diff --git a/modules/mol/alg/molalg.rst b/modules/mol/alg/molalg.rst
index 2daf3ca7597bca27d86b9d86d53e7c67a33b5bb6..7758f3ff290de4812b9635514cf0f7a2f51e2f0a 100644
--- a/modules/mol/alg/molalg.rst
+++ b/modules/mol/alg/molalg.rst
@@ -40,4 +40,30 @@
:param ref: The index of the reference frame to use for superposition. If set
to -1, the each frame is superposed to the previous frame.
- :returns: A newly created coord group containing the superposed frames.
\ No newline at end of file
+ :returns: A newly created coord group containing the superposed frames.
+
+
+Steric Clashes
+--------------------------------------------------------------------------------
+
+The following function detects steric clashes in atomic structures. Two atoms are clashing if their euclidian distance is smaller than a threshold value. The threshold values are calculated from high-resolution X-ray structures for each possible element pair. The value is chosen such that 99.99% of observed distances between 0 and 5 Angstroem are above the threshold.
+
+
+.. function:: FilterClashes(ent, tolerance=0.0)
+
+ This function filters out residues with clashing atoms. If the clashing atom
+ is a backbone atom, the complete residue is removed, if the atom is part of
+ the sidechain, only the sidechain atoms are removed.
+
+ Hydrogen and deuterium atoms are ignored.
+
+ :param ent: The input entity
+ :type ent: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
+ :param tolerance: The tolerance in (Angstroem) is substracted from the
+ thresholds calculated from high resolution X-ray structures to make the
+ function less pedantic. Negative values are also allowed and make the
+ function more stringent.
+
+ :returns: The filtered :class:`~ost.mol.EntityView`
+
+
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 91a9a0904041a90bf502a8c4ecb00e7cbe99c7c0..a5db8de3560a56b1f31bead07cfc70b947850b79 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -21,6 +21,7 @@
#include <ost/config.hh>
#include <ost/mol/alg/local_dist_test.hh>
#include <ost/mol/alg/superpose_frames.hh>
+#include <ost/mol/alg/filter_clashes.hh>
using namespace boost::python;
using namespace ost;
@@ -34,6 +35,8 @@ namespace {
Real (*ldt_a)(const mol::EntityView&, const mol::EntityView& ref, Real, Real)=&mol::alg::LocalDistTest;
Real (*ldt_b)(const seq::AlignmentHandle&,Real, Real, int, int)=&mol::alg::LocalDistTest;
+mol::EntityView (*fc_a)(const mol::EntityView&, Real)=&mol::alg::FilterClashes;
+mol::EntityView (*fc_b)(const mol::EntityHandle&, Real)=&mol::alg::FilterClashes;
}
BOOST_PYTHON_MODULE(_mol_alg)
@@ -45,6 +48,8 @@ BOOST_PYTHON_MODULE(_mol_alg)
def("LocalDistTest", ldt_a);
def("LocalDistTest", ldt_b, (arg("ref_index")=0, arg("mdl_index")=1));
+ def("FilterClashes", fc_a, (arg("ent"), arg("tolerance")=0.1));
+ def("FilterClashes", fc_b, (arg("ent"), arg("tolerance")=0.1));
def("SuperposeFrames", &ost::mol::alg::SuperposeFrames,
(arg("source"), arg("sel")=ost::mol::EntityView(), arg("begin")=0,
