Mercurial > repos > bgruening > openbabel_remduplicates
comparison ob_remIons.py @ 14:b2569e22b40c draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 327c29cc43f56d7067ab9fa51323ea31951db98b"
author | bgruening |
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date | Tue, 10 Nov 2020 20:30:47 +0000 |
parents | 12aca74f07d7 |
children | c5de6c19eb06 |
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13:12aca74f07d7 | 14:b2569e22b40c |
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1 #!/usr/bin/env python | 1 #!/usr/bin/env python |
2 | |
2 """ | 3 """ |
3 Input: molecular input file. | 4 Input: molecular input file. |
4 Output: Molecule file with removed ions and fragments. | 5 Output: Molecule file with removed ions and fragments. |
5 Copyright 2012, Bjoern Gruening and Xavier Lucas | 6 Copyright 2012, Bjoern Gruening and Xavier Lucas |
6 """ | 7 """ |
13 def parse_command_line(): | 14 def parse_command_line(): |
14 parser = argparse.ArgumentParser() | 15 parser = argparse.ArgumentParser() |
15 parser.add_argument('-iformat', default='sdf', help='input file format') | 16 parser.add_argument('-iformat', default='sdf', help='input file format') |
16 parser.add_argument('-i', '--input', required=True, help='input file name') | 17 parser.add_argument('-i', '--input', required=True, help='input file name') |
17 parser.add_argument('-o', '--output', required=True, help='output file name') | 18 parser.add_argument('-o', '--output', required=True, help='output file name') |
19 parser.add_argument('-idx', default=False, action='store_true', help='should output be an indexed text table? works only for inchi/smiles, otherwise is ignored') | |
18 return parser.parse_args() | 20 return parser.parse_args() |
19 | 21 |
20 | 22 |
21 def remove_ions(args): | 23 def remove_ions(args): |
22 outfile = pybel.Outputfile(args.iformat, args.output, overwrite=True) | 24 with open(args.output, 'w') as outfile: |
23 for mol in pybel.readfile(args.iformat, args.input): | 25 for index, mol in enumerate(pybel.readfile(args.iformat, args.input)): |
24 if mol.OBMol.NumHvyAtoms() > 5: | |
25 mol.OBMol.StripSalts(0) | |
26 if 'inchi' in mol.data: | |
27 del mol.data['inchi'] # remove inchi cache so modified mol is saved | |
28 # Check if new small fragments have been created and remove them | |
29 if mol.OBMol.NumHvyAtoms() > 5: | 26 if mol.OBMol.NumHvyAtoms() > 5: |
30 outfile.write(mol) | 27 mol.OBMol.StripSalts(0) |
31 outfile.close() | 28 if 'inchi' in mol.data: |
29 del mol.data['inchi'] # remove inchi cache so modified mol is saved | |
30 | |
31 mol = mol.write(args.iformat) if mol.OBMol.NumHvyAtoms() > 5 else '\n' | |
32 | |
33 if args.idx and args.iformat in ['inchi', 'smi']: | |
34 outfile.write(f'{index}\t{mol}') | |
35 elif mol != '\n': | |
36 outfile.write(f'{mol}') | |
32 | 37 |
33 | 38 |
34 def __main__(): | 39 def __main__(): |
35 """ | 40 """ |
36 Remove any counterion and delete any fragment but the largest one for each molecule. | 41 Remove any counterion and delete any fragment but the largest one for each molecule. |