Added residue name consistency check

modules/mol/alg/pymod/wrap_mol_alg.cc

@@ -23,6 +23,8 @@
 #include <ost/mol/alg/local_dist_diff_test.hh>
 #include <ost/mol/alg/superpose_frames.hh>
 #include <ost/mol/alg/filter_clashes.hh>
+#include <ost/mol/alg/consistency_checks.hh>
+
 using namespace boost::python;
 using namespace ost;
 
@@ -159,5 +161,8 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
   def("IsStandardResidue",&mol::alg::IsStandardResidue);
   def("PrintGlobalRDMap",&mol::alg::PrintGlobalRDMap);
   def("PrintResidueRDMap",&mol::alg::PrintResidueRDMap);
-  
+ 
+  def("CheckResidueTypes",&mol::alg::CheckResidueTypes);
+
+ 
 }

modules/mol/alg/src/CMakeLists.txt

@@ -9,6 +9,7 @@ set(OST_MOL_ALG_HEADERS
   clash_score.hh
   trajectory_analysis.hh
   structure_analysis.hh
+  consistency_checks.hh
 )
 
 set(OST_MOL_ALG_SOURCES
@@ -21,6 +22,7 @@ set(OST_MOL_ALG_SOURCES
   construct_cbeta.cc
   trajectory_analysis.cc
   structure_analysis.cc
+  consistency_checks.cc
 )
 
 set(MOL_ALG_DEPS ost_mol ost_seq)

modules/mol/alg/src/consistency_checks.cc

+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+
+#include <ost/log.hh>
+#include <ost/mol/chain_view.hh>
+#include <ost/mol/residue_view.hh>
+#include <ost/mol/alg/consistency_checks.hh>
+
+namespace ost { namespace mol { namespace alg {
+  
+/// \brief Checks that residue types with the same ResNum in the two structures match
+///
+/// Requires a reference structure and a probe structure. The function checks that all the 
+/// residues in the reference structure that appear in the probe structure (i.e., that have the 
+/// same ResNum) are of the same residue type. 
+
+bool CheckResidueTypes (const mol::EntityView& probe, const mol::EntityView& reference)
+{
+  bool return_value = true;
+  ChainViewList ref_chains = reference.GetChainList();
+  for (ChainViewList::const_iterator rci = ref_chains.begin(), rce=ref_chains.end(); rci!=rce; ++rci) {
+    ChainView probe_chain = probe.FindChain(rci->GetName());
+    if (probe_chain.IsValid()) { 
+      ResidueViewList ref_residues = rci->GetResidueList();       
+      for (ResidueViewList::iterator rri=ref_residues.begin(), rre=ref_residues.end(); rri!=rre; ++rri) {
+        ResidueView probe_residue = probe_chain.FindResidue(rri->GetNumber());
+        if (probe_residue.IsValid()) {
+          if (probe_residue.GetName()!=rri->GetName()) {
+            return_value =false;
+            LOG_VERBOSE("Type mismatch for residue " << probe_residue.GetNumber());
+            LOG_VERBOSE("In reference: " << rri->GetName() << ", in compared structure: " << probe_residue.GetName());
+          } 
+        }            
+      }
+    }
+  }          
+  return return_value;
+}
+ 
+}}}
+
+
+

modules/mol/alg/src/consistency_checks.hh

+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+#ifndef OST_MOL_CONSISTENCY_CHECKS_HH
+#define OST_MOL_CONSISTENCY_CHECKS_HH
+
+#include <ost/mol/entity_view.hh>
+#include <ost/mol/alg/module_config.hh>
+
+namespace ost { namespace mol { namespace alg {
+  
+/// \brief Checks that residue types with the same ResNum in the two structures match
+///
+/// Requires a reference structure and a probe structure. The function checks that all the 
+/// residues in the reference structure that appear in the probe structure (i.e., that have the 
+/// same ResNum) are of the same residue type. 
+
+bool DLLEXPORT_OST_MOL_ALG CheckResidueTypes (const mol::EntityView& probe, const mol::EntityView& reference);
+  
+}}}
+
+#endif
+
+

modules/mol/alg/tests/CMakeLists.txt

 set(OST_MOL_ALG_UNIT_TESTS
   test_superposition.cc
   tests.cc
+  test_consistency_checks.cc
   test_convenient_superpose.py
 )
 

modules/mol/alg/tests/test_consistency_checks.cc

+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+//------------------------------------------------------------------------------
+
+/*
+ * Author Valerio Mariani
+ */
+#define BOOST_TEST_MODULE ost_mol_alg
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+
+#include <ost/mol/mol.hh>
+#include <ost/mol/alg/consistency_checks.hh>
+
+using namespace ost::mol;
+using namespace ost::mol::alg;
+
+
+BOOST_AUTO_TEST_SUITE( mol_alg );
+
+BOOST_AUTO_TEST_CASE(consistency_check) 
+{
+
+  EntityHandle a=CreateEntity();
+  XCSEditor eda=a.EditXCS();
+  ChainHandle ca=eda.InsertChain("A");
+  ResidueHandle r1a = eda.AppendResidue(ca, "ALA",1);
+  ResidueHandle r2a = eda.AppendResidue(ca, "TYR",2);
+  ResidueHandle r3a = eda.AppendResidue(ca, "LEU",3);
+  ResidueHandle r4a = eda.AppendResidue(ca, "GLY",4);
+  ChainHandle ca2=eda.InsertChain("C");
+  ResidueHandle r1a2 = eda.AppendResidue(ca2, "PRO",1);
+
+
+  EntityHandle b=CreateEntity();
+  XCSEditor edb=b.EditXCS();
+  ChainHandle cb=edb.InsertChain("A");
+  ResidueHandle r1b = edb.AppendResidue(cb, "ALA",1);
+  ResidueHandle r2b = edb.AppendResidue(cb, "TYR",2);
+  ResidueHandle r3b = edb.AppendResidue(cb, "LEU",3);
+  ResidueHandle r4b = edb.AppendResidue(cb, "GLY",4);
+  ResidueHandle r5b = edb.AppendResidue(cb, "PRO",5);
+  ChainHandle cb2=edb.InsertChain("B");
+  ResidueHandle r1b2 = edb.AppendResidue(cb2, "ALA",1);
+
+
+  EntityHandle c=CreateEntity();
+  XCSEditor edc=c.EditXCS();
+  ChainHandle cc=edc.InsertChain("A");
+  ResidueHandle r1c = edc.AppendResidue(cc, "ALA",1);
+  ResidueHandle r2c = edc.AppendResidue(cc, "PRO",2);
+  ResidueHandle r3c = edc.AppendResidue(cc, "LEU",3);
+  ResidueHandle r4c = edc.AppendResidue(cc, "GLY",4);
+
+
+  BOOST_CHECK(ost::mol::alg::CheckResidueTypes(a.CreateFullView(),b.CreateFullView())==true);   
+  BOOST_CHECK(ost::mol::alg::CheckResidueTypes(c.CreateFullView(),b.CreateFullView())==false);    
+}
+
+BOOST_AUTO_TEST_SUITE_END();