similarity_search

Perform fingerprint-based similarity screening against a database of molecules. Supports multiple fingerprint types and similarity metrics.

Skills
Scientific
0

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

Install the skill (command above).
In Claude Code, describe what you need - the skill turns on by itself when the context fits.
No commands to memorize: you talk in plain language and the skill does the rest.

Install (Claude Code)

mkdir -p .claude/skills/similarity-search && curl -fsSL https://doutorai.pt/data/lib/skills__similarity-search.md -o .claude/skills/similarity-search/SKILL.md

Paste this command into the terminal, in your project folder, and the component installs automatically.

Content

#!/usr/bin/env python3
"""
Molecular Similarity Search

Perform fingerprint-based similarity screening against a database of molecules.
Supports multiple fingerprint types and similarity metrics.

Usage:
    python similarity_search.py "CCO" database.smi --threshold 0.7
    python similarity_search.py query.smi database.sdf --method morgan --output hits.csv
"""

import argparse
import sys
from pathlib import Path

try:
    from rdkit import Chem
    from rdkit.Chem import AllChem, MACCSkeys
    from rdkit import DataStructs
except ImportError:
    print("Error: RDKit not installed. Install wit

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