schrodinger.seam.yaml.decorators module

class schrodinger.seam.yaml.decorators.SchemadStructureWrapper(ptransform_instance, input_field='structure', output_field='structure')

Bases: PTransform

Wrapper PTransform for applying non-Schemad PTransforms to Structure objects present in Beam Rows. Expects each input Row to have a structure field and yields a new Row with the same fields, with structure field containing the modified Structure object.

Example usage:

>>> from schrodinger import adapter
>>> from schrodinger.application.transforms import filters
>>> key = 'i_user_value'
>>> structs = [adapter.to_structure(smiles) for smiles in ['C'] * 5]
>>> for idx, st in enumerate(structs, start=0):
...     st.property[key] = idx
>>> rows = [beam.Row(test_str='test', test_int=1, structure=st) for st in structs]
>>> with beam.Pipeline() as p:
...     filtered = (p
...     | beam.Create(rows)
...     | SchemadStructureWrapper(filters.StructurePropertyFilter({key: [-5, 2]}))
...     | beam.Map(lambda row: row.structure.property[key]))

ROW_METADATA_FIELD = 's_seam_row_metadata'

__init__(ptransform_instance, input_field='structure', output_field='structure')

expand(pcoll: PCollection)