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SEDenmarkLab / molli_firstgen

In silico library generation tool box
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obabel on windows #22

Open caseyolen opened 2 years ago

caseyolen commented 2 years ago

called optimize on windows system. did not produce stdout or stderr and gave code 1. worked fine on wsl.

blakeo2 commented 2 years ago 
def uff_optimize_chemdraw(chemdraw_file: str, concurrent=4):
    """This will convert chemdraw to xml file to a collection and optimize all collection contents with UFF. DO NOT CONFUSE THIS WITH OPTIMIZE COMBINATORIAL COLLECTION, AS THIS FUNCTION REQUIRES A CHEMDRAW FILE INPUT"""

    file_no_cdxml = chemdraw_file.replace('.cdxml','')

    collection = ml.parsing.split_cdxml(chemdraw_file)

    obabel = ml.OpenBabelDriver("ob", scratch_dir='.')
    # collection.to_zip('admix.zip')
    # #Change the backup directory at some point please
    # collection = ml.Collection.from_zip('admix.zip')
    _preoptimized = ml.Concurrent(collection, backup_dir=".", concurrent=concurrent, update=5)(obabel.hadd_opt)(ff='UFF')

    pprint(_preoptimized)
    uff_optimized = ml.Collection(f'{collection}', _preoptimized)

    uff_optimized.to_zip(f'uff_opt_{file_no_cdxml}.zip')