0.7.1-dev.3

- updated all
- removed unused jest-raw-loader
- removed unused circular-dependency-plugin
- removed unused resolve-url-loader

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.1-dev.2",
+  "version": "0.7.1-dev.3",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -83,68 +83,65 @@
   ],
   "license": "MIT",
   "devDependencies": {
-    "@graphql-codegen/add": "^1.13.3",
-    "@graphql-codegen/cli": "^1.13.3",
-    "@graphql-codegen/time": "^1.13.3",
-    "@graphql-codegen/typescript": "^1.13.3",
-    "@graphql-codegen/typescript-graphql-files-modules": "^1.13.3",
-    "@graphql-codegen/typescript-graphql-request": "^1.13.3",
-    "@graphql-codegen/typescript-operations": "^1.13.3",
+    "@graphql-codegen/add": "^1.13.5",
+    "@graphql-codegen/cli": "^1.13.5",
+    "@graphql-codegen/time": "^1.13.5",
+    "@graphql-codegen/typescript": "^1.13.5",
+    "@graphql-codegen/typescript-graphql-files-modules": "^1.13.5",
+    "@graphql-codegen/typescript-graphql-request": "^1.13.5",
+    "@graphql-codegen/typescript-operations": "^1.13.5",
     "@types/cors": "^2.8.6",
-    "@typescript-eslint/eslint-plugin": "^2.29.0",
-    "@typescript-eslint/parser": "^2.29.0",
+    "@typescript-eslint/eslint-plugin": "^2.32.0",
+    "@typescript-eslint/parser": "^2.32.0",
     "benchmark": "^2.1.4",
-    "circular-dependency-plugin": "^5.2.0",
-    "concurrently": "^5.1.0",
+    "concurrently": "^5.2.0",
     "cpx2": "^2.0.0",
     "css-loader": "^3.5.3",
-    "eslint": "^6.8.0",
+    "eslint": "^7.0.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.0.0",
     "fs-extra": "^9.0.0",
     "graphql": "^15.0.0",
-    "http-server": "^0.12.1",
-    "jest": "^25.4.0",
-    "jest-raw-loader": "^1.0.1",
+    "http-server": "^0.12.3",
+    "jest": "^26.0.1",
     "mini-css-extract-plugin": "^0.9.0",
-    "node-sass": "^4.14.0",
+    "node-sass": "^4.14.1",
     "raw-loader": "^4.0.1",
-    "resolve-url-loader": "^3.1.1",
     "sass-loader": "^8.0.2",
-    "simple-git": "^1.132.0",
-    "style-loader": "^1.2.0",
-    "ts-jest": "^25.4.0",
+    "simple-git": "^2.4.0",
+    "style-loader": "^1.2.1",
+    "ts-jest": "^25.5.1",
     "typescript": "^3.8.3",
     "webpack": "^4.43.0",
     "webpack-cli": "^3.3.11",
     "webpack-version-file-plugin": "^0.4.0"
   },
   "dependencies": {
-    "@material-ui/core": "^4.9.11",
+    "@material-ui/core": "^4.9.13",
     "@material-ui/icons": "^4.9.1",
     "@types/argparse": "^1.0.38",
     "@types/benchmark": "^1.0.31",
     "@types/compression": "1.7.0",
     "@types/express": "^4.17.6",
     "@types/jest": "^25.2.1",
-    "@types/node": "^13.13.2",
+    "@types/node": "^13.13.5",
     "@types/node-fetch": "^2.5.7",
-    "@types/react": "^16.9.34",
-    "@types/react-dom": "^16.9.6",
+    "@types/react": "^16.9.35",
+    "@types/react-dom": "^16.9.8",
     "@types/swagger-ui-dist": "3.0.5",
     "argparse": "^1.0.10",
     "body-parser": "^1.19.0",
     "compression": "^1.7.4",
     "cors": "^2.8.5",
     "express": "^4.17.1",
-    "immer": "^6.0.3",
+    "immer": "^6.0.5",
     "immutable": "^3.8.2",
     "node-fetch": "^2.6.0",
     "react": "^16.13.1",
     "react-dom": "^16.13.1",
     "rxjs": "^6.5.5",
-    "swagger-ui-dist": "^3.25.0",
-    "tslib": "^1.11.1",
+    "swagger-ui-dist": "^3.25.2",
+    "tslib": "^1.11.2",
     "util.promisify": "^1.0.1",
     "xhr2": "^0.2.0"
   }

src/examples/basic-wrapper/index.html

@@ -69,15 +69,8 @@
             $('format').value = format;
             $('format').onchange = function (e) { format = e.target.value; }
 
