added FilterClashes function

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.
+  :returns: A newly created coord group containing the superposed frames.
\ No newline at end of file
+  
+  
+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`
+
+

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));

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)

modules/mol/alg/src/filter_clashes.cc

+//------------------------------------------------------------------------------
+// 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);
+}
+
+
+}}}
+

modules/mol/alg/src/filter_clashes.hh

+//------------------------------------------------------------------------------
+// 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

modules/mol/alg/src/ldt.cc

+//------------------------------------------------------------------------------
+// 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) {

modules/mol/alg/src/local_dist_test.hh

+//------------------------------------------------------------------------------
+// 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