[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M6DBKKW3JAGBT3CK06SW6X2K":3,"skill-same:01M6DBKKW3JAGBT3CK06SW6X2K":66},{"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":18,"publishedAt":31,"linkOnly":32,"markdownContent":33,"markdownBody":34,"frontMatter":35,"refName":36,"commitSha":37,"skillDirectory":38,"forksCount":14,"repositoryHtmlUrl":39,"repositoryHomepageUrl":6,"ownerHtmlUrl":40,"ownerBlogUrl":6,"ownerDescription":6,"updatedAt":41,"install":42,"resources":55},"01M6DBKKW3JAGBT3CK06SW6X2K","mol-filters",null,"Use when mol filters is needed. Synthetic-accessibility SA_Score plus PAINS\u002FBRENK\u002FNIH structural-alert filtering (RDKit FilterCatalog) for a SMILES or SDF. Use when triaging docking or virtual-screening hits, flagging pan-assay-interference \u002F problematic scaffolds, or scoring how hard a molecule.","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\u002Fmol-filters\u002FSKILL.md",[],[19,20,21,22,23,24,25,26,27,28,29,30],"filters","mol filters","accessibility","rdkit","how","virtual","filtering","use","alert","scoring","docking","structural","2026-11-10 10:12:30",false,"---\nname: mol-filters\ndescription: \"Use when mol filters is needed. Synthetic-accessibility SA_Score plus PAINS\u002FBRENK\u002FNIH structural-alert filtering (RDKit FilterCatalog) for a SMILES or SDF. Use when triaging docking or virtual-screening hits, flagging pan-assay-interference \u002F problematic scaffolds, or scoring how hard a molecule.\"\nlicense: MIT\n---\n\n# mol-filters — SA_Score + medicinal-chemistry structural alerts\n\nFills a real gap: the `rdkit` MCP server exposes descriptors\u002Ffingerprints but NOT Ertl's\nsynthetic-accessibility score or RDKit's `FilterCatalog` (PAINS\u002FBRENK\u002FNIH alerts). This skill\nadds both as a small CLI, so you can triage screening\u002Fdocking hits without a Schrodinger license.\n\n## Run\n\nUse the interpreter that has RDKit — the rdkit MCP server's venv:\n\n```\n\"C:\\Users\\Prekzursil\\source\\repos\\rdkit-mcp-server\\.venv\\Scripts\\python.exe\" \\\n  C:\\Users\\Prekzursil\\.agents\\skills\\mol-filters\\scripts\\mol_filters.py \u003CINPUT> [--json]\n```\n\nInput modes:\n- single SMILES:  `... mol_filters.py \"CC(=O)Oc1ccccc1C(=O)O\"`\n- one-per-line:   `... mol_filters.py --smiles-file mols.smi`  (blank \u002F `#` lines skipped; `\u003CSMILES> \u003Cname>` ok)\n- SDF library:    `... mol_filters.py --sdf library.sdf`\n- add `--json` for machine-readable output.\n\n## What it reports (per molecule)\n\n1. **SA_Score** — Ertl & Schuffenhauer (2009) synthetic accessibility, **1 = easy … 10 = hard**\n   to synthesize. Loaded from RDKit's Contrib tree; if a wheel omits Contrib the score degrades\n   to `null` with a note and the alert filters still run.\n2. **Structural-alert hits** across `PAINS_A\u002FB\u002FC`, `BRENK`, `NIH`, `ZINC` — each hit names the\n   catalog and the matched alert (e.g. `PAINS_B: rhod_sat_A(33)`). Zero hits = \"Alerts: none\".\n\nInvalid SMILES are flagged `[INVALID]` and skipped, never crash the run.\n\n## Acceptance (verified 2026-07-04, rdkit 2026.03.3)\n\n- `\"CC(=O)Oc1ccccc1C(=O)O\"` (aspirin) → SA_Score ≈ **1.58**, no alerts.\n- `\"O=C1CSC(=S)N1\"` (rhodanine) → SA_Score ≈ **3.46**, alerts: `PAINS_B: rhod_sat_A(33)`,\n  `Brenk: Thiocarbonyl_group`. A correct run shows a low SA_Score for a simple drug and fires\n  ≥1 alert on a known PAINS\u002FBRENK scaffold.