RDKit compound triage: drug-likeness, PAINS and Brenk

    1

    Validate and standardize SMILES, compute Lipinski/Veber/QED, flag PAINS and Brenk alerts, and get a pass/review/fail verdict per compound.

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    RDKit compound triage: drug-likeness, PAINS and Brenk

    Example session with this skill installed

    Triage the compounds in hits.csv and tell me which are worth following up.

    • Read your context and instructions
    • Compiled the rdkit compound triage
    • Generated the data export

    Script summary: Triaged 5 compounds: 2 pass, 1 review, 1 fail, 1 invalid SMILES.

    idverdictMWcLogPQEDalerts
    benzylidene_rhodaninefail221.32.180.58PAINS:ene_rhod_A; Brenk:Michael_acceptor_1; Brenk:Thiocarbonyl_group
    aspirinreview180.21.310.55Brenk:phenol_ester
    caffeinepass194.2-1.030.54none
    imatinibpass493.64.590.39none
    bad_entryinvalidSMILES did not parse

    Alerts explained

    ene_rhod_A (PAINS): 5-benzylidene rhodanine, a Michael acceptor and frequent assay-interference chemotype. This alone fails it.

    phenol_ester (Brenk): a labile aryl ester. For aspirin that hydrolysis is the mechanism, so it is flagged for review, not rejected.

    Worth following up: caffeine and imatinib (no alerts, no Ro5 violations). Fix or re-check the bad_entry SMILES.

    Full table: triage.csv

    triage.csv

    CSV · data export

    Generated

    Example file from a real run - the skill writes it into your workspace.

    Connects securely to your tools. The creator never sees your data.

    About this skill

    Give your agent a SMILES list or a CSV of hits and get a med-chem triage report back.

    What it does

    • Standardize: RDKit cleanup, salt stripping and neutralization. Invalid SMILES are reported, not silently dropped.
    • Properties: MW, cLogP, HBD/HBA, TPSA, rotatable bonds, QED.
    • Rules: Lipinski Ro5 violations and Veber criteria.
    • Alerts: PAINS (assay interference) and Brenk (unwanted or reactive groups).
    • Verdict: pass / review / fail per compound, plus a full CSV.

    Why it's trustworthy

    Every number comes from a bundled, self-tested RDKit script (scripts/triage.py --selftest); the model never improvises a descriptor. The agent then explains each alert in medicinal-chemistry terms and reminds you that alerts are prompts for a chemist, not automatic rejections.

    Requirements

    uv. RDKit installs automatically on first run. Accepts CSV, .smi/.txt or a single SMILES string.

    How to use

    Skills on Agensi run inside your AI agent. Copy the prompt, paste it into your agent, and it connects to Agensi and installs this skill for you. If a payment is needed, your agent shows it to you first.

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    Astral
    Python

    Listed6 days ago

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