update and adjusted to new molstar version

- use eslint
- allow opening .gz and .zip files
- use validation report property
- use non-covalent interactions property
- use accessible surface area property

.eslintrc.json

@@ -0,0 +1,65 @@
+{
+    "env": {
+        "browser": true,
+        "node": true
+    },
+    "parser": "@typescript-eslint/parser",
+    "parserOptions": {
+        "project": "tsconfig.json",
+        "sourceType": "module"
+    },
+    "plugins": [
+        "@typescript-eslint"
+    ],
+    "rules": {
+        "@typescript-eslint/ban-types": "warn",
+        "@typescript-eslint/class-name-casing": "off",
+        "@typescript-eslint/indent": [
+            "warn",
+            4
+        ],
+        "@typescript-eslint/member-delimiter-style": [
+            "off",
+            {
+                "multiline": {
+                    "delimiter": "none",
+                    "requireLast": true
+                },
+                "singleline": {
+                    "delimiter": "semi",
+                    "requireLast": false
+                }
+            }
+        ],
+        "@typescript-eslint/prefer-namespace-keyword": "warn",
+        "@typescript-eslint/quotes": [
+            "warn",
+            "single",
+            {
+                "avoidEscape": true,
+                "allowTemplateLiterals": true
+            }
+        ],
+        "@typescript-eslint/semi": [
+            "off",
+            null
+        ],
+        "@typescript-eslint/type-annotation-spacing": "warn",
+        "arrow-parens": [
+            "off",
+            "as-needed"
+        ],
+        "comma-dangle": "off",
+        "eqeqeq": [
+            "warn",
+            "smart"
+        ],
+        "import/order": "off",
+        "no-eval": "warn",
+        "no-new-wrappers": "warn",
+        "no-trailing-spaces": "warn",
+        "no-unsafe-finally": "warn",
+        "no-var": "warn",
+        "spaced-comment": "warn"
+    }
+}

package.json

@@ -36,31 +36,34 @@
     "author": "RCSB PDB and Mol* Contributors",
     "license": "MIT",
     "devDependencies": {
-        "@types/argparse": "^1.0.36",
-        "@types/node": "^12.12.9",
-        "@types/node-fetch": "^2.5.3",
-        "@types/react": "^16.9.11",
-        "@types/react-dom": "^16.9.4",
-        "concurrently": "^5.0.0",
-        "cpx": "^1.5.0",
-        "css-loader": "^3.2.0",
+        "@types/argparse": "^1.0.38",
+        "@types/node": "^13.7.4",
+        "@types/node-fetch": "^2.5.4",
+        "@types/react": "^16.9.21",
+        "@types/react-dom": "^16.9.5",
+        "@typescript-eslint/eslint-plugin": "^2.19.2",
+        "@typescript-eslint/eslint-plugin-tslint": "^2.19.2",
+        "@typescript-eslint/parser": "^2.19.2",
+        "concurrently": "^5.1.0",
+        "cpx2": "^2.0.0",
+        "css-loader": "^3.4.2",
+        "eslint": "^6.8.0",
         "extra-watch-webpack-plugin": "^1.0.3",
-        "file-loader": "^4.2.0",
-        "mini-css-extract-plugin": "^0.8.0",
-        "molstar": "^0.4.5",
+        "file-loader": "^5.1.0",
+        "mini-css-extract-plugin": "^0.9.0",
+        "molstar": "^0.5.0",
         "node-fetch": "^2.6.0",
-        "node-sass": "^4.13.0",
-        "raw-loader": "^3.1.0",
+        "node-sass": "^4.13.1",
+        "raw-loader": "^4.0.0",
         "react": "^16.12.0",
         "react-dom": "^16.12.0",
         "resolve-url-loader": "^3.1.1",
-        "rxjs": "^6.5.3",
-        "sass-loader": "^8.0.0",
-        "style-loader": "^1.0.0",
-        "tslint": "^5.20.1",
-        "typescript": "3.7.2",
-        "webpack": "^4.41.2",
-        "webpack-cli": "^3.3.10"
+        "rxjs": "^6.5.4",
+        "sass-loader": "^8.0.2",
+        "style-loader": "^1.1.3",
+        "typescript": "3.7.5",
+        "webpack": "^4.41.6",
+        "webpack-cli": "^3.3.11"
     },
     "dependencies": {}
 }

