diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9ba8bdcc8d60643d99a0ff7e377b0fcc6d63540f..7d483b2215463bd1b8602150df5c693d0f8c41df 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,12 +6,18 @@ Note that since we don't clearly distinguish between a public and private interf
## [Unreleased]
+- 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
- Add ``fov`` (Field of View) Canvas3D parameter
- Add ``sceneRadiusFactor`` Canvas3D parameter
- Add background pass (skybox, image, horizontal/radial gradient)
diff --git a/package-lock.json b/package-lock.json
index 574466fb80e296362a8edd3ffa07466f61cfabde..c576a0d1a68232eecbf5d39f757c3d21893a3af5 100644
Binary files a/package-lock.json and b/package-lock.json differ
diff --git a/package.json b/package.json
index 4ef0af12c3397cc1b2ba736997436aab1d76f45e..7e827994e88b9caab3066949355685d559f866b9 100644
--- a/package.json
+++ b/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"
diff --git a/src/mol-gl/shader/chunks/color-frag-params.glsl.ts b/src/mol-gl/shader/chunks/color-frag-params.glsl.ts
index 4027046f94f18175e895cf440b82aa6623e470ae..b5802f3688be2243b93853b1556226235d1af0bb 100644
--- a/src/mol-gl/shader/chunks/color-frag-params.glsl.ts
+++ b/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;
diff --git a/src/mol-gl/shader/chunks/color-vert-params.glsl.ts b/src/mol-gl/shader/chunks/color-vert-params.glsl.ts
index 0b4c5c45f230aa15a3e846936d23596ae0312ee6..30a830ad73651982363871cbb3fe8b1fcc20d431 100644
--- a/src/mol-gl/shader/chunks/color-vert-params.glsl.ts
+++ b/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;
diff --git a/src/mol-gl/shader/chunks/common-frag-params.glsl.ts b/src/mol-gl/shader/chunks/common-frag-params.glsl.ts
index 5722cb8a2c3ed77e340bcf3354fee9b771f5fdf5..3d694f3e2601c37631439f9e2d5a7f640aa3315b 100644
--- a/src/mol-gl/shader/chunks/common-frag-params.glsl.ts
+++ b/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
diff --git a/src/mol-gl/shader/chunks/common-vert-params.glsl.ts b/src/mol-gl/shader/chunks/common-vert-params.glsl.ts
index 2e391530c42fd9340e6bf3af92c1d379bccfe787..10a7c27ed698a4cd83be892f31bbd34dcc78e5ef 100644
--- a/src/mol-gl/shader/chunks/common-vert-params.glsl.ts
+++ b/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
diff --git a/src/mol-math/geometry/primitives/box3d.ts b/src/mol-math/geometry/primitives/box3d.ts
index d701ae18085f5b45feb9f29cb7cdd5682e9104f9..fff4923615107fddbbe9be77febc27b070182889 100644
--- a/src/mol-math/geometry/primitives/box3d.ts
+++ b/src/mol-math/geometry/primitives/box3d.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 David Sehnal <david.sehnal@gmail.com>
* @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -124,11 +124,19 @@ namespace Box3D {
}
export function containsVec3(box: Box3D, v: Vec3) {
- return (
+ return !(
v[0] < box.min[0] || v[0] > box.max[0] ||
v[1] < box.min[1] || v[1] > box.max[1] ||
v[2] < box.min[2] || v[2] > box.max[2]
- ) ? false : true;
+ );
+ }
+
+ export function overlaps(a: Box3D, b: Box3D) {
+ return !(
+ a.max[0] < b.min[0] || a.min[0] > b.max[0] ||
+ a.max[1] < b.min[1] || a.min[1] > b.max[1] ||
+ a.max[2] < b.min[2] || a.min[2] > b.max[2]
+ );
}
}
diff --git a/src/mol-model-formats/structure/mol.ts b/src/mol-model-formats/structure/mol.ts
index 942f24a597cd0c8bbb18c564d571536e9310f49f..f32849f738b1bb31f4a9aca641bbe2a55adf1e91 100644
--- a/src/mol-model-formats/structure/mol.ts
