{"slug":"learningmatter-mit-chem-react-ot","name":"chem-react-ot","description":"Generate transition state structures for chemical reactions using React-OT.","long_description":"---\nname: chem-react-ot\ndescription: Generate transition state structures for chemical reactions using React-OT.\ncategory: [chemistry]\n---\n\n# `chem-react-ot` — React-OT Transition State Generation\n\n## Goal\n\nGenerate transition state (TS) structures given reactant and product structures using the React-OT model (Optimal Transport). React-OT is a generative model that predicts TS geometries directly without requiring an initial guess path (like NEB).\n\n**Category:** `chemistry`\n**Environment:** `react-ot-agent`\n\n## Key Features\n\n- **Generative TS Prediction:** Predicts 3D transition state structures from 3D reactants and products.\n- **Fast Inference:** Uses an ODE solver for generation, typically much faster than DFT-based NEB.\n- **No Path Guess Required:** Directly generates the TS structure.\n\n## Usage\n\n### 1. Environment Setup\n\nThis skill requires the `react-ot-agent` conda environment. Ensure it is installed:\n\n```bash\n# Env: react-ot-agent\ncd conda-envs/react-ot-agent\nbash install.sh\n```\n\n### 2. Download Models\n\nBefore running the skill for the first time, download the pre-trained model weights:\n\n```bash\n# activate react-ot-agent first\nconda activate react-ot-agent\npython conda-envs/react-ot-agent/download_models.py\n```\n\nThe checkpoint is saved to `~/.cache/react-ot/checkpoints/sb-pretrained.ckpt`.\n\n### 3. Generate Transition State\n\nRun the generation script with reactant and product files (xyz, cif, pdb, etc. - anything ASE reads).\n\n```bash\n# Env: react-ot-agent\npython .agents/skills/chem-react-ot/scripts/generate_ts.py \\\n    --reactants reactant.xyz \\\n    --products product.xyz \\\n    --output_dir results/ts_search\n```\n\n**Arguments:**\n\n- `--reactants`: Path to reactant structure file(s). Can be a single file with multiple molecules or a list of files.\n- `--products`: Path to product structure file(s).\n- `--output_dir`: Directory to save the generated TS structure (`ts_generated.xyz`) and trajectory (`generation_traj.xyz`).\n- `--nfe`: Number of function evaluations for the ODE solver (default: 10). Higher values might be more accurate but slower.\n- `--checkpoint`: Path to custom model checkpoint (optional, defaults to downloaded one).\n\n## Example\n\n```bash\n# Env: react-ot-agent\npython .agents/skills/chem-react-ot/scripts/generate_ts.py \\\n    --reactants .agents/skills/chem-react-ot/examples/oxadiazole_isomerization/reactant.xyz \\\n    --products .agents/skills/chem-react-ot/examples/oxadiazole_isomerization/product.xyz \\\n    --output_dir .agents/skills/chem-react-ot/examples/oxadiazole_isomerization/output\n```\n\n## Constraints\n\n- **Environment**: All scripts require the `react-ot-agent` conda environment.\n- **Input Format**: Reactant and product structures must be in any format readable by ASE (XYZ, CIF, PDB, etc.).\n- **Atom Ordering**: Reactant and product structures must have the same number of atoms with consistent atom ordering.\n- **Model Checkpoint**: The pre-trained checkpoint must be downloaded before first use (see step 2).\n\n## References\n\n- [React-OT GitHub](https://github.com/deepprinciple/react-ot)\n- Duan, C., Liu, G.-H., Du, Y. et al., \"Optimal transport for generating transition states in chemical reactions\", *Nature Machine Intelligence*, 2025. [DOI](https://doi.org/10.1038/s42256-025-01010-0)\n\n---\n\n**Author:** Bowen Deng\n**Contact:** [GitHub @learningmatter-mit](https://github.com/learningmatter-mit)\n","tagline":"Generate transition state structures for chemical reactions using React-OT.","category":"[chemistry]","tags":["agent-skill"],"author":"learningmatter-mit","verified":false,"attribution":{"status":"registry_indexed","statusLabel":"Registry indexed","shortLabel":"REGISTRY INDEXED","sourceLabel":"github candidate review","sourceDetail":"learningmatter-mit/AtomisticSkills","creatorName":"learningmatter-mit","creatorUrl":"https://github.com/learningmatter-mit","sourceUrl":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/learningmatter-mit-chem-react-ot#claim-this-skill","claimCta":"Claim this skill","trustNote":"This listing was indexed from public sources and is not marked official until a maintainer claim is approved.","publicNote":"Attribution links to the public repository or creator profile. 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the example only shows single files, while the description mentions support for lists.","Quality score needs review","Permission surface needs review: secrets or environment access, shell or command execution","Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"outcome_stats":null,"safety":{"score":36,"level":"avoid_auto_install","label":"Avoid automatic install","safety_tier":{"tier":"blocked","label":"Blocked for auto-install","badge":"BLOCKED","summary":"This skill should not be selected by an agent without explicit human security review.","recommended_action":"Do not auto-install. 