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evo-molecule-similarity

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tasks-evolved/find-topk-similiar-chemicals/environment/skills/evo-molecule-similarity/SKILL.md

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Last checked: Nov 6, 2026

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Repository stars (not skill ratings): 97
Repository last updated: Sep 10, 2026
License: Apache-2.0

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# 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