From 7f0829b606251136a416c385d1904a5043567540 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Tue, 15 Feb 2011 11:17:38 +0100
Subject: [PATCH] added NO_PEPTIDE_BONDS flag to ConnectAll.
If set, no peptide bonds will be added. Defaults to off, of course.
---
modules/conop/src/conop.cc | 12 +++++++-----
modules/conop/src/conop.hh | 9 ++++++++-
2 files changed, 15 insertions(+), 6 deletions(-)
diff --git a/modules/conop/src/conop.cc b/modules/conop/src/conop.cc
index 76b45d7bf..b1448aa8f 100644
--- a/modules/conop/src/conop.cc
+++ b/modules/conop/src/conop.cc
@@ -229,9 +229,10 @@ private:
class Connector: public mol::EntityVisitor
{
public:
- Connector(const BuilderP& b):
+ Connector(const BuilderP& b, bool peptide_bonds):
builder_(b),
- prev_()
+ prev_(),
+ peptide_bonds_(peptide_bonds)
{}
virtual bool VisitChain(const mol::ChainHandle& chain) {
@@ -241,7 +242,7 @@ public:
virtual bool VisitResidue(const mol::ResidueHandle& res) {
builder_->ConnectAtomsOfResidue(res);
- if (prev_) {
+ if (peptide_bonds_ && prev_) {
builder_->ConnectResidueToPrev(res,prev_);
}
prev_=res;
@@ -251,6 +252,7 @@ public:
private:
BuilderP builder_;
mol::ResidueHandle prev_;
+ bool peptide_bonds_;
};
class TorsionMaker: public mol::EntityVisitor
@@ -270,7 +272,7 @@ private:
};
} // ns
-void Conopology::ConnectAll(const BuilderP& b, mol::EntityHandle eh, int flag)
+void Conopology::ConnectAll(const BuilderP& b, mol::EntityHandle eh, int flags)
{
Profile profile_connect("ConnectAll");
LOG_DEBUG("Conopology: ConnectAll: building internal coordinate system");
@@ -280,7 +282,7 @@ void Conopology::ConnectAll(const BuilderP& b, mol::EntityHandle eh, int flag)
ChemClassAssigner cca(b);
eh.Apply(cca);
LOG_DEBUG("Conopology: ConnectAll: connecting all bonds");
- Connector connector(b);
+ Connector connector(b, !(flags & NO_PEPTIDE_BONDS));
eh.Apply(connector);
LOG_DEBUG("Conopology: ConnectAll: assigning all torsions");
diff --git a/modules/conop/src/conop.hh b/modules/conop/src/conop.hh
index 7109c83aa..0d9fccf7b 100644
--- a/modules/conop/src/conop.hh
+++ b/modules/conop/src/conop.hh
@@ -26,6 +26,12 @@
namespace ost { namespace conop {
+
+typedef enum {
+ NO_PEPTIDE_BONDS=1,
+} ConopFlag;
+
+
class DLLEXPORT_OST_CONOP Conopology {
typedef std::map<String,BuilderP> BuilderMap;
@@ -42,7 +48,8 @@ public:
does this need to live within Conopology ?
*/
- void ConnectAll(const BuilderP& b, mol::EntityHandle eh, int flag=0);
+ void ConnectAll(const BuilderP& b, mol::EntityHandle eh,
+ int flags=0);
void RegisterBuilder(const BuilderP& b, const String& name);
void SetDefaultBuilder(const String& default_name);
--
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