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Inspect the source, dependencies, and permission surface first.","reasons":["Metadata combines secrets access with shell or command execution","High-risk permission hints: Shell or command execution, Secrets or environment access"]},"eval":{"version":"openagentskill-skill-eval-v1","status":"failed","score":64,"risk_level":"high","decision":{"recommendation":"do_not_auto_install","reason":"Agent safety gate: This skill should not be selected by an agent without explicit human security review.","auto_install_allowed":false,"policy":"block","human_review_required":true},"blockers":["Agent safety gate: This skill should not be selected by an agent without explicit human security review.","Permission surface: secrets or environment access, shell or command execution"],"warnings":["Trust score: Potentially useful, but at least one trust signal needs human inspection.","Audit score: Needs review","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review","Permission surface may require sandboxing","The script's handling of multiple reactant/product files is not fully documented; the example only shows single files, while the description mentions support for lists.","The model weight download step relies on an external URL without explicit checksum verification, which could be a supply chain risk if the source is compromised.","Quality score needs review","Permission surface needs review: secrets or environment access, shell or command execution","Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, credential or environment access"],"validation_plan":["Inspect repository, README/SKILL.md, license, and recent commits before production use.","Install in an isolated workspace or sandbox with no production secrets available.","Run the smallest representative task and record files touched, commands run, network access, and outputs.","Compare the selected skill against at least one alternative when the eval status is review or failed.","Promote only after the agent reports a successful verification result and unresolved warnings are accepted."],"checks":[{"id":"task_fit","label":"Task fit","status":"pass","score":84,"required_for_auto_install":true,"detail":"Task wording matches this skill metadata.","evidence":["Evaluate chem-react-ot before installing it in an agent workflow","[chemistry]","GitHub automation workflows; Claude Code teams; builders willing to evaluate younger projects"]},{"id":"install_path","label":"Install path","status":"pass","score":92,"required_for_auto_install":true,"detail":"Install handoff is available.","evidence":["npx skills add learningmatter-mit/AtomisticSkills --skill chem-react-ot"]},{"id":"install_safety","label":"Install command safety","status":"pass","score":92,"required_for_auto_install":true,"detail":"standard package or runtime install path","evidence":["npx skills add learningmatter-mit/AtomisticSkills --skill chem-react-ot"]},{"id":"trust_score","label":"Trust score","status":"warn","score":66,"required_for_auto_install":true,"detail":"Potentially useful, but at least one trust signal needs human inspection.","evidence":["Manual review","161 GitHub stars","MIT"]},{"id":"audit_score","label":"Audit score","status":"warn","score":76,"required_for_auto_install":true,"detail":"Needs review","evidence":["Dependency or permission surface needs review"]},{"id":"agent_safety_gate","label":"Agent safety gate","status":"fail","score":36,"required_for_auto_install":true,"detail":"This skill should not be selected by an agent without explicit human security review.","evidence":["Do not auto-install. Inspect the source, dependencies, and permission surface first.","Metadata combines secrets access with shell or command execution"]},{"id":"readme_skillmd_completeness","label":"README/SKILL.md completeness","status":"warn","score":70,"required_for_auto_install":false,"detail":"Public metadata needs stronger README/SKILL.md context","evidence":["Usable metadata, review docs"]},{"id":"license_clarity","label":"License clarity","status":"pass","score":86,"required_for_auto_install":true,"detail":"MIT","evidence":["MIT"]},{"id":"recent_maintenance","label":"Recent maintenance","status":"pass","score":100,"required_for_auto_install":false,"detail":"5d since push","evidence":["5d since push"]},{"id":"permission_surface","label":"Permission surface","status":"fail","score":36,"required_for_auto_install":true,"detail":"secrets or environment access, shell or command execution","evidence":["Shell or command execution: high","Network access: medium","Filesystem access: medium"]},{"id":"alternatives","label":"Alternatives available","status":"info","score":55,"required_for_auto_install":false,"detail":"No close alternatives were found in the current shortlist.","evidence":[]}],"endpoints":{"web":"https://www.openagentskill.com/skills/learningmatter-mit-chem-react-ot/evals","api":"/api/agent/evals?slug=learningmatter-mit-chem-react-ot","text":"/api/agent/evals?slug=learningmatter-mit-chem-react-ot&format=text"}},"agent_readable_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"learningmatter-mit-chem-react-ot","name":"chem-react-ot","description":"Generate