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Check the Compound Engineering environment and repository settings, identify configuration issues, and report optional tools. Confirm where generated documents will be stored, make approved configuration fixes, or scaffold a Compound Pack with pack:<id>.
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Carry a request through the appropriate Compound Engineering skills with minimal intervention. For code changes, the workflow covers planning, implementation, review, browser testing, and an open pull request with automated check results assessed.
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Screen compound collections for drug discovery using established drug-likeness rules, structural warnings, and molecular complexity measures. Detect relevant chemical groups, apply property limits, and generate filtering results to support compound selection and prioritization.
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Make compound growth actually click — see how small, consistent amounts become large over time, and why starting now beats starting bigger later. Use when asked explain compound interest, how does compounding work, is it worth investing small amounts, or why should I start now. Produces an intuitive explanation of compounding with concrete illustrative examples for your situation, the outsized effect of time (why an early start beats a later larger one), how fees and inflation eat into it, and the honest caveats — turning an abstract concept into the motivation to start now. Educational, not financial advice.
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Write a compounding worksheet and record that reproduces the preparation exactly and survives inspection — formula, calculations shown, components with lot numbers, in-process checks, and the beyond-use date with its basis. Use when asked to document a compounded preparation, write a master formulation record, create a compounding worksheet, or prepare compounding documentation for inspection. Produces the master formula, the batch record, the component and lot table, in-process checks, labelling, and the beyond-use-date rationale. Documentation only; standards and stability data must come from current official references.
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Dereplicate a putative natural product and assign its chemical taxonomy. Use to answer "is [compound] a known natural product", "what microbe/organism produces [compound]", "what chemical class is [compound]", "dereplicate this metabolite (by formula/exact mass/InChIKey/SMILES)", or "classify this molecule into ChemOnt". Searches NPAtlas for known microbial natural products (producing organism + literature reference), assigns the ChemOnt kingdom→superclass→class→subclass hierarchy via ClassyFire, resolves systematic IUPAC names to structure via OPSIN, and cross-references identity in PubChem. NOT for general drug/compound identity or ADMET (use tooluniverse-chemical-compound-retrieval / tooluniverse-small-molecule-discovery) and NOT for metabolomics pathway/enrichment analysis (use tooluniverse-metabolomics skills).
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Run molecular property predictions, explore molecular shapes, and estimate how compounds bind to proteins through a cloud Python API. Process compound batches and connect modeling steps without maintaining local high-performance computing infrastructure.
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Screen compound libraries for drug discovery using drug-likeness guidelines, structural alerts that flag patterns for review, and molecular complexity measures. Combine criteria to shortlist candidates and retain filtering results with reasons for further assessment.
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Retrieve focused information from PubChem, including molecular formulas, molecular weights, compound descriptions, assay summaries, and substance metadata. Get concise Markdown summaries, with the option to save the full response for further use.
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Turn a recently solved research problem into searchable Markdown documentation. Capture symptoms, failed attempts, root causes, working code, and prevention checks, then organize the solution by category and link it to related records.
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Process and compare mass spectra, measurements used to study chemical compounds, with matchms. Clean peak data, standardize metadata, calculate similarity scores, and search reference libraries for candidate compounds in metabolomics research.
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Query Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization, m/z precursor searches, and gene/protein annotations. Quirks: compound input_item rejects `name` (use pubchem_cid/kegg_id/inchi_key/etc.); free-text → compound is a two-step refmet/match→refmet/name flow; moverz endpoint returns TSV text, not JSON. Use hmdb-database for local XML; pubchem-compound-search for general compound lookup.
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Weekly review partner that compounds productivity gains over time. Use when: (1) "weekly review", "what did I accomplish this week?", "compound my gains", (2) End of work week to review progress, (3) "what patterns are emerging?", (4) "update the system map", (5) Feeling stuck and need to identify friction. Reads all system/ files to synthesize progress. Outputs to system/compounder/week-{date}.md. Feeds insights back to /audit.
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Document a solved and verified problem when its reasoning is missing from code, tests, and existing documentation. Save one durable lesson in the repository so future agents can find it and avoid repeating substantial investigation.
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Evaluate partners and opportunities by asking whether trust, knowledge, and reputation can build over ten years. This skill provides questions for weighing quick returns against lasting cooperation in which everyone benefits.
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Search chemical substances by name or ChEBI ID, retrieve compound details and structure metadata, and explore parent–child relationships in chemical classifications. Results are presented as concise summaries, with raw JSON available on request.
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Screen an existing compound library against a protein target with Boltz. Rank candidates by binding confidence or lead optimization score, download predicted structures, and review solubility, permeability, and lipophilicity results alongside the ranked hits.
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Search ChEMBL for compounds by name, chemical structure, or properties. Retrieve biological activity measurements, target information, and drug mechanisms to investigate inhibitors and compare how structural differences relate to measured activity.
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Generates complete single-compound network-toxicology research designs from one exposure, one disease or toxic phenotype, and a validation direction. Use when a study centers on one compound–one disease link and needs target collection, overlap construction, enrichment, PPI hub prioritization, docking, optional transcriptomic cross-check, and conservative mechanistic synthesis. Covers five study patterns and always outputs Lite / Standard / Advanced / Publication+ with a recommended primary plan, stepwise workflow, figure plan, validation hierarchy, minimal executable version, publication upgrade path, and strictly verified literature retrieval.
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Use when evaluating stocks through Dan Bin's long-term compounder lens: buy great companies, hold through volatility, and let time do the work. Focus on consumer, pharma, and tech compounders.
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This skill should be used when the user says "/compound", "compound this", "document learnings", "save what we learned", or after completing a PR. Extracts knowledge from PR context and saves to docs/learnings/.
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Compound fields (Name, Address, Geolocation): SOQL access rules, DML semantics, component access in Apex/LWC, reporting column behavior, formula field restrictions. NOT for creating a new custom field — use admin/custom-field-creation. NOT for formula syntax and functions — use admin/formula-fields. Trigger keywords: BillingAddress, MailingAddress, ShippingAddress, StateCode, CountryCode, GeocodeAccuracy, Location field type, displayLocationInDecimal, __Latitude__s, __Longitude__s, DISTANCE, GEOLOCATION, Custom Address Fields, AddressSettings, System.Address, System.Location, Person Account name.
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Weekly review partner that compounds productivity gains over time. Tracks velocity, logs friction, sets next-week targets, recognizes patterns across weeks, and feeds insights back to the audit for the next loop. Use when you want a weekly review, need to identify friction, want to see patterns, or want to update your system map. Part of the architect-system loop. Outputs to system/compounder/week-{date}.md.
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Make your AI agent learn and improve automatically. Reviews sessions, extracts learnings, updates memory files, and compounds knowledge over time. Set up nightly review loops that make your agent smarter every day.
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