Mercurial > repos > bgruening > openbabel_remions

comparison ob_filter.py @ 2:bf3b0107c0f4 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 78ac0521d7df684e96c1b9c1ba2a17b02e681608
author bgruening
date Sat, 20 May 2017 20:03:56 -0400
parents c9bee3591df9
children 34fb5da28776
comparison
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1:09cd63251df5 2:bf3b0107c0f4
93 # To keep it readable in the xml file, many white-spaces are included in that string it needs to be removed. 93 # To keep it readable in the xml file, many white-spaces are included in that string it needs to be removed.
94 # Also the last loop creates a ',{' that is not an valid jason expression. 94 # Also the last loop creates a ',{' that is not an valid jason expression.
95 filters = json.loads((args.filters).replace(' ', '').replace(',}', '}')) 95 filters = json.loads((args.filters).replace(' ', '').replace(',}', '}'))
96 if args.iformat == 'sdf': 96 if args.iformat == 'sdf':
97 # Check if the sdf file contains all of the required metadata to invoke the precalculation filtering 97 # Check if the sdf file contains all of the required metadata to invoke the precalculation filtering
98 mol = pybel.readfile('sdf', args.input).next() 98 mol = next(pybel.readfile('sdf', args.input))
99 for key, elem in filters.items(): 99 for key, elem in filters.items():
100 property = cheminfolib.ColumnNames[key] 100 property = cheminfolib.ColumnNames[key]
101 if not property in mol.data: 101 if not property in mol.data:
102 break 102 break
103 else: 103 else: