updated to molstar 0.7 dev

package.json

@@ -15,11 +15,11 @@
         "lint": "eslint src/**/*.ts",
         "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
         "build-tsc": "tsc --incremental",
-        "build-extra": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html,ico}\" build/src/",
+        "build-extra": "cpx \"src/**/*.{scss,html,ico}\" build/src/",
         "build-webpack": "webpack --mode production",
         "watch": "concurrently -c \"green,gray,gray\" --names \"tsc,ext,wpc\" --kill-others \"npm:watch-tsc\" \"npm:watch-extra\" \"npm:watch-webpack\"",
         "watch-tsc": "tsc --watch --incremental",
-        "watch-extra": "cpx \"src/**/*.{scss,woff,woff2,ttf,otf,eot,svg,html,ico}\" build/src/ --watch",
+        "watch-extra": "cpx \"src/**/*.{scss,html,ico}\" build/src/ --watch",
         "watch-webpack": "webpack -w --mode development --display minimal",
         "serve": "http-server -p 1335",
         "preversion": "npm run test",
@@ -37,32 +37,32 @@
     "license": "MIT",
     "devDependencies": {
         "@types/argparse": "^1.0.38",
-        "@types/node": "^13.11.0",
-        "@types/node-fetch": "^2.5.5",
-        "@types/react": "^16.9.32",
+        "@types/node": "^13.13.2",
+        "@types/node-fetch": "^2.5.7",
+        "@types/react": "^16.9.34",
         "@types/react-dom": "^16.9.6",
-        "@typescript-eslint/eslint-plugin": "^2.26.0",
-        "@typescript-eslint/parser": "^2.26.0",
+        "@typescript-eslint/eslint-plugin": "^2.29.0",
+        "@typescript-eslint/parser": "^2.29.0",
         "concurrently": "^5.1.0",
         "cpx2": "^2.0.0",
-        "css-loader": "^3.4.2",
+        "css-loader": "^3.5.3",
         "eslint": "^6.8.0",
         "extra-watch-webpack-plugin": "^1.0.3",
         "file-loader": "^6.0.0",
         "mini-css-extract-plugin": "^0.9.0",
-        "molstar": "^0.6.8",
+        "molstar": "^0.7.0-dev.8",
         "node-fetch": "^2.6.0",
-        "node-sass": "^4.13.1",
-        "raw-loader": "^4.0.0",
+        "node-sass": "^4.14.0",
+        "raw-loader": "^4.0.1",
         "react": "^16.13.1",
         "react-dom": "^16.13.1",
         "resolve-url-loader": "^3.1.1",
         "rxjs": "^6.5.5",
         "sass-loader": "^8.0.2",
-        "style-loader": "^1.1.3",
+        "style-loader": "^1.2.0",
         "tslib": "^1.11.1",
         "typescript": "3.8.3",
-        "webpack": "^4.42.1",
+        "webpack": "^4.43.0",
         "webpack-cli": "^3.3.11"
     }
 }

src/structure-viewer/helpers/model.ts

@@ -8,6 +8,7 @@ import { StructureViewerState, LoadParams } from '../types';
 import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
 import { PluginContext } from 'molstar/lib/mol-plugin/context';
 import { PresetProps, RcsbPreset } from './preset';
+import { Asset } from 'molstar/lib/mol-util/assets';
 
 export class ModelLoader {
     get customState() {
@@ -26,7 +27,7 @@ export class ModelLoader {
         const isBinary = format === 'bcif'
 
         const data = fileOrUrl instanceof File
-            ? (await this.plugin.builders.data.readFile({ file: fileOrUrl, isBinary })).data
+            ? (await this.plugin.builders.data.readFile({ file: Asset.File(fileOrUrl), isBinary })).data
             : await this.plugin.builders.data.download({ url: fileOrUrl, isBinary })
         await this.plugin.builders.structure.parseTrajectory(data, 'mmcif')
 

src/structure-viewer/helpers/preset.ts

@@ -9,8 +9,8 @@ import { MolScriptBuilder as MS } from 'molstar/lib/mol-script/language/builder'
 import Expression from 'molstar/lib/mol-script/language/expression';
 import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
 import { TrajectoryHierarchyPresetProvider } from 'molstar/lib/mol-plugin-state/builder/structure/hierarchy-preset';
-import { ValidationReportGeometryQualityPreset } from 'molstar/lib/mol-plugin/behavior/dynamic/custom-props/rcsb/validation-report';
-import { AssemblySymmetryPreset } from 'molstar/lib/mol-plugin/behavior/dynamic/custom-props/rcsb/assembly-symmetry';
+import { ValidationReportGeometryQualityPreset } from 'molstar/lib/extensions/rcsb/validation-report/behavior';
+import { AssemblySymmetryPreset } from 'molstar/lib/extensions/rcsb/assembly-symmetry/behavior';
 import { PluginStateObject } from 'molstar/lib/mol-plugin-state/objects';
 import { RootStructureDefinition } from 'molstar/lib/mol-plugin-state/helpers/root-structure';
 import { StructureRepresentationPresetProvider } from 'molstar/lib/mol-plugin-state/builder/structure/representation-preset';