src/structure-viewer/helpers/structure.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -45,9 +45,9 @@ export class StructureView {
         const radius = Math.max(assembly.data.lookup3d.boundary.sphere.radius + extraRadius, minRadius);
         const loci = Structure.toStructureElementLoci(assembly.data)
         const principalAxes = StructureElement.Loci.getPrincipalAxes(loci)
-        const { center, normVecA, normVecC } = principalAxes
+        const { origin, dirA, dirC } = principalAxes.boxAxes
 
-        this.plugin.canvas3d.camera.focus(center, radius, durationMs, normVecA, normVecC);
+        this.plugin.canvas3d!.camera.focus(origin, radius, radius, durationMs, dirA, dirC);
     }
 
     private ensureModelUnitcell(tree: StateBuilder.Root, state: State) {
@@ -63,27 +63,42 @@ export class StructureView {
         const state = this.plugin.state.dataState;
         const tree = state.build();
         if (id === AssemblyNames.Unitcell) {
-            const props = { ijkMin: Vec3.create(0, 0, 0), ijkMax: Vec3.create(0, 0, 0) }
+            const props = {
+                type: {
+                    name: 'symmetry' as const,
+                    params: { ijkMin: Vec3.create(0, 0, 0), ijkMax: Vec3.create(0, 0, 0) }
+                }
+            }
             tree.delete(StateElements.Assembly)
                 .to(StateElements.Model).apply(
-                    StateTransforms.Model.StructureSymmetryFromModel,
+                    StateTransforms.Model.StructureFromModel,
                     props, { ref: StateElements.Assembly, tags: [ AssemblyNames.Unitcell ] }
                 )
             this.ensureModelUnitcell(tree, state)
         } else if (id === AssemblyNames.Supercell) {
-            const props = { ijkMin: Vec3.create(-1, -1, -1), ijkMax: Vec3.create(1, 1, 1) }
+            const props = {
+                type: {
+                    name: 'symmetry' as const,
+                    params: { ijkMin: Vec3.create(-1, -1, -1), ijkMax: Vec3.create(1, 1, 1) }
+                }
+            }
             tree.delete(StateElements.Assembly)
                 .to(StateElements.Model).apply(
-                    StateTransforms.Model.StructureSymmetryFromModel,
+                    StateTransforms.Model.StructureFromModel,
                     props, { ref: StateElements.Assembly, tags: [ AssemblyNames.Supercell ] }
                 )
             this.ensureModelUnitcell(tree, state)
         } else if (id === AssemblyNames.CrystalContacts) {
-            const props = { radius: 5 }
+            const props = {
+                type: {
+                    name: 'symmetry-mates' as const,
+                    params: { radius: 5 }
+                }
+            }
             tree.delete(StateElements.ModelUnitcell)
             tree.delete(StateElements.Assembly)
                 .to(StateElements.Model).apply(
-                    StateTransforms.Model.StructureSymmetryMatesFromModel,
+                    StateTransforms.Model.StructureFromModel,
                     props, { ref: StateElements.Assembly, tags: [ AssemblyNames.CrystalContacts ] }
                 )
         } else {

src/structure-viewer/helpers/volume.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -11,6 +11,7 @@ import { PluginContext } from 'molstar/lib/mol-plugin/context';
 import { InitVolumeStreaming, CreateVolumeStreamingInfo } from 'molstar/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers';
 import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
 import { Model } from 'molstar/lib/mol-model/structure';
+import { MmcifFormat } from 'molstar/lib/mol-model-formats/structure/mmcif';
 
 export class VolumeData {
     get state() {
@@ -24,11 +25,12 @@ export class VolumeData {
         if (!model || !asm) return
 
