From e6b1cf9fa9f4e2c1f1184df4cfca1c4a8c2cb7d5 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Mon, 4 Oct 2010 19:37:56 +0200
Subject: [PATCH] rule-based-builder: override the atom element, if it is bogus
---
modules/conop/src/conop.cc | 9 +++++++++
modules/conop/src/conop.hh | 2 ++
modules/conop/src/rule_based_builder.cc | 8 ++++----
3 files changed, 15 insertions(+), 4 deletions(-)
diff --git a/modules/conop/src/conop.cc b/modules/conop/src/conop.cc
index 9d34eba51..d7edd9aa8 100644
--- a/modules/conop/src/conop.cc
+++ b/modules/conop/src/conop.cc
@@ -318,6 +318,15 @@ Real Conopology::GetDefaultAtomRadius(const String& element) const
return it==ele_rad_map_.end() ? 1.5 : it->second;
}
+bool Conopology::IsValidElement(const String& element) const
+{
+ String upper_ele=element;
+ std::transform(upper_ele.begin(),upper_ele.end(),upper_ele.begin(),toupper);
+
+ std::map<String,Real>::const_iterator it = ele_mass_map_.find(upper_ele);
+ return it!=ele_mass_map_.end();
+}
+
Real Conopology::GetDefaultAtomMass(const String& element) const
{
String upper_ele=element;
diff --git a/modules/conop/src/conop.hh b/modules/conop/src/conop.hh
index f8133a078..e8ad4bc0b 100644
--- a/modules/conop/src/conop.hh
+++ b/modules/conop/src/conop.hh
@@ -53,6 +53,8 @@ public:
void RegisterBuilder(const BuilderP& b, const String& name);
void SetDefaultBuilder(const String& default_name);
+
+ bool IsValidElement(const String& element) const;
private:
Conopology();
Conopology(const Conopology&) {}
diff --git a/modules/conop/src/rule_based_builder.cc b/modules/conop/src/rule_based_builder.cc
index 8264dc5ba..e47c96e35 100644
--- a/modules/conop/src/rule_based_builder.cc
+++ b/modules/conop/src/rule_based_builder.cc
@@ -83,11 +83,11 @@ bool RuleBasedBuilder::HasUnknownAtoms(mol::ResidueHandle res)
void RuleBasedBuilder::FillAtomProps(mol::AtomHandle atom, const AtomSpec& spec)
{
+ Conopology& conop_inst=Conopology::Instance();
mol::AtomProp props=atom.GetAtomProps();
- if (props.element=="") {
+ if (!conop_inst.IsValidElement(props.element)) {
props.element=spec.element;
}
- Conopology& conop_inst=Conopology::Instance();
if (props.radius==0.0) {
props.radius=conop_inst.GetDefaultAtomRadius(spec.element);
}
@@ -331,10 +331,10 @@ void RuleBasedBuilder::FillAtomProps(mol::AtomHandle atom)
bool RuleBasedBuilder::OnUnknownAtom(mol::AtomHandle atom)
{
mol::AtomProp props=atom.GetAtomProps();
- if (props.element=="") {
+ Conopology& conop_inst=Conopology::Instance();
+ if (!conop_inst.IsValidElement(props.element)) {
props.element=Builder::GuessAtomElement(atom.GetName(), props.is_hetatm);
}
- Conopology& conop_inst=Conopology::Instance();
if (props.radius==0.0) {
props.radius=conop_inst.GetDefaultAtomRadius(props.element);
}
--
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