molstar 3.3.0 → 3.5.0

package/package.json

@@ -1,160 +1,160 @@
-{
-  "name": "molstar",
-  "version": "3.3.0",
-  "description": "A comprehensive macromolecular library.",
-  "homepage": "https://github.com/molstar/molstar#readme",
-  "repository": {
-    "type": "git",
-    "url": "https://github.com/molstar/molstar.git"
-  },
-  "bugs": {
-    "url": "https://github.com/molstar/molstar/issues"
-  },
-  "scripts": {
-    "lint": "eslint .",
-    "lint-fix": "eslint . --fix",
-    "test": "npm install --no-save \"gl@^5.0.0\" && npm run lint && jest",
-    "jest": "jest",
-    "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
-    "clean": "node ./scripts/clean.js",
-    "rebuild": "npm run clean && npm run build",
-    "build-viewer": "npm run build-tsc && npm run build-extra && npm run build-webpack-viewer",
-    "build-tsc": "concurrently \"tsc --incremental\" \"tsc --build tsconfig.commonjs.json --incremental\"",
-    "build-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/",
-    "build-webpack": "webpack --mode production --config ./webpack.config.production.js",
-    "build-webpack-viewer": "webpack --mode production --config ./webpack.config.viewer.js",
-    "watch": "concurrently -c \"green,green,gray,gray\" --names \"tsc,srv,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-servers\" \"npm:watch-extra\" \"npm:watch-webpack\"",
-    "watch-viewer": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer\"",
-    "watch-viewer-debug": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer-debug\"",
-    "watch-tsc": "tsc --watch --incremental",
-    "watch-servers": "tsc --build tsconfig.commonjs.json --watch --incremental",
-    "watch-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/ --watch",
-    "watch-webpack": "webpack -w --mode development --stats minimal",
-    "watch-webpack-viewer": "webpack -w --mode development --stats minimal --config ./webpack.config.viewer.js",
-    "watch-webpack-viewer-debug": "webpack -w --mode development --stats minimal --config ./webpack.config.viewer.debug.js",
-    "serve": "http-server -p 1338 -g",
-    "model-server": "node lib/commonjs/servers/model/server.js",
-    "model-server-watch": "nodemon --watch lib lib/commonjs/servers/model/server.js",
-    "volume-server-test": "node lib/commonjs/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",
-    "plugin-state": "node lib/commonjs/servers/plugin-state/index.js --working-folder ./build/state --port 1339",
-    "preversion": "npm run test",
-    "version": "npm run rebuild && cpx .npmignore lib/",
-    "postversion": "git push && git push --tags"
-  },
-  "files": [
-    "lib/",
-    "build/viewer/"
-  ],
-  "bin": {
-    "cif2bcif": "lib/commonjs/cli/cif2bcif/index.js",
-    "cifschema": "lib/commonjs/cli/cifschema/index.js",
-    "model-server": "lib/commonjs/servers/model/server.js",
-    "model-server-query": "lib/commonjs/servers/model/query.js",
-    "model-server-preprocess": "lib/commonjs/servers/model/preprocess.js",
-    "volume-server": "lib/commonjs/servers/volume/server.js",
-    "volume-server-query": "lib/commonjs/servers/volume/query.js",
-    "volume-server-pack": "lib/commonjs/servers/volume/pack.js"
-  },
-  "nodemonConfig": {
-    "ignoreRoot": [
-      "./node_modules",
-      ".git"
-    ],
-    "ignore": [],
-    "delay": "2500"
-  },
-  "jest": {
-    "moduleFileExtensions": [