-            // var url = 'https://www.ebi.ac.uk/pdbe/entry-files/pdb' + pdbId + '.ent';
-            // var format = 'pdb';
-            // var assemblyId = 'deposited';
-
             BasicMolStarWrapper.init('app' /** or document.getElementById('app') */);
             BasicMolStarWrapper.setBackground(0xffffff);
-            // BasicMolStarWrapper.load({ url: url, format: format, assemblyId: assemblyId });
-            // BasicMolStarWrapper.toggleSpin();
-
 
             addControl('Load Asym Unit', () => BasicMolStarWrapper.load({ url: url, format: format }));
             addControl('Load Assembly', () => BasicMolStarWrapper.load({ url: url, format: format, assemblyId: assemblyId }));

src/examples/basic-wrapper/index.ts

@@ -56,7 +56,13 @@ class BasicWrapper {
         const trajectory = await this.plugin.builders.structure.parseTrajectory(data, format);
 
         await this.plugin.builders.structure.hierarchy.applyPreset(trajectory, 'default', {
-            structure: assemblyId ? { name: 'assembly', params: { id: assemblyId } } : { name: 'deposited', params: { } },
+            structure: assemblyId ? {
+                name: 'assembly',
+                params: { id: assemblyId }
+            } : {
+                name: 'model',
+                params: { }
+            },
             showUnitcell: false,
             representationPreset: 'auto'
         });

src/examples/lighting/index.ts

@@ -105,7 +105,7 @@ class LightingDemo {
         const data = await this.plugin.builders.data.download({ url: Asset.Url(url), isBinary }, { state: { isGhost: true } });
         const trajectory = await this.plugin.builders.structure.parseTrajectory(data, format);
         const model = await this.plugin.builders.structure.createModel(trajectory);
-        const structure = await this.plugin.builders.structure.createStructure(model, assemblyId ? { name: 'assembly', params: { id: assemblyId } } : { name: 'deposited', params: { } });
+        const structure = await this.plugin.builders.structure.createStructure(model, assemblyId ? { name: 'assembly', params: { id: assemblyId } } : { name: 'model', params: { } });
 
         const polymer = await this.plugin.builders.structure.tryCreateComponentStatic(structure, 'polymer');
         if (polymer) await this.plugin.builders.structure.representation.addRepresentation(polymer, { type: 'spacefill', color: 'illustrative' });

src/examples/proteopedia-wrapper/index.html

@@ -88,10 +88,6 @@
             $('isBinary').checked = isBinary;
             $('isBinary').onchange = function (e) { isBinary = !!e.target.checked; };
 
-            // var url = 'https://www.ebi.ac.uk/pdbe/entry-files/pdb' + pdbId + '.ent';
-            // var format = 'pdb';
-            // var assemblyId = 'deposited';
-
             function loadAndSnapshot(params) {
                 PluginWrapper.load(params).then(() => {
                     setTimeout(() => snapshot = PluginWrapper.plugin.state.getSnapshot({ canvas3d: false /* do not save spinning state */ }), 500);

src/examples/proteopedia-wrapper/index.ts

@@ -89,9 +89,12 @@ class MolStarProteopediaWrapper {
     private structure(assemblyId: string) {
         const model = this.state.build().to(StateElements.Model);
         const props = {
-            type: {
+            type: assemblyId ? {
                 name: 'assembly' as const,
-                params: { id: assemblyId || 'deposited' }
+                params: { id: assemblyId }
+            } : {
+                name: 'model' as const,
+                params: { }
             }
         };
 
@@ -196,7 +199,7 @@ class MolStarProteopediaWrapper {
 
     private emptyLoadedParams: LoadParams = { url: '', format: 'cif', isBinary: false, assemblyId: '' };
     private loadedParams: LoadParams = { url: '', format: 'cif', isBinary: false, assemblyId: '' };
-    async load({ url, format = 'cif', assemblyId = 'deposited', isBinary = false, representationStyle }: LoadParams) {
+    async load({ url, format = 'cif', assemblyId = '', isBinary = false, representationStyle }: LoadParams) {
         let loadType: 'full' | 'update' = 'full';
 
         const state = this.plugin.state.data;
@@ -220,9 +223,12 @@ class MolStarProteopediaWrapper {
             const info = await this.doInfo(true);
             const asmId = (assemblyId === 'preferred' && info && info.preferredAssemblyId) || assemblyId;
             const props = {
-                type: {
+                type: assemblyId ? {
                     name: 'assembly' as const,
-                    params: { id: asmId || 'deposited' }
+                    params: { id: asmId }
+                } : {
+                    name: 'model' as const,
+                    params: { }
                 }
             };
             tree.to(StateElements.Assembly).update(StateTransforms.Model.StructureFromModel, p => ({ ...p, ...props }));

