Quick Start¶

The fastest way to try MOLRAPTOR is with the bundled example configuration.

Install¶

git clone https://github.com/NanoBiostructuresRG/molraptor.git
cd molraptor
python -m pip install -e .

Prepare Your Input¶

MOLRAPTOR expects a CSV file with at least a PubChem CID and Label column:

PubChem CID,Label
2244,1
3672,0
5090,1

Edit examples/example_config.yaml to point to your input file and configure the output paths and fingerprint parameters.

Run the Pipeline¶

molraptor run --config examples/example_config.yaml

With verbose logging:

molraptor run --config examples/example_config.yaml --verbose

Run from Python¶

from molraptor import MolraptorConfig, run

config = MolraptorConfig.load("examples/example_config.yaml")
run(config)

Expected Workflow¶

CSV (CIDs + labels) -> fetch -> curate -> fingerprint -> validate -> .npy / .csv

Output Artifacts¶

After a successful run, the following files are written to artifacts/:

artifacts/
├── morgan_fp.csv          # Morgan fingerprints (human-readable)
├── morgan_db_*.npy        # Morgan fingerprints (NumPy array)
├── labels.npy             # Target labels (NumPy array)
└── summary.txt            # Execution report