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comparison ob_genProp.py @ 13:bd678d7db2ae draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
author bgruening
date Mon, 19 Oct 2020 14:39:41 +0000
parents 171c94786a56
children 9adf3fae2771
comparison
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12:171c94786a56 13:bd678d7db2ae
2 """ 2 """
3 Input: Molecular input file. 3 Input: Molecular input file.
4 Output: Physico-chemical properties are computed and stored as metadata in the sdf output file. 4 Output: Physico-chemical properties are computed and stored as metadata in the sdf output file.
5 Copyright 2012, Bjoern Gruening and Xavier Lucas 5 Copyright 2012, Bjoern Gruening and Xavier Lucas
6 """ 6 """
7 import sys, os
8 import argparse 7 import argparse
8 import sys
9
10 import cheminfolib
9 import openbabel 11 import openbabel
12 from openbabel import pybel
10 openbabel.obErrorLog.StopLogging() 13 openbabel.obErrorLog.StopLogging()
11 import cheminfolib
12 14
13 from openbabel import pybel
14 15
15 def parse_command_line(argv): 16 def parse_command_line(argv):
16 parser = argparse.ArgumentParser() 17 parser = argparse.ArgumentParser()
17 parser.add_argument('--iformat', default='sdf' , help='input file format') 18 parser.add_argument('--iformat', default='sdf', help='input file format')
18 parser.add_argument('-i', '--input', required=True, help='input file name') 19 parser.add_argument('-i', '--input', required=True, help='input file name')
19 parser.add_argument('--oformat', default='sdf', choices = ['sdf', 'table'] , help='output file format') 20 parser.add_argument('--oformat', default='sdf', choices=['sdf', 'table'], help='output file format')
20 parser.add_argument('--header', type=bool, help='Include the header as the first line of the output table') 21 parser.add_argument('--header', type=bool, help='Include the header as the first line of the output table')
21 parser.add_argument('-o', '--output', required=True, help='output file name') 22 parser.add_argument('-o', '--output', required=True, help='output file name')
22 return parser.parse_args() 23 return parser.parse_args()
24
23 25
24 def compute_properties(args): 26 def compute_properties(args):
25 if args.oformat == 'sdf': 27 if args.oformat == 'sdf':
26 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) 28 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
27 else: 29 else:
28 outfile = open(args.output, 'w') 30 outfile = open(args.output, 'w')
29 if args.header: 31 if args.header:
30 mol = next(pybel.readfile(args.iformat, args.input)) 32 mol = next(pybel.readfile(args.iformat, args.input))
31 metadata = cheminfolib.get_properties_ext(mol) 33 metadata = cheminfolib.get_properties_ext(mol)
32 outfile.write( '%s\n' % '\t'.join( [ cheminfolib.ColumnNames[key] for key in metadata ] ) ) 34 outfile.write('%s\n' % '\t'.join([cheminfolib.ColumnNames[key] for key in metadata]))
33 35
34 for mol in pybel.readfile(args.iformat, args.input): 36 for mol in pybel.readfile(args.iformat, args.input):
35 if mol.OBMol.NumHvyAtoms() > 5: 37 if mol.OBMol.NumHvyAtoms() > 5:
36 metadata = cheminfolib.get_properties_ext(mol) 38 metadata = cheminfolib.get_properties_ext(mol)
37 if args.oformat == 'sdf': 39 if args.oformat == 'sdf':
38 [ mol.data.update( { cheminfolib.ColumnNames[key] : metadata[key] } ) for key in metadata ] 40 [mol.data.update({cheminfolib.ColumnNames[key]: metadata[key]}) for key in metadata]
39 outfile.write(mol) 41 outfile.write(mol)
40 else: 42 else:
41 outfile.write( '%s\n' % ('\t'.join( [ str(metadata[key]) for key in metadata ] ) ) ) 43 outfile.write('%s\n' % ('\t'.join([str(metadata[key]) for key in metadata])))
42 outfile.close() 44 outfile.close()
45
43 46
44 def __main__(): 47 def __main__():
45 """ 48 """
46 Physico-chemical properties are computed and stored as metadata in the sdf output file 49 Physico-chemical properties are computed and stored as metadata in the sdf output file
47 """ 50 """
48 args = parse_command_line(sys.argv) 51 args = parse_command_line(sys.argv)
49 compute_properties(args) 52 compute_properties(args)
50 53
51 if __name__ == "__main__" : 54
55 if __name__ == "__main__":
52 __main__() 56 __main__()