From b6dae4263a95fbee43bfb2c1fb348ba96d9fdede Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Wed, 13 Jun 2012 01:51:17 +0200
Subject: [PATCH] Fixed bug for cutoff-sequence dependency. Fixed local ldts in
new LocalDistTest. Other fixes
---
modules/mol/alg/src/ldt.cc | 20 ++++++++++++++++----
modules/mol/alg/src/local_dist_test.cc | 25 ++++++++++++++++---------
2 files changed, 32 insertions(+), 13 deletions(-)
diff --git a/modules/mol/alg/src/ldt.cc b/modules/mol/alg/src/ldt.cc
index a4e5f15e6..bca98880b 100644
--- a/modules/mol/alg/src/ldt.cc
+++ b/modules/mol/alg/src/ldt.cc
@@ -98,7 +98,7 @@ std::pair<int,int> compute_coverage (const EntityView& v,const GlobalRDMap& glob
int main (int argc, char **argv)
{
- String version = "Beta - 2012-05-21";
+ String version = "Beta - 2012-06-13";
Real bond_tolerance = 8.0;
Real angle_tolerance = 8.0;
Real radius=15.0;
@@ -136,7 +136,12 @@ int main (int argc, char **argv)
}
std::vector<String> files;
if (vm.count("files")) {
- files=vm["files"].as<std::vector<String> >();
+ try {
+ files=vm["files"].as<std::vector<String> >();
+ } catch (io::IOException& e) {
+ std::cerr << "ERROR: Problem with file list. " << e.what() << std::endl;
+ exit(-1);
+ }
} else {
usage();
exit(-1);
@@ -152,7 +157,12 @@ int main (int argc, char **argv)
}
String parameter_filename;
if (vm.count("parameter-file")) {
- parameter_filename=vm["parameter-file"].as<String>();
+ try {
+ parameter_filename=vm["parameter-file"].as<String>();
+ } catch (io::IOException& e) {
+ std::cerr << "ERROR: Problem with parameter file name. " << e.what() << std::endl;
+ exit(-1);
+ }
} else if (structural_checks==true) {
std::cout << "Please specify a stereo-chemical parameter file" << std::endl;
exit(-1);
@@ -297,7 +307,9 @@ int main (int argc, char **argv)
if (ritv.HasProp("localldt")) {
ldt_local=ritv.GetFloatProp("localldt");
}
- std::cout << ritv.GetChain() << "\t" << ritv.GetName() << "\t" << ritv.GetNumber() << '\t' << ldt_local << std::endl;
+ if (ldt_local!=0) {
+ std::cout << ritv.GetChain() << "\t" << ritv.GetName() << "\t" << ritv.GetNumber() << '\t' << ldt_local << std::endl;
+ }
}
std::cout << std::endl;
}
diff --git a/modules/mol/alg/src/local_dist_test.cc b/modules/mol/alg/src/local_dist_test.cc
index 7d2e83db1..c15d63927 100644
--- a/modules/mol/alg/src/local_dist_test.cc
+++ b/modules/mol/alg/src/local_dist_test.cc
@@ -91,17 +91,26 @@ std::pair<Real, Real> calc_overlap1(const ResidueRDMap& res_distance_list, const
AtomView av1=mdl_res ? mdl_res.FindAtom(name) : AtomView();
if (only_fixed) {
+ if (first_atom.GetResNum()==second_atom.GetResNum()) {
+ continue;
+ }
if (swappable(second_atom.GetResidueName(), second_atom.GetAtomName())) {
continue;
}
- }
+ }
+ if (!only_fixed) {
+ if (first_atom.GetResNum()<=second_atom.GetResNum()) {
+ continue;
+ }
+ }
+
AtomView av2=mdl_chain.FindAtom(second_atom.GetResNum(),second_atom.GetAtomName());
overlap.second+=tol_list.size();
if (av1) {
- overlap_list[av1.GetResidue().GetIndex()].second+=1.0;
+ overlap_list[av1.GetResidue().GetIndex()].second+=tol_list.size();
}
if (av2) {
- overlap_list[av2.GetResidue().GetIndex()].second+=1.0;
+ overlap_list[av2.GetResidue().GetIndex()].second+=tol_list.size();
}
if (!(av1 && av2)) {
continue;
@@ -441,12 +450,10 @@ GlobalRDMap CreateDistanceList(const EntityView& ref,Real max_dist)
aj->GetResidue().GetChain()!=ai->GetResidue().GetChain()) {
continue;
}
- if (aj->GetResidue().GetNumber()>i->GetNumber()) {
- Real dist=geom::Length(ai->GetPos()-aj->GetPos());
- UAtomIdentifiers atoms = std::make_pair<UniqueAtomIdentifier,UniqueAtomIdentifier>(first_atom,second_atom);
- std::pair<Real,Real> values = std::make_pair<Real,Real>(dist,dist);
- res_dist_list[atoms]=values;
- }
+ Real dist=geom::Length(ai->GetPos()-aj->GetPos());
+ UAtomIdentifiers atoms = std::make_pair<UniqueAtomIdentifier,UniqueAtomIdentifier>(first_atom,second_atom);
+ std::pair<Real,Real> values = std::make_pair<Real,Real>(dist,dist);
+ res_dist_list[atoms]=values;
}
}
dist_list[rnum]=res_dist_list;
--
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