-      "ts",
-      "js"
-    ],
-    "transform": {
-      "\\.ts$": "ts-jest"
-    },
-    "moduleDirectories": [
-      "node_modules",
-      "lib"
-    ],
-    "testURL": "http://localhost/",
-    "testRegex": "\\.spec\\.ts$"
-  },
-  "author": "Mol* Contributors",
-  "contributors": [
-    "Alexander Rose <alexander.rose@weirdbyte.de>",
-    "David Sehnal <david.sehnal@gmail.com>",
-    "Sebastian Bittrich <sebastian.bittrich@rcsb.org>",
-    "Áron Samuel Kovács <aron.kovacs@mail.muni.cz>",
-    "Ludovic Autin <autin@scripps.edu>",
-    "Michal Malý <michal.maly@ibt.cas.cz>",
-    "Jiří Černý <jiri.cerny@ibt.cas.cz>",
-    "Panagiotis Tourlas <panagiot_tourlov@hotmail.com>"
-  ],
-  "license": "MIT",
-  "devDependencies": {
-    "@graphql-codegen/add": "^3.1.1",
-    "@graphql-codegen/cli": "^2.6.2",
-    "@graphql-codegen/time": "^3.1.1",
-    "@graphql-codegen/typescript": "^2.4.5",
-    "@graphql-codegen/typescript-graphql-files-modules": "^2.1.1",
-    "@graphql-codegen/typescript-graphql-request": "^4.3.7",
-    "@graphql-codegen/typescript-operations": "^2.3.2",
-    "@types/cors": "^2.8.12",
-    "@types/gl": "^4.1.0",
-    "@types/jest": "^27.4.1",
-    "@typescript-eslint/eslint-plugin": "^5.12.1",
-    "@typescript-eslint/parser": "^5.12.1",
-    "benchmark": "^2.1.4",
-    "concurrently": "^7.0.0",
-    "cpx2": "^4.2.0",
-    "crypto-browserify": "^3.12.0",
-    "css-loader": "^6.6.0",
-    "eslint": "^8.10.0",
-    "extra-watch-webpack-plugin": "^1.0.3",
-    "file-loader": "^6.2.0",
-    "fs-extra": "^10.0.1",
-    "graphql": "^16.3.0",
-    "http-server": "^14.1.0",
-    "jest": "^27.5.1",
-    "mini-css-extract-plugin": "^2.5.3",
-    "path-browserify": "^1.0.1",
-    "raw-loader": "^4.0.2",
-    "sass": "^1.49.9",
-    "sass-loader": "^12.6.0",
-    "simple-git": "^3.2.6",
-    "stream-browserify": "^3.0.0",
-    "style-loader": "^3.3.1",
-    "ts-jest": "^27.1.3",
-    "typescript": "^4.5.5",
-    "webpack": "^5.69.1",
-    "webpack-cli": "^4.9.2"
-  },
-  "dependencies": {
-    "@types/argparse": "^2.0.10",
-    "@types/benchmark": "^2.1.1",
-    "@types/compression": "1.7.2",
-    "@types/express": "^4.17.13",
-    "@types/node": "^16.11.26",
-    "@types/node-fetch": "^2.6.1",
-    "@types/react": "^17.0.39",
-    "@types/react-dom": "^17.0.11",
-    "@types/swagger-ui-dist": "3.30.1",
-    "argparse": "^2.0.1",
-    "body-parser": "^1.19.2",
-    "compression": "^1.7.4",
-    "cors": "^2.8.5",
-    "express": "^4.17.3",
-    "h264-mp4-encoder": "^1.0.12",
-    "immer": "^9.0.12",
-    "immutable": "^4.0.0",
-    "node-fetch": "^2.6.7",
-    "rxjs": "^7.5.4",
-    "swagger-ui-dist": "^4.5.2",
-    "tslib": "^2.3.1",
-    "util.promisify": "^1.1.1",
-    "xhr2": "^0.2.1"
-  },
-  "peerDependencies": {
-    "react": "^17.0.2 || ^16.14.0",
-    "react-dom": "^17.0.2 || ^16.14.0"
-  }
-}
+{
+  "name": "molstar",
+  "version": "3.5.0",
+  "description": "A comprehensive macromolecular library.",
+  "homepage": "https://github.com/molstar/molstar#readme",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/molstar/molstar.git"
+  },
+  "bugs": {
+    "url": "https://github.com/molstar/molstar/issues"
+  },
+  "scripts": {
+    "lint": "eslint .",
+    "lint-fix": "eslint . --fix",
+    "test": "npm install --no-save \"gl@^5.0.0\" && npm run lint && jest",
+    "jest": "jest",
+    "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
