schrodinger.application.transforms.chemio module

class schrodinger.application.transforms.chemio.WriteBatchesOfStructures(file_prefix: Union[str, Path])

Bases: _LocalOnlyPTransform, WriteBatchesOfStructures

A PTransform that writes each element (which is a list of structures) to a separate file with a unique filename. Note that this transform is an identity step that outputs the input PCollection.

class schrodinger.application.transforms.chemio.ReadFileToStructures(input_file: str)

Bases: PTransform

Read Structure objects from a file.

This is a source transform that reads structures from a file.

Example usage in YAML:

pipeline:
  - type: ReadFileToStructures
    config:
      input_file: "ligands.maegz"

Parameters:

input_file – Path to the structure file to read.

__init__(input_file: str)

expand(pbegin: PBegin)

class schrodinger.application.transforms.chemio.WriteStructures(output_file: str)

Bases: PTransform

Write Structure objects to a file.

This is a sink transform that writes structures to a file. It passes through the input structures unchanged for chaining.

Example usage in YAML:

pipeline:
  - type: ReadFileToStructures
    config:
      input_file: "ligands.maegz"
  - type: LigFilter
    config:
      criteria: ["Num_heavy_atoms > 5"]
  - type: WriteStructures
    config:
      output_file: "filtered.maegz"

Parameters:

output_file – Path to the output structure file.

__init__(output_file: str)

expand(pcoll: PCollection[Structure])

class schrodinger.application.transforms.chemio.CreateStructuresFromSmiles(elements: Iterable[str])

Bases: PTransform

Create Structure objects from a list of SMILES strings.

This is a source transform that creates structures from SMILES.

Example usage in YAML:

pipeline:
  - type: CreateStructuresFromSmiles
    config:
      elements:
        - "c1ccccc1"
        - "CCO"

Parameters:

elements – List of SMILES strings to convert to structures.

__init__(elements: Iterable[str])

expand(pbegin: PBegin)

class schrodinger.application.transforms.chemio.StructureToRow(label: Optional[str] = None)

Bases: PTransform

Convert Structure objects to Beam Rows.

This transform wraps each Structure in a Row with a ‘structure’ field, enabling use of Row-based transforms like MapToFields.

Example usage in YAML:

pipeline:
  - type: CreateStructuresFromSmiles
    config:
      elements:
        - "c1ccccc1"
  - type: LigFilter
    config:
      criteria: ["Num_heavy_atoms > 3"]
  - type: StructureToRow
  - type: MapToFields
    config:
      fields:
        title:
          callable: "lambda row: row.structure.title"

expand(pcoll: PCollection[Structure])