added binding for ialign

temporaly the program is in /import/bc2/home/schwede/bertoni/bin/ialign/bin/ialign.pl

modules/bindings/pymod/ialign.py

+#------------------------------------------------------------------------------
+# This file is part of the OpenStructure project <www.openstructure.org>
+#
+# Copyright (C) 2008-2009 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
+#------------------------------------------------------------------------------
+"""
+Wrappers for the iAlign utility.
+
+References:
+
+Mu Gao and Jeffrey Skolnick, 2010. iAlign: a method for the structural comparison
+of protein-protein interfaces. Bioinformatics, 26(18):2259-65.
+Mu Gao and Jeffrey Skolnick, 2010. Structural space of protein-protein interfaces
+is degenerate, close to complete, and highly connected. PNAS 107(52):22517-22.
+
+Authors: Pascal Benkert, Marco Biasini, Martino Bertoni
+"""
+
+import subprocess, os, tempfile, platform
+from ost import settings, io, geom, seq
+
+def _SetupFiles(models):
+  # create temporary directory
+  tmp_dir_name=tempfile.mkdtemp()
+  dia = 'PDB'
+  for index, model in enumerate(models):
+    for chain in model.chains:
+      if len(chain.name) > 1:
+        dia = 'CHARMM'
+        break;
+      for res in chain.residues:
+        if len(res.name) > 3:
+          dia = 'CHARMM'
+          break;
+    io.SavePDB(model, os.path.join(tmp_dir_name, 'model%02d.pdb' % (index+1)), dialect=dia)
+  return tmp_dir_name
+
+def _CleanupFiles(dir_name):
+  import shutil
+  shutil.rmtree(dir_name)
+
+class iAlignResult:
+  """
+  Holds the result of running iAlign
+  
+  .. attribute:: rmsd
+    
+    The RMSD of the common Calpha atoms of both structures
+  
+  .. attribute:: transform
+  
+    The transform that superposes the model onto the reference structure.
+    
+    :type: :class:`~ost.geom.Mat4`
+  
+  .. attribute:: alignment
+  
+    The alignment of the structures, that is the pairing of Calphas of both 
+    structures. Since the programs only read ATOM records, residues consisting 
+    of HETATMs (MSE) are not included in the alignment.
+    
+    :type: :class:`~ost.seq.AlignmentHandle`
+
+  .. attribute:: IS_score
+
+    The IS-score of the structural superposition
+
+  .. attribute:: aligned_residues
+
+    The total number of aligned residues
+
+  .. attribute:: aligned_contacts
+
+    The total number of aligned contacts
+
+  """
+  def __init__(self, rmsd, transform, alignment, is_score, 
+               aligned_residues, aligned_contacts):
+    
+    self.rmsd=rmsd
+    self.transform=transform
+    self.alignment=alignment
+    self.is_score=is_score    
+    self.aligned_residues=aligned_residues
+    self.aligned_contacts=aligned_contacts
+
+def _ParseiAlign(lines):
+  info_line=lines[18].split(',')
+  is_score=float(info_line[0].split('=')[1].strip())
+  aln_residues=int(lines[19].split('=')[1].strip())
+  aln_contacts=int(lines[20].split('=')[1].strip())
+  info_line=lines[21].split(',')
+  rmsd=float(info_line[0].split('=')[1].strip())
+
+  tf1=[float(i.strip()) for i in lines[25][1:].split()]
+  tf2=[float(i.strip()) for i in lines[26][1:].split()]
+  tf3=[float(i.strip()) for i in lines[27][1:].split()]
+  rot=geom.Mat3(tf1[2], tf1[3], tf1[4], tf2[2], tf2[3],
+                tf2[4], tf3[2], tf3[3], tf3[4])
+  tf=geom.Mat4(rot)
+  tf.PasteTranslation(geom.Vec3(tf1[1], tf2[1], tf3[1]))
+  seq1 = seq.CreateSequence("1",lines[32].strip())
+  seq2 = seq.CreateSequence("2",lines[34].strip())
+  alignment = seq.CreateAlignment()
+  alignment.AddSequence(seq2)
+  alignment.AddSequence(seq1)
+  return iAlignResult(rmsd, tf, alignment, is_score, aln_residues, aln_contacts)
+
+def _RuniAlign(ialign, tmp_dir, options={}):
+  opts = {'a' : 1}   # concise output
+  opts.update(options)
+  cmd_opts = []
+  for k, v in opts.iteritems():
+    if type(v) == type(True):
+      if v == True:
+        cmd_opts.append('-%s' % str(k))
+    else:
+      cmd_opts.append('-%s %s' % (str(k), str(v)))
+  cmd_opts = ' '.join(cmd_opts)
+  model1_filename=os.path.join(tmp_dir, 'model01.pdb')
+  model2_filename=os.path.join(tmp_dir, 'model02.pdb')
+  if platform.system() == "Windows":
+    ialign_path=settings.Locate('ialign.pl', explicit_file_name=ialign)
+    command="\"%s\" %s %s %s" % (os.path.normpath(ialign_path), model1_filename, model2_filename, cmd_opts)
+  else:
+    ialign_path=settings.Locate('ialign.pl', explicit_file_name=ialign)  
+    command="\"%s\" \"%s\" \"%s\" %s" % (ialign_path, model1_filename, model2_filename, cmd_opts)
+  ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+  ps.wait()
+  lines=ps.stdout.readlines()
+  if (len(lines))<22:
+    _CleanupFiles(tmp_dir)
+    raise RuntimeError("iAlign superposition failed")
+  return _ParseiAlign(lines)
+
+
+def iAlign(model1, model2, ialign=None):
+  """
+  Compare protein-protein interfaces of the structures of two pairs of
+  protein complexes and suporpose them.
+  
+
+  :param model1: The model structure. If the superposition is successful, will 
+                 be superposed onto the reference structure
+  :type model1: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
+  :param model2: The reference structure
+  :type model2: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
+  :param ialign: If not None, the path to the ialign executable.
+  :returns: The result of the tmscore superposition
+  :rtype: :class:`iAlignResult`
+  
+  :raises: :class:`~ost.settings.FileNotFound` if tmalign could not be located.
+  :raises: :class:`RuntimeError` if the superposition failed
+  """
+  tmp_dir_name=_SetupFiles((model1, model2))
+  result=_RuniAlign(ialign, tmp_dir_name)
+  model1.handle.EditXCS().ApplyTransform(result.transform)
+  _CleanupFiles(tmp_dir_name)
+  return result