Added a function to compute how well an EntityView superposes with

a denisty map

modules/mol/alg/pymod/CMakeLists.txt

@@ -3,12 +3,14 @@ set(OST_MOL_ALG_PYMOD_SOURCES
   export_svd_superpose.cc
   export_clash.cc
   export_trajectory_analysis.cc
+  export_structure_analysis.cc
 )
 
 set(OST_MOL_ALG_PYMOD_MODULES
   "__init__.py"
   views.py
   superpose.py
+  structure_analysis.py
 )
 
 if (ENABLE_IMG)

modules/mol/alg/pymod/export_structure_analysis.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 <boost/python.hpp>
+using namespace boost::python;
+
+#include <ost/mol/alg/structure_analysis.hh>
+
+using namespace ost;
+using namespace ost::mol::alg;
+
+void export_StructureAnalysis()
+{
+  def("GetPosListFromView",&GetPosListFromView, (arg("view")));
+  def("CalculateAgreementWithDensityMap",&CalculateAgreementWithDensityMap,(arg("pos_list"),arg("density_map")));
+}

modules/mol/alg/pymod/wrap_mol_alg.cc

@@ -27,6 +27,7 @@ using namespace ost;
 
 void export_svdSuperPose();
 void export_TrajectoryAnalysis();
+void export_StructureAnalysis();
 void export_Clash();
 #if OST_IMG_ENABLED
 void export_entity_to_density();
@@ -48,6 +49,7 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
 {
   export_svdSuperPose();
   export_TrajectoryAnalysis();
+  export_StructureAnalysis();
   #if OST_IMG_ENABLED
   export_entity_to_density();
   #endif

modules/mol/alg/src/CMakeLists.txt

@@ -8,6 +8,7 @@ set(OST_MOL_ALG_HEADERS
   construct_cbeta.hh
   clash_score.hh
   trajectory_analysis.hh
+  structure_analysis.hh
 )
 
 set(OST_MOL_ALG_SOURCES
@@ -19,6 +20,7 @@ set(OST_MOL_ALG_SOURCES
   filter_clashes.cc
   construct_cbeta.cc
   trajectory_analysis.cc
+  structure_analysis.cc
 )
 
 set(MOL_ALG_DEPS ost_mol ost_seq)

modules/mol/alg/src/structure_analysis.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 Niklaus Johner
+ */
+
+#include <ost/base.hh>
+#include <ost/mol/mol.hh>
+#include "structure_analysis.hh"
+
+namespace ost { namespace mol { namespace alg {
+
+geom::Vec3List GetPosListFromView(const EntityView& view){
+  CheckHandleValidity(view);
+  geom::Vec3List vl;
+  AtomViewList atoms=view.GetAtomList();
+  vl.reserve(atoms.size());
+  for (AtomViewList::const_iterator i=atoms.begin(), 
+       e=atoms.end(); i!=e; ++i) {
+    vl.push_back(i->GetPos());
+  }
+  return vl;
+}    
+  
+Real CalculateAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map){
+  Real sum,v;
+  sum=0;
+  CheckHandleValidity(density_map);
+  for (geom::Vec3List::const_iterator v1=vl.begin(),e=vl.end(); v1!=e; ++v1) {
+    img::Point p(density_map.CoordToIndex(*v1));
+    v=density_map.GetReal(p);
+    sum=sum+v;
+  }
+  return sum;
+}
+  
+}}} //ns

modules/mol/alg/src/structure_analysis.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
+//------------------------------------------------------------------------------
+
+/*
+ * Niklaus Johner
+ */
+#ifndef OST_STRUCTURE_ANALYSIS_HH
+#define OST_STRUCTURE_ANALYSIS_HH
+
+#include <ost/mol/alg/module_config.hh>
+
+#include <ost/mol/entity_view.hh>
+#include <ost/img/map.hh>
+
+
+namespace ost { namespace mol { namespace alg {
+  geom::Vec3List DLLEXPORT_OST_MOL_ALG GetPosListFromView(const EntityView& view);
+  Real DLLEXPORT_OST_MOL_ALG CalculateAgreementWithDensityMap(const geom::Vec3List& vl, img::MapHandle& density_map);
+}}}//ns
+#endif