moorhen 0.0.1 → 0.6.2

package/moorhen.js.LICENSE.txt

@@ -0,0 +1,101 @@
+/* @license
+ * pixi.js - v1.5.1
+ * Copyright (c) 2012-2014, Mat Groves
+ * http://goodboydigital.com/
+ *
+ * pixi.js is licensed under the MIT License.
+ * http://www.opensource.org/licenses/mit-license.php
+ *
+ * http://stackoverflow.com/users/34441/ellisbben
+ * great solution to the problem!
+ * returns the height of the given font
+ *
+ * @method determineFontHeight
+ * @param fontStyle {Object}
+ * @private
+ */
+
+/*!
+	Copyright (c) 2018 Jed Watson.
+	Licensed under the MIT License (MIT), see
+	http://jedwatson.github.io/classnames
+*/
+
+/*!
+    localForage -- Offline Storage, Improved
+    Version 1.10.0
+    https://localforage.github.io/localForage
+    (c) 2013-2017 Mozilla, Apache License 2.0
+*/
+
+/*!
+ * @kurkle/color v0.2.1
+ * https://github.com/kurkle/color#readme
+ * (c) 2022 Jukka Kurkela
+ * Released under the MIT License
+ */
+
+/*!
+ * Chart.js v3.9.1
+ * https://www.chartjs.org
+ * (c) 2022 Chart.js Contributors
+ * Released under the MIT License
+ */
+
+/**
+ * @license React
+ * react-is.production.min.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
+/**
+ * @license React
+ * react-jsx-runtime.production.min.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
+/**
+ * @license React
+ * use-sync-external-store-shim.production.min.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
+/**
+ * @license React
+ * use-sync-external-store-shim/with-selector.production.min.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
+/**
+ * Prism: Lightweight, robust, elegant syntax highlighting
+ *
+ * @license MIT <https://opensource.org/licenses/MIT>
+ * @author Lea Verou <https://lea.verou.me>
+ * @namespace
+ * @public
+ */
+
+/** @license React v16.13.1
+ * react-is.production.min.js
+ *
+ * Copyright (c) Facebook, Inc. and its affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */

