[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M6DB4761M99M5EQGFZDNB4JK":3,"skill-same:01M6DB4761M99M5EQGFZDNB4JK":67},{"skillNo":4,"name":5,"nameZh":6,"description":7,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":16,"categories":17,"keywords":23,"publishedAt":42,"linkOnly":43,"markdownContent":44,"markdownBody":45,"frontMatter":46,"refName":47,"commitSha":48,"skillDirectory":49,"forksCount":14,"repositoryHtmlUrl":50,"repositoryHomepageUrl":6,"ownerHtmlUrl":51,"ownerBlogUrl":6,"ownerDescription":6,"updatedAt":52,"install":53,"resources":66},"01M6DB4761M99M5EQGFZDNB4JK","cheminformatics-rdkit",null,"Use to drive the standalone rdkit MCP server (tandemai-inc\u002Frdkit-mcp-server, 74 tools, MIT) for license-free chemistry - molecular descriptors, fingerprints, similarity, substructure search, and scaffold analysis on SMILES\u002Fstructures. Covers the stdio registration and two install gotchas. Use when a chemistry question needs RDKit and does not need a Schrodinger license.","Prekzursil\u002Fagent-skills-toolchain","Prekzursil","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F54636077?v=4","01M6DACZ1PCQHD99SCR1YXG28B","Andrei Mihai Visalon","01M6DACZ670WZF535V3WYYSS4Z",0,"MIT","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002F.agents\u002Fskills\u002Fcheminformatics-rdkit\u002FSKILL.md",[18],{"categoryNo":19,"categoryName":20,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000023","Skill与智能体开发","SCENARIO","使用场景",[24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41],"cheminformatics rdkit","cheminformatics","rdkit","question","free","molecular","registration","drive","use","install","MCP","analysis","Tools","server","search","license","scaffold","mcp server","2026-11-10 10:12:30",false,"---\nname: cheminformatics-rdkit\ndescription: Use to drive the standalone rdkit MCP server (tandemai-inc\u002Frdkit-mcp-server, 74 tools, MIT) for license-free chemistry - molecular descriptors, fingerprints, similarity, substructure search, and scaffold analysis on SMILES\u002Fstructures. Covers the stdio registration and two install gotchas. Use when a chemistry question needs RDKit and does not need a Schrodinger license.\n---\n\n# Cheminformatics (RDKit MCP)\n\n## Overview\n\nThe `rdkit` MCP server (tandemai-inc\u002Frdkit-mcp-server, MIT) exposes 74 cheminformatics tools - a license-free, standalone alternative to the bundled-RDKit path inside the `schrodinger` server. Use it for molecular descriptors, fingerprints, similarity, substructure\u002Fscaffold work on SMILES or structures.\n\n- Local checkout: `C:\\Users\\Prekzursil\\source\\repos\\rdkit-mcp-server`\n- Capability categories (call the server's tool list at runtime for exact names): molecular descriptors \u002F physchem properties, fingerprints, similarity scoring, substructure search, and scaffold analysis.\n\n## Registration (verified, stdio)\n\n- command: `C:\\Users\\Prekzursil\\source\\repos\\rdkit-mcp-server\\.venv\\Scripts\\python.exe`\n- args: `C:\\Users\\Prekzursil\\source\\repos\\rdkit-mcp-server\\run_server.py` `--transport` `stdio`\n- env: none.\n- Cross-platform: on POSIX, point command at `rdkit-mcp-server\u002F.venv\u002Fbin\u002Fpython` and keep `run_server.py --transport stdio`.\n\n## Two Install Gotchas (load-bearing)\n\n1. Dead RDKit pin: upstream pins `rdkit==2025.3.1`, which is unavailable. Install a working RDKit (here `rdkit 2026.3.3`) and then install the package WITHOUT re-resolving the dead pin: `pip install --no-deps .` inside the venv. Skipping `--no-deps` re-pulls the broken pin and the install fails.\n2. Transport default: the server defaults to SSE on port 8000. You MUST pass `--transport stdio` in the args (as registered above) or the MCP client cannot connect over stdio.\n\n## Quick Workflow\n\n1. Confirm the `rdkit` MCP server is connected (`claude mcp get rdkit`).\n2. List the server's tools to get exact names\u002Fsignatures - do not assume tool names from the 74-tool set.\n3. Run the chemistry operation (descriptors \u002F fingerprint \u002F similarity \u002F substructure \u002F scaffold) on your SMILES or structure input.\n\n## When to Use vs the Schrodinger Server\n\n- Use `cheminformatics-rdkit` for license-free RDKit cheminformatics (descriptors, fingerprints, similarity, scaffolds) - no Schrodinger token consumed.\n- Use `schrodinger-maestro-driver` when you need suite-specific computation: LigPrep, Glide docking, QikProp ADMET, or `.mae` interchange. Note its `molecule_properties` and `smiles_to_3d` also use a bundled RDKit, so for pure descriptors either server works - prefer this one to avoid touching the licensed suite.