         const m = model.data as Model
-        const d = m.sourceData.data
-        const hasXrayMap = d.pdbx_database_status.status_code_sf.value(0) === 'REL'
+        if (!MmcifFormat.is(m.sourceData)) return
+        const { db } = m.sourceData.data
+        const hasXrayMap = db.pdbx_database_status.status_code_sf.value(0) === 'REL'
         let hasEmMap = false
-        for (let i = 0, il = d.pdbx_database_related._rowCount; i < il; ++i) {
-            if (d.pdbx_database_related.db_name.value(i).toUpperCase() === 'EMDB') {
+        for (let i = 0, il = db.pdbx_database_related._rowCount; i < il; ++i) {
+            if (db.pdbx_database_related.db_name.value(i).toUpperCase() === 'EMDB') {
                 hasEmMap = true
                 break
             }

src/structure-viewer/index.ts

@@ -1,11 +1,11 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { DefaultPluginSpec } from 'molstar/lib/mol-plugin';
-import { Plugin } from 'molstar/lib/mol-plugin/ui/plugin'
+import { Plugin } from 'molstar/lib/mol-plugin-ui/plugin'
 import './index.html'
 import './favicon.ico'
 import { PluginContext } from 'molstar/lib/mol-plugin/context';
@@ -60,10 +60,13 @@ export class StructureViewer {
                     minRadius: 8,
                     extraRadius: 4
                 }),
-                PluginSpec.Behavior(PluginBehaviors.CustomProps.RCSBAssemblySymmetry, {
-                    autoAttach: true
-                }),
-                PluginSpec.Behavior(StructureRepresentationInteraction)
+                PluginSpec.Behavior(StructureRepresentationInteraction),
+
+                PluginSpec.Behavior(PluginBehaviors.CustomProps.AccessibleSurfaceArea),
+                PluginSpec.Behavior(PluginBehaviors.CustomProps.Interactions),
+                PluginSpec.Behavior(PluginBehaviors.CustomProps.RCSBAssemblySymmetry),
+                PluginSpec.Behavior(PluginBehaviors.CustomProps.RCSBValidationReport),
+
             ],
             animations: [
                 AnimateModelIndex
@@ -92,7 +95,7 @@ export class StructureViewer {
 
         ReactDOM.render(React.createElement(Plugin, { plugin: this.plugin }), target)
 
-        const renderer = this.plugin.canvas3d.props.renderer;
+        const renderer = this.plugin.canvas3d!.props.renderer;
         PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { renderer: { ...renderer, backgroundColor: ColorNames.white } } })
 
         PluginCommands.Toast.Show.dispatch(this.plugin, {

src/structure-viewer/skin/rcsb.scss

@@ -27,7 +27,7 @@ $logo-background: lighten(#325880, 60%);
     opacity: 0.8 !important;
 }
 
-@import 'molstar/lib/mol-plugin/skin/base/base';
+@import 'molstar/lib/mol-plugin-ui/skin/base/base';
 
 .msp-help-viewport-controls {
     float: left;

