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pymol
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Daniel Bauer
257
.pymol/startup/tmalign.py
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257
.pymol/startup/tmalign.py
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'''
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(c) 2011-2012 Thomas Holder, MPI for Developmental Biology
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'''
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from __future__ import print_function
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__author__ = 'Thomas Holder'
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__version__ = '1.1'
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__license__ = 'BSD-2-Clause'
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from pymol import cmd, CmdException
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def save_pdb_without_ter(filename, selection, **kwargs):
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'''
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DESCRIPTION
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Save PDB file without TER records. External applications like TMalign and
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DynDom stop reading PDB files at TER records, which might be undesired in
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case of missing loops.
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'''
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v = cmd.get_setting_boolean('pdb_use_ter_records')
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if v:
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cmd.unset('pdb_use_ter_records')
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cmd.save(filename, selection, **kwargs)
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if v:
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cmd.set('pdb_use_ter_records')
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def alignwithanymethod(mobile, target, methods='align super cealign tmalign',
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async=1, quiet=1):
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'''
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DESCRIPTION
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Align copies of mobile to target with several alignment methods
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ARGUMENTS
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mobile = string: atom selection
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target = string: atom selection
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methods = string: space separated list of PyMOL commands which take
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arguments "mobile" and "target" (in any order) {default: align super
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cealign tmalign}
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'''
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import threading
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import time
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methods = methods.split()
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async, quiet = int(async), int(quiet)
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mobile_obj = cmd.get_object_list('first (' + mobile + ')')[0]
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def myalign(method):
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newmobile = cmd.get_unused_name(mobile_obj + '_' + method)
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cmd.create(newmobile, mobile_obj)
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start = time.time()
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cmd.do('%s mobile=%s in %s, target=%s' % (method, newmobile, mobile, target))
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if not quiet:
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print('Finished: %s (%.2f sec)' % (method, time.time() - start))
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for method in methods:
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if async:
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t = threading.Thread(target=myalign, args=(method,))
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t.setDaemon(1)
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t.start()
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else:
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myalign(method)
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def tmalign(mobile, target, args='', exe='TMalign', ter=0, transform=1, object=None, quiet=0):
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'''
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DESCRIPTION
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TMalign wrapper
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Reference: Y. Zhang and J. Skolnick, Nucl. Acids Res. 2005 33, 2302-9
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http://zhanglab.ccmb.med.umich.edu/TM-align/
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USAGE
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tmalign mobile, target [, args [, exe ]]
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ARGUMENTS
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mobile, target = string: atom selections
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args = string: Extra arguments like -d0 5 -L 100
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exe = string: Path to TMalign executable {default: TMalign}
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ter = 0/1: If ter=0, then ignore chain breaks because TMalign will stop
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at first TER record {default: 0}
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SEE ALSO
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tmscore, mmalign
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'''
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import subprocess
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import tempfile
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import os
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import re
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ter, quiet = int(ter), int(quiet)
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mobile_filename = tempfile.mktemp('.pdb', 'mobile')
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target_filename = tempfile.mktemp('.pdb', 'target')
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matrix_filename = tempfile.mktemp('.txt', 'matrix')
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mobile_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % (mobile)
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target_ca_sele = '(%s) and (not hetatm) and name CA and alt +A' % (target)
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if ter:
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save = cmd.save
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else:
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save = save_pdb_without_ter
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save(mobile_filename, mobile_ca_sele)
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save(target_filename, target_ca_sele)
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exe = cmd.exp_path(exe)
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args = [exe, mobile_filename, target_filename, '-m', matrix_filename] + args.split()
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try:
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process = subprocess.Popen(args, stdout=subprocess.PIPE)
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lines = process.stdout.readlines()
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except OSError:
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print('Cannot execute "%s", please provide full path to TMscore or TMalign executable' % (exe))
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raise CmdException
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finally:
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os.remove(mobile_filename)
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os.remove(target_filename)
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# TMalign >= 2012/04/17