\n\n## Notes\n\n- SA_Score is NOT importable by default; the script locates `sascorer` via\n  `RDConfig.RDContribDir\u002FSA_Score` and caches it. A high SA_Score does not mean \"bad\" — read it\n  alongside the alerts (a clean, easy-to-make hit is ideal).\n- For descriptors (TPSA, logP, HBD\u002FHBA, rings) use the `rdkit` MCP or the `cheminformatics-rdkit`\n  skill; for docking\u002FADMET use `structure-based-screening` \u002F `schrodinger-maestro-driver`.\n","# mol-filters — SA_Score + medicinal-chemistry structural alerts\n\nFills a real gap: the `rdkit` MCP server exposes descriptors\u002Ffingerprints but NOT Ertl's\nsynthetic-accessibility score or RDKit's `FilterCatalog` (PAINS\u002FBRENK\u002FNIH alerts). This skill\nadds both as a small CLI, so you can triage screening\u002Fdocking hits without a Schrodinger license.\n\n## Run\n\nUse the interpreter that has RDKit — the rdkit MCP server's venv:\n\n```\n\"C:\\Users\\Prekzursil\\source\\repos\\rdkit-mcp-server\\.venv\\Scripts\\python.exe\" \\\n  C:\\Users\\Prekzursil\\.agents\\skills\\mol-filters\\scripts\\mol_filters.py \u003CINPUT> [--json]\n```\n\nInput modes:\n- single SMILES:  `... mol_filters.py \"CC(=O)Oc1ccccc1C(=O)O\"`\n- one-per-line:   `... mol_filters.py --smiles-file mols.smi`  (blank \u002F `#` lines skipped; `\u003CSMILES> \u003Cname>` ok)\n- SDF library:    `... mol_filters.py --sdf library.sdf`\n- add `--json` for machine-readable output.\n\n## What it reports (per molecule)\n\n1. **SA_Score** — Ertl & Schuffenhauer (2009) synthetic accessibility, **1 = easy … 10 = hard**\n   to synthesize. Loaded from RDKit's Contrib tree; if a wheel omits Contrib the score degrades\n   to `null` with a note and the alert filters still run.\n2. **Structural-alert hits** across `PAINS_A\u002FB\u002FC`, `BRENK`, `NIH`, `ZINC` — each hit names the\n   catalog and the matched alert (e.g. `PAINS_B: rhod_sat_A(33)`). Zero hits = \"Alerts: none\".\n\nInvalid SMILES are flagged `[INVALID]` and skipped, never crash the run.\n\n## Acceptance (verified 2026-07-04, rdkit 2026.03.3)\n\n- `\"CC(=O)Oc1ccccc1C(=O)O\"` (aspirin) → SA_Score ≈ **1.58**, no alerts.\n- `\"O=C1CSC(=S)N1\"` (rhodanine) → SA_Score ≈ **3.46**, alerts: `PAINS_B: rhod_sat_A(33)`,\n  `Brenk: Thiocarbonyl_group`. A correct run shows a low SA_Score for a simple drug and fires\n  ≥1 alert on a known PAINS\u002FBRENK scaffold.\n\n## Notes\n\n- SA_Score is NOT importable by default; the script locates `sascorer` via\n  `RDConfig.RDContribDir\u002FSA_Score` and caches it. A high SA_Score does not mean \"bad\" — read it\n  alongside the alerts (a clean, easy-to-make hit is ideal).\n- For descriptors (TPSA, logP, HBD\u002FHBA, rings) use the `rdkit` MCP or the `cheminformatics-rdkit`\n  skill; for docking\u002FADMET use `structure-based-screening` \u002F `schrodinger-maestro-driver`.\n",{"name":5,"license":15,"description":7},"main","a298c929b6cbd662e1fce54302ce520d5ceea1a5",".agents\u002Fskills\u002Fmol-filters","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain","https:\u002F\u002Fgithub.com\u002FPrekzursil","2026-11-02 14:30:57",{"source":8,"skillName":5,"commands":43,"prompt":53,"zipAvailable":54},[44,47,50],{"tool":45,"command":46},"npx","npx skills add Prekzursil\u002Fagent-skills-toolchain --skill mol-filters",{"tool":48,"command":49},"bunx","bunx skills add Prekzursil\u002Fagent-skills-toolchain --skill mol-filters",{"tool":51,"command":52},"pnpm","pnpm dlx skills add