Small example function for permutating stereochemistry in SMILES strings

permuteSMILESStereo.py

import re
import itertools
import pybel


def permuteSMILESStereo(smile):
    stereo = re.search(r"(\[[^\]]+@+[^\]]*\]|[/\\])", smile)
    if stereo:
        left = smile[:stereo.start()]
        rights = permuteSMILESStereo(smile[stereo.end():])
        if stereo.group() in ['/', '\\']:
            mids = ['/', "\\"]
        else:
            mids = [re.sub('@+', st, stereo.group()) for st in ['@', '@@']]
        lefts = [''.join([left, mid]) for mid in mids]
        return [''.join(i) for i in itertools.product(lefts, rights)]
    else:
        return [smile]


if __name__ == '__main__':
    print('\n'.join([''.join(set([
        pybel.readstring("smi", ps).write("can")
        for ps in permuteSMILESStereo(s)
    ])) for s in ["CC(=O)/C=C/O", "CC[C@](B)(O)C"]]))