diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index e849435819608488ea4230716d96ff41eb077405..4b81ed10b8a81e92b120a2fc51367803a9ed9be9 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -321,9 +321,6 @@ EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParam
for (AtomViewList::const_iterator j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
AtomView atom=*j;
String ele1=atom.GetElement();
- if (atom.GetName()=="OXT") {
- continue;
- }
if (ele1=="H" || ele1=="D") {
continue;
}
@@ -335,9 +332,6 @@ EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParam
if (other_atom.GetResidue()!=res.GetHandle()) {
continue;
}
- if (other_atom.GetName()=="OXT") {
- continue;
- }
String ele2 = other_atom.GetElement();
if (ele2=="H" || ele2=="D") {
continue;
@@ -372,9 +366,6 @@ EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParam
BondHandle bond1=*bond_iter1;
AtomHandle atom1= bond1.GetOther(atom.GetHandle());
String ele_atom1=atom1.GetElement();
- if (atom1.GetName()=="OXT") {
- continue;
- }
if (ele_atom1=="H" || ele_atom1=="D") {
continue;
}
@@ -385,9 +376,6 @@ EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParam
BondHandle bond2=*bond_iter2;
AtomHandle atom2 = bond2.GetOther(atom.GetHandle());
String ele_atom2=atom2.GetElement();
- if (atom2.GetName()=="OXT") {
- continue;
- }
if (ele_atom2=="H" || ele_atom2=="D") {
continue;
}
@@ -474,9 +462,6 @@ EntityView FilterClashes(const EntityView& ent, const ClashingDistances& min_dis
j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
AtomView atom=*j;
String ele1=atom.GetElement();
- if (atom.GetName()=="OXT") {
- continue;
- }
if (ele1=="H" || ele1=="D") {
continue;
}
@@ -488,9 +473,6 @@ EntityView FilterClashes(const EntityView& ent, const ClashingDistances& min_dis
continue;
}
String ele2=atom2.GetElement();
- if (atom2.GetName()=="OXT") {
- continue;
- }
if (ele2=="H" || ele2=="D") {
continue;
}
@@ -508,7 +490,7 @@ EntityView FilterClashes(const EntityView& ent, const ClashingDistances& min_dis
Real tolerance=distance_tolerance.second;
Real threshold=distance-tolerance;
if (d<threshold*threshold) {
- LOG_INFO(atom.GetResidue().GetChain() << " " << atom.GetResidue().GetName() << " " << atom.GetResidue().GetNumber() << " " << atom.GetName() << " " << atom2.GetResidue().GetChain() << " " << atom2.GetResidue().GetName() << " " << atom2.GetResidue().GetName() << " " << atom2.GetName() << " " << threshold << " " << sqrt(d) << " " << sqrt(d)-threshold << " " << "FAIL")
+ LOG_INFO(atom.GetResidue().GetChain() << " " << atom.GetResidue().GetName() << " " << atom.GetResidue().GetNumber() << " " << atom.GetName() << " " << atom2.GetResidue().GetChain() << " " << atom2.GetResidue().GetName() << " " << atom2.GetResidue().GetNumber() << " " << atom2.GetName() << " " << threshold << " " << sqrt(d) << " " << sqrt(d)-threshold << " " << "FAIL")
remove_sc=true;
if (always_remove_bb==true) {
@@ -555,4 +537,3 @@ EntityView FilterClashes(const EntityHandle& ent,
}}}
-
diff --git a/modules/mol/alg/src/ldt.cc b/modules/mol/alg/src/ldt.cc
index 0b9610308ae2850f261ba5594dc988354afaae54..bd5bef27208ad3a5ad0e07eea857b3536be92c39 100644
--- a/modules/mol/alg/src/ldt.cc
+++ b/modules/mol/alg/src/ldt.cc
@@ -80,6 +80,9 @@ std::pair<int,int> compute_coverage (const EntityView& v,const GlobalDistanceLis
{
int second=0;
int first=0;
+ if (v.GetResidueList().size()==0) {
+ return std::make_pair<int,int>(0,1);
+ }
ChainView vchain=v.GetChainList()[0];
for (std::vector<ResidueDistanceList>::const_iterator i=glob_dist_list.begin();i!=glob_dist_list.end();++i)
{