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if os.path.exists(matrix_filename):
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lines += open(matrix_filename).readlines()
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os.remove(matrix_filename)
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r = None
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re_score = re.compile(r'TM-score\s*=\s*(\d*\.\d*)')
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rowcount = 0
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matrix = []
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line_it = iter(lines)
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alignment = []
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for line in line_it:
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if 4 >= rowcount > 0:
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if rowcount >= 2:
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a = list(map(float, line.split()))
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matrix.extend(a[2:5])
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matrix.append(a[1])
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rowcount += 1
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elif line.lower().startswith(' -------- rotation matrix'):
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rowcount = 1
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elif line.startswith('(":" denotes'):
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alignment = [line_it.next().rstrip() for i in range(3)]
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else:
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match = re_score.search(line)
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if match is not None:
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r = float(match.group(1))
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if not quiet:
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print(line.rstrip())
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if not quiet:
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for i in range(0, len(alignment[0]) - 1, 78):
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for line in alignment:
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print(line[i:i + 78])
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print('')
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assert len(matrix) == 3 * 4
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matrix.extend([0, 0, 0, 1])
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if int(transform):
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cmd.transform_selection('byobject (%s)' % (mobile), matrix, homogenous=1)
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# alignment object
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if object is not None:
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mobile_idx, target_idx = [], []
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space = {'mobile_idx': mobile_idx, 'target_idx': target_idx}
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cmd.iterate(mobile_ca_sele, 'mobile_idx.append("%s`%d" % (model, index))', space=space)
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cmd.iterate(target_ca_sele, 'target_idx.append("%s`%d" % (model, index))', space=space)
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for i, aa in enumerate(alignment[0]):
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if aa == '-':
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mobile_idx.insert(i, None)
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for i, aa in enumerate(alignment[2]):
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if aa == '-':
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target_idx.insert(i, None)
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if (len(mobile_idx) == len(target_idx) == len(alignment[2])):
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cmd.rms_cur(
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' '.join(idx for (idx, m) in zip(mobile_idx, alignment[1]) if m in ':.'),
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' '.join(idx for (idx, m) in zip(target_idx, alignment[1]) if m in ':.'),
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cycles=0, matchmaker=4, object=object)
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else:
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print('Could not load alignment object')
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if not quiet and r is not None:
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print('Found in output TM-score = %.4f' % (r))
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return r
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def tmscore(mobile, target, args='', exe='TMscore', quiet=0, **kwargs):
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'''
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DESCRIPTION
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TMscore wrapper
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Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710
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http://zhanglab.ccmb.med.umich.edu/TM-score/
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ARGUMENTS
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mobile, target = string: atom selections
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args = string: Extra arguments like -d 5
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exe = string: Path to TMscore executable {default: TMscore}
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ter = 0/1: If ter=0, then ignore chain breaks because TMscore will stop
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at first TER record {default: 0}
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SEE ALSO
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tmalign, mmalign
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'''
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kwargs.pop('_self', None)
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return tmalign(mobile, target, args, exe, quiet=quiet, **kwargs)
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def mmalign(mobile, target, args='', exe='MMalign', ter=0, transform=1, quiet=0):
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'''
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DESCRIPTION
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MMalign wrapper
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Reference: S. Mukherjee and Y. Zhang, Nucleic Acids Research 2009; 37: e83
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http://zhanglab.ccmb.med.umich.edu/MM-align/
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SEE ALSO
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tmalign, tmscore
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'''
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return tmalign(mobile, target, args, exe, ter, transform, quiet=quiet)
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# pymol commands
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cmd.extend('alignwithanymethod', alignwithanymethod)
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cmd.extend('tmalign', tmalign)
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cmd.extend('tmscore', tmscore)
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cmd.extend('mmalign', tmalign)
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# autocompletion
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cmd.auto_arg[0].update({
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'tmalign': cmd.auto_arg[0]['align'],
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'tmscore': cmd.auto_arg[0]['align'],
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'mmalign': cmd.auto_arg[0]['align'],
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})
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cmd.auto_arg[1].update({
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'tmalign': cmd.auto_arg[1]['align'],
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'tmscore': cmd.auto_arg[1]['align'],
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'mmalign': cmd.auto_arg[1]['align'],
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})
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