.hh
+++ b/modules/mol/alg/src/local_dist_test.hh
@@ -27,12 +27,15 @@ namespace ost { namespace mol { namespace alg {
Real DLLEXPORT_OST_MOL_ALG LocalDistTest(const EntityView& mdl,
const EntityView& ref,
- Real cutoff, Real max_dist);
+ Real cutoff, Real max_dist,
+ const String& local_ldt_property_string="");
Real DLLEXPORT_OST_MOL_ALG LocalDistTest(const ost::seq::AlignmentHandle& aln,
Real cutoff, Real max_dist,
int ref_index=0, int mdl_index=1);
+
}}}
#endif
+
--
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