From 5ccfb4e91ea8c0db69a3c135de165ed0ecee1dfb Mon Sep 17 00:00:00 2001
From: Tobias Schmidt <tobias.schmidt@unibas.ch>
Date: Tue, 19 Jul 2011 17:02:18 +0200
Subject: [PATCH] fixed builder.GetUnknownAtoms for calling it multiple times
with the same residue
---
modules/conop/src/rule_based_builder.cc | 4 +++-
modules/conop/src/rule_based_builder.hh | 6 +++---
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/modules/conop/src/rule_based_builder.cc b/modules/conop/src/rule_based_builder.cc
index 2a0a50010..57c8f5154 100644
--- a/modules/conop/src/rule_based_builder.cc
+++ b/modules/conop/src/rule_based_builder.cc
@@ -89,9 +89,10 @@ mol::AtomHandleList RuleBasedBuilder::GetUnknownAtoms(mol::ResidueHandle res)
if (!last_compound_) {
return unknown;
}
+ mol::AtomHandleList atoms=res.GetAtomList();
+ last_residue_=mol::ResidueHandle();
this->ReorderAtoms(res, last_compound_);
AtomSpecList::const_iterator j=last_compound_->GetAtomSpecs().begin();
- mol::AtomHandleList atoms=res.GetAtomList();
mol::AtomHandleList::iterator i=atoms.begin();
for (mol::AtomHandleList::iterator
i=atoms.begin(), e=atoms.end(); i!=e; ++i) {
@@ -153,6 +154,7 @@ void RuleBasedBuilder::ReorderAtoms(mol::ResidueHandle residue,
mol::impl::AtomImplList::iterator i=impl->GetAtomList().begin();
for (; i!=impl->GetAtomList().end(); ++i) {
mol::impl::AtomImplPtr atom=*i;
+ atom->SetState(std::numeric_limits<unsigned int>::max());
int index=compound->GetAtomSpecIndex(atom->GetName());
if (index==-1) {
if (!this->OnUnknownAtom(mol::AtomHandle(atom))) {
diff --git a/modules/conop/src/rule_based_builder.hh b/modules/conop/src/rule_based_builder.hh
index 9adcc6747..9ecc45c10 100644
--- a/modules/conop/src/rule_based_builder.hh
+++ b/modules/conop/src/rule_based_builder.hh
@@ -116,9 +116,6 @@ public:
/// \brief Set residue properties such as chemical class
virtual void FillResidueProps(mol::ResidueHandle residue);
- /// \brief whether the residue has unknown atoms
- bool HasUnknownAtoms(mol::ResidueHandle res);
-
mol::AtomHandleList GetUnknownAtoms(mol::ResidueHandle res);
/// \brief Check whether the residue has all required atoms. This does not
@@ -131,6 +128,9 @@ private:
CompoundPtr last_compound_;
mol::ResidueHandle last_residue_;
bool unknown_atoms_;
+ /// \brief whether the residue has unknown atoms
+ bool HasUnknownAtoms(mol::ResidueHandle res);
+
void LookupCompound(const mol::ResidueHandle& rh);
/// Change internal order of atoms in residue to the order given by compound
void ReorderAtoms(mol::ResidueHandle residue, CompoundPtr compound);
--
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