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annotate ob_spectrophore_search.py @ 14:4e3b2049a4d3 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"
author bgruening
date Tue, 10 Nov 2020 20:32:05 +0000
parents 3153b6f3087c
children f70b83b730ac
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1 #!/usr/bin/env python
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2 """
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3 Input: tabular format file with one column storing the unique id for the compounds and any other with the Spectrophores(TM) descriptors.
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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.
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5 Copyright 2012, Bjoern Gruening and Xavier Lucas
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6 """
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7 import argparse
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8
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9 import numpy as np
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10 from openbabel import openbabel, pybel
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11 openbabel.obErrorLog.StopLogging()
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12 # TODO get rid of eval()
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14 global spectrophore
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15 spectrophore = pybel.ob.OBSpectrophore()
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18 def parse_command_line():
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19 parser = argparse.ArgumentParser()
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20 parser.add_argument('--target', required=True, help='target file name in sdf format with Spectrophores(TM) descriptors stored as meta-data')
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21 parser.add_argument('--library', required=True, help='library of compounds with pre-computed physico-chemical properties, including Spectrophores(TM) in tabular format')
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22 parser.add_argument('-c', '--column', required=True, type=int, help='#column containing the Spectrophores(TM) descriptors in the library file')
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23 parser.add_argument('-o', '--output', required=True, help='output file name')
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24 parser.add_argument('-n', '--normalization', default="ZeroMeanAndUnitStd", choices=['No', 'ZeroMean', 'UnitStd', 'ZeroMeanAndUnitStd'], help='Normalization method')
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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')
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26 parser.add_argument('-s', '--stereo', default="No", choices=['No', 'Unique', 'Mirror', 'All'], help='Stereospecificity of the cage')
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27 parser.add_argument('-r', '--resolution', type=float, default="3.0", help='Resolution')
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28 return parser.parse_args()
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31 def set_parameters(args):
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32 if args.normalization == 'No':
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33 spectrophore.SetNormalization(spectrophore.NoNormalization)
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34 else:
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35 spectrophore.SetNormalization(eval('spectrophore.NormalizationTowards' + args.normalization))
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36 spectrophore.SetAccuracy(eval('spectrophore.AngStepSize' + args.accuracy))
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37 spectrophore.SetStereo(eval('spectrophore.' + args.stereo + 'StereoSpecificProbes'))
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38 spectrophore.SetResolution(args.resolution)
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39 return True
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42 def Compute_Spectrophores_distance(target_spectrophore, args):
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43 outfile = open(args.output, 'w')
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44 for mol in open(args.library, 'r'):
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45 try:
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46 distance = ((np.asarray(target_spectrophore, dtype=float) - np.asarray(mol.split('\t')[args.column - 1].strip().split(', '), dtype=float))**2).sum()
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47 except ValueError:
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48 distance = 0
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49 outfile.write('%s\t%f\n' % (mol.strip(), distance))
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50 outfile.close()
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53 def __main__():
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54 """
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55 Computation of Spectrophores(TM) distances to a target molecule.
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56 """
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57 args = parse_command_line()
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58 # This sets up the parameters for the Spectrophore generation. Parameters are set to fit those of our standard parsing tool
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59 set_parameters(args)
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61 mol = next(pybel.readfile('sdf', args.target))
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62 target_spectrophore = mol.data["Spectrophores(TM)"].strip().split(', ')
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63 # Compute the paired-distance between every molecule in the library and the target
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64 Compute_Spectrophores_distance(target_spectrophore, args)
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65
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67 if __name__ == "__main__":
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68 __main__()