chembl-molecule-search

Purpose

Search ChEMBL by free-text query and return compact compound summaries suitable for quick cheminformatics triage.

When to use

• You need a ChEMBL identifier and basic compound summary for a known drug or molecule name.
• You want a lightweight compound lookup before deeper cheminformatics or screening workflows.

When not to use

• You need local descriptor calculation or docking.
• You need bulk export of a large ChEMBL slice.
• You need offline execution.

Inputs

• Query string
• Optional result limit and output path

Outputs

• JSON payload with query metadata and compact molecule summaries

Requirements

• Python 3.10+
• Network access to www.ebi.ac.uk

Procedure

1. Run python3 skills/drug-discovery-and-cheminformatics/chembl-molecule-search/scripts/search_chembl_molecules.py --query imatinib --limit 1 --out skills/drug-discovery-and-cheminformatics/chembl-molecule-search/assets/chembl_imatinib.json.
2. Inspect molecules for chembl_id, preferred_name, molecule_type, max_phase, canonical_smiles, and selected properties.
3. Use the returned ChEMBL IDs in downstream compound-knowledge workflows when needed.

Validation

• Command exits successfully.
• molecules contains at least one ChEMBL result for a known query.
• The first result has a non-empty chembl_id and molecule summary fields.

Failure modes and fixes

• No hits: refine the query or use a more canonical drug name.
• Too many hits: lower --limit and inspect the top results manually.
• HTTP errors: retry later and keep the query simple for smoke verification.

Safety and limits

• Knowledge lookup only.
• This skill does not perform synthesis planning, structure optimization, or wet-lab decision making.

Example

• python3 skills/drug-discovery-and-cheminformatics/chembl-molecule-search/scripts/search_chembl_molecules.py --query imatinib --limit 1

Provenance

• ChEMBL web services docs: https://www.ebi.ac.uk/chembl/api/data/docs
• ChEMBL API base path: https://www.ebi.ac.uk/chembl/api/data/

Related skills

• clinicaltrials-study-search