src/structure-viewer/ui/controls.tsx

@@ -5,18 +5,16 @@
  */
 
 import * as React from 'react';
-import { PluginUIComponent } from 'molstar/lib/mol-plugin/ui/base';
-import { TransformUpdaterControl } from 'molstar/lib/mol-plugin/ui/state/update-transform';
-import { StructureSelectionControls } from 'molstar/lib/mol-plugin/ui/structure/selection';
-import { StructureRepresentationControls } from 'molstar/lib/mol-plugin/ui/structure/representation';
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
+import { TransformUpdaterControl } from 'molstar/lib/mol-plugin-ui/state/update-transform';
+import { StructureSelectionControls } from 'molstar/lib/mol-plugin-ui/structure/selection';
+import { StructureRepresentationControls } from 'molstar/lib/mol-plugin-ui/structure/representation';
 import { StateElements, StructureViewerState } from '../types';
-import { Viewport, ViewportControls } from 'molstar/lib/mol-plugin/ui/viewport';
-import { BackgroundTaskProgress } from 'molstar/lib/mol-plugin/ui/task';
-import { ImageControls } from 'molstar/lib/mol-plugin/ui/image';
-import { LociLabels } from 'molstar/lib/mol-plugin/ui/controls';
-import { IconButton } from 'molstar/lib/mol-plugin/ui/controls/common';
-import { Toasts } from 'molstar/lib/mol-plugin/ui/toast';
-import { GeneralSettings } from './general';
+import { Viewport, ViewportControls } from 'molstar/lib/mol-plugin-ui/viewport';
+import { BackgroundTaskProgress } from 'molstar/lib/mol-plugin-ui/task';
+import { LociLabels } from 'molstar/lib/mol-plugin-ui/controls';
+import { IconButton } from 'molstar/lib/mol-plugin-ui/controls/common';
+import { Toasts } from 'molstar/lib/mol-plugin-ui/toast';
 import { StructureControls } from './structure';
 import { HelpContent } from './help';
 import { OpenFile } from './open';
@@ -31,11 +29,9 @@ export class ControlsWrapper extends PluginUIComponent {
         const { showOpenFileControls } = (this.plugin.customState as StructureViewerState).props
         return <div className='msp-scrollable-container msp-right-controls' style={{ paddingTop: '0px' }}>
             {showOpenFileControls && <OpenFile initiallyCollapsed={false} />}
-            <GeneralSettings initiallyCollapsed={true} />
             <StructureControls  />
             <StructureSelectionControls header='Manage Selection' initiallyCollapsed={true} />
             <StructureRepresentationControls header='Change Representation' initiallyCollapsed={true} />
-            <ImageControls initiallyCollapsed={true} />
             <TransformUpdaterControl nodeRef={StateElements.VolumeStreaming} header={{ name: 'Density Controls', description: '' }} initiallyCollapsed={true} />
         </div>;
     }
@@ -66,7 +62,7 @@ export class ViewportWrapper extends PluginUIComponent {
             <div className='msp-viewport-top-left-controls'>
                 <HelpViewportControls />
             </div>
-            <ViewportControls hideSettingsIcon={true} />
+            <ViewportControls />
             <div style={{ position: 'absolute', left: '10px', bottom: '10px' }}>
                 <BackgroundTaskProgress />
             </div>

