rdkit-fp

Parallel RDKit fingerprints with a beginner one-liner and an advanced staged pipeline.

Install

pip install rdfp

Quickstart (10 seconds)

rdfp examples/chembl_1k.smi outputs/fps/

With explicit preset:

rdfp examples/chembl_1k.smi outputs/fps/ --preset ecfp4

This default command is equivalent to rdfp fps INPUT OUTPUT.

Common CLI usage

Simple run with explicit workers/chunk size:

rdfp examples/chembl_1k.smi outputs/fps/ --workers -1 --chunk 100000

Use IDs from a column and keep stable row mapping sidecars:

rdfp data/compounds.smi outputs/fps/ --smiles-col 0 --id-col 1

Resume a stopped large run:

rdfp data/compounds.smi outputs/fps/ --resume

Run built-in demo data:

rdfp demo

Presets

You can override preset values with explicit flags (--fp-type, --fp-size, --radius, --include-chirality).

Advanced lane

Stage 1 only (SMILES -> mols):

rdfp mols examples/chembl_1k.smi outputs/mols/

Stage 2 only (mols -> fingerprints):

rdfp fps-from-mols outputs/mols/ outputs/fps_from_mols/ --resume

Both stages with mol persistence:

rdfp fps examples/chembl_1k.smi outputs/fps/ --save-mols outputs/mols/

Helpful flags

• --workers (alias of --n-jobs)
• --chunk (alias of --chunk-size)
• --preset ecfp4|ecfp6|rdkit|ap|tt|pattern
• --input-smiles-col (alias of --smiles-col)
• --id-col N include IDs in .index.json sidecars
• --resume skip existing chunk outputs
• --no-include-row-mapping disable row/ID mapping sidecars and mapping metadata
• --format numpy|packed|pickle (pickle default)

Python API

from pathlib import Path
import rdfp

smiles_path = Path("examples/chembl_1k.smi")
rdfp.smiles_to_fps_chunked(
    rdfp.iter_smiles_records(smiles_path),
    output_dir="outputs/fps_api/",
    fp_type="morgan",
    fp_size=2048,
    radius=2,
    fmt="pickle",
    n_jobs=-1,
    chunk_size=100_000,
    include_row_mapping=True,
    resume=True,
)

Output layout

pickle output (default):

outputs/fps/
  fps_0000.pkl
  fps_0000.index.json   <- row_idx / id / valid per input row in chunk
  fps_0001.pkl
  fps_0001.index.json
  metadata.json

Each chunk stores only valid fingerprints in fps; mapping metadata + sidecars preserve provenance and failed rows.

Compatibility and packaging

• Repo name stays rdkit-fp.
• Install/import/CLI are centered on rdfp.
• rdkit_fp remains as a compatibility alias for existing code.

Release flow

• CI runs on pushes/PRs to main.
• PyPI publish runs from tags matching v* (for example v0.1.1).