{"slug":"learningmatter-mit-chem-bond-dissociation","name":"chem-bond-dissociation","description":"Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.","long_description":"---\nname: chem-bond-dissociation\ndescription: Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.\ncategory: [chemistry]\n---\n\n# Bond Dissociation Energy Skill\n\n## Goal\n\nCalculate the **homolytic** and/or **heterolytic** bond dissociation energy (BDE) for each single bond in a molecule using Machine Learning Interatomic Potentials (MLIPs).\n\n**Homolytic BDE** (radical fragments):\n$$\\text{BDE}_\\text{homo}(A{-}B) = E(A\\bullet) + E(B\\bullet) - E(A{-}B)$$\n\n**Heterolytic BDE** (ionic fragments, minimum over both polarity variants):\n$$\\text{BDE}_\\text{hetero}(A{-}B) = \\min\\!\\bigl(E(A^+)+E(B^-),\\; E(A^-)+E(B^+)\\bigr) - E(A{-}B)$$\n\n> [!IMPORTANT]\n> This skill computes BDEs by relaxing both the intact molecule and fragments with an MLIP. For purpose-trained GNN models that predict BDE directly from SMILES (MAE ~0.6 kcal/mol), consider [ALFABET](https://bde.ml.nrel.gov) or BonDNet instead.\n\n## Background\n\nBDE is a fundamental thermodynamic quantity that determines:\n- **Drug metabolism**: CYP450 enzymes abstract H from the weakest C–H bond\n- **Electrolyte stability**: Which bonds break first under electrochemical voltage\n- **Combustion chemistry**: Rate-determining bond-breaking steps in fuel oxidation\n- **Polymer degradation**: Weakest links in polymer backbone chains\n\nA 2024 study (Zubatyuk et al., *JCTC*) demonstrated that MACE potentials achieve BDE RMSE of 1.37 kcal/mol for aliphatic C–H bonds in drug-like molecules, outperforming semi-empirical methods and ALFABET for BDE **ranking**.\n\n## 1. Prerequisites\n\n- **Conda Environment**: `mace-agent` (includes RDKit, ASE, and MACE)\n- **Input**: SMILES string or structure file (`.sdf`, `.mol2`)\n- **RDKit**: Required for bond identification and molecular fragmentation\n\n## 2. Choosing a Foundation Potential\n\nRefer to the [foundation-potentials skill](../ml-foundation-potentials/SKILL.md) for model selection.\n\n> [!IMPORTANT]\n> **Model requirements by cleavage mode:**\n>\n> | Mode | Recommended model | `supports_charge_spin` | Validated? |\n> |:---|:---|:---|:---|\n> | `homolytic` | `MACE-OFF23-small/medium/large` | Not required | ✅ |\n> | `heterolytic` or `both` | **`MACE-OMOL-extra-large`** (env: `mace-agent`) | ✅ Required | ✅ |\n> | `heterolytic` or `both` | **`MACE-MH-1`** with omol head (env: `mace-agent`) | ✅ Required | ✅ |\n> | `heterolytic` or `both` | FairChem `uma-s-1p1` with `--task_name omol` (env: `fairchem-agent`) | ✅ Required | ✅ |\n>\n> **Setting charge/spin on MACE models:** use `atoms.info[\"charge\"]` and `atoms.info[\"spin\"]`\n> (the calculator's default `info_keys` maps `\"charge\"` → `total_charge` / `\"spin\"` → `total_spin`).\n> Both MACE-OMOL and MACE-MH use `joint_embedding` to condition the network on these scalars.\n>\n> If you request `--cleavage both` with a model that does **not** support charge/spin,\n> the skill will log a warning and silently fall back to homolytic-only.\n> Using `--cleavage heterolytic` with an unsupported model raises an error.\n>\n> **Note on single-atom fragments:** When a bond produces a bare H (or other single atom),\n> heterolytic BDE is automatically skipped — neither MACE nor FairChem UMA has signed\n> single-atom energies (only neutral H, C, N, O… are in the reference tables).\n\n## 3. Calculation Workflow\n\n### Step 1: Provide a molecule\n\n```bash\n# SMILES input (most common)\n--smiles \"CCO\"\n\n# Or from a structure file\n--structure molecule.sdf\n```\n\n### Step 2: Run BDE calculation\n\n**Homolytic only** (default, no charge/spin needed):\n```bash\n# Env: mace-agent\npython .agents/skills/chem-bond-dissociation/scripts/calculate_bde.py \\\n    --smiles CCO \\\n    --all_bonds \\\n    --cleavage homolytic \\\n    --model_type mace \\\n    --model_name MACE-OFF23-small \\\n    --output_dir research/my_folder/bde_results\n```\n\n**Both homolytic and heterolytic** (MACE-OMOL):\n```bash\n# Env: mace-agent\npython .agents/skills/chem-bond-dissociation/scripts/calculate_bde.py \\\n    --smiles CCO \\\n    --all_bonds \\\n    --cleavage both \\\n    --model_type mace \\\n    --model_name MACE-OMOL-extra-large \\\n    --output_dir research/my_folder/bde_results_both\n```\n\n**Both homolytic and heterolytic** (FairChem UMA omol):\n```bash\n# Env: fairchem-agent\npython .agents/skills/chem-bond-dissociation/scripts/calculate_bde.py \\\n    --smiles CCO \\\n    --all_bonds \\\n    --cleavage both \\\n    --model_type fairchem \\\n    --model_name uma-s-1p1 \\\n    --task_name omol \\\n    --output_dir research/my_folder/bde_results_both\n```\n\n**Heterolytic only** with FairChem UMA:\n```bash\n# Env: fairchem-agent\npython .agents/skills/chem-bond-dissociation/scripts/calculate_bde.py \\\n    --smiles CCO \\\n    --all_bonds \\\n    --cleavage heterolytic \\\n    --model_type fairchem \\\n    --model_name uma-s-1p1 \\\n    --task_name omol \\\n    --output_dir research/my_folder/bde_hetero\n```\n\n### Key Parameters\n\n| Argument | Default | Description |\n|:---|:---|:---|\n| `--smiles` | — | SMILES string of the molecule |\n| `--structure` | — | Path to structure file (`.sdf`, `.mol2`) |\n| `--bond` | — | Specific bond as atom indices `\"i-j\"` (0-indexed) |\n| `--all_bonds` | `True` | Compute BDE for all single bonds |\n| `--include_h_bonds` | `False` | Include X–H bonds |\n| `--cleavage` | `homolytic` | `homolytic`, `heterolytic`, or `both` |\n| `--model_type` | `mace` | MLIP backend (`mace`, `fairchem`) |\n| `--model_name` | auto | Model checkpoint (default: `MACE-OFF23-small` for homolytic; `uma-s-1p1` for hetero/both) |\n| `--task_name` | — | Task head for multi-task models (e.g. `omol` for FairChem UMA) |\n| `--fmax` | `0.01` | Force convergence for relaxation (eV/Å) |\n| `--output_dir` | required | Output directory |\n\n## 4. Output Files\n\n- **`bde_results.json`** — Full results including:\n  - `metadata`: model name, cleavage mode, `supports_charge_spin`, SMILES, etc.\n  - `intact_energy_eV`: Energy of the relaxed intact molecule\n  - `bonds`: List of per-bond results:\n    - `bde_eV`, `bde_kJ_mol`, `bde_kcal_mol`: Homolytic BDE (if computed)\n    - `heterolytic_bde_eV`, `heterolytic_bde_kJ_mol`, `heterolytic_bde_kcal_mol`: Best heterolytic BDE (if computed)\n    - `heterolytic_best_variant`: Which polarity won (`\"frag1+ / frag2-\"` or `\"frag1- / frag2+\"`)\n    - `heterolytic_variants`: Raw results for both polarity variants\n  - `weakest_bond_homolytic`, `weakest_bond_heterolytic`: Summary of weakest bonds\n  - `bonds_ranked_by_homolytic_bde`, `bonds_ranked_by_heterolytic_bde`: Sorted tables\n\n- **`intact_relaxed.xyz`**: Relaxed intact molecule\n- **`frag_bond{N}_homo_{1,2}.xyz`**: Homolytic radical fragments\n- **`frag_bond{N}_hetero_pos_neg_{1,2}.xyz`**: Heterolytic cation/anion fragments (variant A)\n- **`frag_bond{N}_hetero_neg_pos_{1,2}.xyz`**: Heterolytic anion/cation fragments (variant B)\n\n## 5. Examples\n\n| Example | Model | Cleavage | Notes |\n|:---|:---|:---|:---|\n| [`examples/ethanol_mace_off23_small/`](examples/ethanol_mace_off23_small/) | MACE-OFF23-small | `homolytic` | Standard homolytic BDE for ethanol; includes H bonds |\n| [`examples/methanol_mace_omol_both/`](examples/methanol_mace_omol_both/) | MACE-OMOL-extra-large | `both` | Homo + heterolytic for methanol; C–O hetero = 90 vs homo = 143 kcal/mol |\n| [`examples/methanol_uma_omol_both/`](examples/methanol_uma_omol_both/) | FairChem UMA omol | `both` | Homo + heterolytic for methanol; C–O hetero = 157 vs homo = 126 kcal/mol |\n\n### Ethanol — Homolytic BDE (MACE-OFF23)\n\n```bash\n# Env: mace-agent\npython .agents/skills/chem-bond-dissociation/scripts/calculate_bde.py \\\n    --smiles CCO \\\n    --all_bonds \\\n    --include_h_bonds \\\n    --cleavage homolytic \\\n    --model_type mace \\\n    --model_name MACE-OFF23-small \\\n    --output_dir .agents/skills/chem-bond-dissociation/examples/ethanol_mace_off23_small\n```\n\n### Methanol — Both Homo and Heterolytic BDE (FairChem UMA omol)\n\n```bash\n# Env: fairchem-agent\npython .agents/skills/chem-bond-dissociation/scripts/calculate_bde.py \\\n    --smiles CO \\\n    --all_bonds \\\n    --include_h_bonds \\\n    --cleavage both \\\n    --model_type fairchem \\\n    --model_name uma-s-1p1 \\\n    --task_name omol \\\n    --output_dir .agents/skills/chem-bond-dissociation/examples/methanol_uma_omol_both\n```\n\nExperimental BDEs for ethanol (Blanksby & Ellison, 2003):\n| Bond | Experimental BDE (kcal/mol) |\n|:---|:---|\n| O–H | ~104 |\n| C–H (methyl) | ~101 |\n| C–H (methylene) | ~95 |\n| C–C | ~85 |\n| C–O | ~92 |\n\n## 6. Constraints\n\n- **Radical spin states**: For homolytic BDE, MLIPs are generally \"electron-agnostic\" and treat fragments as neutral regardless of spin state. BDE **ranking** is typically more reliable than absolute values.\n- **Ionic states**: Heterolytic BDE requires a charge/spin-aware model (`supports_charge_spin=True`). Validated: **MACE-OMOL**, **MACE-MH** (omol head), and **FairChem UMA omol**. These models use `atoms.info[\"charge\"]` and `atoms.info[\"spin\"]` to condition on the ionic state. Models without this flag raise an error for `--cleavage heterolytic`.\n- **Ring bonds**: Breaking bonds in rings produces a single open-chain diradical. The script will warn and skip ring bonds.\n- **Accuracy**: Expect ~2–5 kcal/mol error for homolytic BDEs with MACE-OFF23. Heterolytic accuracy is less benchmarked with current MLIPs.\n- **Environments**:\n  - `mace-agent` for MACE models\n  - `fairchem-agent` for FairChem/UMA models\n\n## References\n\n- Blanksby & Ellison, \"Bond Dissociation Energies of Organic Molecules\", *Acc. Chem. Res.* **2003**, 36, 255.