evo-molecule-similarity

Description

Find top-k similar chemicals from a PDF molecule pool using Morgan fingerprints with Tanimoto similarity. Converts chemical names to SMILES via PubChemPy, computes Morgan fingerprints (radius=2, chirality=True), and ranks by Tanimoto similarity with alphabetical tie-breaking.

Key Concepts

• PDF Extraction: Uses pdfplumber to extract chemical names (one per line)
• Name-to-SMILES: Uses PubChemPy (external resource, no manual mapping)
• Morgan Fingerprints: radius=2, useChirality=True, default 2048 bits
• Tanimoto Similarity: Standard similarity metric for molecular fingerprints
• Sorting: Descending by similarity, alphabetical for ties

Dependencies

• pdfplumber (PDF text extraction)
• pubchempy (chemical name to SMILES conversion)
• rdkit (fingerprints and similarity)

Usage

import sys
sys.path.insert(0, '/app/environment/skills/evo-molecule-similarity/scripts')
from utils import (
    topk_tanimoto_similarity_molecules,
    extract_molecule_names,
    name_to_smiles,
    smiles_to_fingerprint,
    compute_tanimoto_similarity
)

# Main function - find top k similar molecules
results = topk_tanimoto_similarity_molecules(
    target_molecule_name='Aspirin',
    molecule_pool_filepath='/root/molecules.pdf',
    top_k=5
)
print(results)
# ['Acetylsalicylic acid', 'Aspirin', 'Methyl 2-acetoxybenzoate', ...]

Function Reference

topk_tanimoto_similarity_molecules(target_molecule_name, molecule_pool_filepath, top_k) -> list

Main entry point. Returns list of top-k molecule names sorted by descending Tanimoto similarity, alphabetical for ties.

extract_molecule_names(filepath) -> list

Extract chemical names from PDF file (one per line).

name_to_smiles(name) -> str or None

Convert chemical name to canonical SMILES via PubChemPy.

smiles_to_fingerprint(smiles) -> fingerprint or None

Convert SMILES to Morgan fingerprint (radius=2, chirality=True).

compute_tanimoto_similarity(fp1, fp2) -> float

Compute Tanimoto similarity between two fingerprints.

Notes

• Aspirin and Acetylsalicylic acid are the same molecule (same SMILES)
• The target molecule is NOT excluded from results if it appears in the pool
• Molecules that cannot be resolved via PubChemPy are silently skipped
• PubChemPy requires internet access