src/structure-viewer/ui/general.tsx

@@ -1,131 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import * as React from 'react';
-import { CollapsableControls } from 'molstar/lib/mol-plugin/ui/base';
-import { ParameterControls } from 'molstar/lib/mol-plugin/ui/controls/parameters';
-import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
-import { PluginCommands } from 'molstar/lib/mol-plugin/command';
-import { Canvas3DParams } from 'molstar/lib/mol-canvas3d/canvas3d';
-import { ColorNames } from 'molstar/lib/mol-util/color/names';
-
-const GeneralSettingsParams = {
-    spin: Canvas3DParams.trackball.params.spin,
-    camera: Canvas3DParams.cameraMode,
-    background: PD.Select('white', [['white', 'White'], ['black', 'Black'], ['transparent', 'Transparent']], { description: 'Background of the 3D canvas' }),
-    renderStyle: PD.Select('glossy', [['toon', 'Toon'], ['matte', 'Matte'], ['glossy', 'Glossy'], ['metallic', 'Metallic']], { description: 'Style in which the 3D scene is rendered' }),
-    occlusion: PD.Boolean(false, { description: 'Darken occluded crevices with the ambient occlusion effect' }),
-    outline: PD.Boolean(false, { description: 'Draw outline around 3D objects' }),
-    fog: PD.Boolean(false, { description: 'Show fog in the distance' }),
-}
-
-export class GeneralSettings<P> extends CollapsableControls<P> {
-    setSettings = (p: { param: PD.Base<any>, name: string, value: any }) => {
-        if (p.name === 'spin') {
-            const trackball = this.plugin.canvas3d.props.trackball;
-            PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { trackball: { ...trackball, spin: p.value } } });
-        } else if (p.name === 'camera') {
-            PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { cameraMode: p.value }});
-        } else if (p.name === 'background') {
-            const renderer = this.plugin.canvas3d.props.renderer;
-            if (p.value === 'white') {
-                PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { renderer: { ...renderer, backgroundColor: ColorNames.white, transparentBackground: false } } });
-            } else if (p.value === 'black') {
-                PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { renderer: { ...renderer, backgroundColor: ColorNames.black, transparentBackground: false } } });
-            } else if (p.value === 'transparent') {
-                PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: { renderer: { ...renderer, backgroundColor: ColorNames.white, transparentBackground: true } } });
-            }
-        } else if (p.name === 'renderStyle') {
-            const renderer = this.plugin.canvas3d.props.renderer;
-            if (p.value === 'toon') {
-                PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
-                    renderer: { ...renderer, lightIntensity: 0, ambientIntensity: 1, roughness: 0.4, metalness: 0 }
-                } });
-            } else if (p.value === 'matte') {
-                PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
-                    renderer: { ...renderer, lightIntensity: 0.6, ambientIntensity: 0.4, roughness: 1, metalness: 0 }
-                } });
-            } else if (p.value === 'glossy') {
-                PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
-                    renderer: { ...renderer, lightIntensity: 0.6, ambientIntensity: 0.4, roughness: 0.4, metalness: 0 }
-                } });
-            } else if (p.value === 'metallic') {
-                PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
-                    renderer: { ...renderer, lightIntensity: 0.6, ambientIntensity: 0.4, roughness: 0.6, metalness: 0.4 }
-                } });
-            }
-        } else if (p.name === 'occlusion') {
-            const postprocessing = this.plugin.canvas3d.props.postprocessing;
-            PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
-                postprocessing: { ...postprocessing, occlusionEnable: p.value, occlusionBias: 0.5, occlusionRadius: 64 },
-            } });
-        } else if (p.name === 'outline') {
-            const postprocessing = this.plugin.canvas3d.props.postprocessing;
-            PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
-                postprocessing: { ...postprocessing, outlineEnable: p.value },
-            } });
-        } else if (p.name === 'fog') {;
-            PluginCommands.Canvas3D.SetSettings.dispatch(this.plugin, { settings: {
-                cameraFog: p.value ? 50 : 1,
-            } });
-        }
-    }
-
-    get values () {
-        const renderer = this.plugin.canvas3d.props.renderer;
-
-        let renderStyle = 'custom'
-        if (renderer.lightIntensity === 0 && renderer.ambientIntensity === 1 && renderer.roughness === 0.4 && renderer.metalness === 0) {
-            renderStyle = 'toon'
-        } else if (renderer.lightIntensity === 0.6 && renderer.ambientIntensity === 0.4) {
-            if (renderer.roughness === 1 && renderer.metalness === 0) {
-                renderStyle = 'matte'
-            } else if (renderer.roughness === 0.4 && renderer.metalness === 0) {
-                renderStyle = 'glossy'
-            } else if (renderer.roughness === 0.6 && renderer.metalness === 0.4) {
-                renderStyle = 'metallic'
-            }
-        }
-
-        let background = 'custom'
-        if (renderer.backgroundColor === ColorNames.white && !renderer.transparentBackground) {
-            background = 'white'
-        } else if (renderer.backgroundColor === ColorNames.black && !renderer.transparentBackground) {
-            background = 'black'
-        } else if (renderer.backgroundColor === ColorNames.white && renderer.transparentBackground) {
-            background = 'transparent'
-        }
-
-        return {
-            spin: this.plugin.canvas3d.props.trackball.spin,
-            camera: this.plugin.canvas3d.props.cameraMode,
-            background,
-            renderStyle,
-            occlusion: this.plugin.canvas3d.props.postprocessing.occlusionEnable,
-            outline: this.plugin.canvas3d.props.postprocessing.outlineEnable,
-            fog: this.plugin.canvas3d.props.cameraFog > 1
-        }
-    }
-
-    componentDidMount() {
-        this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
-    }
-
-    defaultState() {
-        return {
-            isCollapsed: false,
-            header: 'General Settings'
-        }
-    }
-
-    renderControls() {
-        if (!this.plugin.canvas3d) return null
-
-        return <div>
-            <ParameterControls params={GeneralSettingsParams} values={this.values} onChange={this.setSettings} />
-        </div>
-    }
-}