\n- St. John et al., \"Prediction of organic homolytic bond dissociation enthalpies at near chemical accuracy with sub-second computational cost\", *Nat. Commun.* **2020**, 11, 2328. (ALFABET)\n- Zubatyuk et al., \"A Transferable MACE Potential for Open- and Closed-Shell Drug-Like Molecules\", *J. Chem. Theory Comput.* **2024**.\n\n---\n\n**Author:** Bowen Deng\n**Contact:** [GitHub @learningmatter-mit](https://github.com/learningmatter-mit)\n","tagline":"Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.","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-bond-dissociation","indexedBy":"OpenAgentSkill community index","claimUrl":"https://www.openagentskill.com/skills/learningmatter-mit-chem-bond-dissociation#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 skill runs local computations with standard scientific libraries and does not perform network operations or access sensitive resources.","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"],"backward_compatible":{"trust_score_v4":{"version":"trust-score-v4","score":67,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection."}}},"trust_score_v4":{"version":"trust-score-v4","score":67,"tier":"review","label":"Manual review","summary":"Potentially useful, but at least one trust signal needs human inspection.","recommendedAction":"Inspect the repository, license, and recent activity before connecting it to agent workflows.","dimensions":[{"id":"github_adoption","label":"GitHub adoption","score":62,"weight":0.13,"status":"info","detail":"161 GitHub stars"},{"id":"repo_activity","label":"Stars/forks activity","score":57,"weight":0.08,"status":"warn","detail":"161 stars, 24 forks; issue activity unavailable in current metadata"},{"id":"maintenance","label":"Recent maintenance","score":100,"weight":0.14,"status":"pass","detail":"5d since push"},{"id":"license","label":"License clarity","score":86,"weight":0.09,"status":"pass","detail":"MIT"},{"id":"documentation","label":"README/SKILL.md completeness","score":86,"weight":0.14,"status":"pass","detail":"Metadata includes enough usage and workflow context"},{"id":"dependency_risk","label":"Dependency/runtime risk","score":54,"weight":0.12,"status":"warn","detail":"command execution surface, credential or environment access"},{"id":"installability","label":"Install availability","score":92,"weight":0.1,"status":"pass","detail":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-bond-dissociation"},{"id":"install_safety","label":"Install command safety","score":92,"weight":0.1,"status":"pass","detail":"standard package or runtime install path"},{"id":"permission_surface","label":"Permission surface","score":22,"weight":0.07,"status":"fail","detail":"secrets or environment access, shell or command execution"},{"id":"repository","label":"Repository evidence","score":86,"weight":0.04,"status":"pass","detail":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation"},{"id":"review_status","label":"Review status","score":66,"weight":0.05,"status":"info","detail":"AI review data available"},{"id":"agent_outcomes","label":"Agent Proven outcomes","score":54,"weight":0.13,"status":"info","detail":"No agent outcome data yet"}],"checks":[{"status":"info","label":"GitHub adoption","detail":"161 GitHub stars"},{"status":"warn","label":"Stars/forks activity","detail":"161 stars, 24 forks; issue activity unavailable in current metadata"},{"status":"pass","label":"Recent maintenance","detail":"5d since push"},{"status":"pass","label":"License clarity","detail":"MIT"},{"status":"pass","label":"README/SKILL.md completeness","detail":"Metadata includes enough usage and workflow context"},{"status":"warn","label":"Dependency/runtime risk","detail":"command execution surface, credential or environment access"},{"status":"pass","label":"Install availability","detail":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-bond-dissociation"},{"status":"pass","label":"Install command safety","detail":"standard package or runtime install path"},{"status":"fail","label":"Permission surface","detail":"secrets or environment access, shell or command execution"},{"status":"pass","label":"Repository evidence","detail":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation"},{"status":"info","label":"Review status","detail":"AI review data available"},{"status":"info","label":"Agent Proven outcomes","detail":"No agent outcome data yet"},{"status":"warn","label":"Ownership","detail":"No approved owner claim yet"},{"status":"info","label":"OpenAgentSkill usage","detail":"No local usage activity yet"},{"status":"info","label":"Agent outcomes","detail":"No agent outcome data yet"}],"strengths":["AI review approved","Install path is available","Repository evidence is available","Recently maintained repository","Install command has no obvious high-risk pattern"],"warnings":["No critical security issues identified; the skill runs local computations