From f837b0bfb3c560a6180bce660d0813242d53e33c Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Mon, 9 Jan 2012 14:09:01 +0100
Subject: [PATCH] Ignore OXT atom type (temporary protocol)
---
modules/mol/alg/src/filter_clashes.cc | 20 +++++++++++++++++++-
1 file changed, 19 insertions(+), 1 deletion(-)
diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index b2bf4fbcf..8bb40bf66 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -161,6 +161,9 @@ 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;
}
@@ -171,7 +174,10 @@ EntityView CheckStereoChemistry(const EntityView& ent, const StereoChemicalParam
AtomHandle other_atom = bond.GetOther(atom.GetHandle());
if (other_atom.GetResidue()!=res.GetHandle()) {
continue;
- }
+ }
+ if (other_atom.GetName()=="OXT") {
+ continue;
+ }
String ele2 = other_atom.GetElement();
if (ele2=="H" || ele2=="D") {
continue;
@@ -206,6 +212,9 @@ 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;
}
@@ -216,6 +225,9 @@ 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;
}
@@ -302,6 +314,9 @@ 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;
}
@@ -313,6 +328,9 @@ 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;
}
--
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