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MolForge Python API

← Back to README · Documentation index

The public API is:

Method Description
MolForge(params) Construct a pipeline from a ForgeParams object, dict, or config file
forge(input_data, ...) Forge a single input (ChEMBL ID, CSV path, or DataFrame) into a DataFrame
forge_to_csv(input_data, output_path, ...) Forge a single input and write the result to a CSV
batch_forge(input_list, output_dir) Forge multiple inputs, writing one CSV per input

Pipeline behavior and per-actor parameters are configured through ForgeParams — see Pipeline Configuration and the per-actor pages linked from it.

Quick Start

from molforge import MolForge, ForgeParams

# Configure pipeline
params = ForgeParams(
    steps=['source', 'chembl', 'curate'],
    source_params={'backend': 'sql'},
    chembl_params={'standard_type': 'IC50', 'standard_units': 'nM'},
    curate_params={'mol_steps': ['desalt', 'neutralize', 'sanitize']}
)

# Run pipeline
forge = MolForge(params)
df = forge.forge("CHEMBL234")

Complete Pipeline Example

from molforge import MolForge, ForgeParams

params = ForgeParams(
    steps=['source', 'chembl', 'curate', 'tokens', 'distributions', 'confs'],

    # Data retrieval
    source_params={'backend': 'sql', 'version': 36},

    # ChEMBL curation
    chembl_params={
        'standard_type': 'IC50',
        'standard_units': 'nM',
        'assay_type': 'B',
        'assay_format': 'protein'
    },

    # Molecule standardization
    curate_params={
        'mol_steps': ['desalt', 'neutralize', 'sanitize', 'handleStereo'],
        'stereo_policy': 'assign',
        'dropna': True
    },

    # Tokenization
    tokens_params={'dynamically_update_vocab': True},

    # Property filtering
    distributions_params={'global_statistical_threshold': 2.0, 'plot_distributions': True},

    # Conformer generation
    confs_params={'backend': 'rdkit', 'max_confs': 200, 'rms_threshold': 0.5}
)

forge = MolForge(params)
df = forge.forge("CHEMBL234")
print(f"Processed {len(df)} molecules")

Loading from a Config File

MolForge can be constructed directly from a YAML or JSON configuration file via the config_path argument, instead of passing a ForgeParams object. Additional keyword arguments override individual config values.

from molforge import MolForge

# From a config file
forge = MolForge(config_path="pipeline_config.yaml")
df = forge.forge("CHEMBL2971")

The same config files are used by the CLI (molforge run --config ...). See the example run for a complete config file (demo/jak2_ic50.yaml).

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