arg("end")=-1, arg("ref")=-1));
diff --git a/modules/mol/alg/src/CMakeLists.txt b/modules/mol/alg/src/CMakeLists.txt
index 15e93c0e72ade2450464aaa55551828073dc1ce3..6d418a16c3691840dceb2eb4c33f968f6a6241e5 100644
--- a/modules/mol/alg/src/CMakeLists.txt
+++ b/modules/mol/alg/src/CMakeLists.txt
@@ -4,6 +4,7 @@ set(OST_MOL_ALG_HEADERS
sec_structure_segments.hh
local_dist_test.hh
superpose_frames.hh
+ filter_clashes.hh
)
set(OST_MOL_ALG_SOURCES
@@ -11,6 +12,7 @@ set(OST_MOL_ALG_SOURCES
sec_structure_segments.cc
local_dist_test.cc
superpose_frames.cc
+ filter_clashes.cc
)
set(MOL_ALG_DEPS mol seq)
diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
new file mode 100644
index 0000000000000000000000000000000000000000..12c539b3ecdd76b7022bed31141675060fa0dd85
--- /dev/null
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -0,0 +1,144 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 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/mol.hh>
+#include "filter_clashes.hh"
+
+namespace ost { namespace mol { namespace alg {
+
+namespace {
+
+Real GetThreshold(const String& ele1, const String& ele2) {
+ if (ele1.length()!=1 || ele2.length()!=1) {
+ return 1.5;
+ }
+ switch (ele1[0]) {
+ case 'C' :
+ switch (ele2[0]) {
+ case 'C' : return 2.10;
+ case 'N' : return 2.10;
+ case 'S' : return 2.45;
+ case 'O' : return 2.25;
+ default: return 1.5;
+ }
+ case 'N':
+ switch (ele2[0]) {
+ case 'C' : return 2.10;
+ case 'N' : return 2.05;
+ case 'S' : return 2.55;
+ case 'O' : return 2.10;
+ default: return 1.5;
+ }
+ case 'O':
+ switch (ele2[0]) {
+ case 'C' : return 2.25;
+ case 'N' : return 2.10;
+ case 'S' : return 2.45;
+ case 'O' : return 2.05;
+ default: return 1.5;
+ }
+ case 'S':
+ switch (ele2[0]) {
+ case 'C' : return 2.45;
+ case 'N' : return 2.55;
+ case 'S' : return 1.80;
+ case 'O' : return 2.45;
+ default: return 1.5;
+ }
+ default:
+ return 1.5;
+ }
+}
+
+
+}
+
+EntityView FilterClashes(const EntityView& ent, Real tolerance)
+{
+ EntityView filtered=ent.CreateEmptyView();
+ ResidueViewList residues=ent.GetResidueList();
+ for (ResidueViewList::iterator
+ i=residues.begin(), e=residues.end(); i!=e; ++i) {
+ bool remove_sc=false, remove_bb=false;
+ ResidueView res=*i;
+ const AtomViewList& atoms=res.GetAtomList();
+ for (AtomViewList::const_iterator
+ j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
+ AtomView atom=*j;
+ String ele1=atom.GetElement();
+ if (ele1=="H" || ele1=="D") {
+ continue;
+ }
+ AtomViewList within=ent.FindWithin(atom.GetPos(), 2.5-tolerance);
+ for (AtomViewList::iterator
+ k=within.begin(), e3=within.end(); k!=e3; ++k) {
+ AtomView atom2=*k;
+ if (atom2==atom) {
+ continue;
+ }
+ String ele2=atom2.GetElement();
+ if (ele2=="H" || ele2=="D") {
+ continue;
+ }
+ // In theory, this should also trigger for disulfide bonds, but
+ // since we don't detect disulfides correctly, we can't count on that
+ // and we instead allow S-S distances down to 1.8.