package/package.json

@@ -1,19 +1,20 @@
 {
   "name": "moorhen",
-  "version": "0.0.1",
+  "version": "0.6.2",
   "private": false,
   "main": "moorhen.js",
+  "types": "./types/main.d.ts",
+  "homepage": "./",
   "author": "Paul Emsley, Filomeno Sanchez Rodriguez, Martin Noble, Stuart McNicholas",
   "description": "Moorhen molecular graphics",
+  "license": "BSD-3-Clause",
   "repository": {
     "type": "git",
-    "url": "git+https://github.com/stuartjamesmcnicholas/Moorhen.git"
+    "url": "git+https://github.com/moorhen-coot/Moorhen.git"
   },
   "bugs": {
-    "url": "https://github.com/stuartjamesmcnicholas/Moorhen/issues"
+    "url": "https://github.com/moorhen-coot/Moorhen/issues"
   },
-  "homepage": "https://github.com/stuartjamesmcnicholas/Moorhen#readme",
-  "types": "src/types/index.d.ts",
   "keywords": [
     "molecular graphics",
     "moorhen",
@@ -61,22 +62,24 @@
       ]
     }
   },
-  "dependencies": {},
+  "dependencies": { },
   "scripts": {
-    "start": "react-scripts start",
-    "start-tsc": "npx nodemon --trace-warnings",
-    "build": "react-scripts build",
-    "build-npm-registry": "webpack --mode development --devtool inline-source-map --env destination='npmRegistry'",
-    "build-cloud-dev": "webpack  --mode development --devtool inline-source-map --env destination='ccp4Cloud'",
-    "build-cloud": "webpack --mode production --env destination='ccp4Cloud'",
-    "test": "react-scripts test",
-    "eject": "react-scripts eject",
+    "create-version": "npx genversion -e -p ./package.json -d -s ./src/version.js",
+    "transpile-ts-worker": "npx tsc --module es2015 --lib webworker --skipLibCheck public/baby-gru/CootWorker.ts && sed -i.bak '/export {}/d' public/baby-gru/CootWorker.js && rm public/baby-gru/CootWorker.js.bak",
+    "transpile-ts-worker-jest": "npx tsc --module es2015 --lib webworker --skipLibCheck public/baby-gru/CootWorker.ts && sed -i.bak 's/export {}/export { doCootCommand, setModules }/g' public/baby-gru/CootWorker.js && sed -i.bak '/importScripts.*;/d' public/baby-gru/CootWorker.js && sed -i.bak 's/onmessage/function setModules(arg0, arg1) { molecules_container = arg0; cootModule = arg1 }; let postMessage = () => {}; let onmessage/g' public/baby-gru/CootWorker.js && rm public/baby-gru/CootWorker.js.bak",
+    "prestart": "npm run create-version && npm run transpile-ts-worker",
+    "start": "vite",
+    "prebuild": "npm run create-version && npm run transpile-ts-worker",
+    "build": "vite build",
+    "build-release": "npm run prebuild && webpack --mode production --devtool inline-source-map",
     "dev": "concurrently -k \"BROWSER=none npm start\" \"npm:electron\"",
     "electron": "wait-on tcp:3000 && electron-forge start",
-    "package": "react-scripts build && electron-forge package",
-    "make-mac": "react-scripts build && electron-forge make --platform darwin",
-    "make-linux": "react-scripts build && electron-forge make --platform linux",
-    "make-win32": "react-scripts build && electron-forge make --platform win32"
+    "package": "npm run build && electron-forge package",
+    "make-mac": "npm run build && electron-forge make --platform darwin",
+    "make-linux": "npm run build && electron-forge make --platform linux",
+    "make-win32": "npm run build && electron-forge make --platform win32",
+    "create-docs": "npm run create-version && npx jsdoc -c jsdoc.json",
+    "test": "npm run create-version && npx tsc && npm run transpile-ts-worker-jest && ln -s ./public/baby-gru/wasm/moorhen.data ./moorhen.data && node --trace-warnings --experimental-vm-modules --experimental-wasm-threads node_modules/jest/bin/jest.js --forceExit"
   },
   "eslintConfig": {
     "extends": [
@@ -97,13 +100,6 @@
     ]
   },
   "devDependencies": {
-    "@emotion/styled": "^11.10.4",
-    "@mui/icons-material": "^5.10.9",
-    "@mui/material": "^5.10.10",
-    "@emotion/react": "^11.10.4",
-    "@testing-library/jest-dom": "^5.16.4",
-    "@testing-library/user-event": "^13.5.0",
