Merge branch 'master' into support-glycam-names

CHANGELOG.md

@@ -6,9 +6,14 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
-- Fix missing ``super.componentWillUnmount()`` calls (@simeonborko)
 - Add support for Glycam saccharide names
 
+## [v3.9.1] - 2022-06-19
+
+- Fix missing ``super.componentWillUnmount()`` calls (@simeonborko)
+- Fix missing ``uGroupCount`` update for visuals
+- Fix missing aromatic bond display
+
 ## [v3.9.0] - 2022-05-30
 
 - Improve picking by using drawbuffers (when available) to reduce number of drawcalls

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.9.0",
+  "version": "3.9.1",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -94,51 +94,51 @@
     "@graphql-codegen/add": "^3.1.1",
     "@graphql-codegen/cli": "^2.6.2",
     "@graphql-codegen/time": "^3.1.1",
-    "@graphql-codegen/typescript": "^2.4.11",
+    "@graphql-codegen/typescript": "^2.5.1",
     "@graphql-codegen/typescript-graphql-files-modules": "^2.1.1",
-    "@graphql-codegen/typescript-graphql-request": "^4.4.8",
-    "@graphql-codegen/typescript-operations": "^2.4.0",
+    "@graphql-codegen/typescript-graphql-request": "^4.4.10",
+    "@graphql-codegen/typescript-operations": "^2.4.2",
     "@types/cors": "^2.8.12",
     "@types/gl": "^4.1.0",
-    "@types/jest": "^27.5.1",
-    "@types/react": "^18.0.9",
+    "@types/jest": "^28.1.2",
+    "@types/react": "^18.0.14",
     "@types/react-dom": "^18.0.5",
-    "@typescript-eslint/eslint-plugin": "^5.27.0",
-    "@typescript-eslint/parser": "^5.27.0",
+    "@typescript-eslint/eslint-plugin": "^5.28.0",
+    "@typescript-eslint/parser": "^5.28.0",
     "benchmark": "^2.1.4",
-    "concurrently": "^7.2.1",
+    "concurrently": "^7.2.2",
     "cpx2": "^4.2.0",
     "crypto-browserify": "^3.12.0",
     "css-loader": "^6.7.1",
-    "eslint": "^8.16.0",
+    "eslint": "^8.18.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
     "fs-extra": "^10.1.0",
     "graphql": "^16.5.0",
-    "http-server": "^14.1.0",
-    "jest": "^28.1.0",
-    "mini-css-extract-plugin": "^2.6.0",
+    "http-server": "^14.1.1",
+    "jest": "^28.1.1",
+    "mini-css-extract-plugin": "^2.6.1",
     "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
-    "react": "^18.1.0",
-    "react-dom": "^18.1.0",
-    "sass": "^1.52.1",
+    "react": "^18.2.0",
+    "react-dom": "^18.2.0",
+    "sass": "^1.52.3",
     "sass-loader": "^13.0.0",
-    "simple-git": "^3.7.1",
+    "simple-git": "^3.8.0",
     "stream-browserify": "^3.0.0",
     "style-loader": "^3.3.1",
-    "ts-jest": "^28.0.3",
-    "typescript": "^4.7.2",
-    "webpack": "^5.72.1",
-    "webpack-cli": "^4.9.2"
+    "ts-jest": "^28.0.5",
+    "typescript": "^4.7.4",
+    "webpack": "^5.73.0",
+    "webpack-cli": "^4.10.0"
   },
   "dependencies": {
     "@types/argparse": "^2.0.10",
     "@types/benchmark": "^2.1.1",
     "@types/compression": "1.7.2",
     "@types/express": "^4.17.13",
-    "@types/node": "^16.11.36",
-    "@types/node-fetch": "^2.6.1",
+    "@types/node": "^16.11.41",
+    "@types/node-fetch": "^2.6.2",
     "@types/swagger-ui-dist": "3.30.1",
     "argparse": "^2.0.1",
     "body-parser": "^1.20.0",
@@ -146,11 +146,11 @@
     "cors": "^2.8.5",
     "express": "^4.18.1",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^9.0.14",
+    "immer": "^9.0.15",
     "immutable": "^4.1.0",
     "node-fetch": "^2.6.7",
     "rxjs": "^7.5.5",
-    "swagger-ui-dist": "^4.11.1",
+    "swagger-ui-dist": "^4.12.0",
     "tslib": "^2.4.0",
     "util.promisify": "^1.1.1",
     "xhr2": "^0.2.1"

src/apps/viewer/app.ts

@@ -400,7 +400,7 @@ export class Viewer {
     async loadTrajectory(params: LoadTrajectoryParams) {
         const plugin = this.plugin;
 
-        let model: StateObjectSelector, coords: StateObjectSelector;
+        let model: StateObjectSelector;
 
         if (params.model.kind === 'model-data' || params.model.kind === 'model-url') {
             const data = params.model.kind === 'model-data'
@@ -418,14 +418,12 @@ export class Viewer {
             model = await provider!.parse(plugin, data);
         }
 
