From 7b5b82a3710bf488f1f299e584d392af833fd35a Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Thu, 25 Aug 2016 10:44:53 +0200
Subject: [PATCH] SCHWED-1316: remove conflicting atoms when building raw
model.
---
modelling/src/model.cc | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
diff --git a/modelling/src/model.cc b/modelling/src/model.cc
index 404b5b13..95fbcc63 100644
--- a/modelling/src/model.cc
+++ b/modelling/src/model.cc
@@ -46,8 +46,25 @@ bool CheckBackboneAtoms(ResidueView res)
return true;
}
+void CleanupAtomConflicts(ResidueView& res) {
+ // remove atoms which are on top of any other atoms in the tpl entity
+ EntityView tpl = res.GetEntity();
+ AtomViewList atom_views = res.GetAtomList();
+ for (uint i = 0; i < atom_views.size(); ++i) {
+ AtomViewList on_top_atoms = tpl.FindWithin(atom_views[i].GetPos(), 0.0);
+ if (on_top_atoms.size() > 1) {
+ res.RemoveAtom(atom_views[i]);
+ // report
+ std::stringstream ss;
+ ss << "residue " << res.GetQualifiedName() << " has conflicting atom "
+ << atom_views[i].GetName() << " - skipping atom.";
+ LOG_WARNING(ss.str());
+ }
+ }
}
+} // anon ns
+
int CountEnclosedGaps(ModellingHandle& mhandle, const StructuralGap& gap,
bool insertions_only)
{
@@ -541,6 +558,8 @@ void BuildRawChain(const ost::seq::AlignmentHandle& aln,
src_res.GetOneLetterCode() << "'";
throw promod3::Error(ss.str());
}
+ // remove atoms with conflicting positions (i.e. on top of each other)
+ CleanupAtomConflicts(src_res);
// check for complete backbone, or in case of Calpha only model building,
// if the src_res has a Calpha atom
if(!CheckBackboneAtoms(src_res)){
--
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