+++ b/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);
}
diff --git a/src/mol-model-formats/structure/mol2.ts b/src/mol-model-formats/structure/mol2.ts
index ac8b4e75c1119a06afa11a91d18709f888129418..19723a6fd1987e77bb382bafb2621f98e95bfbeb 100644
--- a/src/mol-model-formats/structure/mol2.ts
+++ b/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);
diff --git a/src/mol-model/structure/structure/carbohydrates/constants.ts b/src/mol-model/structure/structure/carbohydrates/constants.ts
index bc9e49e728e386db75c92dfd118ee3e875d3de9d..aeb5fd82a1c2515becfcf439750f9fb7ccb35d8d 100644
--- a/src/mol-model/structure/structure/carbohydrates/constants.ts
+++ b/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);
diff --git a/src/mol-model/structure/structure/structure.ts b/src/mol-model/structure/structure/structure.ts
index 81f84f447fa5c17191641c2d8c3b81594bcdc08d..3c2dfdc6322d5895bf82dbd5c6689c78b58d4bae 100644
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -23,7 +23,7 @@ import { Carbohydrates } from './carbohydrates/data';
import { computeCarbohydrates } from './carbohydrates/compute';
import { Vec3, Mat4 } from '../../../mol-math/linear-algebra';
import { idFactory } from '../../../mol-util/id-factory';
-import { GridLookup3D } from '../../../mol-math/geometry';
+import { Box3D, GridLookup3D } from '../../../mol-math/geometry';
import { UUID } from '../../../mol-util';
import { CustomProperties } from '../../custom-property';
import { AtomicHierarchy } from '../model/properties/atomic';
@@ -43,6 +43,8 @@ type State = {
lookup3d?: StructureLookup3D,
interUnitBonds?: InterUnitBonds,
dynamicBonds: boolean,
+ interBondsValidUnit?: (unit: Unit) => boolean,
+ interBondsValidUnitPair?: (structure: Structure, unitA: Unit, unitB: Unit) => boolean,
unitSymmetryGroups?: ReadonlyArray<Unit.SymmetryGroup>,
unitSymmetryGroupsIndexMap?: IntMap<number>,
unitsSortedByVolume?: ReadonlyArray<Unit>;
@@ -241,6 +243,8 @@ class Structure {
this.state.interUnitBonds = computeInterUnitBonds(this, {
ignoreWater: !this.dynamicBonds,
ignoreIon: !this.dynamicBonds,
+ validUnit: this.state.interBondsValidUnit,
+ validUnitPair: this.state.interBondsValidUnitPair,
});
}
return this.state.interUnitBonds;
@@ -250,6 +254,14 @@ class Structure {
return this.state.dynamicBonds;
}
+ get interBondsValidUnit() {
+ return this.state.interBondsValidUnit;
+ }
+
+ get interBondsValidUnitPair() {
+ return this.state.interBondsValidUnitPair;
+ }
+
get unitSymmetryGroups(): ReadonlyArray<Unit.SymmetryGroup> {
if (this.state.unitSymmetryGroups) return this.state.unitSymmetryGroups;
this.state.unitSymmetryGroups = StructureSymmetry.computeTransformGroups(this);
@@ -380,7 +392,12 @@ class Structure {
parent: parent?.remapModel(m),
label: this.label,
interUnitBonds: dynamicBonds ? undefined : interUnitBonds,
- dynamicBonds
+ dynamicBonds,
+ interBondsValidUnit: this.state.interBondsValidUnit,
+ interBondsValidUnitPair: this.state.interBondsValidUnitPair,
+ coordinateSystem: this.state.coordinateSystem,
+ masterModel: this.state.masterModel,
+ representativeModel: this.state.representativeModel,
});
}
@@ -428,7 +445,6 @@ class Structure {
function cmpUnits(units: ArrayLike<Unit>, i: number, j: number) {
return units[i].id - units[j].id;
-
}
function getModels(s: Structure) {
@@ -634,6 +650,8 @@ namespace Structure {
* Also enables calculation of inter-unit bonds in water molecules.