\n\n## Common Mistakes\n\n- Forgetting `--transport stdio` and getting an SSE:8000 server the client cannot reach.\n- Running a plain `pip install .` and failing on the dead `rdkit==2025.3.1` pin (use `--no-deps` with a separately installed working RDKit).\n- Inventing tool names instead of listing the server's 74 tools at runtime.\n\n## Related Skills\n\n- `schrodinger-maestro-driver` - licensed suite tools (LigPrep\u002FGlide\u002FQikProp) and its own bundled-RDKit descriptor panel.\n- `ddi-admet-research` - ToolUniverse biomedical knowledge front-end.\n","# Cheminformatics (RDKit MCP)\n\n## Overview\n\nThe `rdkit` MCP server (tandemai-inc\u002Frdkit-mcp-server, MIT) exposes 74 cheminformatics tools - a license-free, standalone alternative to the bundled-RDKit path inside the `schrodinger` server. Use it for molecular descriptors, fingerprints, similarity, substructure\u002Fscaffold work on SMILES or structures.\n\n- Local checkout: `C:\\Users\\Prekzursil\\source\\repos\\rdkit-mcp-server`\n- Capability categories (call the server's tool list at runtime for exact names): molecular descriptors \u002F physchem properties, fingerprints, similarity scoring, substructure search, and scaffold analysis.\n\n## Registration (verified, stdio)\n\n- command: `C:\\Users\\Prekzursil\\source\\repos\\rdkit-mcp-server\\.venv\\Scripts\\python.exe`\n- args: `C:\\Users\\Prekzursil\\source\\repos\\rdkit-mcp-server\\run_server.py` `--transport` `stdio`\n- env: none.\n- Cross-platform: on POSIX, point command at `rdkit-mcp-server\u002F.venv\u002Fbin\u002Fpython` and keep `run_server.py --transport stdio`.\n\n## Two Install Gotchas (load-bearing)\n\n1. Dead RDKit pin: upstream pins `rdkit==2025.3.1`, which is unavailable. Install a working RDKit (here `rdkit 2026.3.3`) and then install the package WITHOUT re-resolving the dead pin: `pip install --no-deps .` inside the venv. Skipping `--no-deps` re-pulls the broken pin and the install fails.\n2. Transport default: the server defaults to SSE on port 8000. You MUST pass `--transport stdio` in the args (as registered above) or the MCP client cannot connect over stdio.\n\n## Quick Workflow\n\n1. Confirm the `rdkit` MCP server is connected (`claude mcp get rdkit`).\n2. List the server's tools to get exact names\u002Fsignatures - do not assume tool names from the 74-tool set.\n3. Run the chemistry operation (descriptors \u002F fingerprint \u002F similarity \u002F substructure \u002F scaffold) on your SMILES or structure input.\n\n## When to Use vs the Schrodinger Server\n\n- Use `cheminformatics-rdkit` for license-free RDKit cheminformatics (descriptors, fingerprints, similarity, scaffolds) - no Schrodinger token consumed.\n- Use `schrodinger-maestro-driver` when you need suite-specific computation: LigPrep, Glide docking, QikProp ADMET, or `.mae` interchange. Note its `molecule_properties` and `smiles_to_3d` also use a bundled RDKit, so for pure descriptors either server works - prefer this one to avoid touching the licensed suite.\n\n## Common Mistakes\n\n- Forgetting `--transport stdio` and getting an SSE:8000 server the client cannot reach.\n- Running a plain `pip install .` and failing on the dead `rdkit==2025.3.1` pin (use `--no-deps` with a separately installed working RDKit).\n- Inventing tool names instead of listing the server's 74 tools at runtime.\n\n## Related Skills\n\n- `schrodinger-maestro-driver` - licensed suite tools (LigPrep\u002FGlide\u002FQikProp) and its own bundled-RDKit descriptor panel.\n- `ddi-admet-research` - ToolUniverse biomedical knowledge front-end.\n",{"name":5,"description":7},"main","a298c929b6cbd662e1fce54302ce520d5ceea1a5",".agents\u002Fskills\u002Fcheminformatics-rdkit","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain","https:\u002F\u002Fgithub.com\u002FPrekzursil","2026-11-02 14:30:57",{"source":8,"skillName":5,"commands":54,"prompt":64,"zipAvailable":65},[55,58,61],{"tool":56,"command":57},"npx","npx skills add Prekzursil\u002Fagent-skills-toolchain --skill cheminformatics-rdkit",{"tool":59,"command":60},"bunx","bunx skills add Prekzursil\u002Fagent-skills-toolchain --skill cheminformatics-rdkit",{"tool":62,"command":63},"pnpm","pnpm dlx skills add Prekzursil\u002Fagent-skills-toolchain --skill