schrodinger.application.transforms.ligprep module¶
- class schrodinger.application.transforms.ligprep.LigandPrep(arg_string: str = '', filter_string: str = '')¶
Bases:
apache_beam.transforms.ptransform.PTransform
A PTransform that ligpreps molecules.
Example usage:
>>> benzene = Chem.MolFromSmiles('c1ccccc1') >>> with beam.Pipeline() as p: ... ligprepped_benzene = (p ... | beam.Create([benzene]) ... | LigandPrep() ... | beam.Map(lambda mol: Chem.MolToSmiles(mol)) ... | beam.LogElements()) c1ccccc1
NOTE:: If the input is a Mol PCollection, the Mol will first be converted to a Structure and then ligprep will be run on the Structure. The output will be a Mol PCollection. If any structures fail to convert to Mols, they will be dropped from the output.
- Parameters
arg_string – command line arguments to pass to ligprep, e.g. ‘-nt’, or ‘-nt -bff 16 -epik -s 32’.
filter_string – a filter string to pass to ligprep.
Note: the filter_string is a single string, so if multiple filters are needed they need to be separated by “n”.
- __init__(arg_string: str = '', filter_string: str = '')¶
- expand(pcoll: apache_beam.pvalue.PCollection[schrodinger.application.transforms.ligprep.T])¶
- classmethod FromFile(path: Union[str, pathlib.Path], *, arg_string: str)¶
- Parameters
path – the path to the ligprep filter file.
arg_string – the command line arguments to pass to ligprep excluding the input and output arguments.