schrodinger.application.transforms.debug module

Apache Beam transforms for debugging and utility operations in YAML pipelines.

class schrodinger.application.transforms.debug.PrettyPrint(expand: bool = False)

Bases: PTransform

Pretty-print Beam Rows as JSON strings.

The expand configuration option controls the formatting:

• If expand is True, the JSON output is printed with indentation across multiple lines.

• If expand is False (default), the JSON output is compact and printed on a single line.

Example usage in YAML:

pipeline:
  - type: ReadFileToStructures
    config:
      input_file: "ligands.maegz"
  - type: StructureToRow
  - type: PrettyPrint
    config:
      expand: true

Parameters:

expand – Whether to pretty-print with indentation.

__init__(expand: bool = False)

class schrodinger.application.transforms.debug.ExtractFieldFromRow(field_name: str)

Bases: PTransform

Extract a field from Row objects, yielding the field value.

This is useful when a transform expects a specific type (like Structure) but the pipeline uses Row objects. Extract the field before the transform, then optionally wrap it back in a Row after.

Example usage in YAML:

pipeline:
  - type: ReadFromPDB
    config:
      pdb_codes:
        - "1A2B"
  - type: StructureToRow
  - type: ExtractFieldFromRow
    config:
      field_name: "structure"

This would transform Row(structure=Structure(...), other=value) into just the Structure object.

Parameters:

field_name – The name of the Row field to extract.

__init__(field_name: str)

class schrodinger.application.transforms.debug.WrapInRow(field_name: str)

Bases: PTransform

Wrap values in a Row with a specified field name.

This is useful when a transform returns bare values (like Structure) but the pipeline expects Row objects. Wrap the values in a Row so subsequent transforms can access them via the field name.

Example usage in YAML:

pipeline:
  - type: CreateMolsFromSmiles
    config:
      elements:
        - "c1ccccc1"
  - type: WrapInRow
    config:
      field_name: "mol"

This would transform a bare Mol into Row(mol=Mol(...)).

Parameters:

field_name – The name of the Row field to create.

__init__(field_name: str)