-    "@testing-library/react": "^13.2.0",
     "@babel/preset-env": "^7.20.2",
     "@babel/preset-react": "^7.18.6",
     "@electron-forge/cli": "^6.0.5",
@@ -111,41 +107,50 @@
     "@electron-forge/maker-rpm": "^6.0.5",
     "@electron-forge/maker-squirrel": "^6.0.5",
     "@electron-forge/maker-zip": "^6.0.5",
+    "@emotion/react": "^11.10.4",
+    "@emotion/styled": "^11.10.4",
+    "@mui/icons-material": "^5.10.9",
+    "@mui/lab": "^5.0.0-alpha.140",
+    "@mui/material": "^5.10.10",
+    "@reduxjs/toolkit": "^1.9.7",
+    "@testing-library/jest-dom": "^5.16.4",
+    "@testing-library/react": "^13.2.0",
+    "@testing-library/user-event": "^13.5.0",
     "@types/node": "^18.16.14",
     "@types/react": "^18.2.6",
-    "babel-preset-react-app": "^3.1.2",
+    "@vitejs/plugin-react-swc": "^3.4.1",
+    "acorn": "^8.10.0",
+    "babel-cli": "^6.26.0",
     "babel-core": "^6.26.3",
     "babel-loader": "^9.1.0",
     "babel-preset-env": "^1.7.0",
+    "babel-preset-react-app": "^3.1.2",
+    "bootstrap": "^5.1.3",
+    "chart.js": "^3.7.1",
+    "chartjs-plugin-annotation": "^2.1.2",
     "concurrently": "^7.6.0",
     "copy-webpack-plugin": "^11.0.0",
     "css-loader": "^6.7.2",
+    "d3": "^5.15.0",
     "electron": "^23.1.3",
     "electron-devtools-installer": "^3.2.0",
-    "html-webpack-plugin": "^5.5.0",
-    "nodemon": "^2.0.22",
-    "style-loader": "^3.3.1",
-    "ts-loader": "^9.4.3",
-    "ts-node": "^10.9.1",
-    "webpack": "^5.75.0",
-    "webpack-cli": "^5.0.1",
-    "webpack-dev-server": "^4.11.1",
-    "webpack-node-externals": "^3.0.0",
-    "worker-loader": "^3.0.8",
-    "html-react-parser": "^1.4.14",
-    "babel-cli": "^6.26.0",
-    "bootstrap": "^5.1.3",
-    "chart.js": "^3.7.1",
-    "chartjs-plugin-annotation": "^2.1.2",
-    "d3": "^5.15.0",
     "electron-is-dev": "^2.0.0",
     "electron-squirrel-startup": "^1.0.0",
     "express": "^4.18.2",
+    "genversion": "^3.1.1",
     "gl-matrix": "^3.4.3",
+    "html-react-parser": "^1.4.14",
+    "html-webpack-plugin": "^5.5.0",
+    "jest": "^27.5.1",
+    "jsdoc": "^4.0.2",
     "localforage": "^1.10.0",
+    "mini-css-extract-plugin": "^2.7.6",
     "nested-worker": "git+https://github.com/johanholmerin/nested-worker.git#semver:^1.0.0",
     "nightingale-linegraph-track": "^3.8.10",
+    "node-fetch": "^2.7.0",
+    "nodemon": "^2.0.22",
     "pako": "^2.0.4",
+    "parcel-bundler": "^1.12.5",
     "pca-js": "^1.0.2",
     "plotly.js": "^2.12.1",
     "prismjs": "^1.29.0",
@@ -155,22 +160,38 @@
     "protvista-sequence": "^3.5.1",
     "protvista-track": "^3.4.0",
     "rc-tree": "4.2.2",
-    "styled-components": "^5.3.9",
-    "typescript": "^4.0.0",
-    "util": "^0.12.5",
-    "uuid": "^9.0.0",
-    "wait-on": "^7.0.1",
-    "web-vitals": "^2.1.4",
+    "re-resizable": "^6.9.11",
     "react": "^18.1.0",
-    "react-dom": "^18.1.0",
     "react-bootstrap": "^2.3.1",
     "react-bootstrap-typeahead": "^6.0.0-alpha.11",
     "react-chartjs-2": "^4.1.0",
     "react-color": "^2.19.3",
+    "react-colorful": "^5.6.1",
+    "react-dom": "^18.1.0",
     "react-draggable": "^4.4.5",
     "react-plotly.js": "^2.5.1",
-    "react-scripts": "5.0.1",
+    "react-redux": "^8.1.3",
     "react-simple-code-editor": "^0.13.1",
-    "reactcss": "^1.2.3"
+    "reactcss": "^1.2.3",
+    "style-loader": "^3.3.1",
+    "styled-components": "^5.3.9",
+    "taffydb": "^2.7.3",
+    "ts-loader": "^9.4.3",
+    "ts-node": "^10.9.1",
+    "typescript": "^4.0.0",
+    "util": "^0.12.5",
+    "uuid": "^9.0.0",
+    "vite": "^4.5.0",
+    "vite-plugin-checker": "^0.6.2",
+    "vite-plugin-cross-origin-isolation": "^0.1.6",
+    "vite-plugin-top-level-await": "^1.3.1",
+    "vite-plugin-wasm": "^3.2.2",
+    "wait-on": "^7.0.1",
+    "web-vitals": "^2.1.4",
+    "webpack": "^5.86.0",
+    "webpack-cli": "^5.0.1",
+    "webpack-dev-server": "^4.11.1",
+    "webpack-node-externals": "^3.0.0",
+    "worker-loader": "^3.0.8"
   }
 }

