diff --git a/CHANGELOG.md b/CHANGELOG.md
index fb197b561692c51e992a5db220ab32a75390f9d1..c9cbed82a0c88e0e0bdc06e045ca3c46f55628e1 100644
--- a/CHANGELOG.md
+++ b/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
diff --git a/package-lock.json b/package-lock.json
index 70d6a914c46d23eb7a636d5764e06eb628c91ac9..ebd04c44d0c87794983dc11511ccf5262b833d4f 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index 5cd468df8921aed97c1facb2eed2ef49d20e84fb..f287a08c01ebc4746eb437be117e66512235fe80 100644
--- a/package.json
+++ b/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"
diff --git a/src/apps/viewer/app.ts b/src/apps/viewer/app.ts
index 8896b1e02026a53ee221835d2c8ff99b2029cf3a..cee2646c35f3239230979bb3e6ff1686b327c285 100644
--- a/src/apps/viewer/app.ts
+++ b/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, {
diff --git a/src/mol-repr/shape/representation.ts b/src/mol-repr/shape/representation.ts
index 70dc3d05aa347981c21827428fb93f1c77921b71..8571dc7353e2c74e326c338c708548133a2d3278 100644
--- a/src/mol-repr/shape/representation.ts
+++ b/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) {
diff --git a/src/mol-repr/structure/complex-visual.ts b/src/mol-repr/structure/complex-visual.ts
index 54a7378334d0ba087333dc1028afa8db357fe0af..e1b13148d48555b8d5bf670e40839783d80952d4 100644
--- a/src/mol-repr/structure/complex-visual.ts
+++ b/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');
}
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index 760028920025c278aaa5eab6096920da05c5939e..2325d08b91d80ce263548634d5a19b31b1fcaafd 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/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');
}
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
index 013a584e157d160cba46adebd435061e99a503e3..ec837f48eebd89e02b9fbcf1af3095eb6785560e 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
+++ b/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;
}
}
}
diff --git a/src/mol-repr/structure/visual/bond-intra-unit-line.ts b/src/mol-repr/structure/visual/bond-intra-unit-line.ts
index 351c190c300c50f2c68205bcaa521b8d35e42e51..68d1ca4f957cdaa27a37a280f6c41cc7823f9eeb 100644
--- a/src/mol-repr/structure/visual/bond-intra-unit-line.ts
+++ b/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;
}
}
}
diff --git a/src/mol-repr/volume/representation.ts b/src/mol-repr/volume/representation.ts
index 55c8250f7579c44a8d5519a12d215bad13b22eb4..bb90f67659a04e2192ad3e5367eac3da97204eb0 100644
--- a/src/mol-repr/volume/representation.ts
+++ b/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');
}