#------------------------------------------------------------------------------ # This file is part of the OpenStructure project # # Copyright (C) 2008-2020 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 tmalign and tmscore utilities. References: tmscore: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 tmalign: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9 Authors: Pascal Benkert, Marco Biasini """ import subprocess, os, tempfile, platform import ost 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) def _ParseTmAlign(lines,lines_matrix): info_line=lines[12].split(',') aln_length=int(info_line[0].split('=')[1].strip()) rmsd=float(info_line[1].split('=')[1].strip()) tm_score=float(lines[14].split('=')[1].split('(')[0].strip()) tf1=[float(i.strip()) for i in lines_matrix[2].split()] tf2=[float(i.strip()) for i in lines_matrix[3].split()] tf3=[float(i.strip()) for i in lines_matrix[4].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[18].strip()) seq2 = seq.CreateSequence("2",lines[20].strip()) alignment = seq.CreateAlignment() alignment.AddSequence(seq2) alignment.AddSequence(seq1) return ost.bindings.TMAlignResult(rmsd, tm_score, aln_length, tf, alignment) def _RunTmAlign(tmalign, tmp_dir): model1_filename=os.path.join(tmp_dir, 'model01.pdb') model2_filename=os.path.join(tmp_dir, 'model02.pdb') if platform.system() == "Windows": tmalign_path=settings.Locate('tmalign.exe', explicit_file_name=tmalign) command="\"%s\" %s %s -m %s" %(os.path.normpath(tmalign_path), model1_filename, model2_filename, os.path.join(tmp_dir,'matrix.txt')) else: tmalign_path=settings.Locate('tmalign', explicit_file_name=tmalign) command="\"%s\" \"%s\" \"%s\" -m \"%s\"" %(tmalign_path, model1_filename, model2_filename, os.path.join(tmp_dir,'matrix.txt')) ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE) stdout,_=ps.communicate() lines=stdout.decode().splitlines() if (len(lines))<22: _CleanupFiles(tmp_dir) raise RuntimeError("tmalign superposition failed") matrix_file=open(os.path.join(tmp_dir,'matrix.txt')) lines_matrix=matrix_file.readlines() matrix_file.close() return _ParseTmAlign(lines,lines_matrix) class TMScoreResult: """ Holds the result of running TMscore .. attribute:: rmsd_common The RMSD of the common Calpha atoms of both structures .. attribute:: rmsd_below_five The RMSD of all Calpha atoms that can be superposed below five Angstroem .. attribute:: tm_score The TM-score of the structural superposition .. attribute:: transform The transform that superposes the model onto the reference structure. :type: :class:`~ost.geom.Mat4` .. attribute:: gdt_ha The GDT_HA of the model to the reference structure. .. attribute:: gdt_ts The GDT_TS of the model to the reference structure. """ def __init__(self, rmsd_common, tm_score, max_sub, gdt_ts, gdt_ha, rmsd_below_five, transform): self.rmsd_common=rmsd_common self.tm_score=tm_score self.max_sub=max_sub self.gdt_ts=gdt_ts self.gdt_ha=gdt_ha self.rmsd_below_five=rmsd_below_five self.transform=transform def _ParseTmScore(lines): tf1=[float(i.strip()) for i in lines[23].split()] tf2=[float(i.strip()) for i in lines[24].split()] tf3=[float(i.strip()) for i in lines[25].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])) result=TMScoreResult(float(lines[14].split()[-1].strip()), float(lines[16].split()[2].strip()), float(lines[17].split()[1].strip()), float(lines[18].split()[1].strip()), float(lines[19].split()[1].strip()), float(lines[27].split()[-1].strip()), tf) return result def _RunTmScore(tmscore, tmp_dir): model1_filename=os.path.join(tmp_dir, 'model01.pdb') model2_filename=os.path.join(tmp_dir, 'model02.pdb') if platform.system() == "Windows": tmscore_path=settings.Locate('tmscore.exe', explicit_file_name=tmscore) command="\"%s\" %s %s" %(os.path.normpath(tmscore_path), model1_filename, model2_filename) else: tmscore_path=settings.Locate('tmscore', explicit_file_name=tmscore) command="\"%s\" \"%s\" \"%s\"" % (tmscore_path, model1_filename, model2_filename) ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE) stdout,_=ps.communicate() lines=stdout.decode().splitlines() if (len(lines))<22: _CleanupFiles(tmp_dir) raise RuntimeError("tmscore superposition failed") return _ParseTmScore(lines) def TMAlign(model1, model2, tmalign=None): """ Performs a sequence independent superposition of model1 onto model2, the reference. :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 tmalign: If not None, the path to the tmalign executable. :returns: The result of the tmscore superposition :rtype: :class:`ost.bindings.TMAlignResult` :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=_RunTmAlign(tmalign, tmp_dir_name) model1.handle.EditXCS().ApplyTransform(result.transform) _CleanupFiles(tmp_dir_name) return result def TMScore(model1, model2, tmscore=None): """ Performs a sequence dependent superposition of model1 onto model2, the reference. :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 tmscore: If not None, the path to the tmscore executable. :returns: The result of the tmscore superposition :rtype: :class:`TMScoreResult` :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=_RunTmScore(tmscore, tmp_dir_name) model1.handle.EditXCS().ApplyTransform(result.transform) _CleanupFiles(tmp_dir_name) return result