Mercurial > repos > bgruening > openbabel_change_title
diff 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 |
---|---|
date | Thu, 15 Aug 2024 11:02:57 +0000 |
parents | 2cd8aee0d830 |
children |
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--- a/ob_spectrophore_search.py Tue Nov 10 20:30:04 2020 +0000 +++ b/ob_spectrophore_search.py Thu Aug 15 11:02:57 2024 +0000 @@ -8,6 +8,7 @@ import numpy as np from openbabel import openbabel, pybel + openbabel.obErrorLog.StopLogging() # TODO get rid of eval() @@ -17,49 +18,94 @@ def parse_command_line(): parser = argparse.ArgumentParser() - parser.add_argument('--target', required=True, help='target file name in sdf format with Spectrophores(TM) descriptors stored as meta-data') - parser.add_argument('--library', required=True, help='library of compounds with pre-computed physico-chemical properties, including Spectrophores(TM) in tabular format') - parser.add_argument('-c', '--column', required=True, type=int, help='#column containing the Spectrophores(TM) descriptors in the library file') - parser.add_argument('-o', '--output', required=True, help='output file name') - parser.add_argument('-n', '--normalization', default="ZeroMeanAndUnitStd", choices=['No', 'ZeroMean', 'UnitStd', 'ZeroMeanAndUnitStd'], help='Normalization method') - parser.add_argument('-a', '--accuracy', default="20", choices=['1', '2', '5', '10', '15', '20', '30', '36', '45', '60'], help='Accuracy expressed as angular stepsize') - parser.add_argument('-s', '--stereo', default="No", choices=['No', 'Unique', 'Mirror', 'All'], help='Stereospecificity of the cage') - parser.add_argument('-r', '--resolution', type=float, default="3.0", help='Resolution') + parser.add_argument( + "--target", + required=True, + help="target file name in sdf format with Spectrophores(TM) descriptors stored as meta-data", + ) + parser.add_argument( + "--library", + required=True, + help="library of compounds with pre-computed physico-chemical properties, including Spectrophores(TM) in tabular format", + ) + parser.add_argument( + "-c", + "--column", + required=True, + type=int, + help="#column containing the Spectrophores(TM) descriptors in the library file", + ) + parser.add_argument("-o", "--output", required=True, help="output file name") + parser.add_argument( + "-n", + "--normalization", + default="ZeroMeanAndUnitStd", + choices=["No", "ZeroMean", "UnitStd", "ZeroMeanAndUnitStd"], + help="Normalization method", + ) + parser.add_argument( + "-a", + "--accuracy", + default="20", + choices=["1", "2", "5", "10", "15", "20", "30", "36", "45", "60"], + help="Accuracy expressed as angular stepsize", + ) + parser.add_argument( + "-s", + "--stereo", + default="No", + choices=["No", "Unique", "Mirror", "All"], + help="Stereospecificity of the cage", + ) + parser.add_argument( + "-r", "--resolution", type=float, default="3.0", help="Resolution" + ) return parser.parse_args() def set_parameters(args): - if args.normalization == 'No': + if args.normalization == "No": spectrophore.SetNormalization(spectrophore.NoNormalization) else: - spectrophore.SetNormalization(eval('spectrophore.NormalizationTowards' + args.normalization)) - spectrophore.SetAccuracy(eval('spectrophore.AngStepSize' + args.accuracy)) - spectrophore.SetStereo(eval('spectrophore.' + args.stereo + 'StereoSpecificProbes')) + spectrophore.SetNormalization( + eval("spectrophore.NormalizationTowards" + args.normalization) + ) + spectrophore.SetAccuracy(eval("spectrophore.AngStepSize" + args.accuracy)) + spectrophore.SetStereo(eval("spectrophore." + args.stereo + "StereoSpecificProbes")) spectrophore.SetResolution(args.resolution) return True def Compute_Spectrophores_distance(target_spectrophore, args): - outfile = open(args.output, 'w') - for mol in open(args.library, 'r'): + outfile = open(args.output, "w") + for mol in open(args.library, "r"): try: - distance = ((np.asarray(target_spectrophore, dtype=float) - np.asarray(mol.split('\t')[args.column - 1].strip().split(', '), dtype=float))**2).sum() + distance = ( + ( + np.asarray(target_spectrophore, dtype=float) + - np.asarray( + mol.split("\t")[args.column - 1].strip().split(", "), + dtype=float, + ) + ) + ** 2 + ).sum() except ValueError: distance = 0 - outfile.write('%s\t%f\n' % (mol.strip(), distance)) + outfile.write("%s\t%f\n" % (mol.strip(), distance)) outfile.close() def __main__(): """ - Computation of Spectrophores(TM) distances to a target molecule. + Computation of Spectrophores(TM) distances to a target molecule. """ args = parse_command_line() # This sets up the parameters for the Spectrophore generation. Parameters are set to fit those of our standard parsing tool set_parameters(args) - mol = next(pybel.readfile('sdf', args.target)) - target_spectrophore = mol.data["Spectrophores(TM)"].strip().split(', ') + mol = next(pybel.readfile("sdf", args.target)) + target_spectrophore = mol.data["Spectrophores(TM)"].strip().split(", ") # Compute the paired-distance between every molecule in the library and the target Compute_Spectrophores_distance(target_spectrophore, args)