From 6bf3a6108ea96c468ed9a35728d487f6460a4e41 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Wed, 21 Mar 2012 17:38:23 +0100
Subject: [PATCH] Updated LDT to use now distance list implementation
---
modules/mol/alg/pymod/wrap_mol_alg.cc | 4 +-
modules/mol/alg/src/ldt.cc | 3 +-
modules/mol/alg/src/local_dist_test.cc | 325 ++++++++++++++++---------
modules/mol/alg/src/local_dist_test.hh | 57 ++++-
4 files changed, 261 insertions(+), 128 deletions(-)
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 52b7a703f..d14474df0 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -34,8 +34,8 @@ void export_entity_to_density();
namespace {
-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;
+Real (*ldt_a)(const mol::EntityView&, const mol::alg::GlobalDistanceList& glob_dist_list, Real, const String&)=&mol::alg::LocalDistTest;
+Real (*ldt_b)(const seq::AlignmentHandle&,Real, int, int)=&mol::alg::LocalDistTest;
mol::EntityView (*fc_a)(const mol::EntityView&, const mol::alg::ClashingDistances&,bool)=&mol::alg::FilterClashes;
mol::EntityView (*fc_b)(const mol::EntityHandle&, const mol::alg::ClashingDistances&, bool)=&mol::alg::FilterClashes;
mol::EntityView (*csc_a)(const mol::EntityView&, const mol::alg::StereoChemicalParams&, const mol::alg::StereoChemicalParams&, Real, Real, bool)=&mol::alg::CheckStereoChemistry;
diff --git a/modules/mol/alg/src/ldt.cc b/modules/mol/alg/src/ldt.cc
index 6b343838c..3b37839c6 100644
--- a/modules/mol/alg/src/ldt.cc
+++ b/modules/mol/alg/src/ldt.cc
@@ -235,7 +235,8 @@ int main (int argc, char **argv)
v=alg::FilterClashes(v,nonbonded_table);
}
- Real ldt=LDTHA(v, ref_view, radius);
+ GlobalDistanceList glob_dist_list = CreateDistanceList(ref_view,radius);
+ Real ldt=LDTHA(v, glob_dist_list);
std::cout << "File: " << files[i] << std::endl;
std::cout << "Global LDT score: " << ldt << std::endl;
diff --git a/modules/mol/alg/src/local_dist_test.cc b/modules/mol/alg/src/local_dist_test.cc
index 274a32aa1..13f37e2e0 100644
--- a/modules/mol/alg/src/local_dist_test.cc
+++ b/modules/mol/alg/src/local_dist_test.cc
@@ -1,6 +1,7 @@
#include <ost/log.hh>
#include <ost/mol/mol.hh>
#include "local_dist_test.hh"
+#include <boost/concept_check.hpp>
namespace ost { namespace mol { namespace alg {
@@ -37,7 +38,8 @@ bool swappable(const String& rname, const String& aname)
if (rname=="ASP") {
return (aname=="OD1" || aname=="OD2");
}
- if (rname=="VAL") {
+ if (rname=="VAL") {
+
return (aname=="CG1" || aname=="CG2");
}
if (rname=="TYR" || rname=="PHE") {
@@ -49,84 +51,103 @@ bool swappable(const String& rname, const String& aname)
return false;
}
-std::pair<Real, Real> calc_overlap1(ResidueView ref_res,
- EntityView ref,
+std::pair<bool,Real> within_tolerance(Real mdl_dist, const ReferenceDistance& ref_dist, Real tol)
+{
+ Real min = ref_dist.GetMaxDistance();
+ Real max = ref_dist.GetMaxDistance();
+ bool within_tol = false;
+ Real difference = 0;
+ if (mdl_dist>=min && mdl_dist <=max) {
+ within_tol=true;
+ } else if (mdl_dist < min && abs(min-mdl_dist) < tol) {
+ within_tol = true;
+ } else if (mdl_dist > max && abs(mdl_dist-max) < tol) {
+ within_tol = true;
+ }