transition state structures for chemical reactions using React-OT.","category":"[chemistry]","url":"https://www.openagentskill.com/skills/learningmatter-mit-chem-react-ot","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot","github_repo":"learningmatter-mit/AtomisticSkills"},"suited_tasks":["GitHub automation workflows","Claude Code teams","builders willing to evaluate younger projects","Inspect repository metadata","Compare code changes","Write concise engineering summaries","Navigate pages","Click and type safely"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-react-ot","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add learningmatter-mit-chem-react-ot"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"chem-react-ot\" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Generate transition state structures for chemical reactions using React-OT. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-react-ot\",\"task\":\"Install chem-react-ot\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"chem-react-ot\" as a Claude Code skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Generate transition state structures for chemical reactions using React-OT. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-react-ot\",\"task\":\"Install chem-react-ot\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"chem-react-ot\" from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Generate transition state structures for chemical reactions using React-OT. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-react-ot\",\"task\":\"Install chem-react-ot\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/learningmatter-mit-chem-react-ot/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-react-ot"},"trust":{"score":66,"label":"Manual review","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"161 GitHub stars","repoActivity":"161 stars, 24 forks","lastPushed":"5d since push","license":"MIT","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot","install":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-react-ot","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Usable metadata, review docs","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["[chemistry]","agent-skill"],"known_risks":["The script's handling of multiple reactant/product files is not fully documented; the example only shows single files, while the description mentions support for lists.","Quality score needs review","Permission surface needs review: secrets or environment access, shell or command execution","Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":76,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","The script's handling of multiple reactant/product files is not fully documented; the example only shows single files, while the description mentions support for lists.","The model weight download step relies on an external URL without explicit checksum verification, which could be a supply chain risk if the source is compromised.","Quality score needs review","Permission surface needs review: secrets or environment access, shell or command execution","Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, credential or environment access"]},"safety_gate":{"tier":"blocked","label":"Blocked for auto-install","auto_install_policy":"block","auto_install_allowed":false,"human_review_required":true,"blocked":true,"recommended_action":"Do not auto-install. Inspect the source, dependencies, and permission surface first."},"quality":{"score":69,"label":"Promising"},"supply":{"track":"Coding and developer agents","scenario":"GitHub automation","maintenance":"5d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","The script's handling of multiple reactant/product files is not fully documented; the example only shows single files, while the description mentions support for lists.","No OpenAgentSkill engagement data yet","High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review","Permission surface may require sandboxing","The model weight download step relies on an external URL without explicit checksum verification, which could be a supply chain risk if the source is compromised."],"agent_contract":{"task_input":"Use chem-react-ot in an agent workflow","recommended_action":"Do not auto-install. Inspect the source, dependencies, and permission surface first.","install_policy":"block","minimum_review_before_use":["Trust: 66/100 Manual review","Audit: 76/100 Needs review","Safety: 36/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"learningmatter-mit-chem-react-ot (chem-react-ot)","install_command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-react-ot","risk_summary":"Needs review; Blocked for auto-install; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"learningmatter-mit-chem-react-ot","task":"Use chem-react-ot