From 3eba172e2bfde50fc2e7ec70027159682f62abf7 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@stud.unibas.ch>
Date: Mon, 27 May 2013 18:51:50 +0200
Subject: [PATCH] added checker function for residue completeness in compound
lib. not tested yet.
---
modules/conop/pymod/export_compound.cc | 3 +++
modules/conop/src/compound_lib_base.cc | 26 ++++++++++++++++++++++++++
modules/conop/src/compound_lib_base.hh | 5 +++++
3 files changed, 34 insertions(+)
diff --git a/modules/conop/pymod/export_compound.cc b/modules/conop/pymod/export_compound.cc
index 33cbe0536..4ed7248f4 100644
--- a/modules/conop/pymod/export_compound.cc
+++ b/modules/conop/pymod/export_compound.cc
@@ -135,6 +135,9 @@ void export_Compound() {
.def("Load", &CompoundLib::Load, arg("readonly")=true).staticmethod("Load")
.def("FindCompound", &find_compound,
(arg("tlc"), arg("dialect")="PDB"))
+ .def("IsResidueComplete",&CompoundLib::IsResidueComplete, (arg("residue"),
+ arg("check_hydrogens")=false,
+ arg("dialect")="PDB"))
.def("ClearCache", &CompoundLib::ClearCache)
.def("GetOSTVersionUsed", &CompoundLib::GetOSTVersionUsed)
.def("GetCreationDate", &get_creation_date, (arg("comp_lib")))
diff --git a/modules/conop/src/compound_lib_base.cc b/modules/conop/src/compound_lib_base.cc
index e69de29bb..b5071e00f 100644
--- a/modules/conop/src/compound_lib_base.cc
+++ b/modules/conop/src/compound_lib_base.cc
@@ -0,0 +1,26 @@
+#include "compound_lib_base.hh"
+
+namespace ost { namespace conop {
+
+bool CompoundLibBase::IsResidueComplete(const ost::mol::ResidueHandle& res, bool check_hydrogens, Compound::Dialect dialect) const{
+
+ CompoundPtr compound = this->FindCompound(res.GetName(), dialect);
+
+ AtomSpecList a_spec = compound->GetAtomSpecs();
+
+ for(AtomSpecList::const_iterator it=a_spec.begin(); it!=a_spec.end();++it){
+ if(it->element=="H" || it->element=="D"){
+ if(check_hydrogens){
+ if(!res.FindAtom(it->name).IsValid()){
+ return false;
+ }
+ }
+ }
+ if(!res.FindAtom(it->name).IsValid()){
+ return false;
+ }
+ }
+ return true;
+}
+
+}}//namespace
diff --git a/modules/conop/src/compound_lib_base.hh b/modules/conop/src/compound_lib_base.hh
index 350307eb5..aee5215b9 100644
--- a/modules/conop/src/compound_lib_base.hh
+++ b/modules/conop/src/compound_lib_base.hh
@@ -2,6 +2,7 @@
#define OST_CONOP_COMPOUND_LIB_BASE_HH
#include "compound.hh"
+#include <ost/mol/residue_handle.hh>
namespace ost { namespace conop {
@@ -13,6 +14,10 @@ public:
virtual ~CompoundLibBase() {}
virtual CompoundPtr FindCompound(const String& id,
Compound::Dialect dialect) const = 0;
+
+ bool IsResidueComplete(const ost::mol::ResidueHandle& res,
+ bool check_hydrogens,
+ Compound::Dialect) const;
};
}}
--
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