+ if (within_tol == false) {
+ if (mdl_dist > max) {
+ difference = mdl_dist-(max+tol);
+ } else {
+ difference = mdl_dist-(min-tol);
+ }
+ }
+ return std::make_pair<bool,Real>(within_tol,difference);
+}
+
+
+std::pair<Real, Real> calc_overlap1(const ResidueDistanceList& res_distance_list,
ChainView mdl_chain,
- Real tol, Real max_dist, bool only_fixed,
- bool swap,std::vector<std::pair<Real, Real> >& overlap_list )
+ Real tol, bool only_fixed,
+ bool swap,std::vector<std::pair<Real, Real> >& overlap_list, bool log )
{
std::pair<Real, Real> overlap(0.0, 0.0);
- AtomViewList ref_atoms=ref_res.GetAtomList();
- ResidueView mdl_res=mdl_chain.FindResidue(ref_res.GetNumber());
- AtomViewList within;
- if (max_dist<0){
- within=ref.GetAtomList();
- }
- for (AtomViewList::iterator ai=ref_atoms.begin(),
- ae=ref_atoms.end(); ai!=ae; ++ai) {
- if (ai->GetElement()=="H") { continue; }
- String name=swap ? swapped_name(ai->GetName()) : ai->GetName();
+ ResidueView mdl_res=mdl_chain.FindResidue(res_distance_list[0].GetFirstAtom().GetResNum());
+ for (ResidueDistanceList::const_iterator ai=res_distance_list.begin(),
+ ae=res_distance_list.end(); ai!=ae; ++ai) {
+ UniqueAtomIdentifier first_atom=ai->GetFirstAtom();
+ UniqueAtomIdentifier second_atom=ai->GetSecondAtom();
+ String name=swap ? swapped_name(first_atom.GetAtomName()) : first_atom.GetAtomName();
AtomView av1=mdl_res ? mdl_res.FindAtom(name) : AtomView();
- if (max_dist>=0){
- within=ref.FindWithin(ai->GetPos(), max_dist);
- }
- for (AtomViewList::iterator aj=within.begin(),
- ae2=within.end(); aj!=ae2; ++aj) {
- if (aj->GetElement()=="H" ||
- aj->GetResidue().GetChain()!=ai->GetResidue().GetChain()) {
+
+ if (only_fixed) {
+ if (swappable(second_atom.GetResidueName(), second_atom.GetAtomName())) {
continue;
}
-
- if (only_fixed) {
- if (aj->GetResidue().GetNumber()==ref_res.GetNumber()) {
- continue;
- }
- if (swappable(aj->GetResidue().GetName(), aj->GetName())) {
- continue;
- }
- AtomView av2=mdl_chain.FindAtom(aj->GetResidue().GetNumber(),
- aj->GetName());
- overlap.second+=1.0;
- if (!(av1 && av2)) {
- continue;
- }
- Real mdl_dist=geom::Length(av1.GetPos()-av2.GetPos());
- Real ref_dist=geom::Length(ai->GetPos()-aj->GetPos());
- if (std::abs(mdl_dist-ref_dist)<tol) {
- overlap.first+=1;
- }
+ AtomView av2=mdl_chain.FindAtom(second_atom.GetResNum(),second_atom.GetAtomName());
+ overlap.second+=1.0;
+ if (!(av1 && av2)) {
continue;
}
- if (aj->GetResidue().GetNumber()>ref_res.GetNumber()) {
- 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;
- }
- Real mdl_dist=geom::Length(av1.GetPos()-av2.GetPos());
- Real ref_dist=geom::Length(ai->GetPos()-aj->GetPos());
- if (std::abs(mdl_dist-ref_dist)<tol) {
+ Real mdl_dist=geom::Length(av1.GetPos()-av2.GetPos());
+ ReferenceDistance ref_dist=*ai;
+ if (within_tolerance(mdl_dist,ref_dist,tol).first) {
+ if (log) {
LOG_VERBOSE("LDT:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
<< " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetName() << " " << av2.GetResidue().GetNumber() << " " << av2.GetName() << " "
- << mdl_dist << " " << ref_dist << " " << mdl_dist-ref_dist << " " << tol << " " << "PASS")
