comparison ob_filter.py @ 11:e4ece69f1b32 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit cda909c5e0b88fa3d12abe43fc72b8dd0729417a"

10:c427987b54fd

def filter_precalculated_compounds(args, filters):
    outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
    for mol in pybel.readfile('sdf', args.input):
        for key, elem in filters.items():
            # map the short description to the larger metadata names stored in the sdf file
            property = cheminfolib.ColumnNames[key]
            min = elem[0]
            max = elem[1]
            if float(mol.data[property]) >= float(min) and float(mol.data[property]) <= float(max):
                pass
            else:

    filters = json.loads((args.filters).replace(' ', '').replace(',}', '}'))
    if args.iformat == 'sdf':
        # Check if the sdf file contains all of the required metadata to invoke the precalculation filtering
        mol = next(pybel.readfile('sdf', args.input))
        for key, elem in filters.items():
            property = cheminfolib.ColumnNames[key]
            if not property in mol.data:
                break
        else:
            # if the for loop finishes in a normal way, we should habe all properties at least in the first molecule
            # assume it is the same for all other molecules and start the precalculated filtering

11:e4ece69f1b32

def filter_precalculated_compounds(args, filters):
    outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
    for mol in pybel.readfile('sdf', args.input):
        for key, elem in filters.items():
            # map the short description to the larger metadata names stored in the sdf file
            property = cheminfolib.ColumnNames.get(key, key)
            min = elem[0]
            max = elem[1]
            if float(mol.data[property]) >= float(min) and float(mol.data[property]) <= float(max):
                pass
            else:

    filters = json.loads((args.filters).replace(' ', '').replace(',}', '}'))
    if args.iformat == 'sdf':
        # Check if the sdf file contains all of the required metadata to invoke the precalculation filtering
        mol = next(pybel.readfile('sdf', args.input))
        for key, elem in filters.items():
            property = cheminfolib.ColumnNames.get(key, key)
            if not property in mol.data:
                break
        else:
            # if the for loop finishes in a normal way, we should habe all properties at least in the first molecule
            # assume it is the same for all other molecules and start the precalculated filtering