Mercurial > repos > bgruening > openbabel_change_title
comparison ob_spectrophore_search.py @ 16:a638d8d13bb3 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author | bgruening |
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date | Thu, 15 Aug 2024 11:02:57 +0000 |
parents | 2cd8aee0d830 |
children |
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15:01ab890bf0ad | 16:a638d8d13bb3 |
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6 """ | 6 """ |
7 import argparse | 7 import argparse |
8 | 8 |
9 import numpy as np | 9 import numpy as np |
10 from openbabel import openbabel, pybel | 10 from openbabel import openbabel, pybel |
11 | |
11 openbabel.obErrorLog.StopLogging() | 12 openbabel.obErrorLog.StopLogging() |
12 # TODO get rid of eval() | 13 # TODO get rid of eval() |
13 | 14 |
14 global spectrophore | 15 global spectrophore |
15 spectrophore = pybel.ob.OBSpectrophore() | 16 spectrophore = pybel.ob.OBSpectrophore() |
16 | 17 |
17 | 18 |
18 def parse_command_line(): | 19 def parse_command_line(): |
19 parser = argparse.ArgumentParser() | 20 parser = argparse.ArgumentParser() |
20 parser.add_argument('--target', required=True, help='target file name in sdf format with Spectrophores(TM) descriptors stored as meta-data') | 21 parser.add_argument( |
21 parser.add_argument('--library', required=True, help='library of compounds with pre-computed physico-chemical properties, including Spectrophores(TM) in tabular format') | 22 "--target", |
22 parser.add_argument('-c', '--column', required=True, type=int, help='#column containing the Spectrophores(TM) descriptors in the library file') | 23 required=True, |
23 parser.add_argument('-o', '--output', required=True, help='output file name') | 24 help="target file name in sdf format with Spectrophores(TM) descriptors stored as meta-data", |
24 parser.add_argument('-n', '--normalization', default="ZeroMeanAndUnitStd", choices=['No', 'ZeroMean', 'UnitStd', 'ZeroMeanAndUnitStd'], help='Normalization method') | 25 ) |
25 parser.add_argument('-a', '--accuracy', default="20", choices=['1', '2', '5', '10', '15', '20', '30', '36', '45', '60'], help='Accuracy expressed as angular stepsize') | 26 parser.add_argument( |
26 parser.add_argument('-s', '--stereo', default="No", choices=['No', 'Unique', 'Mirror', 'All'], help='Stereospecificity of the cage') | 27 "--library", |
27 parser.add_argument('-r', '--resolution', type=float, default="3.0", help='Resolution') | 28 required=True, |
29 help="library of compounds with pre-computed physico-chemical properties, including Spectrophores(TM) in tabular format", | |
30 ) | |
31 parser.add_argument( | |
32 "-c", | |
33 "--column", | |
34 required=True, | |
35 type=int, | |
36 help="#column containing the Spectrophores(TM) descriptors in the library file", | |
37 ) | |
38 parser.add_argument("-o", "--output", required=True, help="output file name") | |
39 parser.add_argument( | |
40 "-n", | |
41 "--normalization", | |
42 default="ZeroMeanAndUnitStd", | |
43 choices=["No", "ZeroMean", "UnitStd", "ZeroMeanAndUnitStd"], | |
44 help="Normalization method", | |
45 ) | |
46 parser.add_argument( | |
47 "-a", | |
48 "--accuracy", | |
49 default="20", | |
50 choices=["1", "2", "5", "10", "15", "20", "30", "36", "45", "60"], | |
51 help="Accuracy expressed as angular stepsize", | |
52 ) | |
53 parser.add_argument( | |
54 "-s", | |
55 "--stereo", | |
56 default="No", | |
57 choices=["No", "Unique", "Mirror", "All"], | |
58 help="Stereospecificity of the cage", | |
59 ) | |
60 parser.add_argument( | |
61 "-r", "--resolution", type=float, default="3.0", help="Resolution" | |
62 ) | |
28 return parser.parse_args() | 63 return parser.parse_args() |
29 | 64 |
30 | 65 |
31 def set_parameters(args): | 66 def set_parameters(args): |
32 if args.normalization == 'No': | 67 if args.normalization == "No": |
33 spectrophore.SetNormalization(spectrophore.NoNormalization) | 68 spectrophore.SetNormalization(spectrophore.NoNormalization) |
34 else: | 69 else: |
35 spectrophore.SetNormalization(eval('spectrophore.NormalizationTowards' + args.normalization)) | 70 spectrophore.SetNormalization( |
36 spectrophore.SetAccuracy(eval('spectrophore.AngStepSize' + args.accuracy)) | 71 eval("spectrophore.NormalizationTowards" + args.normalization) |
37 spectrophore.SetStereo(eval('spectrophore.' + args.stereo + 'StereoSpecificProbes')) | 72 ) |
73 spectrophore.SetAccuracy(eval("spectrophore.AngStepSize" + args.accuracy)) | |
74 spectrophore.SetStereo(eval("spectrophore." + args.stereo + "StereoSpecificProbes")) | |
38 spectrophore.SetResolution(args.resolution) | 75 spectrophore.SetResolution(args.resolution) |
39 return True | 76 return True |
40 | 77 |
41 | 78 |
42 def Compute_Spectrophores_distance(target_spectrophore, args): | 79 def Compute_Spectrophores_distance(target_spectrophore, args): |
43 outfile = open(args.output, 'w') | 80 outfile = open(args.output, "w") |
44 for mol in open(args.library, 'r'): | 81 for mol in open(args.library, "r"): |
45 try: | 82 try: |
46 distance = ((np.asarray(target_spectrophore, dtype=float) - np.asarray(mol.split('\t')[args.column - 1].strip().split(', '), dtype=float))**2).sum() | 83 distance = ( |
84 ( | |
85 np.asarray(target_spectrophore, dtype=float) | |
86 - np.asarray( | |
87 mol.split("\t")[args.column - 1].strip().split(", "), | |
88 dtype=float, | |
89 ) | |
90 ) | |
91 ** 2 | |
92 ).sum() | |
47 except ValueError: | 93 except ValueError: |
48 distance = 0 | 94 distance = 0 |
49 outfile.write('%s\t%f\n' % (mol.strip(), distance)) | 95 outfile.write("%s\t%f\n" % (mol.strip(), distance)) |
50 outfile.close() | 96 outfile.close() |
51 | 97 |
52 | 98 |
53 def __main__(): | 99 def __main__(): |
54 """ | 100 """ |
55 Computation of Spectrophores(TM) distances to a target molecule. | 101 Computation of Spectrophores(TM) distances to a target molecule. |
56 """ | 102 """ |
57 args = parse_command_line() | 103 args = parse_command_line() |
58 # This sets up the parameters for the Spectrophore generation. Parameters are set to fit those of our standard parsing tool | 104 # This sets up the parameters for the Spectrophore generation. Parameters are set to fit those of our standard parsing tool |
59 set_parameters(args) | 105 set_parameters(args) |
60 | 106 |
61 mol = next(pybel.readfile('sdf', args.target)) | 107 mol = next(pybel.readfile("sdf", args.target)) |
62 target_spectrophore = mol.data["Spectrophores(TM)"].strip().split(', ') | 108 target_spectrophore = mol.data["Spectrophores(TM)"].strip().split(", ") |
63 # Compute the paired-distance between every molecule in the library and the target | 109 # Compute the paired-distance between every molecule in the library and the target |
64 Compute_Spectrophores_distance(target_spectrophore, args) | 110 Compute_Spectrophores_distance(target_spectrophore, args) |
65 | 111 |
66 | 112 |
67 if __name__ == "__main__": | 113 if __name__ == "__main__": |