- overlap.first+=1;
- overlap_list[ref_res.GetIndex()].first+=1.0;
- overlap_list[aj->GetResidue().GetIndex()].first+=1.0;
- } else {
+ << mdl_dist << " " << ref_dist.GetMinDistance() << " " << ref_dist.GetMaxDistance() << " " << tol << " " << "PASS")
+ }
+ overlap.first+=1;
+ } else {
+ if (log) {
LOG_VERBOSE("LDT:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
<< " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetName() << " " << av2.GetResidue().GetNumber() << " " << av2.GetName() << " "
- << mdl_dist << " " << ref_dist << " " << mdl_dist-ref_dist << " " << tol << " " << "FAIL")
- }
+ << mdl_dist << " " << ref_dist.GetMinDistance() << " " << mdl_dist-ref_dist.GetMinDistance() << " " << tol << " " << "FAIL")
+ }
}
- }
- }
+ continue;
+ }
+ AtomView av2=mdl_chain.FindAtom(second_atom.GetResNum(), second_atom.GetAtomName());
+ overlap.second+=1.0;
+ if (av1) {
+ overlap_list[av1.GetResidue().GetIndex()].second+=1.0;
+ }
+ if (av2) {
+ overlap_list[av2.GetResidue().GetIndex()].second+=1.0;
+ }
+ if (!(av1 && av2)) {
+ continue;
+ }
+
+ Real mdl_dist=geom::Length(av1.GetPos()-av2.GetPos());
+ ReferenceDistance ref_dist=*ai;
+ if (within_tolerance(mdl_dist,ref_dist,tol).first) {
+ LOG_VERBOSE("LDT:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
+ << " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetName() << " " << av2.GetResidue().GetNumber() << " " << av2.GetName() << " "
+ << mdl_dist << " " << ref_dist.GetMinDistance() << " " << mdl_dist-ref_dist.GetMinDistance() << " " << tol << " " << "PASS")
+ overlap.first+=1;
+ overlap_list[av1.GetResidue().GetIndex()].first+=1.0;
+ overlap_list[av2.GetResidue().GetIndex()].first+=1.0;
+ } else {
+ LOG_VERBOSE("LDT:" << " " << av1.GetResidue().GetChain() << " " << av1.GetResidue().GetName() << " " << av1.GetResidue().GetNumber() << " " << av1.GetName()
+ << " " << av2.GetResidue().GetChain() << " " << av2.GetResidue().GetName() << " " << av2.GetResidue().GetNumber() << " " << av2.GetName() << " "
+ << mdl_dist << " " << ref_dist.GetMinDistance() << " " << mdl_dist-ref_dist.GetMinDistance() << " " << tol << " " << "FAIL")
+ }
+ }
return overlap;
}
+
std::pair<Real, Real> calc_overlap2(const seq::ConstSequenceHandle& ref_seq,
const seq::ConstSequenceHandle& mdl_seq,
int pos, Real tol, Real max_dist,
@@ -186,7 +207,8 @@ std::pair<Real, Real> calc_overlap2(const seq::ConstSequenceHandle& ref_seq,
continue;
} else {
if (aj->GetResidue().GetNumber()>ref_res.GetNumber()) {
- overlap.second+=1.0;
+ overlap.second+=1.0;
+
try {
int aln_pos=ref_seq.GetPos(aj->GetResidue().GetIndex());
ResidueView r2=mdl_seq.GetResidue(aln_pos);
@@ -212,81 +234,141 @@ std::pair<Real, Real> calc_overlap2(const seq::ConstSequenceHandle& ref_seq,
}
-Real LocalDistTest(const EntityView& mdl, const EntityView& ref,
- Real cutoff, Real max_dist, const String& local_ldt_property_string)
+bool ReferenceDistance::IsValid() const
+{
+ if (mind_ == -1.0 and maxd_ == -1.0) {
+ return false;
+ }
+ return true;
+}
+
+void ReferenceDistance::Print() const
+{
+ if (this->IsValid() == true) {