src/extensions/rcsb/assembly-symmetry/prop.ts

@@ -35,7 +35,7 @@ export function isBiologicalAssembly(structure: Structure): boolean {
     const mmcif = structure.models[0].sourceData.data.db;
     if (!mmcif.pdbx_struct_assembly.details.isDefined) return false;
     const id = structure.units[0].conformation.operator.assembly?.id || '';
-    if (id === '' || id === 'deposited') return true;
+    if (id === '') return true;
     const indices = Column.indicesOf(mmcif.pdbx_struct_assembly.id, e => e === id);
     if (indices.length !== 1) return false;
     const details = mmcif.pdbx_struct_assembly.details.value(indices[0]);
@@ -63,7 +63,7 @@ export namespace AssemblySymmetry {
 
         const client = new GraphQLClient(props.serverUrl, ctx.assetManager);
         const variables: AssemblySymmetryQueryVariables = {
-            assembly_id: structure.units[0].conformation.operator.assembly?.id || 'deposited',
+            assembly_id: structure.units[0].conformation.operator.assembly?.id || '',
             entry_id: structure.units[0].model.entryId
         };
         const result = await client.request(ctx.runtime, query, variables);

src/mol-plugin-state/builder/structure.ts

@@ -90,7 +90,7 @@ export class StructureBuilder {
             const model = StateObjectRef.resolveAndCheck(state, modelRef);
             if (model) {
                 const symm = ModelSymmetry.Provider.get(model.obj?.data!);
-                if (!symm || symm?.assemblies.length === 0) params = { name: 'deposited', params: { } };
+                if (!symm || symm?.assemblies.length === 0) params = { name: 'model', params: { } };
             }
         }
 

src/mol-plugin-state/builder/structure/hierarchy-preset.ts

@@ -43,7 +43,7 @@ const defaultPreset = TrajectoryHierarchyPresetProvider({
     id: 'preset-trajectory-default',
     display: {
         name: 'Default (Assembly)', group: 'Preset',
-        description: 'Shows the first assembly or, if that is unavailable, the first deposited model.'
+        description: 'Shows the first assembly or, if that is unavailable, the first model.'
     },
     isApplicable: o => {
         return true;
@@ -93,7 +93,7 @@ const allModels = TrajectoryHierarchyPresetProvider({
         for (let i = 0; i < tr.length; i++) {
             const model = await builder.createModel(trajectory, { modelIndex: i });
             const modelProperties = await builder.insertModelProperties(model, params.modelProperties, { isCollapsed: true });
-            const structure = await builder.createStructure(modelProperties || model, { name: 'deposited', params: {} });
+            const structure = await builder.createStructure(modelProperties || model, { name: 'model', params: {} });
             const structureProperties = await builder.insertStructureProperties(structure, params.structureProperties);
 
             models.push(model);

src/mol-plugin-state/helpers/root-structure.ts

@@ -17,7 +17,7 @@ import { PluginStateObject as SO } from '../objects';
 import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
 
 export namespace RootStructureDefinition {
-    export function getParams(model?: Model, defaultValue?: 'auto' | 'deposited' | 'assembly' | 'symmetry' | 'symmetry-mates' | 'symmetry-assembly') {
+    export function getParams(model?: Model, defaultValue?: 'auto' | 'model' | 'assembly' | 'symmetry' | 'symmetry-mates' | 'symmetry-assembly') {
         const symmetry = model && ModelSymmetry.Provider.get(model);
 
         const assemblyIds = symmetry ? symmetry.assemblies.map(a => [a.id, `${a.id}: ${stringToWords(a.details)}`] as [string, string]) : [];
@@ -41,7 +41,7 @@ export namespace RootStructureDefinition {
 
         const modes = {
             auto: PD.EmptyGroup(),
-            deposited: PD.EmptyGroup(),
+            model: PD.EmptyGroup(),
             assembly: PD.Group({
                 id: PD.Optional(model
                     ? PD.Select(assemblyIds.length ? assemblyIds[0][0] : '', assemblyIds, { label: 'Asm Id', description: 'Assembly Id' })
@@ -75,7 +75,7 @@ export namespace RootStructureDefinition {
             options.push(['auto', 'Auto']);
         }
 
-        options.push(['deposited', 'Deposited']);
+        options.push(['model', 'Model']);
 
         if (assemblyIds.length > 0) {
             options.push(['assembly', 'Assembly']);
@@ -88,7 +88,7 @@ export namespace RootStructureDefinition {
         }
 
         return {
-            type: PD.MappedStatic(defaultValue || 'deposited', modes, { options })
+            type: PD.MappedStatic(defaultValue || 'model', modes, { options })
         };
     }
 
