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Design new small-molecule binders with Boltz. Use when generating novel ligands or hits for a target without a fixed compound library. Not for screening existing molecules or one-off docking.
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インストールを決める前に、SKILL.md と SkillsMP に表示されている付属ファイルをお読みください。
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
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npx skills add https://github.com/openai/plugins --skill boltz-small-molecule-designコマンドは1行のまま表示されます。コピー前に横へスクロールして全体を確認してください。
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Use this skill when implementing a Figma design as code (design → code) — the read-FROM-Figma direction. Triggers: 'implement this Figma design', 'build this screen from Figma', 'turn this Figma into code', 'code this up from Figma', 'design to code', or a figma.com design URL provided alongside a codebase. Encodes the workflow for reading a node out of Figma with get_design_context and adapting its reference output to the target project — reusing existing components, tokens, and conventions, and honoring Code Connect mappings, component docs, design annotations, and design tokens by priority. Complements figma-code-connect (component mapping) and figma-generate-design / figma-use (the reverse, code → design direction).
Build or update a professional-grade design system in Figma from a codebase. Use when the user wants to create variables/tokens, build component libraries, create individual components with proper variant sets and variable bindings, set up theming (light/dark modes), document foundations, or reconcile gaps between code and Figma. Also use when the user asks to create or generate any component in Figma — even a single one — since components require proper variable foundations, variant states, and design token bindings to be production-quality. This skill teaches WHAT to build and in WHAT ORDER — it complements the `figma-use` skill which teaches HOW to call the Plugin API. Both skills should be loaded together.
**MANDATORY prerequisite** — you MUST invoke this skill BEFORE every `use_figma` tool call. NEVER call `use_figma` directly without loading this skill first. Skipping it causes common, hard-to-debug failures. Trigger whenever the user wants to perform a write action or a unique read action that requires JavaScript execution in the Figma file context — e.g. create/edit/delete nodes, set up variables or tokens, build components and variants, modify auto-layout or fills, bind variables to properties, or inspect file structure programmatically.
SKILL.md を表示中
SOC 職業分類に基づく
| name | boltz-small-molecule-design |
| description | Design new small-molecule binders with Boltz. Use when generating novel ligands or hits for a target without a fixed compound library. Not for screening existing molecules or one-off docking. |
If boltz-api is missing from PATH, use boltz-cli-setup for install/update guidance before retrying.
If a command reports missing or expired authentication, use boltz-cli-setup to start boltz-api auth login --device-code before retrying; do not ask permission first.
If the agent host sandbox blocks boltz-api install/auth/API calls, use boltz-cli-setup to request the host sandbox bypass/escalation needed for user-wide CLI install, browser login, credential storage, temp files, or API access before retrying.
Use this skill when the user wants de novo small-molecule binders (no existing library).
target.entities, plus optional pocket_residues (0-based) and/or reference_ligands (known binders to help locate the pocket).num_molecules — valid range 10 to 1,000,000 (server rejects outside it). If the user says fewer than 10, explain the floor and propose 10.chemical_space (e.g. "enamine_real") if the user explicitly wants generation restricted to synthesizable molecules within that library.chemical_space and molecule_filters; only add them on explicit request. Read references/api.md for exact shapes and filter options.estimate-cost, show the USD cost, wait for explicit confirmation. Cost is a flat $0.025 per molecule (size-independent); still quote estimated_cost_usd from the response as the authoritative total.start to submit (synchronous). Capture the ID.download-results with the agent runtime's background/non-blocking command facility; it polls, paginates, downloads per-hit structures, and exits when terminal. In Claude Code, use Bash with run_in_background: true. In Codex, run download-results as a foreground shell command with yield_time_ms: 1000; if Codex returns a session_id, keep it for optional same-thread polling, but treat download-status plus the run directory as the durable source of truth. In Codex app/desktop runtimes that expose same-thread heartbeat automations, create a heartbeat that checks download-status periodically and posts a concise completion or failure update when the download reaches a terminal state. After launching the downloader, always report the job ID, run name, and output directory. Include the next check cadence if the heartbeat was created; otherwise include the download-status command.<output-root>/<run-name>/results/index.jsonl by binding_confidence for hit discovery or optimization_score for lead optimization. Each generated molecule also carries a free adme block (solubility, permeability, lipophilicity) — surface it for developability triage when the user cares about ADME, or when a top hit looks risky. Read references/results.md for output layout and metric details.# Replace placeholders with concrete absolute paths before running.