in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/learningmatter-mit-chem-react-ot","api":"https://www.openagentskill.com/api/agent/skills/learningmatter-mit-chem-react-ot","audit":"https://www.openagentskill.com/skills/learningmatter-mit-chem-react-ot/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=learningmatter-mit-chem-react-ot&task=Use%20chem-react-ot%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20chem-react-ot%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20chem-react-ot%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/learningmatter-mit-chem-react-ot/install","manifest":"https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-react-ot"}},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"learningmatter-mit-chem-react-ot","name":"chem-react-ot","description":"Generate transition state structures for chemical reactions using React-OT.","category":"[chemistry]","url":"https://www.openagentskill.com/skills/learningmatter-mit-chem-react-ot","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot","github_repo":"learningmatter-mit/AtomisticSkills"},"suited_tasks":["GitHub automation workflows","Claude Code teams","builders willing to evaluate younger projects","Inspect repository metadata","Compare code changes","Write concise engineering summaries","Navigate pages","Click and type safely"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-react-ot","ready":true,"targets":[{"id":"openagentskill-cli","label":"CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add learningmatter-mit-chem-react-ot"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"chem-react-ot\" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Generate transition state structures for chemical reactions using React-OT. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-react-ot\",\"task\":\"Install chem-react-ot\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"claude-code","label":"Claude Code","kind":"agent-prompt","value":"Add \"chem-react-ot\" as a Claude Code skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Generate transition state structures for chemical reactions using React-OT. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-react-ot\",\"task\":\"Install chem-react-ot\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."},{"id":"cursor","label":"Cursor","kind":"agent-prompt","value":"Turn \"chem-react-ot\" from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Generate transition state structures for chemical reactions using React-OT. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-react-ot\",\"task\":\"Install chem-react-ot\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes."}],"handoff_url":"https://www.openagentskill.com/api/skills/learningmatter-mit-chem-react-ot/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-react-ot"},"trust":{"score":66,"label":"Manual review","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"161 GitHub stars","repoActivity":"161 stars, 24 forks","lastPushed":"5d since push","license":"MIT","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot","install":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-react-ot","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Usable metadata, review docs","agentOutcomes":"No agent outcome data yet"},"outcome_evidence":{"total":0,"successes":0,"failures":0,"not_relevant":0,"success_rate":null,"recent_success_rate":null,"recent_failure_rate":null,"install_attempts":0,"install_success_rate":null,"risk_blocked":0,"setup_required":0,"avg_output_quality":null,"production_outcomes":0,"last_outcome_at":null,"label":"No agent outcome data yet"},"auto_install":{"allowed":false,"sandbox_required":true,"reason":"Human review or sandbox validation is required before automatic installation."},"best_for":["[chemistry]","agent-skill"],"known_risks":["The script's handling of multiple reactant/product files is not fully documented; the example only shows single files, while the description mentions support for lists.","Quality score needs review","Permission surface needs review: secrets or environment access, shell or command execution","Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"agent_proven":{"version":"agent-proven-v1","score":0,"tier":"unproven","label":"Needs first agent run","summary":"No agent outcome reports yet. Use Resolve, run one narrow sandbox task, then report the result.","metrics":{"totalOutcomes":0,"successfulOutcomes":0,"failedOutcomes":0,"installAttempts":0,"installSuccessRate":null,"successRate":null,"recentSuccessRate":null,"recentFailureRate":null,"riskBlocked":0,"setupRequired":0,"notRelevant":0,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"uniqueAgents":0,"lastOutcomeAt":null},"signals":[],"penalties":["No real agent outcome evidence yet"]},"audit":{"score":76,"risk_level":"needs_review","risk_label":"Needs review","warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","The script's handling of multiple reactant/product files is not fully documented; the example only shows single files, while the description mentions support for lists.","The model weight download step relies on an external URL without explicit checksum verification, which could be a supply chain risk if the source is compromised.","Quality score needs review","Permission surface needs review: secrets or environment access, shell or command execution","Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, credential or environment access"]},"safety_gate":{"tier":"blocked","label":"Blocked for auto-install","auto_install_policy":"block","auto_install_allowed":false,"human_review_required":true,"blocked":true,"recommended_action":"Do not auto-install. Inspect the source, dependencies, and permission surface first."