@@ -110,19 +110,17 @@ export namespace RootStructureDefinition {
         }
 
         if (!symmetry || symmetry.assemblies.length === 0) {
-            if (id !== 'deposited') {
-                plugin.log.warn(`Model '${model.entryId}' has no assembly, returning deposited structure.`);
-            }
+            plugin.log.warn(`Model '${model.entryId}' has no assembly, returning model structure.`);
         } else {
             asm = Symmetry.findAssembly(model, id || '');
             if (!asm) {
-                plugin.log.warn(`Model '${model.entryId}' has no assembly called '${id}', returning deposited structure.`);
+                plugin.log.warn(`Model '${model.entryId}' has no assembly called '${id}', returning model structure.`);
             }
         }
 
         const base = Structure.ofModel(model);
         if (!asm) {
-            const label = { label: 'Deposited', description: Structure.elementDescription(base) };
+            const label = { label: 'Model', description: Structure.elementDescription(base) };
             return new SO.Molecule.Structure(base, label);
         }
 
@@ -155,14 +153,14 @@ export namespace RootStructureDefinition {
 
     export async function create(plugin: PluginContext, ctx: RuntimeContext, model: Model, params?: Params): Promise<SO.Molecule.Structure> {
         const symmetry = ModelSymmetry.Provider.get(model);
-        if (!symmetry || !params || params.name === 'deposited') {
+        if (!symmetry || !params || params.name === 'model') {
             const s = Structure.ofModel(model);
-            return new SO.Molecule.Structure(s, { label: 'Deposited', description: Structure.elementDescription(s) });
+            return new SO.Molecule.Structure(s, { label: 'Model', description: Structure.elementDescription(s) });
         }
         if (params.name === 'auto') {
             if (symmetry.assemblies.length === 0) {
                 const s = Structure.ofModel(model);
-                return new SO.Molecule.Structure(s, { label: 'Deposited', description: Structure.elementDescription(s) });
+                return new SO.Molecule.Structure(s, { label: 'Model', description: Structure.elementDescription(s) });
             } else {
                 return buildAssembly(plugin, ctx, model);
             }

src/mol-plugin-state/transforms/model.ts

@@ -371,7 +371,7 @@ const StructureFromTrajectory = PluginStateTransform.BuiltIn({
 type StructureFromModel = typeof StructureFromModel
 const StructureFromModel = PluginStateTransform.BuiltIn({
     name: 'structure-from-model',
-    display: { name: 'Structure', description: 'Create a molecular structure (deposited, assembly, or symmetry) from the specified model.' },
+    display: { name: 'Structure', description: 'Create a molecular structure (model, assembly, or symmetry) from the specified model.' },
     from: SO.Molecule.Model,
     to: SO.Molecule.Structure,
     params(a) { return RootStructureDefinition.getParams(a && a.data); }

src/mol-plugin-ui/skin/base/base.scss

@@ -1,5 +1,4 @@
-// @import url(https://fonts.googleapis.com/css?family=Source+Sans+Pro:400,400italic,700);
-
+
 @mixin user-select($select) {
   -webkit-user-select: $select;
      -moz-user-select: $select;

webpack.config.common.js

@@ -3,7 +3,6 @@ const webpack = require('webpack');
 const ExtraWatchWebpackPlugin = require('extra-watch-webpack-plugin');
 const MiniCssExtractPlugin = require('mini-css-extract-plugin');
 const VersionFile = require('webpack-version-file-plugin');
-// const CircularDependencyPlugin = require('circular-dependency-plugin');
 
 const sharedConfig = {
     module: {
@@ -20,18 +19,12 @@ const sharedConfig = {
                 use: [
                     MiniCssExtractPlugin.loader,
                     { loader: 'css-loader', options: { sourceMap: false } },
-                    { loader: 'resolve-url-loader', options: { sourceMap: false } },
                     { loader: 'sass-loader', options: { sourceMap: false } },
                 ]
             }
         ]
     },
     plugins: [
-        // new CircularDependencyPlugin({
-        //     include: [ path.resolve(__dirname, 'lib/') ],
-        //     failOnError: false,
-        //     cwd: process.cwd(),
-        // }),
         new ExtraWatchWebpackPlugin({
             files: [
                 './lib/**/*.scss',
@@ -39,8 +32,6 @@ const sharedConfig = {
             ],
         }),
         new webpack.DefinePlugin({
-            // __VERSION__: webpack.DefinePlugin.runtimeValue(() => JSON.stringify(require('./package.json').version), true),
-            // __VERSION_TIMESTAMP__: webpack.DefinePlugin.runtimeValue(() => `${new Date().valueOf()}`, true),
             'process.env.DEBUG': JSON.stringify(process.env.DEBUG)
         }),
         new MiniCssExtractPlugin({ filename: 'molstar.css',  }),