+ if (atom.GetHandle().FindBondToAtom(atom2.GetHandle()).IsValid()) {
+ continue;
+ }
+ Real d=geom::Length2(atom.GetPos()-atom2.GetPos());
+ Real threshold=GetThreshold(ele1, ele2)-tolerance;
+ if (d<threshold*threshold) {
+ remove_sc=true;
+ String name=atom.GetName();
+ if (name=="CA" || name=="N" || name=="O" || name=="C") {
+ remove_bb=true;
+ }
+ }
+ }
+ }
+ if (remove_bb) {
+ LOG_VERBOSE("removing whole residue " << res);
+ continue;
+ }
+ if (remove_sc) {
+ LOG_VERBOSE("removing sidechain of residue " << res);
+ for (AtomViewList::const_iterator
+ j=atoms.begin(), e2=atoms.end(); j!=e2; ++j) {
+ AtomView atom=*j;
+ String name=atom.GetName();
+ if (name=="CA" || name=="N" || name=="O" || name=="C") {
+ filtered.AddAtom(atom);
+ }
+ }
+ }
+ filtered.AddResidue(res, ViewAddFlag::INCLUDE_ATOMS);
+ }
+ return filtered;
+}
+
+
+EntityView FilterClashes(const EntityHandle& ent, Real tolerance)
+{
+ return FilterClashes(ent.CreateFullView(), tolerance);
+}
+
+
+}}}
+
diff --git a/modules/mol/alg/src/filter_clashes.hh b/modules/mol/alg/src/filter_clashes.hh
new file mode 100644
index 0000000000000000000000000000000000000000..87fd770311435ec4115311c342aa2bec7fd4309f
--- /dev/null
+++ b/modules/mol/alg/src/filter_clashes.hh
@@ -0,0 +1,36 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 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_ALG_FILTER_CLASHES_HH
+#define OST_MOL_ALG_FILTER_CLASHES_HH
+
+#include <ost/mol/entity_view.hh>
+#include <ost/mol/alg/module_config.hh>
+
+namespace ost { namespace mol { namespace alg {
+
+
+EntityView DLLEXPORT_OST_MOL_ALG FilterClashes(const EntityView& ent,
+ Real tolerance=0.1);
+
+EntityView DLLEXPORT_OST_MOL_ALG FilterClashes(const EntityHandle& ent,
+ Real tolerance=0.1);
+}}}
+
+
+#endif
diff --git a/modules/mol/alg/src/ldt.cc b/modules/mol/alg/src/ldt.cc
index 589bd125f72b2abbba2921877a8b7b64618a3417..7a676b00ae74eceea3fa4cac96b7b18575896590 100644
--- a/modules/mol/alg/src/ldt.cc
+++ b/modules/mol/alg/src/ldt.cc
@@ -1,6 +1,26 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 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/mol/alg/local_dist_test.hh>
+#include <ost/mol/alg/filter_clashes.hh>
#include <ost/io/mol/pdb_reader.hh>
#include <ost/io/io_exception.hh>
+#include <ost/conop/conop.hh>
using namespace ost;
using namespace ost::io;
using namespace ost::mol;
@@ -12,6 +32,8 @@ EntityHandle load(const String& file)
if (reader.HasNext()) {
EntityHandle ent=CreateEntity();
reader.Import(ent);
+ conop::Conopology& conop_inst=conop::Conopology::Instance();
+ conop_inst.ConnectAll(conop_inst.GetBuilder(), ent);
return ent;
}
std::cerr << "ERROR: '" << file << "' does not contain any ATOM records. "
@@ -82,6 +104,9 @@ int main (int argc, char* const *argv)
continue;
}
EntityView v=model.CreateFullView();
+ if (filter_clashes) {
+ v=alg::FilterClashes(v);
+ }
float cutoffs[]={0.5,1,2,4};
float ldt=0.0;
for (int n=0; n<4; ++n) {
diff --git a/modules/mol/alg/src/local_dist_test.hh b/modules/mol/alg/src/local_dist_test.hh
index ab7588cdf84d401aaee052bcfe2b390da8174b15..a4e645acce1e5ae8d490e34a52860af0ac9705b7 100644
--- a/modules/mol/alg/src/local_dist_test.hh
+++ b/modules/mol/alg/src/local_dist_test.hh
@@ -1,3 +1,21 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2010 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_ALG_LOCAL_DIST_TEST_HH
#define OST_MOL_ALG_LOCAL_DIST_TEST_HH