schrodinger.application.transforms.prepwizard module

class schrodinger.application.transforms.prepwizard.ProteinPrep(settings: schrodinger.application.prepwizard.PrepWizardSettings)

Bases: apache_beam.transforms.ptransform.PTransform

A PTransform that prepares protein structure using PrepWizard.

Example usage:

>>> from schrodinger.seam.io import chemio
>>> from schrodinger.test import mmshare_testfile
>>> SMALL_PEPTIDE_FILE = mmshare_testfile('phosphoThr.mae')
>>> settings = prepwizard.PrepWizardSettings(
... cap_termini=True,
... cap_termini_min_atoms=5,
... run_impref=False)
>>> with beam.Pipeline() as p:
...     _ = (p
...     | chemio.ReadStructuresFromFile(SMALL_PEPTIDE_FILE)
...     | ProteinPrep(settings)
...     | chemio.WriteStructuresToFile('output.mae'))

__init__(settings: schrodinger.application.prepwizard.PrepWizardSettings)

expand(pcoll)