annotate ob_spectrophore_search.py @ 12:afd14e10a318 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:35:45 -0400
parents a1db432874e5
children 9ce9f996b941
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
1 #!/usr/bin/env python
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
2 """
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
3 Input: tabular format file with one column storing the unique id for the compounds and any other with the Spectrophores(TM) descriptors.
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
4 Output: parse the target file using the same protocol used to generate the databases in our servers. Physico-chemical properties are computed and stored as metadata in the sdf output file.
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
5 Copyright 2012, Bjoern Gruening and Xavier Lucas
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
6 """
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
7 import sys, os
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
8 import argparse
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
9 import math
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
10 import numpy as np
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
11
12
afd14e10a318 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 3
diff changeset
12 from openbabel import openbabel, pybel
afd14e10a318 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 3
diff changeset
13 openbabel.obErrorLog.StopLogging()
0
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
14 #TODO get rid of eval()
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
15
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
16 global spectrophore
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
17 spectrophore = pybel.ob.OBSpectrophore()
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
18
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
19 def parse_command_line():
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
20 parser = argparse.ArgumentParser()
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
21 parser.add_argument('--target', required=True, help='target file name in sdf format with Spectrophores(TM) descriptors stored as meta-data')
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
22 parser.add_argument('--library', required=True, help='library of compounds with pre-computed physico-chemical properties, including Spectrophores(TM) in tabular format')
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
23 parser.add_argument('-c', '--column', required=True, type=int, help='#column containing the Spectrophores(TM) descriptors in the library file')
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
24 parser.add_argument('-o', '--output', required=True, help='output file name')
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
25 parser.add_argument('-n', '--normalization', default="ZeroMeanAndUnitStd", choices=['No', 'ZeroMean', 'UnitStd', 'ZeroMeanAndUnitStd'], help='Normalization method')
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
26 parser.add_argument('-a', '--accuracy', default="20", choices=['1', '2', '5', '10', '15', '20', '30', '36', '45', '60'], help='Accuracy expressed as angular stepsize')
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
27 parser.add_argument('-s', '--stereo', default="No", choices=['No', 'Unique', 'Mirror', 'All'], help='Stereospecificity of the cage')
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
28 parser.add_argument('-r', '--resolution', type=float, default="3.0", help='Resolution')
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
29 return parser.parse_args()
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
30
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
31 def set_parameters(args):
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
32 if args.normalization == 'No':
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
33 spectrophore.SetNormalization( spectrophore.NoNormalization )
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
34 else:
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
35 spectrophore.SetNormalization( eval('spectrophore.NormalizationTowards' + args.normalization) )
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
36 spectrophore.SetAccuracy( eval('spectrophore.AngStepSize' + args.accuracy) )
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
37 spectrophore.SetStereo( eval('spectrophore.' + args.stereo + 'StereoSpecificProbes') )
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
38 spectrophore.SetResolution( args.resolution )
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
39 return True
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
40
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
41 def Compute_Spectrophores_distance(target_spectrophore, args):
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
42 outfile = open(args.output, 'w')
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
43 for mol in open(args.library, 'r'):
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
44 try:
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
45 distance = ( ( np.asarray( target_spectrophore, dtype=float ) - np.asarray( mol.split('\t')[ args.column - 1 ].strip().split(', '), dtype=float) )**2).sum()
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
46 except ValueError:
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
47 distance = 0
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
48 outfile.write( '%s\t%f\n' % (mol.strip(), distance ) )
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
49 outfile.close()
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
50
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
51 def __main__():
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
52 """
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
53 Computation of Spectrophores(TM) distances to a target molecule.
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
54 """
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
55 args = parse_command_line()
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
56 # This sets up the parameters for the Spectrophore generation. Parameters are set to fit those of our standard parsing tool
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
57 set_parameters(args)
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
58
3
a1db432874e5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c376ab981fafb25f0c04a2a313968fa2e55f5196
bgruening
parents: 0
diff changeset
59 mol = next(pybel.readfile('sdf', args.target))
0
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
60 target_spectrophore = mol.data["Spectrophores(TM)"].strip().split(', ')
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
61 # Compute the paired-distance between every molecule in the library and the target
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
62 distances = Compute_Spectrophores_distance(target_spectrophore, args)
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
63
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
64 if __name__ == "__main__" :
7133973beaf0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
bgruening
parents:
diff changeset
65 __main__()