{"query":"packmol-generate-mixture","filters":{"category":null,"platform":null,"track":null,"safety":null,"include_blocked":false,"min_stars":0},"total":1,"skills":[{"rank":1,"match_type":"exact","match_score":99,"raw_match_score":852.2,"semantic_relevance":100,"ranking_signals":{"retrieval":832,"semantic":100,"quality":9.5,"projectPopularity":10.7,"verifiedOutcomes":0,"verifiedSource":0},"slug":"jinzhezenggroup-packmol-generate-mixture","name":"packmol-generate-mixture","description":"A tool for generating initial packed molecular configurations (XYZ format) from single-molecule structures by calculating box dimensions, writing input scripts, and executing Packmol. 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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\":\"jinzhezenggroup-packmol-generate-mixture\",\"task\":\"Install packmol-generate-mixture\",\"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 \"packmol-generate-mixture\" from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/packmol-generate-mixture 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: A tool for generating initial packed molecular configurations (XYZ format) from single-molecule structures by calculating box dimensions, writing input scripts, and executing Packmol. USE WHEN you need to randomly pack a specific number of molecules into a simulation box (defined by target density or fixed lengths) to create starting geometries for molecular dynamics or related computational chemistry workflows. 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\":\"jinzhezenggroup-packmol-generate-mixture\",\"task\":\"Install packmol-generate-mixture\",\"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/jinzhezenggroup-packmol-generate-mixture/install","manifest_url":"https://www.openagentskill.com/api/registry/manifest/jinzhezenggroup-packmol-generate-mixture"},"trust":{"score":78,"label":"Strong shortlist","version":"trust-score-v4","install_policy":"human_review_before_install","evidence":{"stars":"135 GitHub stars","repoActivity":"135 stars, 27 forks","lastPushed":"1d since push","license":"LGPL-3.0-or-later","repository":"https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/packmol-generate-mixture","install":"npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill packmol-generate-mixture","installSafety":"standard package or runtime install path","permissionSurface":"no high-risk permission surface in public metadata","documentation":"Thin public metadata","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":["research","agent-skill"],"known_risks":["Quality score needs review","Stars/forks activity: 135 stars, 27 forks; issue activity unavailable in current metadata","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"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":82,"risk_level":"safe_to_try","risk_label":"Safe to try","warnings":["Quality score needs review","Stars/forks activity: 135 stars, 27 forks; issue activity unavailable in current metadata","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context"]},"safety_gate":{"tier":"reviewed","label":"Reviewed","auto_install_policy":"review","auto_install_allowed":false,"human_review_required":true,"blocked":false,"recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow."},"quality":{"score":68,"label":"Promising"},"supply":{"track":"Research and knowledge work","scenario":"Research agents","maintenance":"1d since push","risk":"Safe to try"},"alternative_skills":[],"do_not_use_when":["teams that need a vendor-supported SLA","high-compliance environments without internal security review","No OpenAgentSkill engagement data yet","Quality score needs review","Stars/forks activity: 135 stars, 27 forks; issue activity unavailable in current metadata","README/SKILL.md completeness: Public metadata needs stronger README/SKILL.md context","Production credentials, payments, or irreversible account changes without explicit human review","Sensitive private data before reviewing repository code, license, and permission surface"],"agent_contract":{"task_input":"Use packmol-generate-mixture in an agent workflow","recommended_action":"Review the audit page, then allow agent install in a sandboxed workflow.","install_policy":"review","minimum_review_before_use":["Trust: 78/100 Strong shortlist","Audit: 82/100 Safe to try","Safety: 70/100 Review before install","Review repository, license, install command, and permission surface before production use."],"expected_agent_output":{"selected_skill":"jinzhezenggroup-packmol-generate-mixture (packmol-generate-mixture)","install_command":"npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill packmol-generate-mixture","risk_summary":"Safe to try; Reviewed; 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":"jinzhezenggroup-packmol-generate-mixture","task":"Use packmol-generate-mixture 