},"quality":{"score":69,"label":"Promising"},"supply":{"track":"Coding and developer agents","scenario":"GitHub automation","maintenance":"5d since push","risk":"Needs review"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","production agents without a repository review","The script's handling of multiple reactant/product files is not fully documented; the example only shows single files, while the description mentions support for lists.","No OpenAgentSkill engagement data yet","High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review","Permission surface may require sandboxing","The model weight download step relies on an external URL without explicit checksum verification, which could be a supply chain risk if the source is compromised."],"agent_contract":{"task_input":"Use chem-react-ot in an agent workflow","recommended_action":"Do not auto-install. Inspect the source, dependencies, and permission surface first.","install_policy":"block","minimum_review_before_use":["Trust: 66/100 Manual review","Audit: 76/100 Needs review","Safety: 36/100 Avoid automatic install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"learningmatter-mit-chem-react-ot (chem-react-ot)","install_command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-react-ot","risk_summary":"Needs review; Blocked for auto-install; Review before production","verification_result":"Report the smallest successful task, files touched, warnings, and any missing setup."}},"outcome_feedback":{"endpoint":"https://www.openagentskill.com/api/agent/outcome","method":"POST","requires_resolve_event_id":true,"event_id_source":"Use install_receipt.outcome_feedback.event_id or feedback.event_id returned by /api/agent/resolve for the current task.","expected_outcomes":["success","failed","not_relevant","blocked_by_risk","setup_required"],"payload_template":{"event_id":"<install_receipt.outcome_feedback.event_id or feedback.event_id from /api/agent/resolve>","skill_slug":"learningmatter-mit-chem-react-ot","task":"Use chem-react-ot in an agent workflow","agent":"codex","outcome":"success","install_used":true,"risk_blocked":false,"setup_required":false,"task_success":true,"output_quality":4,"error_type":null,"human_review_required":false,"workspace":"sandbox","time_to_useful_ms":120000,"notes":"Report the smallest successful task, setup friction, files touched, and risk notes."}},"endpoints":{"web":"https://www.openagentskill.com/skills/learningmatter-mit-chem-react-ot","api":"https://www.openagentskill.com/api/agent/skills/learningmatter-mit-chem-react-ot","audit":"https://www.openagentskill.com/skills/learningmatter-mit-chem-react-ot/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=learningmatter-mit-chem-react-ot&task=Use%20chem-react-ot%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20chem-react-ot%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20chem-react-ot%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/learningmatter-mit-chem-react-ot/install","manifest":"https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-react-ot"}},"supply_profile":{"track":{"slug":"coding","label":"Coding and developer agents","shortLabel":"Coding","description":"Code review, repo analysis, testing, CI, GitHub, DevOps, and developer workflow skills."},"scenario":{"label":"GitHub automation","description":"I need my agent to triage GitHub issues, review pull requests, and summarize repository changes.","useCases":[{"slug":"github-automation","title":"GitHub automation"},{"slug":"browser-automation","title":"Browser automation"},{"slug":"coding-agents","title":"Coding agents"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-react-ot","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":161,"starsLabel":"161","forks":24,"license":"MIT","qualityScore":69,"trustScore":66,"auditScore":76},"maintenance":{"status":"fresh","label":"5d since push","daysSincePush":5,"lastPushedAt":"2026-09-03T06:44:16+00:00"},"risk":{"level":"needs_review","label":"Needs review","requiresReview":true,"notes":["Dependency or permission surface needs review","Permission surface may require sandboxing","The script's handling of multiple reactant/product files is not fully documented; the example only shows single files, while the description mentions support for lists.","The model weight download step relies on an external URL without explicit checksum verification, which could be a supply chain risk if the source is compromised.","Quality score needs review"]},"coverageTags":["Coding","GitHub automation","[chemistry]","agent-skill"]},"audit":{"audit_score":76,"risk_level":"needs_review","risk_label":"Needs review","quality_score":69,"trust_score":66,"maintenance_score":100,"security_score":73,"install_score":92,"warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","The script's handling of multiple reactant/product files is not fully documented; the example