From 3e02346f0290bed9a2c6510955acdb6a4f49f5ef Mon Sep 17 00:00:00 2001
From: Niklaus Johner <nij2003@med.cornell.edu>
Date: Thu, 22 Mar 2012 18:26:09 -0400
Subject: [PATCH] Added a function to compute how well an EntityView superposes
with a denisty map
---
modules/mol/alg/pymod/CMakeLists.txt | 2 +
.../alg/pymod/export_structure_analysis.cc | 31 +++++++++++
modules/mol/alg/pymod/wrap_mol_alg.cc | 2 +
modules/mol/alg/src/CMakeLists.txt | 2 +
modules/mol/alg/src/structure_analysis.cc | 54 +++++++++++++++++++
modules/mol/alg/src/structure_analysis.hh | 36 +++++++++++++
6 files changed, 127 insertions(+)
create mode 100644 modules/mol/alg/pymod/export_structure_analysis.cc
create mode 100644 modules/mol/alg/src/structure_analysis.cc
create mode 100644 modules/mol/alg/src/structure_analysis.hh
diff --git a/modules/mol/alg/pymod/CMakeLists.txt b/modules/mol/alg/pymod/CMakeLists.txt
index 0ffb3f651..a89211dce 100644
--- a/modules/mol/alg/pymod/CMakeLists.txt
+++ b/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)
diff --git a/modules/mol/alg/pymod/export_structure_analysis.cc b/modules/mol/alg/pymod/export_structure_analysis.cc
new file mode 100644
index 000000000..c4df71e3f
--- /dev/null
+++ b/modules/mol/alg/pymod/export_structure_analysis.cc
@@ -0,0 +1,31 @@
+//------------------------------------------------------------------------------
+// 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")));
+}
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 4f974d940..4e4ccc2f5 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/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
diff --git a/modules/mol/alg/src/CMakeLists.txt b/modules/mol/alg/src/CMakeLists.txt
index 2e3d94b13..259f7f7dc 100644
--- a/modules/mol/alg/src/CMakeLists.txt
+++ b/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)
diff --git a/modules/mol/alg/src/structure_analysis.cc b/modules/mol/alg/src/structure_analysis.cc
new file mode 100644
index 000000000..a590cf0e4
--- /dev/null
+++ b/modules/mol/alg/src/structure_analysis.cc
@@ -0,0 +1,54 @@
+//------------------------------------------------------------------------------
+// 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
diff --git a/modules/mol/alg/src/structure_analysis.hh b/modules/mol/alg/src/structure_analysis.hh
new file mode 100644
index 000000000..aa9e72041
--- /dev/null
+++ b/modules/mol/alg/src/structure_analysis.hh
@@ -0,0 +1,36 @@
+//------------------------------------------------------------------------------
+// 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
--
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