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/jinzhezenggroup-packmol-generate-mixture","api":"https://www.openagentskill.com/api/agent/skills/jinzhezenggroup-packmol-generate-mixture","audit":"https://www.openagentskill.com/skills/jinzhezenggroup-packmol-generate-mixture/audit","eval":"https://www.openagentskill.com/api/agent/evals?slug=jinzhezenggroup-packmol-generate-mixture&task=Use%20packmol-generate-mixture%20in%20an%20agent%20workflow&max_risk=medium","resolve":"https://www.openagentskill.com/api/agent/resolve?task=Use%20packmol-generate-mixture%20in%20an%20agent%20workflow&agent=codex&max_risk=medium","receipt":"https://www.openagentskill.com/api/agent/receipt?task=Use%20packmol-generate-mixture%20in%20an%20agent%20workflow&agent=codex&max_risk=medium&format=text","install":"https://www.openagentskill.com/api/skills/jinzhezenggroup-packmol-generate-mixture/install","manifest":"https://www.openagentskill.com/api/registry/manifest/jinzhezenggroup-packmol-generate-mixture"}},"platforms":["Claude Code"],"use_cases":[{"slug":"research-agents","title":"Research agents","url":"https://www.openagentskill.com/use-cases/research-agents"},{"slug":"rag-knowledge","title":"RAG and knowledge","url":"https://www.openagentskill.com/use-cases/rag-knowledge"},{"slug":"browser-automation","title":"Browser automation","url":"https://www.openagentskill.com/use-cases/browser-automation"},{"slug":"workflow-automation","title":"Workflow automation","url":"https://www.openagentskill.com/use-cases/workflow-automation"}],"install":"npx skills add jinzhezenggroup/computational-chemistry-agent-skills --skill packmol-generate-mixture","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 jinzhezenggroup-packmol-generate-mixture","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 \"packmol-generate-mixture\" agent skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/packmol-generate-mixture. 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: A tool for generating initial packed molecular configurations (XYZ format) from single-molecule structures by calculating box dimensions, writing input scripts, and executing Packmol. USE WHEN you need to randomly pack a specific number of molecules into a simulation box (defined by target density or fixed lengths) to create starting geometries for molecular dynamics or related computational chemistry workflows. 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\":\"jinzhezenggroup-packmol-generate-mixture\",\"task\":\"Install packmol-generate-mixture\",\"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 \"packmol-generate-mixture\" as a Claude Code skill from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/packmol-generate-mixture. 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: A tool for generating initial packed molecular configurations (XYZ format) from single-molecule structures by calculating box dimensions, writing input scripts, and executing Packmol. USE WHEN you need to randomly pack a specific number of molecules into a simulation box (defined by target density or fixed lengths) to create starting geometries for molecular dynamics or related computational chemistry workflows. 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\":\"jinzhezenggroup-packmol-generate-mixture\",\"task\":\"Install packmol-generate-mixture\",\"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 \"packmol-generate-mixture\" from https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/packmol-generate-mixture 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: A tool for generating initial packed molecular configurations (XYZ format) from single-molecule structures by calculating box dimensions, writing input scripts, and executing Packmol. USE WHEN you need to randomly pack a specific number of molecules into a simulation box (defined by target density or fixed lengths) to create starting geometries for molecular dynamics or related computational chemistry workflows. 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\":\"jinzhezenggroup-packmol-generate-mixture\",\"task\":\"Install packmol-generate-mixture\",\"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/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/packmol-generate-mixture","github_repo":"jinzhezenggroup/computational-chemistry-agent-skills","version":"1.0.0","license":"LGPL-3.0-or-later","updated_at":"2026-09-04T13:10:45.956277+00:00","canonical_key":"jinzhezenggroup/computational-chemistry-agent-skills#data-processing/packmol-generate-mixture","recommendation_reasons":["Matches task terms: packmol, generate, mixture","Install handoff is available","Repository freshness signal is available","Registry match score 99"],"urls":{"web":"https://www.openagentskill.com/skills/jinzhezenggroup-packmol-generate-mixture","api":"https://www.openagentskill.com/api/agent/skills/jinzhezenggroup-packmol-generate-mixture","install_api":"https://www.openagentskill.com/api/skills/jinzhezenggroup-packmol-generate-mixture/install","audit":"https://www.openagentskill.com/skills/jinzhezenggroup-packmol-generate-mixture/audit","repository":"https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/master/data-processing/packmol-generate-mixture"}}],"meta":{"endpoint":"/api/skills/search","canonical_agent_endpoint":"/api/agent/resolve","ranking_model":"hybrid-v2-task-fit-quality-outcomes","shortlist_policy":"Return one best match plus up to four distinct alternatives; suppress unrelated direct-name matches.","lookup_intent":true,"exact_match_found":true,"match_counts":{"exact":1,"near":0,"related":0},"no_match_message":null,"safety_policy":"Blocked candidates are excluded by default. Pass include_blocked=true only for manual audit workflows.","agent_friendly":true,"api_version":"1.0","generated_at":"2026-09-06T06:43:41.148Z"}}