with standard scientific libraries and does not perform network operations or access sensitive resources.","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"],"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-bond-dissociation","install":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-bond-dissociation","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Strong README/SKILL.md context","agentOutcomes":"No agent outcome data yet"},"installReadiness":{"ready":true,"command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-bond-dissociation","policy":"human_review_before_install","label":"Human review before install","notes":["Install path is available","Repository evidence is available","License is declared","No Agent Proven outcome evidence yet","5d since push"]},"agentCompatibility":["Codex","Claude Code","Cursor","OpenAgentSkill CLI"],"riskSummary":{"level":"medium","label":"Review before production","notes":["No critical security issues identified; the skill runs local computations with standard scientific libraries and does not perform network operations or access sensitive resources.","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"]},"outcomeEvidence":{"total":0,"successes":0,"failures":0,"notRelevant":0,"successRate":null,"installAttempts":0,"riskBlocked":0,"setupRequired":0,"installSuccessRate":null,"avgOutputQuality":null,"avgTimeToUsefulMs":null,"productionOutcomes":0,"humanReviewRequired":0,"recentSuccessRate":null,"recentFailureRate":null,"uniqueAgents":0,"agentProvenScore":0,"agentProvenLabel":"Needs first agent run","lastOutcomeAt":null,"label":"No agent outcome data yet"},"autoInstall":{"allowed":false,"sandboxRequired":true,"policy":"human_review_before_install","reason":"Human review or sandbox validation is required before automatic installation."},"bestFor":["[chemistry]","agent-skill"],"doNotUseFor":["Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface","Automatic installation in a production workspace"],"knownRisks":["No critical security issues identified; the skill runs local computations with standard scientific libraries and does not perform network operations or access sensitive resources.","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. Inspect the source, dependencies, and permission surface first.","auto_install_policy":"block","reasons":["Metadata combines secrets access with shell or command execution","High-risk permission hints: Shell or command execution, Secrets or environment access"]},"auto_install_allowed":false,"human_review_required":true,"blocked":true,"audit_risk":"needs_review","permission_hints":[{"id":"shell","label":"Shell or command execution","reason":"Skill metadata references terminal, CLI, shell, subprocess, or command execution workflows.","severity":"high"},{"id":"network","label":"Network access","reason":"Skill likely fetches remote pages, APIs, repositories, or external services.","severity":"medium"},{"id":"filesystem","label":"Filesystem access","reason":"Skill may read or write project files, documents, generated artifacts, or local workspace state.","severity":"medium"},{"id":"secrets","label":"Secrets or environment access","reason":"Skill metadata references credentials, tokens, environment variables, or secret-bearing workflows.","severity":"high"}],"policy_warnings":["High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review"],"constraints_applied":{"max_risk":"medium","needs_install_command":true,"min_stars":0}},"safety_gate":{"tier":"blocked","label":"Blocked for auto-install","badge":"BLOCKED","auto_install_policy":"block","auto_install_allowed":false,"blocked":true,"human_review_required":true,"recommended_action":"Do not auto-install. 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":65,"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","High-risk permission hints: Shell or command execution, Secrets or environment access","Dependency or permission surface needs review","Permission surface may require sandboxing","No critical security issues identified; the skill runs local computations with standard scientific libraries and does not perform network operations or access sensitive resources.","The SKILL.md excerpt is truncated in the review, but the provided sections are clear and comprehensive.","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"],"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-bond-dissociation before installing it in an agent workflow","[chemistry]","RAG and knowledge 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-bond-dissociation"]},{"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-bond-dissociation"]},{"id":"trust_score","label":"Trust score","status":"warn","score":67,"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":"pass","score":86,"required_for_auto_install":false,"detail":"Metadata includes enough usage and workflow context","evidence":["Strong