Prekzursil\u002Fagent-skills-toolchain --skill mol-filters","安装技能，技能地址：https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002F.agents\u002Fskills\u002Fmol-filters\u002FSKILL.md",true,[56,62],{"path":57,"resourceType":58,"resourceTypeDesc":59,"sizeBytes":60,"sourceHtmlUrl":61},"scripts\u002Fmol_filters.py","SCRIPT","脚本",8237,"https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002F.agents\u002Fskills\u002Fmol-filters\u002Fscripts\u002Fmol_filters.py",{"path":63,"resourceType":58,"resourceTypeDesc":59,"sizeBytes":64,"sourceHtmlUrl":65},"tests\u002Ftest_mol_filters.py",6478,"https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002F.agents\u002Fskills\u002Fmol-filters\u002Ftests\u002Ftest_mol_filters.py",[67,88,118,145,159,175],{"skillNo":68,"name":69,"nameZh":6,"description":70,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":71,"categories":72,"keywords":73,"publishedAt":31},"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",[],[74,75,76,77,78,79,80,81,82,26,83,84,85,86,87],"clarify requirements","clarify","requirements","risk","options","task","prompts","goal","scanning","context","repo","injection","execution","file",{"skillNo":89,"name":90,"nameZh":6,"description":91,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":92,"categories":93,"keywords":99,"publishedAt":31},"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",[94],{"categoryNo":95,"categoryName":96,"taxonomyType":97,"taxonomyTypeDesc":98},"01JBSEEDCAT000000000000023","Skill与智能体开发","SCENARIO","使用场景",[100,23,101,102,103,104,105,106,107,108,109,110,111,112,26,113,114,115,116,117],"openmm md","decision","pick","linux","analyze","tool","stack","open","NVIDIA","gpu","license","workflow","windows","free","molecular dynamics","local","do","MCP",{"skillNo":119,"name":120,"nameZh":6,"description":121,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":122,"categories":123,"keywords":130,"publishedAt":31},"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",[124,127],{"categoryNo":125,"categoryName":126,"taxonomyType":97,"taxonomyTypeDesc":98},"01JBSEEDCAT000000000000003","演示文稿",{"categoryNo":128,"categoryName":129,"taxonomyType":97,"taxonomyTypeDesc":98},"01JBSEEDCAT000000000000008","测试与质量",[131,132,133,134,135,136,137,138,139,140,23,141,142,143,144],"review","visual","visual review","pages","web","false","iteration","take","check","slides","ui","screenshot","playwright","screenshots",{"skillNo":146,"name":147,"nameZh":6,"description":148,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":149,"categories":150,"keywords":151,"publishedAt":31},"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",[],[147,152,153,154,155,156,157,158],"setup","report","project","installation","project setup","issues","state",{"skillNo":160,"name":161,"nameZh":6,"description":162,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":163,"categories":164,"keywords":166,"publishedAt":31},"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",[165],{"categoryNo":95,"categoryName":96,"taxonomyType":97,"taxonomyTypeDesc":98},[161,167,79,168,169,170,26,171,172,173,174],"start issue","issue","ready","work on issue","user","work","work on","development",{"skillNo":176,"name":152,"nameZh":6,"description":177,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":178,"categories":179,"keywords":180,"publishedAt":31},"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",[],[152,154,115,181,156,182],"files","interactive"]