schrodinger.application.transforms.prime module

Transforms to run Prime calculations

Example:

>>> from schrodinger.test import mmshare_data_file
>>> from schrodinger.seam.io.chemio import ReadStructuresFromFile
>>> from schrodinger.seam.io.chemio import WriteStructuresToFile
>>> settings = PrimeSettings({})
>>> with beam.Pipeline() as p:
...     _ = (p
...     | ReadStructuresFromFile(mmshare_data_file('cookbook/stereoisomers-form-1.maegz'))
...     | Prime.Refine(RefinmentType.ENERGY, settings)
...     | WriteStructuresFromFile('output.maegz'))

class schrodinger.application.transforms.prime.PrimeSettings(input_config: dict[str, str])

Bases: object

Settings necessary for running a Prime calculation.

Variables:

input_config – A dictionary containing backend options for Prime in key-value pairs.

input_config: dict[str, str]

validate()

__init__(input_config: dict[str, str]) → None

class schrodinger.application.transforms.prime.JobType

Bases: StrEnum

REFINE = 'REFINE'

MODEL = 'MODEL'

class schrodinger.application.transforms.prime.RefineType

Bases: StrEnum

SIDE_PRED = 'SIDE_PRED'

SIDE_COMBI = 'SIDE_COMBI'

LOOP_BLD = 'LOOP_BLD'

EXTENDED = 'EXTENDED'

LONG_LOOP_2 = 'LONG_LOOP_2'

LOOP_PAIR = 'LOOP_PAIR'

HELIX_BLD = 'HELIX_BLD'

REAL_MIN = 'REAL_MIN'

SITE_OPT = 'SITE_OPT'

ENERGY = 'ENERGY'

class schrodinger.application.transforms.prime.Prime(settings: PrimeSettings)

Bases: PTransform

Run a Prime calculation on a structure.

static Refine(refinement_type: RefineType, settings: PrimeSettings) → Prime

Run a Prime Refinement calculation on a structure.

static Model(settings: PrimeSettings) → Prime

Run a Prime Homology Modeling calculation on a structure.

__init__(settings: PrimeSettings)