README/SKILL.md context"]},{"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":22,"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-bond-dissociation/evals","api":"/api/agent/evals?slug=learningmatter-mit-chem-bond-dissociation","text":"/api/agent/evals?slug=learningmatter-mit-chem-bond-dissociation&format=text"}},"agent_readable_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"learningmatter-mit-chem-bond-dissociation","name":"chem-bond-dissociation","description":"Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.","category":"[chemistry]","url":"https://www.openagentskill.com/skills/learningmatter-mit-chem-bond-dissociation","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation","github_repo":"learningmatter-mit/AtomisticSkills"},"suited_tasks":["RAG and knowledge workflows","Claude Code teams","builders willing to evaluate younger projects","Chunk documents","Create embeddings","Retrieve and cite relevant passages","Search sources","Extract claims"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-bond-dissociation","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-bond-dissociation"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"chem-bond-dissociation\" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation. 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: Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation. 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-bond-dissociation\",\"task\":\"Install chem-bond-dissociation\",\"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-bond-dissociation\" as a Claude Code skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation. 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: Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation. 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-bond-dissociation\",\"task\":\"Install chem-bond-dissociation\",\"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-bond-dissociation\" from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation 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: Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation. 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-bond-dissociation\",\"task\":\"Install chem-bond-dissociation\",\"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-bond-dissociation/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-bond-dissociation"},"trust":{"score":67,"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-bond-dissociation","install":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-bond-dissociation","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Strong README/SKILL.md context","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":["No critical security issues identified; the skill runs local computations with standard scientific libraries and does not perform network operations or access sensitive resources.","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","No critical security issues identified; the skill runs local computations with standard scientific libraries and does not perform network operations or access sensitive resources.","The SKILL.md excerpt is truncated in the review, but the provided sections are clear and comprehensive.","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":"Research and knowledge work","scenario":"RAG and knowledge","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","No critical security issues identified; the skill runs local computations with standard scientific libraries and does not perform network operations or access sensitive resources.","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 SKILL.md excerpt is truncated in the review, but the provided sections are clear and comprehensive."],"agent_contract":{"task_input":"Use chem-bond-dissociation 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: 67/100 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-bond-dissociation (chem-bond-dissociation)","install_command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-bond-dissociation","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-bond-dissociation","task":"Use chem-bond-dissociation 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-bond-dissociation","api":"https://www.openagentskill.com/api/agent/skills/learningmatter-mit-chem-bond-dissociation","audit":"https://www.openagentskill.com/skills/learningmatter-mit-chem-bond-dissociation/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=learningmatter-mit-chem-bond-dissociation&task=Use%20chem-bond-dissociation%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20chem-bond-dissociation%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20chem-bond-dissociation%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/learningmatter-mit-chem-bond-dissociation/install","manifest":"https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-bond-dissociation"}},"machine_metadata":{"version":"openagentskill-agent-metadata-v2","skill":{"slug":"learningmatter-mit-chem-bond-dissociation","name":"chem-bond-dissociation","description":"Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation.","category":"[chemistry]","url":"https://www.openagentskill.com/skills/learningmatter-mit-chem-bond-dissociation","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation","github_repo":"learningmatter-mit/AtomisticSkills"},"suited_tasks":["RAG