view @ 5:8b5c8f51074e draft

planemo upload for repository commit 81bccfe3545098dc46a377102816e7fae642c95f
author bgruening
date Wed, 03 Jan 2018 13:12:34 -0500
parents ada6daa717d2
children 43167f164076
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#!/usr/bin/env python
    Input: Molecular input file.
    Output: Physico-chemical properties are computed and stored as metadata in the sdf output file.
    Copyright 2012, Bjoern Gruening and Xavier Lucas
import sys, os
import argparse
import openbabel
import pybel
import cheminfolib

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)
        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':
                [ { cheminfolib.ColumnNames[key] : metadata[key] } ) for key in metadata ]
                outfile.write( '%s\n' % ('\t'.join( [ str(metadata[key]) for key in metadata ] ) ) )

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

if __name__ == "__main__" :