From 03b194ffccbe59debbef21772b1fb96b0df0ad8d Mon Sep 17 00:00:00 2001
From: marco <marco@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Mon, 10 May 2010 05:38:55 +0000
Subject: [PATCH] fix import of compounds with only one atom
components.cif does not use a loop_ section if the residue only
has one atom. Now we also handle these single atom residues
properly
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2214 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/conop/src/chemdict_tool.cc | 12 ++++++++++++
1 file changed, 12 insertions(+)
diff --git a/modules/conop/src/chemdict_tool.cc b/modules/conop/src/chemdict_tool.cc
index 79b36b7b1..865425d8c 100644
--- a/modules/conop/src/chemdict_tool.cc
+++ b/modules/conop/src/chemdict_tool.cc
@@ -140,12 +140,23 @@ public:
} else if (item.GetName()==StringRef("pdbx_modified_date", 18)) {
compound_->SetModificationDate(conop::Date::FromString(item.GetValue()));
}
+ } else if (item.GetName()==StringRef("atom_id", 7)) {
+ atom_.name=item.GetValue().str();
+ } else if (item.GetName()==StringRef("alt_atom_id", 11)) {
+ atom_.alt_name=item.GetValue().str();
+ } else if (item.GetName()==StringRef("type_symbol", 11)) {
+ atom_.element=item.GetValue().str();
+ } else if (item.GetName()==StringRef("pdbx_ordinal", 12)) {
+ atom_.ordinal=item.GetValue().to_int().second-1;
}
}
virtual void OnEndData()
{
if (insert_) {
+ if (compound_->GetAtomSpecs().empty()) {
+ compound_->AddAtom(atom_);
+ }
lib_->AddCompound(compound_);
}
}
@@ -176,6 +187,7 @@ private:
static std::map<String, mol::ChemClass> tm_;
std::map<String, int> atom_map_;
LoopType loop_type_;
+ conop::AtomSpec atom_;
};
std::map<String, mol::ChemClass> ChemDictParser::tm_=std::map<String, mol::ChemClass>();
--
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