src/structure-viewer/index.ts

@@ -11,11 +11,9 @@ import './index.html'
 import './favicon.ico'
 import { PluginContext } from 'molstar/lib/mol-plugin/context';
 import { PluginCommands } from 'molstar/lib/mol-plugin/commands';
-import { PluginBehaviors } from 'molstar/lib/mol-plugin/behavior';
 import { AnimateModelIndex } from 'molstar/lib/mol-plugin-state/animation/built-in';
 import { StructureViewerState, StructureViewerProps, CollapsedState } from './types';
 import { PluginSpec } from 'molstar/lib/mol-plugin/spec';
-import { StructureFocusRepresentation } from 'molstar/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation';
 
 import { ColorNames } from 'molstar/lib/mol-util/color/names';
 import ReactDOM = require('react-dom');
@@ -24,6 +22,8 @@ import { ModelLoader } from './helpers/model';
 import { PresetProps } from './helpers/preset';
 import { ControlsWrapper, ViewportWrapper } from './ui/controls';
 import { PluginConfig } from 'molstar/lib/mol-plugin/config';
+import { RCSBAssemblySymmetry } from 'molstar/lib/extensions/rcsb/assembly-symmetry/behavior';
+import { RCSBValidationReport } from 'molstar/lib/extensions/rcsb/validation-report/behavior';
 require('./skin/rcsb.scss')
 
 /** package version, filled in at bundle build time */
@@ -31,8 +31,8 @@ declare const __RCSB_MOLSTAR_VERSION__: string
 export const RCSB_MOLSTAR_VERSION = __RCSB_MOLSTAR_VERSION__;
 
 /** unix time stamp, to be filled in at bundle build time */
-declare const __VERSION_TIMESTAMP__: number
-export const BUILD_TIMESTAMP = __VERSION_TIMESTAMP__;
+declare const __BUILD_TIMESTAMP__: number
+export const BUILD_TIMESTAMP = __BUILD_TIMESTAMP__;
 export const BUILD_DATE = new Date(BUILD_TIMESTAMP);
 
 export const DefaultStructureViewerProps: StructureViewerProps = {
@@ -66,21 +66,9 @@ export class StructureViewer {
         this.plugin = new PluginContext({
             ...DefaultPluginSpec,
             behaviors: [
-                PluginSpec.Behavior(PluginBehaviors.Representation.HighlightLoci),
-                PluginSpec.Behavior(PluginBehaviors.Representation.SelectLoci),
-                PluginSpec.Behavior(PluginBehaviors.Representation.DefaultLociLabelProvider),
-                PluginSpec.Behavior(PluginBehaviors.Representation.FocusLoci),
-                PluginSpec.Behavior(PluginBehaviors.Camera.FocusLoci),
-                PluginSpec.Behavior(StructureFocusRepresentation),
-
-                PluginSpec.Behavior(PluginBehaviors.CustomProps.AccessibleSurfaceArea),
-                PluginSpec.Behavior(PluginBehaviors.CustomProps.Interactions),
-                PluginSpec.Behavior(PluginBehaviors.CustomProps.SecondaryStructure),
-                PluginSpec.Behavior(PluginBehaviors.CustomProps.ValenceModel),
-                PluginSpec.Behavior(PluginBehaviors.CustomProps.CrossLinkRestraint),
-
-                PluginSpec.Behavior(PluginBehaviors.CustomProps.RCSBAssemblySymmetry),
-                PluginSpec.Behavior(PluginBehaviors.CustomProps.RCSBValidationReport),
+                ...DefaultPluginSpec.behaviors,
+                PluginSpec.Behavior(RCSBAssemblySymmetry),
+                PluginSpec.Behavior(RCSBValidationReport),
             ],
             animations: [
                 AnimateModelIndex

