comparison ob_genProp.py @ 16:a638d8d13bb3 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf

15:01ab890bf0ad

import sys

import cheminfolib
import openbabel
from openbabel import pybel
openbabel.obErrorLog.StopLogging()


def parse_command_line(argv):
    parser = argparse.ArgumentParser()
    parser.add_argument('--iformat', default='sdf', help='input file format')
    parser.add_argument('-i', '--input', required=True, help='input file name')
    parser.add_argument('--oformat', default='sdf', choices=['sdf', 'table'], help='output file format')
    parser.add_argument('--header', type=bool, help='Include the header as the first line of the output table')
    parser.add_argument('-o', '--output', required=True, help='output file name')
    return parser.parse_args()


def compute_properties(args):
    if args.oformat == 'sdf':
        outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
    else:
        outfile = open(args.output, 'w')
        if args.header:
            mol = next(pybel.readfile(args.iformat, args.input))
            metadata = cheminfolib.get_properties_ext(mol)
            outfile.write('%s\n' % '\t'.join([cheminfolib.ColumnNames[key] for key in metadata]))

    for mol in pybel.readfile(args.iformat, args.input):
        if mol.OBMol.NumHvyAtoms() > 5:
            metadata = cheminfolib.get_properties_ext(mol)
            if args.oformat == 'sdf':
                [mol.data.update({cheminfolib.ColumnNames[key]: metadata[key]}) for key in metadata]
                outfile.write(mol)
            else:
                outfile.write('%s\n' % ('\t'.join([str(metadata[key]) for key in metadata])))
    outfile.close()


def __main__():
    """
        Physico-chemical properties are computed and stored as metadata in the sdf output file
    """
    args = parse_command_line(sys.argv)
    compute_properties(args)

16:a638d8d13bb3

import sys

import cheminfolib
import openbabel
from openbabel import pybel

openbabel.obErrorLog.StopLogging()


def parse_command_line(argv):
    parser = argparse.ArgumentParser()
    parser.add_argument("--iformat", default="sdf", help="input file format")
    parser.add_argument("-i", "--input", required=True, help="input file name")
    parser.add_argument(
        "--oformat", default="sdf", choices=["sdf", "table"], help="output file format"
    )
    parser.add_argument(
        "--header",
        type=bool,
        help="Include the header as the first line of the output table",
    )
    parser.add_argument("-o", "--output", required=True, help="output file name")
    return parser.parse_args()


def compute_properties(args):
    if args.oformat == "sdf":
        outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
    else:
        outfile = open(args.output, "w")
        if args.header:
            mol = next(pybel.readfile(args.iformat, args.input))
            metadata = cheminfolib.get_properties_ext(mol)
            outfile.write(
                "%s\n" % "\t".join([cheminfolib.ColumnNames[key] for key in metadata])
            )

    for mol in pybel.readfile(args.iformat, args.input):
        if mol.OBMol.NumHvyAtoms() > 5:
            metadata = cheminfolib.get_properties_ext(mol)
            if args.oformat == "sdf":
                [
                    mol.data.update({cheminfolib.ColumnNames[key]: metadata[key]})
                    for key in metadata
                ]
                outfile.write(mol)
            else:
                outfile.write(
                    "%s\n" % ("\t".join([str(metadata[key]) for key in metadata]))
                )
    outfile.close()


def __main__():
    """
    Physico-chemical properties are computed and stored as metadata in the sdf output file
    """
    args = parse_command_line(sys.argv)
    compute_properties(args)