cheminformatics-rdkit","安装技能，技能地址：https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002F.agents\u002Fskills\u002Fcheminformatics-rdkit\u002FSKILL.md",true,[],[68,89,113,140,154,170],{"skillNo":69,"name":70,"nameZh":6,"description":71,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":72,"categories":73,"keywords":74,"publishedAt":42},"01M6DF7D7478R55P46REYH4QAC","clarify-requirements","Resolve genuine pre-execution ambiguity by scanning repo context, generating 1-6 grounded options, and asking 1-3 focused questions via AskUserQuestion. NOT for mid-task use (injection risk); NOT when the goal is already unambiguous; use to disambiguate vague prompts before any file edits.","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Fworkspace-hooks\u002Fskills\u002Fclarify-requirements\u002FSKILL.md",[],[75,76,77,78,79,80,81,82,83,32,84,85,86,87,88],"clarify requirements","clarify","requirements","risk","options","task","prompts","goal","scanning","context","repo","injection","execution","file",{"skillNo":90,"name":91,"nameZh":6,"description":92,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":93,"categories":94,"keywords":96,"publishedAt":42},"01M6DF79CA4BHJS66J8EZDBPWJ","openmm-md","Run FREE, open-source, Windows-native GPU molecular dynamics via the openmm-md MCP (OpenMM + CUDA on the local NVIDIA GPU). Use for protein \u002F protein-ligand MD when you want a free stack or are on Windows without a Schrodinger license. Covers the full workflow (prepare, solvate, minimize, equilibrate, production, analyze, mmgbsa) AND an honest decision guide vs Schrodinger Desmond, including how to run Desmond legitimately on Linux or a cloud GPU with a real license. This is a deliberately LESSER free alternative and does NOT replace the schrodinger MCP tools. Do NOT use it to pick a free tool when a validated FEP+, WaterMap, IFD-MD, or Prime MM-GBSA result is actually required.","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Fmcp\u002Fopenmm-md-mcp\u002Fskill\u002Fopenmm-md\u002FSKILL.md",[95],{"categoryNo":19,"categoryName":20,"taxonomyType":21,"taxonomyTypeDesc":22},[97,98,99,100,101,102,103,104,105,106,107,39,108,109,32,28,110,111,112,34],"openmm md","how","decision","pick","linux","analyze","tool","stack","open","NVIDIA","gpu","workflow","windows","molecular dynamics","local","do",{"skillNo":114,"name":115,"nameZh":6,"description":116,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":117,"categories":118,"keywords":125,"publishedAt":42},"01M6DF76C1MG85VEWP8VZCBNMN","visual-review","Take screenshots of web pages and UI using Playwright for visual review and iteration","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fvisual-review\u002FSKILL.md",[119,122],{"categoryNo":120,"categoryName":121,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000003","演示文稿",{"categoryNo":123,"categoryName":124,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000008","测试与质量",[126,127,128,129,130,131,132,133,134,135,98,136,137,138,139],"review","visual","visual review","pages","web","false","iteration","take","check","slides","ui","screenshot","playwright","screenshots",{"skillNo":141,"name":142,"nameZh":6,"description":143,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":144,"categories":145,"keywords":146,"publishedAt":42},"01M6DF73AQVCBZKEN0YXEX9FXP","status","Diagnostic status report — shows metaswarm installation state, project setup, and potential issues","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fstatus\u002FSKILL.md",[],[142,147,148,149,150,151,152,153],"setup","report","project","installation","project setup","issues","state",{"skillNo":155,"name":156,"nameZh":6,"description":157,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":158,"categories":159,"keywords":161,"publishedAt":42},"01M6DF6X6C2XB0P6GX76P7TTYV","start","Use when starting work on any task, when the user mentions metaswarm, or when the user wants to begin tracked development work","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fstart\u002FSKILL.md",[160],{"categoryNo":19,"categoryName":20,"taxonomyType":21,"taxonomyTypeDesc":22},[156,162,80,163,164,165,32,166,167,168,169],"start issue","issue","ready","work on issue","user","work","work on","development",{"skillNo":171,"name":147,"nameZh":6,"description":172,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":173,"categories":174,"keywords":175,"publishedAt":42},"01M6DF6QMJ9AJKFKHHKRT005PQ","Interactive project setup — detects your project, configures metaswarm, writes project-local files","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fsetup\u002FSKILL.md",[],[147,149,111,176,151,177],"files","interactive"]