# Use a short descriptive run name, for example: sm-design-<target>-<batch>-v1
boltz-api small-molecule:design estimate-cost \
--input @yaml:///absolute/path/payload.yaml
boltz-api small-molecule:design start \
--idempotency-key "<run-name>" \
--input @yaml:///absolute/path/payload.yaml \
--raw-output --transform id
# Copy the printed job ID into this command, then launch it in the agent
# runtime's background/non-blocking mode.
# Claude Code: Bash with run_in_background=true.
# Codex: foreground shell command with yield_time_ms=1000; keep the returned session_id if one is provided.
# Do not append "&" or use nohup in Codex.
boltz-api download-results \
--id "<job-id-from-start>" --name "<run-name>" \
--root-dir "/absolute/path/boltz-experiments" \
--poll-interval-seconds 60
# -> /absolute/path/boltz-experiments/<run-name>/results/<pres_*>/...
Payload keys are num_molecules, target, chemical_space, molecule_filters — the API body field names.
10 <= num_molecules <= 1,000,000 before calling estimate-cost. The server rejects values outside that range.estimate-cost returns the authoritative total.references/api.md.cd into the run directory for follow-up commands; pass the same --root-dir and use absolute paths so later relative paths do not drift.--input @yaml:///absolute/path/payload.yaml or @json:///absolute/path/payload.json for estimate-cost and start. Keep --idempotency-key and --workspace-id top-level; if they also appear inside --input, the top-level flags win.--target @yaml:///absolute/path/target.yaml or --molecule-filters @json:///absolute/path/filters.json. Piped YAML / JSON on stdin also works, but it must use API body field names. Never use @file://.--idempotency-key at submit and --name on download-results.boltz-api. Prefer concrete arguments over sh -c, inline environment assignments, aliases, wrapper scripts, loops, or pipelines around the boltz-api invocation unless the user already allowed that exact command form. Use --raw-output --transform id, read the printed ID, then paste that literal ID into the next download-results command.download-results. In Codex specifically, keep download-results in the foreground and set the shell tool yield to 1000 ms; Codex will return a session_id if the command is still running. Do not append & or use nohup in Codex because the tool runner may clean up shell-backgrounded descendants before .boltz-run.json is fully written.boltz-api small-molecule:design start --helpRead references/api.md for the target, chemical_space, and molecule_filters shapes (filter catalog matches the screen endpoint). Read references/results.md after download when ranking generated molecules or explaining outputs.
Rank from results/index.jsonl after download-results; use references/results.md for local file layout and metric meanings.
num_molecules: under 100 often finishes in a few minutes, 100-1,000 may take several minutes to tens of minutes, and larger runs can take longer or hours depending on inputs and system load. Don't quote a fixed duration. --poll-interval-seconds 60 is a sensible default for the downloader. download-results emits JSONL progress on stderr by default; add --progress-format text --verbose only when you explicitly want human-readable logs.download-results. The heartbeat should run boltz-api --format json download-status --name "<run-name>" --root-dir "/absolute/path/boltz-experiments" and stop once terminal. Choose cadence by num_molecules: under 100 -> every 1-2 minutes; 100-1,000 -> every 5 minutes; over 1,000 -> every 15 minutes. Post only material status changes or terminal completion/failure. Poll the saved session_id with an empty write_stdin only for interactive, user-requested progress checks. Never run a manual poll loop in the current turn.download-status.boltz-api download-results with the same --name "<run-name>" and the same --root-dir.molecule_filters on user request.