| name | chembl_database |
| description | ChEMBL bioactive molecules and drugs via VenusFactory download tools. Use for molecule/drug by ID, similarity/substructure by SMILES, SAR starting points. Do NOT use for openFDA regulatory data (fda) or RDKit-only local chemistry (rdkit). |
| license | Unknown |
| metadata | {"version":"1.2","skill-author":"VenusFactory2"} |
ChEMBL Database
Project Tools (VenusFactory2)
| Tool | Key args | Purpose |
|---|
| download_chembl_molecule_by_id | mol_id, out_path | Molecule record |
| download_chembl_drug_by_id | chembl_id / drug id, out_path | Drug record |
| download_chembl_similarity_by_smiles | smiles, threshold, out_path | Similarity neighbors |
| download_chembl_substructure_by_smiles | smiles, out_path | Substructure hits |
Returns rich JSON with file_info. Output path arg is out_path (not out_dir). Follow with rdkit for descriptors/filters if needed.
Workflow
- Resolve ChEMBL ID or start from SMILES.
- Download → parse JSON/TSV on disk.
- Optional RDKit property filter / figure of activity distributions.
When NOT to use
- FDA labels / adverse events →
fda
- Pure local fingerprinting without ChEMBL →
rdkit
References (progressive disclosure)
Trust order: SKILL.md (hub tools & envelopes) → topic refs → references/legacy_guide.md (archived; may be outdated).
read_skill(skill_id="chembl_database", relative_path="references/legacy_guide.md")
Load legacy only after the hub workflow in this file is insufficient.
