From 8fc60a0c3345cb0557f81410b04effc902a4142a Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Fri, 6 Sep 2013 15:51:50 +0200
Subject: [PATCH] fix rule-based conop with strict_hydrogens=false
---
modules/conop/src/processor.cc | 27 ++++++++-------------------
modules/conop/src/rule_based.cc | 12 +++++++++++-
2 files changed, 19 insertions(+), 20 deletions(-)
diff --git a/modules/conop/src/processor.cc b/modules/conop/src/processor.cc
index a2e32c0bf..141003c65 100644
--- a/modules/conop/src/processor.cc
+++ b/modules/conop/src/processor.cc
@@ -290,15 +290,6 @@ void Processor::ConnectAtomsOfResidue(mol::ResidueHandle rh,
CompoundPtr compound,
bool strict_hydrogens) const
{
-
- //if (!compound) {
- // dist_connect(this, rh.GetAtomList());
- // return;
- //}
- //if (unknown_atoms_) {
- // dist_connect(this, rh.GetAtomList());
- // return;
- //}
mol::XCSEditor e=rh.GetEntity().EditXCS(mol::BUFFERED_EDIT);
BondSpecList::const_iterator j=compound->GetBondSpecs().begin();
mol::AtomHandleList atoms=rh.GetAtomList();
@@ -307,18 +298,16 @@ void Processor::ConnectAtomsOfResidue(mol::ResidueHandle rh,
mol::AtomHandle a1=this->LocateAtom(atoms, bond.atom_one);
mol::AtomHandle a2=this->LocateAtom(atoms, bond.atom_two);
if (a1.IsValid() && a2.IsValid()) {
+ if (!strict_hydrogens && (a1.GetElement()=="H" ||
+ a1.GetElement()=="D" ||
+ a2.GetElement()=="H" ||
+ a2.GetElement()=="D")) {
+ continue;
+ }
if (!this->GetCheckBondFeasibility()) {
- if (strict_hydrogens && (a1.GetElement()=="H" ||
- a2.GetElement()=="D")) {
- continue;
- }
e.Connect(a1, a2, bond.order);
} else {
if (IsBondFeasible(a1, a2)) {
- if (strict_hydrogens && (a1.GetElement()=="H" ||
- a2.GetElement()=="D")) {
- continue;
- }
e.Connect(a1, a2, bond.order);
}
}
@@ -405,8 +394,8 @@ void Processor::DistanceBasedConnect(mol::AtomHandle atom) const
e=alist.end();it!=e;++it) {
if (*it!=atom) {
if (IsBondFeasible(atom, *it)) {
- if (Processor::AreResiduesConsecutive(res_a, it->GetResidue()) ||
- it->GetResidue()==res_a) {
+ if (it->GetResidue()==res_a ||
+ Processor::AreResiduesConsecutive(res_a, it->GetResidue())) {
editor.Connect(*it, atom);
}
}
diff --git a/modules/conop/src/rule_based.cc b/modules/conop/src/rule_based.cc
index 902aec33d..6e8b712fe 100644
--- a/modules/conop/src/rule_based.cc
+++ b/modules/conop/src/rule_based.cc
@@ -47,7 +47,7 @@ void RuleBasedProcessor::DoProcess(DiagnosticsPtr diags,
mol::ResidueHandle residue = *j;
mol::AtomHandleList atoms_to_connect;
CompoundPtr compound = lib_->FindCompound(residue.GetName(), Compound::PDB);
- if (!compound) {
+ if (!compound && this->GetConnect()) {
// process unknown residue...
this->ProcessUnkResidue(diags, residue, atoms_to_connect);
for (mol::AtomHandleList::iterator k = atoms_to_connect.begin(),
@@ -79,6 +79,16 @@ void RuleBasedProcessor::DoProcess(DiagnosticsPtr diags,
e3=atoms_to_connect.end(); k!= e3; ++k) {
this->DistanceBasedConnect(*k);
}
+ if (!this->GetStrictHydrogens()) {
+ mol::AtomHandleList atoms = residue.GetAtomList();
+ for (mol::AtomHandleList::iterator k = atoms.begin(),
+ e3 = atoms.end(); k != e3; ++k) {
+ const String& ele = k->GetElement();
+ if ((ele == "D" || ele == "H") && k->GetBondCount() == 0) {
+ this->DistanceBasedConnect(*k);
+ }
+ }
+ }
}
prev = residue;
}
--
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