From 5252923cab6fb1bd4db952c507415f676092d3aa Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Sat, 13 Oct 2012 15:31:33 +0200
Subject: [PATCH] added option to disable connecting adjacent residues
---
modules/conop/src/heuristic.cc | 3 ++-
modules/conop/src/processor.hh | 9 ++++++++-
modules/conop/src/rule_based.cc | 3 ++-
3 files changed, 12 insertions(+), 3 deletions(-)
diff --git a/modules/conop/src/heuristic.cc b/modules/conop/src/heuristic.cc
index 335f14f12..d21c13fd5 100644
--- a/modules/conop/src/heuristic.cc
+++ b/modules/conop/src/heuristic.cc
@@ -70,7 +70,8 @@ void HeuristicProcessor::DoProcess(DiagnosticsPtr diags,
this->FillResidueProps(residue, compound);
if (this->GetConnect()) {
this->ConnectAtomsOfResidue(residue, compound, false);
- this->ConnectResidues(prev, residue);
+ if (this->GetConnectAminoAcids())
+ this->ConnectResidues(prev, residue);
}
prev = residue;
if (!this->GetConnect()) { continue; }
diff --git a/modules/conop/src/processor.hh b/modules/conop/src/processor.hh
index 0bf71a896..29acec191 100644
--- a/modules/conop/src/processor.hh
+++ b/modules/conop/src/processor.hh
@@ -66,7 +66,7 @@ protected:
mol::AtomHandle LocateAtom(const mol::AtomHandleList&, int ordinal) const;
public:
Processor(): check_bond_feasibility_(false),
- assign_torsions_(false), connect_(true),
+ assign_torsions_(false), connect_(true), connect_aa_(true),
zero_occ_treatment_(CONOP_SILENT) {}
void SetConnect(bool connect) {
connect_ = connect;
@@ -82,6 +82,12 @@ public:
return assign_torsions_;
}
+ bool GetConnectAminoAcids() const {
+ return connect_aa_;
+ }
+ void SetConnectAminoAcids(bool c) {
+ connect_aa_ = c;
+ }
bool GetCheckBondFeasibility() const {
return check_bond_feasibility_;
}
@@ -103,6 +109,7 @@ private:
bool check_bond_feasibility_;
bool assign_torsions_;
bool connect_;
+ bool connect_aa_;
ConopAction zero_occ_treatment_;
};
diff --git a/modules/conop/src/rule_based.cc b/modules/conop/src/rule_based.cc
index 862faffad..65b89988f 100644
--- a/modules/conop/src/rule_based.cc
+++ b/modules/conop/src/rule_based.cc
@@ -73,7 +73,8 @@ void RuleBasedProcessor::DoProcess(DiagnosticsPtr diags,
if (this->GetConnect()) {
this->ConnectAtomsOfResidue(residue, compound,
this->GetStrictHydrogens());
- this->ConnectResidues(prev, residue);
+ if (this->GetConnectAminoAcids())
+ this->ConnectResidues(prev, residue);
for (mol::AtomHandleList::iterator k = atoms_to_connect.begin(),
e3=atoms_to_connect.end(); k!= e3; ++k) {
this->DistanceBasedConnect(*k);
--
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