chembl-database

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

1. Resolve ChEMBL ID or start from SMILES.
2. Download → parse JSON/TSV on disk.
3. 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Trust order: SKILL.md (hub tools & envelopes) → topic refs → references/legacy_guide.md (archived; may be outdated).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.