package.json

{
  "name": "@datagrok/bio",
  "friendlyName": "Bio",
  "author": {
    "name": "Leonid Stolbov",
    "email": "lstolbov@datagrok.ai"
  },
  "version": "2.18.0",
  "description": "Bioinformatics support (import/export of sequences, conversion, visualization, analysis). [See more](https://github.com/datagrok-ai/public/blob/master/packages/Bio/README.md) for details.",
  "repository": {
    "type": "git",
    "url": "https://github.com/datagrok-ai/public.git",
    "directory": "packages/Bio"
  },
  "properties": [
    {
      "name": "FontSize",
      "description": "Font size for monomer symbols in the sequence renderer",
      "propertyType": "int",
      "defaultValue": "12",
      "nullable": false
    },
    {
      "name": "MaxMonomerLength",
      "description": "The max length of monomer symbol displayed without shortening, 'long' to no limit",
      "propertyType": "string",
      "defaultValue": "4",
      "nullable": false
    },
    {
      "name": "TooltipWebLogo",
      "description": "Display WebLogo in a Macromolecule column header tooltip",
      "propertyType": "bool",
      "defaultValue": "true",
      "nullable": false
    },
    {
      "name": "DefaultSeparator",
      "description": "Default separator using to convert sequences into separator notation",
      "propertyType": "string",
      "defaultValue": ".",
      "nullable": false
    }
  ],
  "dependencies": {
    "@biowasm/aioli": "^3.1.0",
    "@datagrok-libraries/bio": "^5.46.0",
    "@datagrok-libraries/chem-meta": "^1.2.7",
    "@datagrok-libraries/math": "^1.2.4",
    "@datagrok-libraries/ml": "^6.7.6",
    "@datagrok-libraries/tutorials": "^1.4.3",
    "@datagrok-libraries/utils": "^4.4.0",
    "datagrok-api": "^1.23.0",
    "@webgpu/types": "^0.1.40",
    "ajv": "^8.12.0",
    "ajv-errors": "^3.0.0",
    "cash-dom": "^8.0.0",
    "css-loader": "^6.7.3",
    "dayjs": "^1.11.4",
    "fastest-levenshtein": "^1.0.16",
    "openchemlib": "^7.2.3",
    "rxjs": "^6.5.5",
    "style-loader": "^3.3.1",
    "umap-js": "^1.3.3",
    "wu": "^2.1.0"
  },
  "devDependencies": {
    "@datagrok-libraries/helm-web-editor": "^1.1.13",
    "@datagrok-libraries/js-draw-lite": "^0.0.10",
    "@datagrok/chem": "^1.13.0",
    "@datagrok/dendrogram": "^1.2.33",
    "@datagrok/helm": "^2.7.0",
    "@types/node": "^17.0.24",
    "@types/wu": "^2.1.44",
    "@typescript-eslint/eslint-plugin": "^8.8.1",
    "@typescript-eslint/parser": "^8.8.1",
    "datagrok-tools": "latest",
    "eslint": "^8.57.1",
    "eslint-config-google": "^0.14.0",
    "eslint-plugin-rxjs": "^5.0.3",
    "source-map-loader": "^5.0.0",
    "ts-loader": "^9.5.1",
    "typescript": "^5.5.3",
    "webpack": "^5.92.1",
    "webpack-bundle-analyzer": "^4.10.2",
    "webpack-cli": "^5.1.4"
  },
  "scripts": {
    "link-api": "npm link datagrok-api",
    "link-bio": "npm link @datagrok-libraries/bio",
    "link-ml": "npm link @datagrok-libraries/ml",
    "link-utils": "npm link @datagrok-libraries/utils",
    "link-all": "npm link @datagrok-libraries/chem-meta datagrok-api @datagrok-libraries/utils @datagrok-libraries/math @datagrok-libraries/ml @datagrok-libraries/bio @datagrok-libraries/tutorials",
    "debug-sequences1": "webpack && grok publish",
    "release-sequences1": "webpack && grok publish --release",
    "build-sequences1": "webpack",
    "build": "webpack",
    "build-all": "npm --prefix ./../../libraries/chem-meta run build && npm --prefix ./../../js-api run build && npm --prefix ./../../libraries/utils run build && npm --prefix ./../../libraries/math run build && npm --prefix ./../../libraries/ml run build && npm --prefix ./../../libraries/bio run build && npm --prefix ./../../libraries/tutorials run build && npm run build",
    "debug-sequences1-local": "webpack && grok publish local",
    "release-sequences1-local": "webpack && grok publish local --release",
    "debug-sequences1-dev": "webpack && grok publish dev",
    "release-sequences1-dev": "webpack && grok publish dev --release",
    "debug-sequences1-public": "webpack && grok publish public",
    "release-sequences1-public": "webpack && grok publish public --release",
    "lint": "eslint \"./src/**/*.ts\"",
    "lint-fix": "eslint \"./src/**/*.ts\" --fix",
    "test": "grok test",
    "test-local": "grok test --host localhost",
    "build-bio-local": "npm --prefix ./../../js-api run build && npm --prefix ./../../libraries/utils run build && npm --prefix ./../../libraries/ml run build && npm run build && npm --prefix ./../../libraries/bio run build && npm run build",
    "analyze": "webpack --profile --json > ./stats.json && npx webpack-bundle-analyzer ./stats.json"
  },
  "canEdit": [
    "Developers"
  ],
  "canView": [
    "All users"
  ],
  "sources": [
    "css/helm.css",
    "common/openchemlib-full.js"
  ],
  "category": "Bioinformatics",
  "meta": {
    "dartium": false,
    "menu": {
      "Bio": {
        "Analyze": {
          "SAR...": null,
          "Sequence Space...": null,
          "Hierarchical Clustering...": null,
          "Activity Cliffs...": null,
          "Sequence Space": null,
          "MSA...": null,
          "Composition": null
        },
        "Search": {
          "Diversity Search": null,
          "Similarity Search": null,
          "Subsequence Search...": null
        },
        "Calculate": {
          "Identity...": null,
          "Similarity...": null
        },
        "Convert": {
          "Split to Monomerts...": null,
          "Get Region...": null,
          "Notation...": null,
          "SDF to JSON Library...": null,
          "To Atomic Level...": null
        },
        "Manage": {
          "Monomer Libraries": null
        },
        "PolyTool": {
          "Convert...": null,
          "Enumerate Chem...": null,
          "Enumerate HELM...": null
        }
      }
    }
  }
}