Mercurial > repos > bgruening > openbabel_remove_protonation_state

comparison ob_remIons.py @ 15:22a866858b81 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf
author bgruening
date Thu, 15 Aug 2024 11:00:20 +0000
parents e376ba0fcde0
children
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14:e376ba0fcde0 15:22a866858b81
6 Copyright 2012, Bjoern Gruening and Xavier Lucas 6 Copyright 2012, Bjoern Gruening and Xavier Lucas
7 """ 7 """
8 import argparse 8 import argparse
9 9
10 from openbabel import openbabel, pybel 10 from openbabel import openbabel, pybel
11
11 openbabel.obErrorLog.StopLogging() 12 openbabel.obErrorLog.StopLogging()
12 13
13 14
14 def parse_command_line(): 15 def parse_command_line():
15 parser = argparse.ArgumentParser() 16 parser = argparse.ArgumentParser()
16 parser.add_argument('-iformat', default='sdf', help='input file format') 17 parser.add_argument("-iformat", default="sdf", help="input file format")
17 parser.add_argument('-i', '--input', required=True, help='input file name') 18 parser.add_argument("-i", "--input", required=True, help="input file name")
18 parser.add_argument('-o', '--output', required=True, help='output file name') 19 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') 20 parser.add_argument(
21 "-idx",
22 default=False,
23 action="store_true",
24 help="should output be an indexed text table? works only for inchi/smiles, otherwise is ignored",
25 )
20 return parser.parse_args() 26 return parser.parse_args()
21 27
22 28
23 def remove_ions(args): 29 def remove_ions(args):
24 with open(args.output, 'w') as outfile: 30 with open(args.output, "w") as outfile:
25 for index, mol in enumerate(pybel.readfile(args.iformat, args.input)): 31 for index, mol in enumerate(pybel.readfile(args.iformat, args.input)):
26 if mol.OBMol.NumHvyAtoms() > 5: 32 if mol.OBMol.NumHvyAtoms() > 5:
27 mol.OBMol.StripSalts(0) 33 mol.OBMol.StripSalts(0)
28 if 'inchi' in mol.data: 34 if "inchi" in mol.data:
29 del mol.data['inchi'] # remove inchi cache so modified mol is saved 35 del mol.data["inchi"] # remove inchi cache so modified mol is saved
30 36
31 mol = mol.write(args.iformat) if mol.OBMol.NumHvyAtoms() > 5 else '\n' 37 mol = mol.write(args.iformat) if mol.OBMol.NumHvyAtoms() > 5 else "\n"
32 38
33 if args.idx and args.iformat in ['inchi', 'smi']: 39 if args.idx and args.iformat in ["inchi", "smi"]:
34 outfile.write(f'{index}\t{mol}') 40 outfile.write(f"{index}\t{mol}")
35 elif mol != '\n': 41 elif mol != "\n":
36 outfile.write(f'{mol}') 42 outfile.write(f"{mol}")
37 43
38 44
39 def __main__(): 45 def __main__():
40 """ 46 """
41 Remove any counterion and delete any fragment but the largest one for each molecule. 47 Remove any counterion and delete any fragment but the largest one for each molecule.
42 """ 48 """
43 args = parse_command_line() 49 args = parse_command_line()
44 remove_ions(args) 50 remove_ions(args)
45 51
46 52