API Reference

This section contains detailed documentation for all functions, classes, and modules in ord_rxn_converter.

Main Functions

Core Modules

Dataset Processing

ord_rxn_converter.dataset_module.extract_dataset(filepath, compounds=Empty DataFrame Columns: [] Index: [], persons=Empty DataFrame Columns: [] Index: [])[source]

Extracts all structured data from an ORD dataset file and organizes it into a dictionary of DataFrames.

This function loads a dataset from a .pb or .pbtxt file (compressed or uncompressed), then extracts and organizes its reactions and associated metadata into tabular form. Each component of the reaction—identifiers, inputs, conditions, setup, workups, outcomes, and more—is parsed into a separate pandas.DataFrame.

If compound or person tables are provided, they will be updated to include any new compounds or people found during extraction.

Parameters:

  • filepath (str) – Path to the input file (either zipped or unzipped Google Protobuf format).

  • compounds (pd.DataFrame, optional) – Existing compound table to update or append to. Defaults to an empty DataFrame.

  • persons (pd.DataFrame, optional) – Existing person table to update or append to. Defaults to an empty DataFrame.

Returns:

A dictionary containing the following keys, each mapping to a pandas.DataFrame:

  • ”dataset_metadata”: Dataset-level metadata.

  • ”reaction_metadata”: Reaction-level metadata including provenance and contributor info.

  • ”reaction_identifiers”: SMILES, InChI, and other identifiers for each reaction.

  • ”input_components”: Details of each input component (compound, amount, role, etc.).

  • ”input_addition”: Temporal details for the addition of inputs.

  • ”reaction_setup”: Setup information including vessels and automation.

  • ”reaction_conditions”: Environmental and operational reaction conditions.

  • ”reaction_notes”: Observations and experimental notes.

  • ”reaction_workups”: Post-reaction processing steps.

  • ”reaction_outcomes”: Products and analyses of reaction outcomes.

  • ”compound”: A table of all compounds involved across reactions.

  • ”person”: A table of contributors extracted from provenance.

Return type:

dict

Raises:

  • FileNotFoundError – If the filepath does not exist.

  • ValueError – If the Protobuf file is invalid or does not conform to dataset_pb2.Dataset.

Example

>>> from ord_rxn_converter.dataset_module import extract_dataset
>>> out = extract_dataset("example_dataset.pb")
>>> out["reaction_metadata"].head()

Reaction Components

Utilities