package/types/emscriptem.d.ts

@@ -0,0 +1,25 @@
+export namespace emscriptem {
+
+    type instance<T> = {
+        clone: () => T;
+        delete: () => void;
+        isDeleted: () => boolean;
+    }
+
+    interface vector<T> extends instance<T> {
+        size: () => number;
+        get: (idx: number) => T;
+        at: (idx: number) => T;
+        length: () => number;
+        push_back: (arg0: T) => void;
+    }
+
+    interface map<T1, T2> extends instance<T1> {
+        set(idx: T2, value: T1): void;
+        size: () => number;
+        get: (idx: T2) => T1;
+        length: () => number;
+        keys: () => vector<T2>;
+    }
+    
+}

package/types/gemmi.d.ts

@@ -0,0 +1,115 @@
+import { emscriptem } from "./emscriptem"
+
+export namespace gemmi {
+    interface NeighborSearch extends emscriptem.instance<NeighborSearch> {
+        populate: (arg0: boolean) => void;
+        find_atoms: (arg0: Position, arg1: string, arg2: number) => emscriptem.vector<Mark>;
+        find_neighbors: (arg0: Atom, arg1: number, ag2: number) =>  emscriptem.vector<Mark>;
+    }
+    interface Mark extends emscriptem.instance<Mark> {
+        x: number;
+        y: number;
+        z: number;
+        altloc: number;
+        element: emscriptem.instance<string>;
+        chain_idx: number;
+        residue_idx: number;
+        atom_idx: number;
+        image_idx: number;
+        pos: () => Position;
+    }
+    interface Position extends emscriptem.instance<Position> {
+        x: number;
+        y: number;
+        z: number;
+    }
+    interface Fractional extends emscriptem.instance<Fractional> {
+        x: number;
+        y: number;
+        z: number;
+    }
+    interface cifDocument extends emscriptem.instance<Fractional> {
+        blocks: emscriptem.vector<cifBlock>;
+    }
+    interface cifBlock extends emscriptem.instance<cifBlock> {
+        name: string;
+        find_loop: (arg0: string) => cifLoop;
+    }
+    interface cifLoop extends emscriptem.instance<cifLoop> {
+        length: () => number;
+        str: (arg0: number) => string;
+    }
+    interface Selection extends emscriptem.instance<Selection> {
+        residue_names: any;
+        matches_model: (model: Model) => boolean;
+        matches_chain: (chain: Chain) => boolean;
+        matches_residue: (residue: Residue) => boolean;
+        matches_atom: (atom: Atom) => boolean;
+        models: (struct: Structure) => emscriptem.vector<Model>;
+        chains: (model: Model) => emscriptem.vector<Chain>;
+        residues: (chain: Chain) => emscriptem.vector<Residue>;
+        atoms: (res: Residue) => emscriptem.vector<Atom>;
+        chain_ids: SelectionChainList;
+        to_seqid: SelectionSeqId;
+        from_seqid: SelectionSeqId;
+    }
+    interface SelectionResidueNamesList extends emscriptem.instance<SelectionResidueNamesList> {
+        str: () => string;
+        all: boolean;
+    }
+    interface SelectionChainList extends emscriptem.instance<SelectionChainList> {
+        str: () => string;
+        all: boolean;
+    }
+    interface SelectionSeqId extends emscriptem.instance<SelectionSeqId> {
+        str: () => string;
+        empty: () => boolean;
+        seqnum: number;
+    }
+    interface Atom extends emscriptem.instance<Atom> {
+        name: string;
+        element: emscriptem.instance<string>;
+        pos: { x: number, y: number, z: number, delete: () => void };
+        altloc: number;
+        charge: number;
+        b_iso: number;
+        serial: number;
+        has_altloc: () => boolean;
+    }
+    interface ResidueSeqId extends emscriptem.instance<ResidueSeqId> {
+        str: () => string;
+        num: { value: number };
+    }
+    interface Residue extends emscriptem.instance<Residue> {
+        name: string;
+        seqid: ResidueSeqId;
+        atoms: emscriptem.vector<Atom>;
+    }
+    interface Chain extends emscriptem.instance<Chain> {
+        residues: emscriptem.vector<Residue>;
+        name: string;
+        get_ligands: () => emscriptem.vector<Residue>;
+        get_polymer_const: () => emscriptem.instance<number>;
+        get_ligands_const: () => emscriptem.vector<Residue>;
+    }
+    interface Model extends emscriptem.instance<Model> {
+        name: string;
+        chains: emscriptem.vector<Chain>;
+    }
+    interface UnitCell extends emscriptem.instance<UnitCell> {
+        a: number;
+        b: number;
+        c: number;
+        alpha: number;
+        beta: number;
+        gamma: number;
+        orthogonalize: (arg0: emscriptem.instance<Fractional>) => Position;
+        set: (a: number, b: number, c: number, alpha: number, beta: number, gamma: number) => void
+    }
+    interface Structure extends emscriptem.instance<Structure> {
+        models: emscriptem.vector<Model>;
+        cell: UnitCell;
+        first_model: () => Model;
+        remove_empty_chains: () => void;
+    }
+}

package/types/index.d.ts

@@ -0,0 +1,18 @@
+import { libcootApi } from "./libcoot";
+
+export {};
+
+declare global {
+    namespace JSX {
+        interface IntrinsicElements {
+          "protvista-manager": ProtvistaManager;
+          "protvista-sequence": ProtvistaSequence;
+          "protvista-navigation": ProtvistaNavigation;
+          "protvista-track": ProtvistaTrack;
+        }
+    }    
+    interface Window {
+        CCP4Module: libcootApi.CCP4ModuleType;
+    }
+}
+