rdkit

name	rdkit
description	RDKit cheminformatics via VenusFactory bioinfo scripts and agent_generated_code. Use for SMILES/SDF, descriptors, fingerprints, substructure filters, similarity. Do NOT use for ChEMBL bioactivity download (chembl_database) or openFDA (fda). No dedicated rdkit_* LangChain tool — run scripts or import modules.
license	BSD-3-Clause
metadata	{"version":"1.2","skill-author":"VenusFactory2"}

RDKit Cheminformatics

Overview

Fine-grained molecular control in Python. Platform helpers live under src/tools/bioinfo/rdkit/ (CLI + importable functions). Prefer them over re-implementing RDKit from scratch.

VenusFactory execution

• No rdkit_* @tool in the hub — use agent_generated_code (or python_repl) and import the modules below.
• Extended tutorials: read_skill("rdkit", relative_path="references/legacy_guide.md").
• Bioactivity from ChEMBL first → chembl_database, then RDKit for chemistry ops.

Project scripts (src/tools/bioinfo/rdkit/)

Script	Purpose
molecular_properties.py	MW, LogP, TPSA, Lipinski, QED → CSV
substructure_filter.py	SMARTS/SMILES include/exclude filters
similarity_search.py	Morgan/RDKit/MACCS fingerprints + Tanimoto

from src.tools.bioinfo.rdkit import calculate_properties, filter_molecules, similarity_search
# loaders: substructure_filter.load_molecules / similarity_search.load_molecules

python -m src.tools.bioinfo.rdkit.molecular_properties "CCO"
python -m src.tools.bioinfo.rdkit.similarity_search "CCO" database.smi --threshold 0.7 -o hits.csv

When NOT to use

• Download ChEMBL molecules/activities → chembl_database
• Simple FDA label search → fda / query_fda

Common mistakes

• Importing load_molecules from package root (use module-specific loaders)
• Assuming a LangChain tool named rdkit_* exists
• Sanitization failures on dirty SMILES — handle None mols

References

• references/api_reference.md, descriptors_reference.md, smarts_patterns.md
• references/legacy_guide.md — full capability cookbook