From 7d6fdf3af706129846ba1a11b450a41d63a2cf92 Mon Sep 17 00:00:00 2001
From: Marco Biasini <marco.biasini@unibas.ch>
Date: Mon, 4 Apr 2011 00:15:54 +0200
Subject: [PATCH] added RuleBasedBuilder::GetUnknownAtoms
---
modules/conop/doc/connectivity.rst | 7 +++++++
modules/conop/pymod/export_builder.cc | 1 +
modules/conop/src/chemdict_tool.cc | 4 +++-
modules/conop/src/rule_based_builder.cc | 24 ++++++++++++++++++++++++
modules/conop/src/rule_based_builder.hh | 5 ++++-
5 files changed, 39 insertions(+), 2 deletions(-)
diff --git a/modules/conop/doc/connectivity.rst b/modules/conop/doc/connectivity.rst
index 1b0610770..9b56d6566 100644
--- a/modules/conop/doc/connectivity.rst
+++ b/modules/conop/doc/connectivity.rst
@@ -250,4 +250,11 @@ The RuleBasedBuilder class
:param atom: The missing atom's name
:type atom: string
+
+ .. method:: GetUnknownAtoms(residue)
+
+ Returns the unknown atoms of this residue, that is all atoms that
+ are not part of the compound lib definition.
+
+ :rtype: list of :class:`~ost.mol.AtomHandle` instances
diff --git a/modules/conop/pymod/export_builder.cc b/modules/conop/pymod/export_builder.cc
index 871329a47..4bd468f36 100644
--- a/modules/conop/pymod/export_builder.cc
+++ b/modules/conop/pymod/export_builder.cc
@@ -55,5 +55,6 @@ void export_Builder() {
class_<RuleBasedBuilder, bases<Builder> >("RuleBasedBuilder",
init<const CompoundLibPtr&>())
.add_property("compound_lib", &RuleBasedBuilder::GetCompoundLib)
+ .def("GetUnknownAtoms", &RuleBasedBuilder::GetUnknownAtoms)
;
}
diff --git a/modules/conop/src/chemdict_tool.cc b/modules/conop/src/chemdict_tool.cc
index 21ff69293..6e5720675 100644
--- a/modules/conop/src/chemdict_tool.cc
+++ b/modules/conop/src/chemdict_tool.cc
@@ -80,7 +80,9 @@ int main(int argc, char const *argv[])
PrintUsage();
return 0;
}
-
+ if (!compound_lib) {
+ return 0;
+ }
assert(compound_lib);
conop::CompoundLibPtr in_mem_lib=compound_lib->Copy(":memory:");
compound_lib.reset();
diff --git a/modules/conop/src/rule_based_builder.cc b/modules/conop/src/rule_based_builder.cc
index 9cd65b269..9a0e87851 100644
--- a/modules/conop/src/rule_based_builder.cc
+++ b/modules/conop/src/rule_based_builder.cc
@@ -82,6 +82,30 @@ bool RuleBasedBuilder::HasUnknownAtoms(mol::ResidueHandle res)
return false;
}
+mol::AtomHandleList RuleBasedBuilder::GetUnknownAtoms(mol::ResidueHandle res)
+{
+ mol::AtomHandleList unknown;
+ this->LookupCompound(res);
+ if (!last_compound_) {
+ return unknown;
+ }
+ 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) {
+ if ((*i).Impl()->GetState()==std::numeric_limits<unsigned int>::max()) {
+ if (((*i).GetElement()=="H" || (*i).GetElement()=="D") &&
+ this->GetStrictHydrogenMode()==false) {
+ continue;
+ }
+ unknown.push_back(*i);
+ }
+ }
+ return unknown;
+}
+
void RuleBasedBuilder::FillAtomProps(mol::AtomHandle atom, const AtomSpec& spec)
{
Conopology& conop_inst=Conopology::Instance();
diff --git a/modules/conop/src/rule_based_builder.hh b/modules/conop/src/rule_based_builder.hh
index 5eea4b42e..9adcc6747 100644
--- a/modules/conop/src/rule_based_builder.hh
+++ b/modules/conop/src/rule_based_builder.hh
@@ -117,7 +117,10 @@ public:
virtual void FillResidueProps(mol::ResidueHandle residue);
/// \brief whether the residue has unknown atoms
- bool HasUnknownAtoms(mol::ResidueHandle res);
+ bool HasUnknownAtoms(mol::ResidueHandle res);
+
+ mol::AtomHandleList GetUnknownAtoms(mol::ResidueHandle res);
+
/// \brief Check whether the residue has all required atoms. This does not
/// include hydrogens and leaving atoms such as the terminal OXT.
virtual bool IsResidueComplete(const mol::ResidueHandle& residue);
--
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