src/structure-viewer/skin/fonts/fontello.svg

@@ -1,442 +0,0 @@
-<?xml version="1.0" standalone="no"?>
-<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<svg xmlns="http://www.w3.org/2000/svg">
-<metadata>Copyright (C) 2016 by original authors @ fontello.com</metadata>
-<defs>
-<font id="fontello" horiz-adv-x="1000" >
-<font-face font-family="fontello" font-weight="400" font-stretch="normal" units-per-em="1000" ascent="850" descent="-150" />
-<missing-glyph horiz-adv-x="1000" />
-<glyph glyph-name="palette" unicode="&#xe800;" d="M857 622q72-48 101-110t20-104-35-48q-16-4-54 10t-80 10-80-46q-30-46-21-75t34-65 23-50q-2-26-36-63t-126-74-216-37q-186 0-291 101t-95 245q8 118 104 235t216 151q290 84 536-80z m-318-466q30 0 52 22t22 54-22 53-52 21q-32 0-54-21t-22-53 22-54 54-22z" horiz-adv-x="980" />
-
-<glyph glyph-name="search" unicode="&#xe803;" d="M772 78q30-34 6-62l-46-46q-36-32-68 0l-190 190q-74-42-156-42-128 0-223 95t-95 223 90 219 218 91 224-95 96-223q0-88-46-162z m-678 358q0-88 68-156t156-68 151 63 63 153q0 88-68 155t-156 67-151-63-63-151z" horiz-adv-x="789" />
-
-<glyph glyph-name="flashlight" unicode="&#xe804;" d="M807 706q62-62 85-130t-5-92l-134-134q-16-16-62-26t-96-4l-408-408q-18-18-57-6t-75 50q-36 36-49 74t5 56l408 408q-6 50 4 96t26 62l136 136q24 28 92 4t130-86z m-448-408q32-32 80 14 46 46 14 82-14 14-38 10t-44-24-23-43 11-39z m336 298q30-30 68-50t62-25 28-1q2 4-4 27t-26 60-50 67-66 50-59 26-27 2 1-28 25-62 48-66z" horiz-adv-x="902" />
-
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-
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-
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src/structure-viewer/ui/controls.tsx

@@ -12,7 +12,6 @@ import { BackgroundTaskProgress } from 'molstar/lib/mol-plugin-ui/task';
 import { LociLabels, CustomStructureControls, SelectionViewportControls } from 'molstar/lib/mol-plugin-ui/controls';
 import { Toasts } from 'molstar/lib/mol-plugin-ui/toast';
 import { OpenFile } from './open';
-import { Icon } from 'molstar/lib/mol-plugin-ui/controls/icons';
 import { StructureSourceControls } from 'molstar/lib/mol-plugin-ui/structure/source';
 import { StructureMeasurementsControls } from 'molstar/lib/mol-plugin-ui/structure/measurements';
 import { StructureComponentControls } from 'molstar/lib/mol-plugin-ui/structure/components';
@@ -30,8 +29,6 @@ export class StructureTools extends PluginUIComponent {
     render() {
         const collapsed = this.customState.collapsed.value
         return <>
-            <div className='msp-section-header'><Icon name='tools' />Structure Tools</div>
-
             <StructureSourceControls />
             <StructureMeasurementsControls initiallyCollapsed={collapsed.measurements}  />
             <StructureComponentControls initiallyCollapsed={collapsed.component}  />

src/structure-viewer/ui/open.tsx

@@ -23,14 +23,14 @@ const OpenFileAction = StateAction.build({
         }
     }
 })(({ params, state }, ctx: PluginContext) => Task.create('Open File', async taskCtx => {
-
-    if (params.file === null) {
+    const file = params.file?.file;
+    if (!file) {
         throw new Error('no file selected')
     }
-    if (params.file.type !== 'cif' && params.file.type !== 'bcif') {
-        throw new Error(`unsupported file format '${params.file.type}`)
+    if (file.type !== 'cif' && file.type !== 'bcif') {
+        throw new Error(`unsupported file format '${file.type}`)
     }
-    await StructureViewerState(ctx).modelLoader.load({ fileOrUrl: params.file, format: params.file.type, })
+    await StructureViewerState(ctx).modelLoader.load({ fileOrUrl: file, format: file.type, })
 }));
 
 export class OpenFile extends PluginUIComponent<{ initiallyCollapsed?: boolean }> {

webpack.config.js

@@ -33,8 +33,7 @@ const sharedConfig = {
             ],
         }),
         new webpack.DefinePlugin({
-            __VERSION__: webpack.DefinePlugin.runtimeValue(() => JSON.stringify(require('./node_modules/molstar/package.json').version), true),
-            __VERSION_TIMESTAMP__: webpack.DefinePlugin.runtimeValue(() => `${new Date().valueOf()}`, true),
+            __BUILD_TIMESTAMP__: webpack.DefinePlugin.runtimeValue(() => `${new Date().valueOf()}`, true),
             __RCSB_MOLSTAR_VERSION__: webpack.DefinePlugin.runtimeValue(() => JSON.stringify(require('./package.json').version), true),
             'process.env.DEBUG': JSON.stringify(process.env.DEBUG)
         }),