only shows single files, while the description mentions support for lists.","The model weight download step relies on an external URL without explicit checksum verification, which could be a supply chain risk if the source is compromised.","Quality score needs review","Permission surface needs review: secrets or environment access, shell or command execution","Stars/forks activity: 161 stars, 24 forks; issue activity unavailable in current metadata","Dependency/runtime risk: command execution surface, credential or environment access","Permission surface: secrets or environment access, shell or command execution"]},"quality_signals":{"model":"v2","star_score":15.47,"usage_score":0,"review_score":5.25,"metadata_score":3,"freshness_score":15},"platforms":["Claude Code"],"use_cases":[{"slug":"github-automation","title":"GitHub automation","url":"https://www.openagentskill.com/use-cases/github-automation"},{"slug":"browser-automation","title":"Browser automation","url":"https://www.openagentskill.com/use-cases/browser-automation"},{"slug":"coding-agents","title":"Coding agents","url":"https://www.openagentskill.com/use-cases/coding-agents"},{"slug":"rag-knowledge","title":"RAG and knowledge","url":"https://www.openagentskill.com/use-cases/rag-knowledge"}],"stacks":[{"slug":"browser-qa-agent","title":"Browser QA agent","url":"https://www.openagentskill.com/collections/browser-qa-agent"},{"slug":"coding-review-agent","title":"Coding review agent","url":"https://www.openagentskill.com/collections/coding-review-agent"},{"slug":"rag-knowledge-base","title":"RAG knowledge base","url":"https://www.openagentskill.com/collections/rag-knowledge-base"}],"install":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-react-ot","install_targets":[{"id":"openagentskill-cli","label":"CLI","title":"OpenAgentSkill CLI","kind":"command","value":"npx --yes https://github.com/Leon-Drq/openagentskill/releases/download/cli-v0.3.0/openagentskill-0.3.0.tgz add learningmatter-mit-chem-react-ot","description":"Resolve policy, run the source installer safely, and report a verified install receipt.","copyLabel":"Copy command"},{"id":"codex","label":"Codex","title":"Codex install prompt","kind":"agent-prompt","value":"Install the \"chem-react-ot\" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot. Read its SKILL.md or equivalent instructions first, install only the files needed for this workspace, and summarize any required setup before using it. Skill purpose: Generate transition state structures for chemical reactions using React-OT. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-react-ot\",\"task\":\"Install chem-react-ot\",\"agent\":\"codex\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Give Codex a repo-aware install prompt when the skill is not available through a local CLI.","copyLabel":"Copy prompt"},{"id":"claude-code","label":"Claude Code","title":"Claude Code skill prompt","kind":"agent-prompt","value":"Add \"chem-react-ot\" as a Claude Code skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot. Inspect the skill instructions, place the reusable skill files in the appropriate local skills location for this project, and report the activation steps. Skill purpose: Generate transition state structures for chemical reactions using React-OT. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-react-ot\",\"task\":\"Install chem-react-ot\",\"agent\":\"claude-code\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this prompt to ask Claude Code to add the skill and explain the local activation steps.","copyLabel":"Copy prompt"},{"id":"cursor","label":"Cursor","title":"Cursor rule prompt","kind":"agent-prompt","value":"Turn \"chem-react-ot\" from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot into a reusable Cursor project rule or agent instruction. Preserve the core workflow, adapt paths to this repo, and keep the rule scoped to tasks where it is relevant. Skill purpose: Generate transition state structures for chemical reactions using React-OT. After the install attempt, report the result to https://www.openagentskill.com/api/agent/outcome with POST JSON {\"event_id\":\"install_<unique-id>\",\"skill_slug\":\"learningmatter-mit-chem-react-ot\",\"task\":\"Install chem-react-ot\",\"agent\":\"cursor\",\"outcome\":\"success\",\"install_used\":true}. Replace event_id with a unique value and outcome with success or failed. Report success only after the skill is installed and a minimal verification passes.","description":"Use this when installing as Cursor project rules or reusable agent instructions.","copyLabel":"Copy prompt"}],"repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot","github_repo":"learningmatter-mit/AtomisticSkills","version":"1.0.0","license":"MIT","urls":{"web":"https://www.openagentskill.com/skills/learningmatter-mit-chem-react-ot","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-react-ot","api":"/api/agent/skills/learningmatter-mit-chem-react-ot","install_api":"/api/skills/learningmatter-mit-chem-react-ot/install"},"meta":{"created_at":"2026-09-06T12:01:09.250192+00:00","updated_at":"2026-09-06T12:01:09.429179+00:00","agent_friendly":true}}