v4 changes

molstar · Jan 29, 2024 · 1e963ea · 1e963ea
1 parent a03f3dd
commit 1e963ea
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Showing 8 changed files with 56 additions and 36 deletions.
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -10,7 +10,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: actions/setup-node@v2
         with:
-          node-version: 16
+          node-version: 18
       - run: npm ci
       - name: Lint
         run: npm run lint
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,10 @@
 
 [Semantic Versioning](https://semver.org/)
 
+## [Unreleased]
+### General
+- Dependency update to Mol* v4
+
 ## [2.9.1] - 2024-01-24
 ### General
 - Dependency update

diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -62,7 +62,7 @@
     "dependencies": {
         "@types/react": "^18.2.48",
         "@types/react-dom": "^18.2.18",
-        "molstar": "^3.44.0",
+        "molstar": "^4.0.0-beta.0",
         "react": "^18.2.0",
         "react-dom": "^18.2.0",
         "rxjs": "^7.8.1",

diff --git a/src/viewer/helpers/preset.ts b/src/viewer/helpers/preset.ts
@@ -8,7 +8,7 @@ import { PluginContext } from 'molstar/lib/mol-plugin/context';
 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/extensions/rcsb/validation-report/behavior';
-import { AssemblySymmetryPreset } from 'molstar/lib/extensions/rcsb/assembly-symmetry/behavior';
+import { AssemblySymmetryPreset } from 'molstar/lib/extensions/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';
@@ -44,7 +44,7 @@ import { RcsbSuperpositionRepresentationPreset } from './superpose/preset';
 import {
     AssemblySymmetryDataProvider,
     AssemblySymmetryProvider
-} from 'molstar/lib/extensions/rcsb/assembly-symmetry/prop';
+} from 'molstar/lib/extensions/assembly-symmetry/prop';
 import { Task } from 'molstar/lib/mol-task';
 import { PLDDTConfidenceColorThemeProvider } from 'molstar/lib/extensions/model-archive/quality-assessment/color/plddt';
 

diff --git a/src/viewer/index.ts b/src/viewer/index.ts
@@ -20,7 +20,7 @@ import { ModelLoader } from './helpers/model';
 import { PresetProps } from './helpers/preset';
 import { ControlsWrapper } from './ui/controls';
 import { PluginConfig } from 'molstar/lib/mol-plugin/config';
-import { RCSBAssemblySymmetry } from 'molstar/lib/extensions/rcsb/assembly-symmetry/behavior';
+import { AssemblySymmetry } from 'molstar/lib/extensions/assembly-symmetry/behavior';
 import { RCSBValidationReport } from 'molstar/lib/extensions/rcsb/validation-report/behavior';
 import { Mat4 } from 'molstar/lib/mol-math/linear-algebra';
 import { PluginState } from 'molstar/lib/mol-plugin/state';
@@ -49,7 +49,7 @@ import { Mp4Export } from 'molstar/lib/extensions/mp4-export';
 import { PartialCanvas3DProps } from 'molstar/lib/mol-canvas3d/canvas3d';
 import { RSCCScore } from './helpers/rscc/behavior';
 import { createRoot } from 'react-dom/client';
-import { AssemblySymmetry } from 'molstar/lib/extensions/rcsb/assembly-symmetry/prop';
+import { AssemblySymmetryData } from 'molstar/lib/extensions/assembly-symmetry/prop';
 import { wwPDBChemicalComponentDictionary } from 'molstar/lib/extensions/wwpdb/ccd/behavior';
 import { ChemicalCompontentTrajectoryHierarchyPreset } from 'molstar/lib/extensions/wwpdb/ccd/representation';
 import { StateTransforms } from 'molstar/lib/mol-plugin-state/transforms';
@@ -65,7 +65,7 @@ export const BUILD_TIMESTAMP = typeof __BUILD_TIMESTAMP__ != 'undefined' ? __BUI
 export const BUILD_DATE = new Date(BUILD_TIMESTAMP);
 
 const Extensions = {
-    'rcsb-assembly-symmetry': PluginSpec.Behavior(RCSBAssemblySymmetry),
+    'assembly-symmetry': PluginSpec.Behavior(AssemblySymmetry),
     'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
     'rscc': PluginSpec.Behavior(RSCCScore),
     'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
@@ -220,7 +220,7 @@ export class Viewer {
                 [PluginConfig.Download.DefaultEmdbProvider, 'rcsb'],
                 [PluginConfig.Structure.DefaultRepresentationPreset, PresetStructureRepresentations.auto.id],
                 // wboit & webgl1 checks are needed to work properly on recent Safari versions
-                [PluginConfig.General.EnableWboit, PluginFeatureDetection.preferWebGl1],
+                [PluginConfig.General.Transparency, PluginFeatureDetection.preferWebGl1 ? 'wboit' : undefined],
                 [PluginConfig.General.PreferWebGl1, PluginFeatureDetection.preferWebGl1]
             ]
         };
@@ -265,7 +265,7 @@ export class Viewer {
                     this._plugin.representation.structure.registry.remove(MembraneOrientationRepresentationProvider);
                 }
                 // normally, this would be part of CustomStructureControls -- we want to manage its collapsed state individually though
-                this._plugin.customStructureControls.delete(AssemblySymmetry.Tag.Representation);
+                this._plugin.customStructureControls.delete(AssemblySymmetryData.Tag.Representation);
 
                 const root = createRoot(element);
                 root.render(React.createElement(Plugin, { plugin: this._plugin }));
@@ -449,7 +449,7 @@ export class LigandViewer {
                 [PluginConfig.Download.DefaultEmdbProvider, 'rcsb'],
                 [PluginConfig.Structure.DefaultRepresentationPreset, PresetStructureRepresentations.auto.id],
                 // wboit & webgl1 checks are needed to work properly on recent Safari versions
-                [PluginConfig.General.EnableWboit, PluginFeatureDetection.preferWebGl1],
+                [PluginConfig.General.Transparency, PluginFeatureDetection.preferWebGl1 ? 'wboit' : undefined],
                 [PluginConfig.General.PreferWebGl1, PluginFeatureDetection.preferWebGl1]
             ]
         };

diff --git a/src/viewer/ui/controls.tsx b/src/viewer/ui/controls.tsx
@@ -17,7 +17,7 @@ import { SessionControls } from './session';
 import { StrucmotifSubmitControls } from './strucmotif';
 import { ValidationReportControls } from './validation';
 import { StructureQuickStylesControls } from 'molstar/lib/mol-plugin-ui/structure/quick-styles';
-import { AssemblySymmetryControls } from 'molstar/lib/extensions/rcsb/assembly-symmetry/ui';
+import { AssemblySymmetryControls } from 'molstar/lib/extensions/assembly-symmetry/ui';
 
 export class StructureTools extends PluginUIComponent {
     get customState() {

diff --git a/tsconfig.json b/tsconfig.json
@@ -1,7 +1,7 @@
 {
     "compilerOptions": {
         "declaration": true,
-        "target": "es5",
+        "target": "es2018",
         "alwaysStrict": true,
         "noImplicitAny": true,
         "noImplicitThis": true,
@@ -16,7 +16,7 @@
         "importHelpers": true,
         "noEmitHelpers": true,
         "jsx": "react-jsx",
-        "lib": [ "es6", "dom", "esnext.asynciterable", "es2016" ],
+        "lib": [ "es2018", "dom", "ES2022.Object" ],
         "outDir": "build/src",
         "rootDir": "src",
         "resolveJsonModule": true,