@@ -102,7 +105,7 @@ int main (int argc, char **argv)
Real min_distance_tolerance = 0.0;
Real bond_tolerance = 8.0;
Real angle_tolerance = 8.0;
- Real radius=8.0;
+ Real radius=12.0;
IOProfile profile;
profile.bond_feasibility_check=false;
@@ -193,6 +196,7 @@ int main (int argc, char **argv)
}
files.pop_back();
EntityView ref_view=ref.Select(sel);
+ GlobalDistanceList glob_dist_list = CreateDistanceList(ref_view,radius);
std::cout << "Verbosity level: " << verbosity_level << std::endl;
if (structural_checks) {
std::cout << "Stereo-chemical and steric clash checks: On " << std::endl;
@@ -209,7 +213,7 @@ int main (int argc, char **argv)
LOG_INFO("ANGLE INFO FORMAT: Chain Residue ResNum Angle Min Max Observed Z-score Status");
LOG_INFO("CLASH INFO FORMAT: Chain1 Residue1 ResNum1 Atom1 Chain2 Residue2 ResNum2 Atom2 Observed Difference Status");
LOG_INFO("LDT INFO FORMAT: Chain1 Residue1 ResNum1 Atom1 Chain2 Residue2 ResNum2 Atom2 ModelDist TargetDist Difference Tolerance Status");
- }
+ }
for (size_t i=0; i<files.size(); ++i) {
EntityHandle model=load(files[i], profile);
if (!model) {
@@ -219,6 +223,24 @@ int main (int argc, char **argv)
continue;
}
EntityView v=model.CreateFullView();
+
+ // The code in this following block is only used to make CASP9 models load correctly and normally commented out
+ //EntityView model2=model.Select("aname!=CEN,NV,OT1,OT,CAY,CY,OXT,1OCT,NT,OT2,2OCT,OVL1,OC1,O1,OC2,O2,OVU1");
+ //EntityView v1=model2.Select("not (rname==GLY and aname==CB)");
+ //boost::filesystem::path pathstring(files[i]);
+ //String filestring=pathstring.filename();
+ //if (filestring.substr(5,5)=="TS257" || filestring.substr(5,5)=="TS458" ) {
+ // for (AtomHandleIter ait=v1.GetHandle().AtomsBegin();ait!=v1.GetHandle().AtomsEnd();++ait){
+ // AtomHandle aitv = *ait;
+ // String atomname=aitv.GetName();
+ // String firstletter=atomname.substr(0,1);
+ // aitv.SetElement(firstletter);
+ // }
+ }
+ std::cout << "File: " << files[i] << std::endl;
+ std::pair<int,int> cov = compute_coverage(v,glob_dist_list);
+ std::cout << "Coverage: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
+
if (structural_checks) {
boost::filesystem::path loc(parameter_filename);
boost::filesystem::ifstream infile(loc);
@@ -250,17 +272,19 @@ int main (int argc, char **argv)
std::cout << "Error reading the Clashing section of the stereo-chemical parameter file." << std::endl;
exit(-1);
}
-
- v=alg::CheckStereoChemistry(v,bond_table,angle_table,bond_tolerance,angle_tolerance);
- v=alg::FilterClashes(v,nonbonded_table);
+ EntityView v2=alg::CheckStereoChemistry(v,bond_table,angle_table,bond_tolerance,angle_tolerance);
+ cov = compute_coverage(v2,glob_dist_list);
+ std::cout << "Coverage after stereo-chemical checks: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
+ v=alg::FilterClashes(v2,nonbonded_table);
+ cov = compute_coverage(v,glob_dist_list);
+ std::cout << "Coverage after clashing checks: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
}
-
- GlobalDistanceList glob_dist_list = CreateDistanceList(ref_view,radius);
- std::pair<int,int> cov = compute_coverage(v,glob_dist_list);
+ if (cov.first==0) {
+ std::cout << "Global LDT score: 0.0" << std::endl;
+ return 0;
+ }
Real ldt=LDTHA(v, glob_dist_list);
- std::cout << "File: " << files[i] << std::endl;
- std::cout << "Coverage: " << (float(cov.first)/float(cov.second)) << " (" << cov.first << " out of " << cov.second << " residues)" << std::endl;
std::cout << "Global LDT score: " << ldt << std::endl;
std::cout << "Local LDT Score:" << std::endl;
std::cout << "Chain\tResName\tResNum\tScore" << std::endl;