Merge branch 'master' of https://github.com/molstar/molstar into inter-bonds-props

CHANGELOG.md

@@ -9,11 +9,15 @@ Note that since we don't clearly distinguish between a public and private interf
 - Expose inter-bonds compute params in structure
 - Improve performance of inter/intra-bonds compute
 - Fix defaultAttribs handling in Canvas3DContext.fromCanvas
-- Add custom labels to Confal pyramids
-- Improve naming of some internal types in Confal pyramids extension coordinate
-- Add example mmCIF file with categories necessary to display Confal pyramids
-- Change the lookup logic of NtC steps from residues
+- Confal pyramids extension improvements
+    - Add custom labels to Confal pyramids
+    - Improve naming of some internal types in Confal pyramids extension coordinate
+    - Add example mmCIF file with categories necessary to display Confal pyramids
+    - Change the lookup logic of NtC steps from residues
 - Add support for download of gzipped files
+- Don't filter IndexPairBonds by element-based rules in MOL/SDF and MOL2 (without symmetry) models
+- Fix Glycam Saccharide Names used by default
+- Prefer WebGL1 for more Safari versions to avoid broken GPU surfaces rendering
 
 ## [v3.13.0] - 2022-07-24
 

package.json

@@ -75,7 +75,9 @@
       "node_modules",
       "lib"
     ],
-    "testURL": "http://localhost/",
+    "testEnvironmentOptions": {
+      "url": "http://localhost/"
+    },
     "testRegex": "\\.spec\\.ts$"
   },
   "author": "Mol* Contributors",
@@ -91,30 +93,30 @@
   ],
   "license": "MIT",
   "devDependencies": {
-    "@graphql-codegen/add": "^3.2.0",
-    "@graphql-codegen/cli": "^2.9.1",
-    "@graphql-codegen/time": "^3.2.0",
-    "@graphql-codegen/typescript": "^2.7.2",
-    "@graphql-codegen/typescript-graphql-files-modules": "^2.2.0",
-    "@graphql-codegen/typescript-graphql-request": "^4.5.2",
-    "@graphql-codegen/typescript-operations": "^2.5.2",
+    "@graphql-codegen/add": "^3.2.1",
+    "@graphql-codegen/cli": "^2.11.6",
+    "@graphql-codegen/time": "^3.2.1",
+    "@graphql-codegen/typescript": "^2.7.3",
+    "@graphql-codegen/typescript-graphql-files-modules": "^2.2.1",
+    "@graphql-codegen/typescript-graphql-request": "^4.5.3",
+    "@graphql-codegen/typescript-operations": "^2.5.3",
     "@types/cors": "^2.8.12",
     "@types/gl": "^4.1.1",
-    "@types/jest": "^28.1.6",
-    "@types/react": "^18.0.15",
+    "@types/jest": "^28.1.7",
+    "@types/react": "^18.0.17",
     "@types/react-dom": "^18.0.6",
-    "@typescript-eslint/eslint-plugin": "^5.30.7",
-    "@typescript-eslint/parser": "^5.30.7",
+    "@typescript-eslint/eslint-plugin": "^5.33.1",
+    "@typescript-eslint/parser": "^5.33.1",
     "benchmark": "^2.1.4",
     "concurrently": "^7.3.0",
     "cpx2": "^4.2.0",
     "crypto-browserify": "^3.12.0",
     "css-loader": "^6.7.1",
-    "eslint": "^8.20.0",
+    "eslint": "^8.22.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
     "fs-extra": "^10.1.0",
-    "graphql": "^16.5.0",
+    "graphql": "^16.6.0",
     "http-server": "^14.1.1",
     "jest": "^28.1.3",
     "mini-css-extract-plugin": "^2.6.1",
@@ -122,14 +124,14 @@
     "raw-loader": "^4.0.2",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
-    "sass": "^1.54.0",
+    "sass": "^1.54.4",
     "sass-loader": "^13.0.2",
-    "simple-git": "^3.10.0",
+    "simple-git": "^3.12.0",
     "stream-browserify": "^3.0.0",
     "style-loader": "^3.3.1",
-    "ts-jest": "^28.0.7",
+    "ts-jest": "^28.0.8",
     "typescript": "^4.7.4",
-    "webpack": "^5.73.0",
+    "webpack": "^5.74.0",
     "webpack-cli": "^4.10.0"
   },
   "dependencies": {
@@ -137,7 +139,7 @@
     "@types/benchmark": "^2.1.1",
     "@types/compression": "1.7.2",
     "@types/express": "^4.17.13",
-    "@types/node": "^16.11.45",
+    "@types/node": "^16.11.49",
     "@types/node-fetch": "^2.6.2",
     "@types/swagger-ui-dist": "3.30.1",
     "argparse": "^2.0.1",
@@ -150,7 +152,7 @@
     "immutable": "^4.1.0",
     "node-fetch": "^2.6.7",
     "rxjs": "^7.5.6",
-    "swagger-ui-dist": "^4.13.0",
+    "swagger-ui-dist": "^4.14.0",
     "tslib": "^2.4.0",
     "util.promisify": "^1.1.1",
     "xhr2": "^0.2.1"