src/structure-viewer/ui/help.tsx

@@ -5,7 +5,7 @@
  */
 
 import * as React from 'react';
-import { CollapsableControls, PluginUIComponent } from 'molstar/lib/mol-plugin/ui/base';
+import { CollapsableControls, PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
 import { Binding } from 'molstar/lib/mol-util/binding';
 import { StateSelection, StateTransformer } from 'molstar/lib/mol-state';
 import { StructureRepresentationInteraction } from 'molstar/lib/mol-plugin/behavior/dynamic/selection/structure-representation-interaction';
@@ -94,7 +94,7 @@ export class HelpContent extends PluginUIComponent {
         })
         return [
             <HelpGroup key='trackball' header='Moving in 3D'>
-                <BindingsHelp bindings={this.plugin.canvas3d.props.trackball.bindings} />
+                <BindingsHelp bindings={this.plugin.canvas3d?.props.trackball.bindings ?? {}} />
             </HelpGroup>,
             <HelpGroup key='interactions' header='Select, Highlight, Focus'>
                 <BindingsHelp bindings={interactionBindings} />

src/structure-viewer/ui/open.tsx

@@ -10,8 +10,8 @@ import { StateAction, StateTransform } from 'molstar/lib/mol-state';
 import { PluginStateObject } from 'molstar/lib/mol-plugin/state/objects';
 import { PluginContext } from 'molstar/lib/mol-plugin/context';
 import { Task } from 'molstar/lib/mol-task';
-import { ApplyActionControl } from 'molstar/lib/mol-plugin/ui/state/apply-action';
-import { PluginUIComponent } from 'molstar/lib/mol-plugin/ui/base';
+import { ApplyActionControl } from 'molstar/lib/mol-plugin-ui/state/apply-action';
+import { PluginUIComponent } from 'molstar/lib/mol-plugin-ui/base';
 import { StructureViewerState } from '../types';
 
 const OpenFileAction = StateAction.build({
@@ -19,7 +19,7 @@ const OpenFileAction = StateAction.build({
     from: PluginStateObject.Root,
     params: (a, ctx: PluginContext) => {
         return {
-            file: PD.File({ accept: '.cif, .mcif, .mmcif, .bcif' })
+            file: PD.File({ accept: '.cif, .mcif, .mmcif, .bcif, .gz, .zip' })
         }
     }
 })(({ params, state }, ctx: PluginContext) => Task.create('Open File', async taskCtx => {

src/structure-viewer/ui/structure.tsx

@@ -1,19 +1,21 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import * as React from 'react';
-import { CollapsableControls, CollapsableState } from 'molstar/lib/mol-plugin/ui/base';
+import { CollapsableControls, CollapsableState } from 'molstar/lib/mol-plugin-ui/base';
 import { StateElements, AssemblyNames, StructureViewerState } from '../types';
-import { ParameterControls } from 'molstar/lib/mol-plugin/ui/controls/parameters';
+import { ParameterControls } from 'molstar/lib/mol-plugin-ui/controls/parameters';
 import { ParamDefinition as PD } from 'molstar/lib/mol-util/param-definition';
 import { StateObject, StateTree, StateSelection } from 'molstar/lib/mol-state';
 import { PluginStateObject as PSO } from 'molstar/lib/mol-plugin/state/objects';
 import { StateTransforms } from 'molstar/lib/mol-plugin/state/transforms';
 import { Model } from 'molstar/lib/mol-model/structure';
+import { MmcifFormat } from 'molstar/lib/mol-model-formats/structure/mmcif';
 import { stringToWords } from 'molstar/lib/mol-util/string';
+import { ModelSymmetry } from 'molstar/lib/mol-model-formats/structure/property/symmetry';
 
 interface StructureControlsState extends CollapsableState {
     trajectoryRef: string
@@ -96,11 +98,16 @@ export class StructureControls<P, S extends StructureControlsState> extends Coll
 
         let modelValue = 0
         if (model) {
-            if (trajectory) modelValue = trajectory.data.indexOf(model.data)
-            const { assemblies } = model.data.symmetry
-            for (let i = 0, il = assemblies.length; i < il; ++i) {
-                const a = assemblies[i]
-                assemblyOptions.push([a.id, `${a.id}: ${stringToWords(a.details)}`])
+            const symmetry = ModelSymmetry.Provider.get(model.data)
+            if (symmetry) {
+                if (trajectory) modelValue = trajectory.data.indexOf(model.data)
+                const { assemblies } = symmetry
+                for (let i = 0, il = assemblies.length; i < il; ++i) {
+                    const a = assemblies[i]
+                    assemblyOptions.push([a.id, `${a.id}: ${stringToWords(a.details)}`])
+                }
+            } else {
+                modelValue = -1
             }
         } else if (assembly) {
             // assembly from trajectory, no model
@@ -265,24 +272,26 @@ export class StructureControls<P, S extends StructureControlsState> extends Coll
 }
 