+    "clean": "node ./scripts/clean.js",
+    "rebuild": "npm run clean && npm run build",
+    "build-viewer": "npm run build-tsc && npm run build-extra && npm run build-webpack-viewer",
+    "build-tsc": "concurrently \"tsc --incremental\" \"tsc --build tsconfig.commonjs.json --incremental\"",
+    "build-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/",
+    "build-webpack": "webpack --mode production --config ./webpack.config.production.js",
+    "build-webpack-viewer": "webpack --mode production --config ./webpack.config.viewer.js",
+    "watch": "concurrently -c \"green,green,gray,gray\" --names \"tsc,srv,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-servers\" \"npm:watch-extra\" \"npm:watch-webpack\"",
+    "watch-viewer": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer\"",
+    "watch-viewer-debug": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack-viewer-debug\"",
+    "watch-tsc": "tsc --watch --incremental",
+    "watch-servers": "tsc --build tsconfig.commonjs.json --watch --incremental",
+    "watch-extra": "cpx \"src/**/*.{scss,html,ico}\" lib/ --watch",
+    "watch-webpack": "webpack -w --mode development --stats minimal",
+    "watch-webpack-viewer": "webpack -w --mode development --stats minimal --config ./webpack.config.viewer.js",
+    "watch-webpack-viewer-debug": "webpack -w --mode development --stats minimal --config ./webpack.config.viewer.debug.js",
+    "serve": "http-server -p 1338 -g",
+    "model-server": "node lib/commonjs/servers/model/server.js",
+    "model-server-watch": "nodemon --watch lib lib/commonjs/servers/model/server.js",
+    "volume-server-test": "node lib/commonjs/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",
+    "plugin-state": "node lib/commonjs/servers/plugin-state/index.js --working-folder ./build/state --port 1339",
+    "preversion": "npm run test",
+    "version": "npm run rebuild && cpx .npmignore lib/",
+    "postversion": "git push && git push --tags"
+  },
+  "files": [
+    "lib/",
+    "build/viewer/"
+  ],
+  "bin": {
+    "cif2bcif": "lib/commonjs/cli/cif2bcif/index.js",
+    "cifschema": "lib/commonjs/cli/cifschema/index.js",
+    "model-server": "lib/commonjs/servers/model/server.js",
+    "model-server-query": "lib/commonjs/servers/model/query.js",
+    "model-server-preprocess": "lib/commonjs/servers/model/preprocess.js",
+    "volume-server": "lib/commonjs/servers/volume/server.js",
+    "volume-server-query": "lib/commonjs/servers/volume/query.js",
+    "volume-server-pack": "lib/commonjs/servers/volume/pack.js"
+  },
+  "nodemonConfig": {
+    "ignoreRoot": [
+      "./node_modules",
+      ".git"
+    ],
+    "ignore": [],
+    "delay": "2500"
+  },
+  "jest": {
+    "moduleFileExtensions": [
+      "ts",
+      "js"
+    ],
+    "transform": {
+      "\\.ts$": "ts-jest"
+    },
+    "moduleDirectories": [
+      "node_modules",
+      "lib"
+    ],
+    "testURL": "http://localhost/",
+    "testRegex": "\\.spec\\.ts$"
+  },
+  "author": "Mol* Contributors",
+  "contributors": [
+    "Alexander Rose <alexander.rose@weirdbyte.de>",
+    "David Sehnal <david.sehnal@gmail.com>",
+    "Sebastian Bittrich <sebastian.bittrich@rcsb.org>",
+    "Áron Samuel Kovács <aron.kovacs@mail.muni.cz>",
+    "Ludovic Autin <autin@scripps.edu>",
+    "Michal Malý <michal.maly@ibt.cas.cz>",
+    "Jiří Černý <jiri.cerny@ibt.cas.cz>",
