From fe1c532f471f0d8eb5da68d3aec3057a9032ccd1 Mon Sep 17 00:00:00 2001
From: Martino Bertoni <martino.bertoni@unibas.ch>
Date: Mon, 30 Sep 2013 10:27:06 +0200
Subject: [PATCH] added binding for ialign temporaly the program is in
/import/bc2/home/schwede/bertoni/bin/ialign/bin/ialign.pl
---
modules/bindings/pymod/ialign.py | 172 +++++++++++++++++++++++++++++++
1 file changed, 172 insertions(+)
create mode 100644 modules/bindings/pymod/ialign.py
diff --git a/modules/bindings/pymod/ialign.py b/modules/bindings/pymod/ialign.py
new file mode 100644
index 000000000..673f1b78a
--- /dev/null
+++ b/modules/bindings/pymod/ialign.py
@@ -0,0 +1,172 @@
+#------------------------------------------------------------------------------
+# 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
--
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