 function modelHasSymmetry(model: Model) {
-    const mmcif = model.sourceData.data
+    if (!MmcifFormat.is(model.sourceData)) return false
+    const { db } = model.sourceData.data
     return (
-        mmcif.symmetry._rowCount === 1 && mmcif.cell._rowCount === 1 && !(
-            mmcif.symmetry.Int_Tables_number.value(0) === 1 &&
-            mmcif.cell.angle_alpha.value(0) === 90 &&
-            mmcif.cell.angle_beta.value(0) === 90 &&
-            mmcif.cell.angle_gamma.value(0) === 90 &&
-            mmcif.cell.length_a.value(0) === 1 &&
-            mmcif.cell.length_b.value(0) === 1 &&
-            mmcif.cell.length_c.value(0) === 1
+        db.symmetry._rowCount === 1 && db.cell._rowCount === 1 && !(
+            db.symmetry.Int_Tables_number.value(0) === 1 &&
+            db.cell.angle_alpha.value(0) === 90 &&
+            db.cell.angle_beta.value(0) === 90 &&
+            db.cell.angle_gamma.value(0) === 90 &&
+            db.cell.length_a.value(0) === 1 &&
+            db.cell.length_b.value(0) === 1 &&
+            db.cell.length_c.value(0) === 1
         )
     )
 }
 
 function modelFromCrystallography(model: Model) {
-    const mmcif = model.sourceData.data
-    for (let i = 0; i < mmcif.exptl.method.rowCount; i++) {
-        const v = mmcif.exptl.method.value(i).toUpperCase()
+    if (!MmcifFormat.is(model.sourceData)) return false
+    const { db } = model.sourceData.data
+    for (let i = 0; i < db.exptl.method.rowCount; i++) {
+        const v = db.exptl.method.value(i).toUpperCase()
         if (v.indexOf('DIFFRACTION') >= 0) return true
     }
     return false

tslint.json

@@ -1,74 +0,0 @@
-{
-    "rules": {
-        "array-type": [
-            true,
-            "array"
-        ],
-        "arrow-parens": false,
-        "no-var-keyword": true,
-        "no-construct": true,
-        "ordered-imports": [false],
-        "trailing-comma": [false],
-        "class-name": false,
-        "comment-format": [
-            true,
-            "check-space"
-        ],
-        "indent": [
-            true,
-            "spaces"
-        ],
-        "ban-types": [
-            true,
-            ["String", "Use primitive 'string' instead."],
-            ["Boolean", "Use primitive 'boolean' instead."],
-            ["Number", "Use primitive 'number' instead."]
-        ],
-        "no-eval": true,
-        "no-internal-module": true,
-        "no-trailing-whitespace": true,
-        "no-unsafe-finally": true,
-        "one-line": [
-            true,
-            "check-open-brace",
-            "check-whitespace"
-        ],
-        "quotemark": [
-            true,
-            "single"
-        ],
-        "semicolon": [ false ],
-        "triple-equals": [
-            true,
-            "allow-null-check"
-        ],
-        "typedef-whitespace": [
-            true,
-            {
-                "call-signature": "nospace",
-                "index-signature": "nospace",
-                "parameter": "nospace",
-                "property-declaration": "nospace",
-                "variable-declaration": "nospace"
-            }
-        ],
-        "variable-name": [
-            true,
-            "ban-keywords"
-        ],
-        "whitespace": [
-            true,
-            "check-branch",
-            "check-decl",
-            "check-separator",
-            "check-type"
-        ]
-    },
-    "jsRules": {
-        "triple-equals": [
-            true,
-            "allow-null-check"
-        ]
-    },
-    "defaultSeverity": "warning"
-}