annotate structure_pipeline.py @ 9:a446ea7e2bc1 draft default tip

"planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 7ca965e469cce3951d22c854dc7b6cb2a3a4f9f6"

import argparse

from chembl_structure_pipeline import checker, standardizer


def load_mols(input_file):
    """
    Returns a list of strings, each a molblock
    """
    with open(input_file) as f:
        mols = [''.join(('\n', mol.strip())) for mol in f.read().strip().split('$$$$\n')]
    return mols


def write_mols(mols, output_file):
    """
    Writes a list of molblocks to an SDF
    """
    with open(output_file, 'w') as f:
        f.write('\n$$$$'.join(mols))


def standardize_molblock(mol):
    return standardizer.standardize_molblock(mol)


def get_parent_molblock(mol):
    return standardizer.get_parent_molblock(mol)[0]


def check_molblock(mol):
    issues = checker.check_molblock(mol)
    max_penalty_score = str(max([issue[0] for issue in issues])) if issues else '0'
    message = '; '.join([issue[1] for issue in issues])
    mol_with_issues = '\n'.join((mol, '> <MaxPenaltyScore>', max_penalty_score, '> <IssueMessages>', message))
    return mol_with_issues


def main():
    parser = argparse.ArgumentParser(description='Search ChEMBL database for compounds')
    parser.add_argument('-i', '--input', help='SDF/MOL input')
    parser.add_argument('-o', '--output', help="Standardized output")
    parser.add_argument('--standardize', action='store_true', help="Standardize molblock")
    parser.add_argument('--get_parent', action='store_true', help="Get parent molblock.")
    parser.add_argument('--check', action='store_true', help="Check molblock")
    args = parser.parse_args()

    mols = load_mols(args.input)
    if args.standardize:
        mols = [standardize_molblock(mol) for mol in mols]
    if args.get_parent:
        mols = [get_parent_molblock(mol) for mol in mols]
    if args.check:
        mols = [check_molblock(mol) for mol in mols]
    write_mols(mols, args.output)


if __name__ == "__main__":
    main()