and knowledge workflows","Claude Code teams","builders willing to evaluate younger projects","Chunk documents","Create embeddings","Retrieve and cite relevant passages","Search sources","Extract claims"],"suited_agents":["Codex","Claude Code","Cursor","OpenAgentSkill CLI","CLI"],"install":{"command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-bond-dissociation","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-bond-dissociation"},{"id":"codex","label":"Codex","kind":"agent-prompt","value":"Install the \"chem-bond-dissociation\" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation. 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: Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation. 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-bond-dissociation\",\"task\":\"Install chem-bond-dissociation\",\"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-bond-dissociation\" as a Claude Code skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation. 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: Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation. 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-bond-dissociation\",\"task\":\"Install chem-bond-dissociation\",\"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-bond-dissociation\" from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation 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: Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation. 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-bond-dissociation\",\"task\":\"Install chem-bond-dissociation\",\"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-bond-dissociation/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-bond-dissociation"},"trust":{"score":67,"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-bond-dissociation","install":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-bond-dissociation","installSafety":"standard package or runtime install path","permissionSurface":"secrets or environment access, shell or command execution","documentation":"Strong README/SKILL.md context","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":["No critical security issues identified; the skill runs local computations with standard scientific libraries and does not perform network operations or access sensitive resources.","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","No critical security issues identified; the skill runs local computations with standard scientific libraries and does not perform network operations or access sensitive resources.","The SKILL.md excerpt is truncated in the review, but the provided sections are clear and comprehensive.","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":"Research and knowledge work","scenario":"RAG and knowledge","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","No critical security issues identified; the skill runs local computations with standard scientific libraries and does not perform network operations or access sensitive resources.","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 SKILL.md excerpt is truncated in the review, but the provided sections are clear and comprehensive."],"agent_contract":{"task_input":"Use chem-bond-dissociation 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: 67/100 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-bond-dissociation (chem-bond-dissociation)","install_command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-bond-dissociation","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-bond-dissociation","task":"Use chem-bond-dissociation 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-bond-dissociation","api":"https://www.openagentskill.com/api/agent/skills/learningmatter-mit-chem-bond-dissociation","audit":"https://www.openagentskill.com/skills/learningmatter-mit-chem-bond-dissociation/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=learningmatter-mit-chem-bond-dissociation&task=Use%20chem-bond-dissociation%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20chem-bond-dissociation%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20chem-bond-dissociation%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/learningmatter-mit-chem-bond-dissociation/install","manifest":"https://www.openagentskill.com/api/registry/manifest/learningmatter-mit-chem-bond-dissociation"}},"supply_profile":{"track":{"slug":"research","label":"Research and knowledge work","shortLabel":"Research","description":"Deep research, source comparison, literature review, RAG, knowledge search, and reports."