-        {
-            const data = params.coordinates.kind === 'coordinates-data'
-                ? await plugin.builders.data.rawData({ data: params.coordinates.data, label: params.coordinatesLabel })
-                : await plugin.builders.data.download({ url: params.coordinates.url, isBinary: params.coordinates.isBinary, label: params.coordinatesLabel });
+        const data = params.coordinates.kind === 'coordinates-data'
+            ? await plugin.builders.data.rawData({ data: params.coordinates.data, label: params.coordinatesLabel })
+            : await plugin.builders.data.download({ url: params.coordinates.url, isBinary: params.coordinates.isBinary, label: params.coordinatesLabel });
 
-            const provider = plugin.dataFormats.get(params.coordinates.format);
-            coords = await provider!.parse(plugin, data);
-        }
+        const provider = plugin.dataFormats.get(params.coordinates.format);
+        const coords = await provider!.parse(plugin, data);
 
         const trajectory = await plugin.build().toRoot()
             .apply(TrajectoryFromModelAndCoordinates, {

src/mol-repr/shape/representation.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -132,6 +132,7 @@ export function ShapeRepresentation<D, G extends Geometry, P extends Geometry.Pa
                     // console.log('update geometry')
                     ValueCell.updateIfChanged(_renderObject.values.drawCount, Geometry.getDrawCount(_shape.geometry));
                     ValueCell.updateIfChanged(_renderObject.values.uVertexCount, Geometry.getVertexCount(_shape.geometry));
+                    ValueCell.updateIfChanged(_renderObject.values.uGroupCount, Geometry.getGroupCount(_shape.geometry));
                 }
 
                 if (updateState.updateTransform || updateState.createGeometry) {

src/mol-repr/structure/complex-visual.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -161,6 +161,7 @@ export function ComplexVisual<G extends Geometry, P extends StructureParams & Ge
                 if (newGeometry) {
                     ValueCell.updateIfChanged(renderObject.values.drawCount, Geometry.getDrawCount(newGeometry));
                     ValueCell.updateIfChanged(renderObject.values.uVertexCount, Geometry.getVertexCount(newGeometry));
+                    ValueCell.updateIfChanged(renderObject.values.uGroupCount, Geometry.getGroupCount(newGeometry));
                 } else {
                     throw new Error('expected geometry to be given');
                 }

src/mol-repr/structure/units-visual.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -207,6 +207,7 @@ export function UnitsVisual<G extends Geometry, P extends StructureParams & Geom
                 if (newGeometry) {
                     ValueCell.updateIfChanged(renderObject.values.drawCount, Geometry.getDrawCount(newGeometry));
                     ValueCell.updateIfChanged(renderObject.values.uVertexCount, Geometry.getVertexCount(newGeometry));
+                    ValueCell.updateIfChanged(renderObject.values.uGroupCount, Geometry.getGroupCount(newGeometry));
                 } else {
                     throw new Error('expected geometry to be given');
                 }

src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts

@@ -149,10 +149,8 @@ function getIntraUnitBondCylinderBuilderProps(unit: Unit.Atomic, structure: Stru
                 if (isBondType(f, BondType.Flag.Aromatic) || (arCount && !ignoreComputedAromatic)) {
                     if (arCount === 2) {
                         return LinkStyle.MirroredAromatic;
-                    } else if (arCount === 1 || deloTriplets?.getThirdElement(aI, bI)) {
-                        return LinkStyle.Aromatic;
                     } else {
-                        // case for bonds between two aromatic rings
+                        return LinkStyle.Aromatic;
                     }
                 }
             }

src/mol-repr/structure/visual/bond-intra-unit-line.ts

@@ -110,10 +110,8 @@ function createIntraUnitBondLines(ctx: VisualContext, unit: Unit, structure: Str
                 if (isBondType(f, BondType.Flag.Aromatic) || (arCount && !ignoreComputedAromatic)) {
                     if (arCount === 2) {
                         return LinkStyle.MirroredAromatic;
-                    } else if (arCount === 1 || deloTriplets?.getThirdElement(aI, bI)) {
-                        return LinkStyle.Aromatic;
                     } else {
-                        // case for bonds between two aromatic rings
+                        return LinkStyle.Aromatic;
                     }
                 }
             }

src/mol-repr/volume/representation.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -130,6 +130,7 @@ export function VolumeVisual<G extends Geometry, P extends VolumeParams & Geomet
                 if (newGeometry) {
                     ValueCell.updateIfChanged(renderObject.values.drawCount, Geometry.getDrawCount(newGeometry));
                     ValueCell.updateIfChanged(renderObject.values.uVertexCount, Geometry.getVertexCount(newGeometry));
+                    ValueCell.updateIfChanged(renderObject.values.uGroupCount, Geometry.getGroupCount(newGeometry));
                 } else {
                     throw new Error('expected geometry to be given');
                 }