schrodinger.application.transforms.ligprep module¶

class schrodinger.application.transforms.ligprep.LigandPrep(arg_string: str, filter_string: apache_beam.pvalue.PCollection[str])¶

Bases: apache_beam.typehints.decorators.WithTypeHints, apache_beam.transforms.display.HasDisplayData, Generic[apache_beam.transforms.ptransform.InputT, apache_beam.transforms.ptransform.OutputT]

A PTransform that returns ligand prepped molecules.

To be used with Mol or Structure PCollections.

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.

__init__(arg_string: str, filter_string: apache_beam.pvalue.PCollection[str])¶

Parameters

arg_string – the command line arguments to pass to ligprep excluding the input and output arguments.
filter_string – the filter string which will be written to a temporary file and passed to ligprep.

Note: the filter_string is a single string, so if multiple filters are needed they need to be separated by “n”.

expand(pcoll: apache_beam.pvalue.PCollection[schrodinger.application.transforms.ligprep.T])¶

annotations() → Dict[str, Union[bytes, str, google.protobuf.message.Message]]¶

default_label() → str¶

default_type_hints()¶

display_data() → dict¶

Returns the display data associated to a pipeline component.

It should be reimplemented in pipeline components that wish to have static display data.

Returns:

Dict[str, Any]: A dictionary containing key:value pairs. The value might be an integer, float or string value; a DisplayDataItem for values that have more data (e.g. short value, label, url); or a HasDisplayData instance that has more display data that should be picked up. For example:

{
  'key1': 'string_value',
  'key2': 1234,
  'key3': 3.14159265,
  'key4': DisplayDataItem('apache.org', url='http://apache.org'),
  'key5': subComponent
}

classmethod from_runner_api(proto: Optional[beam_runner_api_pb2.PTransform], context: PipelineContext) → Optional[PTransform]¶

get_resource_hints() → Dict[str, bytes]¶

get_type_hints()¶

Gets and/or initializes type hints for this object.

If type hints have not been set, attempts to initialize type hints in this order: - Using self.default_type_hints(). - Using self.__class__ type hints.

get_windowing(inputs: Any) → Windowing¶

Returns the window function to be associated with transform’s output.

By default most transforms just return the windowing function associated with the input PCollection (or the first input if several).

infer_output_type(unused_input_type)¶

property label¶

pipeline: Optional[Pipeline] = None¶

classmethod register_urn(urn, parameter_type, constructor=None)¶

runner_api_requires_keyed_input()¶

side_inputs: Sequence[pvalue.AsSideInput] = ()¶

to_runner_api(context: PipelineContext, has_parts: bool = False, **extra_kwargs: Any) → beam_runner_api_pb2.FunctionSpec¶

to_runner_api_parameter(unused_context: PipelineContext) → Tuple[str, Optional[Union[message.Message, bytes, str]]]¶

to_runner_api_pickled(unused_context: PipelineContext) → Tuple[str, bytes]¶

type_check_inputs(pvalueish)¶

type_check_inputs_or_outputs(pvalueish, input_or_output)¶

type_check_outputs(pvalueish)¶

with_input_types(input_type_hint)¶

Annotates the input type of a PTransform with a type-hint.

Args:

input_type_hint (type): An instance of an allowed built-in type, a custom: class, or an instance of a TypeConstraint.

Raises:

TypeError: If input_type_hint is not a valid type-hint.: See apache_beam.typehints.typehints.validate_composite_type_param() for further details.

Returns:

PTransform: A reference to the instance of this particular PTransform object. This allows chaining type-hinting related methods.

with_output_types(type_hint)¶

Annotates the output type of a PTransform with a type-hint.

Args:

type_hint (type): An instance of an allowed built-in type, a custom class,: or a TypeConstraint.

Raises:

TypeError: If type_hint is not a valid type-hint. See: validate_composite_type_param() for further details.

Returns:

PTransform: A reference to the instance of this particular PTransform object. This allows chaining type-hinting related methods.

with_resource_hints(**kwargs) → apache_beam.transforms.ptransform.PTransform¶

Adds resource hints to the PTransform.

Resource hints allow users to express constraints on the environment where the transform should be executed. Interpretation of the resource hints is defined by Beam Runners. Runners may ignore the unsupported hints.

Args:

**kwargs: key-value pairs describing hints and their values.

Raises:

ValueError: if provided hints are unknown to the SDK. See: apache_beam.transforms.resources for a list of known hints.

Returns:

PTransform: A reference to the instance of this particular PTransform object.