+    "Panagiotis Tourlas <panagiot_tourlov@hotmail.com>"
+  ],
+  "license": "MIT",
+  "devDependencies": {
+    "@graphql-codegen/add": "^3.1.1",
+    "@graphql-codegen/cli": "^2.6.2",
+    "@graphql-codegen/time": "^3.1.1",
+    "@graphql-codegen/typescript": "^2.4.7",
+    "@graphql-codegen/typescript-graphql-files-modules": "^2.1.1",
+    "@graphql-codegen/typescript-graphql-request": "^4.4.2",
+    "@graphql-codegen/typescript-operations": "^2.3.4",
+    "@types/cors": "^2.8.12",
+    "@types/gl": "^4.1.0",
+    "@types/jest": "^27.4.1",
+    "@typescript-eslint/eslint-plugin": "^5.14.0",
+    "@typescript-eslint/parser": "^5.14.0",
+    "benchmark": "^2.1.4",
+    "concurrently": "^7.0.0",
+    "cpx2": "^4.2.0",
+    "crypto-browserify": "^3.12.0",
+    "css-loader": "^6.7.1",
+    "eslint": "^8.11.0",
+    "extra-watch-webpack-plugin": "^1.0.3",
+    "file-loader": "^6.2.0",
+    "fs-extra": "^10.0.1",
+    "graphql": "^16.3.0",
+    "http-server": "^14.1.0",
+    "jest": "^27.5.1",
+    "mini-css-extract-plugin": "^2.6.0",
+    "path-browserify": "^1.0.1",
+    "raw-loader": "^4.0.2",
+    "sass": "^1.49.9",
+    "sass-loader": "^12.6.0",
+    "simple-git": "^3.3.0",
+    "stream-browserify": "^3.0.0",
+    "style-loader": "^3.3.1",
+    "ts-jest": "^27.1.3",
+    "typescript": "^4.6.2",
+    "webpack": "^5.70.0",
+    "webpack-cli": "^4.9.2"
+  },
+  "dependencies": {
+    "@types/argparse": "^2.0.10",
+    "@types/benchmark": "^2.1.1",
+    "@types/compression": "1.7.2",
+    "@types/express": "^4.17.13",
+    "@types/node": "^16.11.26",
+    "@types/node-fetch": "^2.6.1",
+    "@types/react": "^17.0.40",
+    "@types/react-dom": "^17.0.13",
+    "@types/swagger-ui-dist": "3.30.1",
+    "argparse": "^2.0.1",
+    "body-parser": "^1.19.2",
+    "compression": "^1.7.4",
+    "cors": "^2.8.5",
+    "express": "^4.17.3",
+    "h264-mp4-encoder": "^1.0.12",
+    "immer": "^9.0.12",
+    "immutable": "^4.0.0",
+    "node-fetch": "^2.6.7",
+    "rxjs": "^7.5.5",
+    "swagger-ui-dist": "^4.6.2",
+    "tslib": "^2.3.1",
+    "util.promisify": "^1.1.1",
+    "xhr2": "^0.2.1"
+  },
+  "peerDependencies": {
+    "react": "^17.0.2 || ^16.14.0",
+    "react-dom": "^17.0.2 || ^16.14.0"
+  }
+}

package/lib/commonjs/mol-plugin-state/formats/structure.js

@@ -1,64 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.BuiltInStructureFormats = exports.XtcProvider = exports.DcdProvider = exports.PsfProvider = exports.StructureFormatCategory = void 0;
-var tslib_1 = require("tslib");
-var transforms_1 = require("../transforms");
-var provider_1 = require("./provider");
-exports.StructureFormatCategory = 'Structure';
-exports.PsfProvider = (0, provider_1.DataFormatProvider)({
-    label: 'PSF',
-    description: 'PSF',
-    category: exports.StructureFormatCategory,
-    stringExtensions: ['psf'],
-    parse: function (plugin, data) { return (0, tslib_1.__awaiter)(void 0, void 0, void 0, function () {
-        var format, topology;
-        return (0, tslib_1.__generator)(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    format = plugin.state.data.build()
-                        .to(data)
-                        .apply(transforms_1.StateTransforms.Data.ParsePsf, {}, { state: { isGhost: true } });
-                    topology = format.apply(transforms_1.StateTransforms.Model.TopologyFromPsf);