src/mol-gl/shader/chunks/color-frag-params.glsl.ts

@@ -36,7 +36,6 @@ uniform float uBumpiness;
             varying vec4 vColor;
         #endif
     #else
-        // avoid flat until EXT_provoking_vertex is supported
         #ifdef requiredDrawBuffers
             flat in vec4 vObject;
             flat in vec4 vInstance;

src/mol-gl/shader/chunks/color-vert-params.glsl.ts

@@ -64,7 +64,6 @@ uniform float uBumpiness;
             varying vec4 vColor;
         #endif
     #else
-        // avoid flat until EXT_provoking_vertex is supported
         #ifdef requiredDrawBuffers
             flat out vec4 vObject;
             flat out vec4 vInstance;

src/mol-gl/shader/chunks/common-frag-params.glsl.ts

@@ -17,7 +17,6 @@ uniform int uMarkingType;
         #if __VERSION__ == 100 || defined(dClippingType_instance) || !defined(dVaryingGroup)
             varying float vClipping;
         #else
-            // avoid flat until EXT_provoking_vertex is supported
             flat in float vClipping;
         #endif
     #endif
@@ -36,7 +35,6 @@ uniform int uMarkingType;
     #if __VERSION__ == 100 || defined(dMarkerType_instance) || !defined(dVaryingGroup)
         varying float vMarker;
     #else
-        // avoid flat until EXT_provoking_vertex is supported
         flat in float vMarker;
     #endif
 #endif

src/mol-gl/shader/chunks/common-vert-params.glsl.ts

@@ -24,7 +24,6 @@ uniform int uPickType;
         #if __VERSION__ == 100 || defined(dClippingType_instance) || !defined(dVaryingGroup)
             varying float vClipping;
         #else
-            // avoid flat until EXT_provoking_vertex is supported
             flat out float vClipping;
         #endif
     #endif
@@ -37,7 +36,6 @@ uniform int uPickType;
     #if __VERSION__ == 100 || defined(dMarkerType_instance) || !defined(dVaryingGroup)
         varying float vMarker;
     #else
-        // avoid flat until EXT_provoking_vertex is supported
         flat out float vMarker;
     #endif
 #endif

src/mol-model-formats/structure/mol.ts

@@ -80,7 +80,10 @@ export async function getMolModels(mol: MolFile, format: ModelFormat<any> | unde
         const indexA = Column.ofIntArray(Column.mapToArray(bonds.atomIdxA, x => x - 1, Int32Array));
         const indexB = Column.ofIntArray(Column.mapToArray(bonds.atomIdxB, x => x - 1, Int32Array));
         const order = Column.asArrayColumn(bonds.order, Int32Array);
-        const pairBonds = IndexPairBonds.fromData({ pairs: { indexA, indexB, order }, count: atoms.count });
+        const pairBonds = IndexPairBonds.fromData(
+            { pairs: { indexA, indexB, order }, count: atoms.count },
+            { maxDistance: Infinity }
+        );
         IndexPairBonds.Provider.set(models.representative, pairBonds);
     }
 

src/mol-model-formats/structure/mol2.ts

@@ -113,7 +113,10 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
                         return BondType.Flag.Covalent;
                 }
             }, Int8Array));
-            const pairBonds = IndexPairBonds.fromData({ pairs: { key, indexA, indexB, order, flag }, count: atoms.count });
+            const pairBonds = IndexPairBonds.fromData(
+                { pairs: { key, indexA, indexB, order, flag }, count: atoms.count },
+                { maxDistance: crysin ? -1 : Infinity }
+            );
 
             const first = _models.representative;
             IndexPairBonds.Provider.set(first, pairBonds);

src/mol-model/structure/structure/carbohydrates/constants.ts

@@ -386,16 +386,6 @@ const DefaultSaccharideCompIdMap = (function () {
                 map.set(charmm[j], saccharide);
             }
         }
-
-        const glycam = GlycamSaccharideNames[saccharide.abbr];
-        if (glycam) {
-            for (let j = 0, jl = glycam.length; j < jl; ++j) {
-                // On collision, use PDB name as default.
-                if (!map.has(glycam[j])) {
-                    map.set(glycam[j], saccharide);
-                }
-            }
-        }
     }
     SaccharideNames.forEach(name => {
         if (!map.has(name)) map.set(name, UnknownSaccharideComponent);

src/mol-plugin/features.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 export const PluginFeatureDetection = {
@@ -13,7 +14,11 @@ export const PluginFeatureDetection = {
         const unpportedSafariVersions = [
             'Version/15.1 Safari',
             'Version/15.2 Safari',
-            'Version/15.3 Safari'
+            'Version/15.3 Safari',
+            // the following 'only' break GPU surfaces
+            'Version/15.4 Safari',
+            'Version/15.5 Safari',
+            'Version/16.0 Safari',
         ];
         if (unpportedSafariVersions.some(v => navigator.userAgent.indexOf(v) > 0)) {
             return true;