| 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
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.mdreferences/legacy_guide.md — full capability cookbook
