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MOLRAPTOR

SMILES-first fingerprinting

MOLRAPTOR

Scientific library and command-line tool for generating reproducible binary molecular fingerprints from user-provided molecular representations.

Install API Reference Changelog
CI PyPI Python versions License: LGPL v3+

Pre-stable

MOLRAPTOR is currently in alpha-stage development. Public APIs may change before 1.0.

Workflow

Input Python / CSV / TXT user-provided SMILES
Parse RDKit molecular graph construction
Encode Fingerprint selected binary bit vectors
Trace Status + hashes alignment and provenance
Output NumPy / CSV / JSON reproducible artifacts
01

Supply

Provide ordered SMILES directly through Python or from a CSV or UTF-8 TXT file.

02

Encode

Generate the selected binary molecular fingerprint using a serializable effective profile.

03

Trace

Preserve input order and duplicates while recording validity, matrix-row alignment, hashes, and runtime versions.

04

Export

Write fingerprint matrices, per-input statuses, and encoding metadata for downstream scientific workflows.

Scope

MOLRAPTOR does MOLRAPTOR does not
Accept user-provided SMILES through Python, CSV, or TXT. Retrieve molecular records from PubChem or other databases.
Parse SMILES with RDKit for fingerprint calculation. Curate, harmonize, canonicalize, or replace supplied SMILES.
Generate supported binary molecular fingerprints. Generate labels or activity classes.
Record profiles, hashes, versions, and row alignment. Select or recommend a scientifically preferred fingerprint.
Preserve input order and duplicates. Train or evaluate machine-learning models.
Isolate invalid individual inputs. Calculate molecular descriptors or 3D conformations.

Quick Example

python -m pip install molraptor

molraptor run \
  --input molecules.csv \
  --smiles-column SMILES \
  --fingerprint maccs \
  --output-dir artifacts

from molraptor import MorganFingerprintProfile, encode_fingerprints

profile = MorganFingerprintProfile(radius=2, fp_size=2048)

result = encode_fingerprints(
    ["CCO", "not-a-smiles", "c1ccccc1"],
    profile,
)

print(result.fingerprints.shape)
# (2, 2048)

Morgan is the default fingerprint and supports configurable settings. Other fingerprint types use their fixed effective profiles.

The in-memory API, file workflow, and command-line interface use the same scientific encoding core.

Documentation

Page Purpose
Usage Installation, CLI, CSV/TXT inputs, Python workflows, outputs, and failure handling.
API Reference Current public Python contracts and examples.
Changelog Project history sourced from the repository changelog.

Citation

Contreras-Torres, F. F. (2026). MOLRAPTOR: Molecular Fingerprint Rapid Generator. Zenodo. https://doi.org/10.5281/zenodo.20434420

License

This project is licensed under the terms of the GNU Lesser General Public License v3.0 or later. SPDX identifier: LGPL-3.0-or-later.