+ std::cout << first_atom_.GetChainName() << " " << first_atom_.GetResNum() << " " << first_atom_.GetResidueName() << " " << first_atom_.GetAtomName() << " " <<
+ second_atom_.GetChainName() << " " << second_atom_.GetResNum() << " " << second_atom_.GetResidueName() << " " << second_atom_.GetAtomName() << " " <<
+ mind_ << " " << maxd_ << std::endl;
+ } else {
+ std::cout << first_atom_.GetChainName() << " " << first_atom_.GetResNum() << " " << first_atom_.GetResidueName() << " Placeholder" << std::endl;
+ }
+}
+
+GlobalDistanceList CreateDistanceList(const EntityView& ref,Real max_dist)
+{
+ GlobalDistanceList dist_list;
+ ResidueViewList ref_residues=ref.GetChainList()[0].GetResidueList();
+ for (ResidueViewList::iterator i=ref_residues.begin(), e=ref_residues.end(); i!=e; ++i) {
+ ResidueView rview = (*i);
+//# if (rview.IsPeptideLinking()) {
+ if (true) {
+ ResidueDistanceList res_dist_list;
+ AtomViewList ref_atoms=(*i).GetAtomList();
+ AtomViewList within;
+ if (max_dist<0){
+ dist_list.push_back(res_dist_list);
+ within=ref.GetAtomList();
+ }
+ for (AtomViewList::iterator ai=ref_atoms.begin(), ae=ref_atoms.end(); ai!=ae; ++ai) {
+ UniqueAtomIdentifier first_atom(ai->GetResidue().GetChain().GetName(),ai->GetResidue().GetNumber(),ai->GetResidue().GetName(),ai->GetName());
+ if (ai->GetElement()=="H") { continue; }
+ if (max_dist>=0){
+ within=ref.FindWithin(ai->GetPos(), max_dist);
+ }
+ for (AtomViewList::iterator aj=within.begin(), ae2=within.end(); aj!=ae2; ++aj) {
+ UniqueAtomIdentifier second_atom(aj->GetResidue().GetChain().GetName(),aj->GetResidue().GetNumber(),aj->GetResidue().GetName(),aj->GetName());
+ if (aj->GetElement()=="H" ||
+ aj->GetResidue().GetChain()!=ai->GetResidue().GetChain()) {
+ continue;
+ }
+ if (aj->GetResidue().GetNumber()>i->GetNumber()) {
+ Real dist=geom::Length(ai->GetPos()-aj->GetPos());
+ ReferenceDistance ref_dist(first_atom,second_atom,dist,dist);
+ res_dist_list.push_back(ref_dist);
+ }
+ }
+ }
+ if (res_dist_list.size()==0) {
+ UniqueAtomIdentifier current_residue_fake_atom(rview.GetChain().GetName(),rview.GetNumber(),rview.GetName(),"CA");
+ ReferenceDistance fake_ref_distance(current_residue_fake_atom,current_residue_fake_atom,-1.0,-1.0);
+ res_dist_list.push_back(fake_ref_distance);
+ }
+ dist_list.push_back(res_dist_list);
+ }
+ }
+ return dist_list;
+}
+
+
+Real LocalDistTest(const EntityView& mdl, const GlobalDistanceList& glob_dist_list,
+ Real cutoff, const String& local_ldt_property_string)
{
-
if (!mdl.GetResidueCount()) {
LOG_WARNING("model structures doesn't contain any residues");
return 0.0;
}
-
- if (!ref.GetResidueCount()) {
- LOG_WARNING("reference structures doesn't contain any residues");
+ if (glob_dist_list.size()==0) {
+ LOG_WARNING("global reference list is empty");
return 0.0;
}
- ResidueViewList ref_residues=ref.GetChainList()[0].GetResidueList();
- std::vector<std::pair<Real, Real> > overlap_list(ref_residues.size(), std::pair<Real, Real>(0.0, 0.0));
+ std::vector<std::pair<Real, Real> > overlap_list(mdl.GetResidueCount(), 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
// fixed atoms and take the solution that gives bigger scores.
