Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add ma-compbio-lab/SkillFoundry --skill chembl-molecule-searchgit clone --depth 1 https://github.com/ma-compbio-lab/SkillFoundryWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/chembl-molecule-search)<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/chembl-molecule-search"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/chembl-molecule-search/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/chembl-molecule-search"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/chembl-molecule-search.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00037 | $0.00541 |
| Opus 5 | $0.00018 | $0.00270 |
| Sonnet 5 | $0.00007 | $0.00108 |
| Haiku 4.5 | $0.00004 | $0.00054 |
Grade A, and why
chembl-molecule-search scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 57 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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
- 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. - Inspect
moleculesforchembl_id,preferred_name,molecule_type,max_phase,canonical_smiles, and selected properties. - Use the returned ChEMBL IDs in downstream compound-knowledge workflows when needed.
Validation
- Command exits successfully.
moleculescontains at least one ChEMBL result for a known query.- The first result has a non-empty
chembl_idand molecule summary fields.
Failure modes and fixes
- No hits: refine the query or use a more canonical drug name.
- Too many hits: lower
--limitand 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/
What ships with it
9 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 57 lines · 37 tokens per session scan A 6544fd8a2ab0
chembl-molecule-search is a skill published in the GitHub repository ma-compbio-lab/SkillFoundry (38 stars, last pushed 4mo ago), licensed Apache-2.0. It adds 37 tokens to every session and 541 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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