-                    return [4 /*yield*/, format.commit()];
-                case 1:
-                    _a.sent();
-                    return [2 /*return*/, { format: format.selector, topology: topology.selector }];
-            }
-        });
-    }); }
-});
-exports.DcdProvider = (0, provider_1.DataFormatProvider)({
-    label: 'DCD',
-    description: 'DCD',
-    category: exports.StructureFormatCategory,
-    binaryExtensions: ['dcd'],
-    parse: function (plugin, data) {
-        var coordinates = plugin.state.data.build()
-            .to(data)
-            .apply(transforms_1.StateTransforms.Model.CoordinatesFromDcd);
-        return coordinates.commit();
-    }
-});
-exports.XtcProvider = (0, provider_1.DataFormatProvider)({
-    label: 'XTC',
-    description: 'XTC',
-    category: exports.StructureFormatCategory,
-    binaryExtensions: ['xtc'],
-    parse: function (plugin, data) {
-        var coordinates = plugin.state.data.build()
-            .to(data)
-            .apply(transforms_1.StateTransforms.Model.CoordinatesFromXtc);
-        return coordinates.commit();
-    }
-});
-exports.BuiltInStructureFormats = [
-    ['psf', exports.PsfProvider],
-    ['dcd', exports.DcdProvider],
-    ['xtc', exports.XtcProvider],
-];

package/lib/mol-plugin-state/formats/structure.js

@@ -1,61 +0,0 @@
-/**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { __awaiter, __generator } from "tslib";
-import { StateTransforms } from '../transforms';
-import { DataFormatProvider } from './provider';
-export var StructureFormatCategory = 'Structure';
-export var PsfProvider = DataFormatProvider({
-    label: 'PSF',
-    description: 'PSF',
-    category: StructureFormatCategory,
-    stringExtensions: ['psf'],
-    parse: function (plugin, data) { return __awaiter(void 0, void 0, void 0, function () {
-        var format, topology;
-        return __generator(this, function (_a) {
-            switch (_a.label) {
-                case 0:
-                    format = plugin.state.data.build()
-                        .to(data)
-                        .apply(StateTransforms.Data.ParsePsf, {}, { state: { isGhost: true } });
-                    topology = format.apply(StateTransforms.Model.TopologyFromPsf);
-                    return [4 /*yield*/, format.commit()];
-                case 1:
-                    _a.sent();
-                    return [2 /*return*/, { format: format.selector, topology: topology.selector }];
-            }
-        });
-    }); }
-});
-export var DcdProvider = DataFormatProvider({
-    label: 'DCD',
-    description: 'DCD',
-    category: StructureFormatCategory,
-    binaryExtensions: ['dcd'],
-    parse: function (plugin, data) {
-        var coordinates = plugin.state.data.build()
-            .to(data)
-            .apply(StateTransforms.Model.CoordinatesFromDcd);
-        return coordinates.commit();
-    }
-});
-export var XtcProvider = DataFormatProvider({
-    label: 'XTC',
-    description: 'XTC',
-    category: StructureFormatCategory,
-    binaryExtensions: ['xtc'],
-    parse: function (plugin, data) {
-        var coordinates = plugin.state.data.build()
-            .to(data)
-            .apply(StateTransforms.Model.CoordinatesFromXtc);
-        return coordinates.commit();
-    }
-});
-export var BuiltInStructureFormats = [
-    ['psf', PsfProvider],
-    ['dcd', DcdProvider],
-    ['xtc', XtcProvider],
-];