- XCSEditor edi=ref.GetHandle().EditXCS(BUFFERED_EDIT);
- for (ResidueViewList::iterator
- i=ref_residues.begin(), e=ref_residues.end(); i!=e; ++i) {
- const String rname=i->GetName();
- ResidueView mdl_res=mdl_chain.FindResidue(i->GetNumber());
- if (!mdl_res) {
- continue;
- }
- if (!(rname=="GLU" || rname=="ASP" || rname=="VAL" || rname=="TYR" ||
- rname=="PHE" || rname=="LYS" || rname=="ARG")) {
+ XCSEditor edi=mdl.GetHandle().EditXCS(BUFFERED_EDIT);
+ for (GlobalDistanceList::const_iterator i=glob_dist_list.begin(), e=glob_dist_list.end(); i!=e; ++i) {
+ ResidueDistanceList rdl = *i;
+ if (!rdl[0].IsValid()) {
continue;
}
-
- std::pair<Real, Real> ov1=calc_overlap1(*i, ref, mdl_chain,
- cutoff, max_dist, true,
- false, overlap_list);
- std::pair<Real, Real> ov2=calc_overlap1(*i, ref, mdl_chain,
- cutoff, max_dist, true,
- true, overlap_list);
+
+ ResNum rnum = rdl[0].GetFirstAtom().GetResNum() ;
+ String rname=rdl[0].GetFirstAtom().GetResidueName();
+ ResidueView mdl_res=mdl_chain.FindResidue(rnum);
+ if (!mdl_res) {
+ continue;
+ }
+ if (!(rname=="GLU" || rname=="ASP" || rname=="VAL" || rname=="TYR" || rname=="PHE" || rname=="LYS" || rname=="ARG")) {
+ continue;
+ }
+ std::pair<Real, Real> ov1=calc_overlap1(*i, mdl_chain,
+ cutoff, true,
+ false, overlap_list,false);
+
+ std::pair<Real, Real> ov2=calc_overlap1(*i, mdl_chain,
+ cutoff, true,
+ true, overlap_list,false);
if (ov1.first/ov1.second<ov2.first/ov2.second) {
- AtomViewList atoms=mdl_res.GetAtomList();
- for (AtomViewList::iterator j=atoms.begin(),
- e2=atoms.end(); j!=e2; ++j) {
- if (swappable(rname, j->GetName())) {
- edi.RenameAtom(j->GetHandle(), swapped_name(j->GetName()));
- }
- }
+ AtomViewList atoms=mdl_res.GetAtomList();
+ for (AtomViewList::iterator j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
+ if (swappable(rname, j->GetName())) {
+ edi.RenameAtom(j->GetHandle(), swapped_name(j->GetName()));
+ }
+ }
}
}
+ overlap_list.clear();
std::pair<Real, Real> total_ov(0.0, 0.0);
- 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;
- }
-
- // 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);
- }
+ for (GlobalDistanceList::const_iterator i=glob_dist_list.begin(), e=glob_dist_list.end(); i!=e; ++i) {
+ ResidueDistanceList rdl = *i;
+ if (rdl[0].IsValid()) {
+ std::pair<Real, Real> ov1=calc_overlap1(*i, mdl_chain, cutoff,
+ false, false, overlap_list,true);
+ total_ov.first+=ov1.first;
+ total_ov.second+=ov1.second;
}
- mdl_chain.SetFloatProp(local_ldt_property_string, total_ov.first/(total_ov.second ? total_ov.second : 1));
+ if(local_ldt_property_string!="") {
+ ResNum rn = rdl[0].GetFirstAtom().GetResNum();
+ ResidueView mdlr=mdl_chain.FindResidue(rn);
+ if (mdlr.IsValid()) {
+ int mdl_res_index =mdlr.GetIndex();
+ Real local_ldt=overlap_list[mdl_res_index].first/(overlap_list[mdl_res_index].second ? overlap_list[mdl_res_index].second : 1);
+ ResidueView res_to_wr = mdl_chain.FindResidue((*i)[0].GetFirstAtom().GetResNum());
