schrodinger.application.transforms.qikprop module

class schrodinger.application.transforms.qikprop.QikPropResult(*, source_id: SourceID, structure: Structure)

Bases: BaseModel

Result of running QikProp on a single input structure.

Parameters:

  • source_id – Source ID of the input structure.

  • output_structure – Structure with QikProp properties attached.

source_id: SourceID
structure: Structure
model_config: ClassVar[ConfigDict] = {'arbitrary_types_allowed': True, 'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

class schrodinger.application.transforms.qikprop.QikPropConfig(*, fast: bool = False, neutralize: bool = True, altclass: bool = False, altprobe: Optional[float] = None, recap: bool = False, nofailout: bool = False, legacy_arg_string: str | None = None, error_handling: ErrorHandling | None = None)

Bases: BaseModel

Configuration for QikProp transforms.

Use named fields directly (preferred for new code):

config = QikPropConfig(fast=True, neutralize=False)
Parameters:

  • fast – Run in fast mode (no dipole, HOMO, or LUMO).

  • neutralize – Neutralize molecules before processing.

  • altclass – Use alternative SASA/PSA class definition.

  • altprobe – Alternative probe radius for SASA (must be positive).

  • recap – CombiGlide preprocessing (replace functional group with methyl).

  • nofailout – Do not write failed structures to output.

  • legacy_arg_string – Legacy CLI args (mutually exclusive with other fields).

  • error_handling – Optional error handling configuration.

fast: bool
neutralize: bool
altclass: bool
altprobe: Optional[float]
recap: bool
nofailout: bool
legacy_arg_string: str | None
error_handling: ErrorHandling | None
model_config: ClassVar[ConfigDict] = {'frozen': True}

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

classmethod parseLegacyArgString(data: Any) → Any

Parse legacy_arg_string into explicit config fields.

toArgList() → list[str]

Convert config fields to a CLI argument list for the qikprop binary.

Returns:

List of CLI arguments.

class schrodinger.application.transforms.qikprop.RunQikPropDoFn(config: QikPropConfig)

Bases: _GetLicenseHintsMixin, RunQikPropDoFn

A DoFn that runs QikProp on a batch of structures via subprocess.

When used with OutcomeParDo, structures that fail yield DroppedRecord that is automatically routed to the dropped output.

Parameters:

config – An instance of QikPropConfig.

class schrodinger.application.transforms.qikprop.RunQikProp(**kwargs)

Bases: PTransformWithConfig

A PTransform that runs QikProp on structures and yields QikPropResult objects.

Returns an OutcomePCollections with:

  • main: PCollection[QikPropResult] containing structures with QikProp properties

See QikPropConfig for all available configuration options.

config_class

alias of QikPropConfig

class schrodinger.application.transforms.qikprop.ComputeQikPropProperties(**kwargs)

Bases: PTransformWithConfig

A PTransform that computes QikProp ADME properties on structures.

Returns an OutcomePCollections with:

  • main: PCollection[Structure] of structures with QikProp properties

Example usage:

>>> with beam.Pipeline() as p:
...     result = (p
...         | beam.Create([st])
...         | ComputeQikPropProperties(fast=True))
...     structures_with_props = result.main

See QikPropConfig for all available configuration options.

config_class

alias of QikPropConfig

schrodinger.application.transforms.qikprop.QikProp

alias of ComputeQikPropProperties