},"scenario":{"label":"RAG and knowledge","description":"I need my agent to build a RAG workflow over documents and retrieve reliable context.","useCases":[{"slug":"rag-knowledge","title":"RAG and knowledge"},{"slug":"research-agents","title":"Research agents"},{"slug":"workflow-automation","title":"Workflow automation"}]},"applicableAgents":["Claude Code","CLI","Codex","Cursor"],"install":{"ready":true,"command":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-bond-dissociation","primaryTarget":"CLI","targetCount":4},"githubQuality":{"stars":161,"starsLabel":"161","forks":24,"license":"MIT","qualityScore":69,"trustScore":67,"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","No critical security issues identified; the skill runs local computations with standard scientific libraries and does not perform network operations or access sensitive resources.","The SKILL.md excerpt is truncated in the review, but the provided sections are clear and comprehensive.","Quality score needs review"]},"coverageTags":["Research","RAG and knowledge","[chemistry]","agent-skill"]},"audit":{"audit_score":76,"risk_level":"needs_review","risk_label":"Needs review","quality_score":69,"trust_score":67,"maintenance_score":100,"security_score":72,"install_score":92,"warnings":["Dependency or permission surface needs review","Permission surface may require sandboxing","No critical security issues identified; the skill runs local computations with standard scientific libraries and does not perform network operations or access sensitive resources.","The SKILL.md excerpt is truncated in the review, but the provided sections are clear and comprehensive.","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":5.55,"metadata_score":3,"freshness_score":15},"platforms":["Claude Code"],"use_cases":[{"slug":"rag-knowledge","title":"RAG and knowledge","url":"https://www.openagentskill.com/use-cases/rag-knowledge"},{"slug":"research-agents","title":"Research agents","url":"https://www.openagentskill.com/use-cases/research-agents"},{"slug":"workflow-automation","title":"Workflow automation","url":"https://www.openagentskill.com/use-cases/workflow-automation"},{"slug":"github-automation","title":"GitHub automation","url":"https://www.openagentskill.com/use-cases/github-automation"}],"stacks":[{"slug":"rag-knowledge-base","title":"RAG knowledge base","url":"https://www.openagentskill.com/collections/rag-knowledge-base"},{"slug":"content-growth-agent","title":"Content growth agent","url":"https://www.openagentskill.com/collections/content-growth-agent"},{"slug":"research-report-agent","title":"Research report agent","url":"https://www.openagentskill.com/collections/research-report-agent"}],"install":"npx skills add learningmatter-mit/AtomisticSkills --skill chem-bond-dissociation","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-bond-dissociation","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-bond-dissociation\" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation. 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: Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation. 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-bond-dissociation\",\"task\":\"Install chem-bond-dissociation\",\"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-bond-dissociation\" as a Claude Code skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation. 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: Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation. 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-bond-dissociation\",\"task\":\"Install chem-bond-dissociation\",\"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-bond-dissociation\" from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation 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: Calculate homolytic and heterolytic bond dissociation energies (BDEs) for all single bonds in a molecule using MLIPs with RDKit fragmentation. 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-bond-dissociation\",\"task\":\"Install chem-bond-dissociation\",\"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-bond-dissociation","github_repo":"learningmatter-mit/AtomisticSkills","version":"1.0.0","license":"MIT","urls":{"web":"https://www.openagentskill.com/skills/learningmatter-mit-chem-bond-dissociation","repository":"https://github.com/learningmatter-mit/AtomisticSkills/tree/main/.agents/skills/chem-bond-dissociation","api":"/api/agent/skills/learningmatter-mit-chem-bond-dissociation","install_api":"/api/skills/learningmatter-mit-chem-bond-dissociation/install"},"meta":{"created_at":"2026-09-06T11:41:43.403268+00:00","updated_at":"2026-09-06T11:41:43.468559+00:00","agent_friendly":true}}