+ res_to_wr.SetFloatProp(local_ldt_property_string, local_ldt);
+ }
+ }
}
overlap_list.clear();
-
return total_ov.first/(total_ov.second ? total_ov.second : 1);
}
@@ -341,16 +423,17 @@ Real LocalDistTest(const ost::seq::AlignmentHandle& aln,
return 0.0;
}
-Real LDTHA(EntityView&v, const EntityView& ref_view, Real radius)
+Real LDTHA(EntityView& v, const GlobalDistanceList& global_dist_list)
{
+
Real cutoffs[]={0.5,1,2,4};
String labels[]={"localldt0.5","localldt1","localldt2","ldtlocal4"};
Real ldt=0.0;
for (int n=0; n<4; ++n) {
- ldt+=alg::LocalDistTest(v, ref_view, cutoffs[n], radius,labels[n]);
+ ldt+=alg::LocalDistTest(v, global_dist_list, cutoffs[n], labels[n]);
}
ldt/=4.0;
return ldt;
}
-}}}
\ No newline at end of file
+}}}
diff --git a/modules/mol/alg/src/local_dist_test.hh b/modules/mol/alg/src/local_dist_test.hh
index c6dd4d7e0..74473ba29 100644
--- a/modules/mol/alg/src/local_dist_test.hh
+++ b/modules/mol/alg/src/local_dist_test.hh
@@ -25,17 +25,66 @@
namespace ost { namespace mol { namespace alg {
+
+class UniqueAtomIdentifier
+{
+
+public:
+ UniqueAtomIdentifier(const String& chain,const ResNum& residue,const String& residue_name, const String& atom): chain_(chain),residue_(residue),residue_name_(residue_name),atom_(atom) {}
+
+ String GetChainName() const { return chain_; }
+ ResNum GetResNum() const { return residue_; }
+ String GetResidueName() const { return residue_name_; }
+ String GetAtomName() const { return atom_; }
+
+private:
+
+ String chain_;
+ ResNum residue_;
+ String residue_name_;
+ String atom_;
+};
+
+class ReferenceDistance
+{
+
+public:
+
+ ReferenceDistance(UniqueAtomIdentifier first_atom, UniqueAtomIdentifier second_atom, Real mind, Real maxd):
+ first_atom_(first_atom),second_atom_(second_atom),mind_(mind),maxd_(maxd) {}
+ UniqueAtomIdentifier GetFirstAtom() const {return first_atom_;}
+ UniqueAtomIdentifier GetSecondAtom() const {return second_atom_;}
+ Real GetMinDistance() const {return mind_ ;}
+ Real GetMaxDistance() const {return maxd_ ;}
+ bool IsValid() const;
+ void Print() const;
+
+private:
+
+ UniqueAtomIdentifier first_atom_;
+ UniqueAtomIdentifier second_atom_;
+ Real mind_;
+ Real maxd_;
+ bool valid;
+
+};
+
+typedef std::vector<ReferenceDistance> ResidueDistanceList;
+typedef std::vector<ResidueDistanceList> GlobalDistanceList;
+
Real DLLEXPORT_OST_MOL_ALG LocalDistTest(const EntityView& mdl,
- const EntityView& ref,
- Real cutoff, Real max_dist,
+ const GlobalDistanceList& dist_list,
+ Real cutoff,
const String& local_ldt_property_string="");
Real DLLEXPORT_OST_MOL_ALG LocalDistTest(const ost::seq::AlignmentHandle& aln,
- Real cutoff, Real max_dist,
+ Real cutoff,
int ref_index=0, int mdl_index=1);
-Real DLLEXPORT_OST_MOL_ALG LDTHA(EntityView&v, const EntityView& ref_view, Real radius);
+Real DLLEXPORT_OST_MOL_ALG LDTHA(EntityView& v, const GlobalDistanceList& global_dist_list);
+
+GlobalDistanceList CreateDistanceList(const EntityView& ref,Real max_dist);
}}}
--
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