*/
dynamicBonds?: boolean,
+ interBondsValidUnit?: (unit: Unit) => boolean,
+ interBondsValidUnitPair?: (structure: Structure, unitA: Unit, unitB: Unit) => boolean,
coordinateSystem?: SymmetryOperator
label?: string
/** Master model for structures of a protein model and multiple ligand models */
@@ -722,6 +740,12 @@ namespace Structure {
if (props.parent) state.parent = props.parent.parent || props.parent;
if (props.interUnitBonds) state.interUnitBonds = props.interUnitBonds;
+ if (props.interBondsValidUnit) state.interBondsValidUnit = props.interBondsValidUnit;
+ else if (props.parent) state.interBondsValidUnit = props.parent.interBondsValidUnit;
+
+ if (props.interBondsValidUnitPair) state.interBondsValidUnitPair = props.interBondsValidUnitPair;
+ else if (props.parent) state.interBondsValidUnitPair = props.parent.interBondsValidUnitPair;
+
if (props.dynamicBonds) state.dynamicBonds = props.dynamicBonds;
else if (props.parent) state.dynamicBonds = props.parent.dynamicBonds;
@@ -1180,7 +1204,7 @@ namespace Structure {
/**
* Iterate over all unit pairs of a structure and invokes callback for valid units
- * and unit pairs if within a max distance.
+ * and unit pairs if their boundaries are within a max distance.
*/
export function eachUnitPair(structure: Structure, callback: (unitA: Unit, unitB: Unit) => void, props: EachUnitPairProps) {
const { maxRadius, validUnit, validUnitPair } = props;
@@ -1188,15 +1212,19 @@ namespace Structure {
const lookup = structure.lookup3d;
const imageCenter = Vec3();
+ const bbox = Box3D();
+ const rvec = Vec3.create(maxRadius, maxRadius, maxRadius);
for (const unit of structure.units) {
if (!validUnit(unit)) continue;
const bs = unit.boundary.sphere;
+ Box3D.expand(bbox, unit.boundary.box, rvec);
Vec3.transformMat4(imageCenter, bs.center, unit.conformation.operator.matrix);
const closeUnits = lookup.findUnitIndices(imageCenter[0], imageCenter[1], imageCenter[2], bs.radius + maxRadius);
for (let i = 0; i < closeUnits.count; i++) {
const other = structure.units[closeUnits.indices[i]];
+ if (!Box3D.overlaps(bbox, other.boundary.box)) continue;
if (!validUnit(other) || unit.id >= other.id || !validUnitPair(unit, other)) continue;
if (other.elements.length >= unit.elements.length) callback(unit, other);
diff --git a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
index 535a6d09bca596e00119faffd2cf2fcefafd9344..ba0327c3fc2ffaecbc25b4abe2ed8b434a40373d 100644
--- a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
@@ -21,12 +21,18 @@ import { StructConn } from '../../../../../mol-model-formats/structure/property/
import { equalEps } from '../../../../../mol-math/linear-algebra/3d/common';
import { Model } from '../../../model';
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+const v3distance = Vec3.distance;
+const v3set = Vec3.set;
+const v3squaredDistance = Vec3.squaredDistance;
+const v3transformMat4 = Vec3.transformMat4;
+
const tmpDistVecA = Vec3();
const tmpDistVecB = Vec3();
function getDistance(unitA: Unit.Atomic, indexA: ElementIndex, unitB: Unit.Atomic, indexB: ElementIndex) {
unitA.conformation.position(indexA, tmpDistVecA);
unitB.conformation.position(indexB, tmpDistVecB);
- return Vec3.distance(tmpDistVecA, tmpDistVecB);
+ return v3distance(tmpDistVecA, tmpDistVecB);
}
const _imageTransform = Mat4();
@@ -68,22 +74,22 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
const aI = atomsA[_aI];
- Vec3.set(_imageA, xA[aI], yA[aI], zA[aI]);
- if (isNotIdentity) Vec3.transformMat4(_imageA, _imageA, imageTransform);
- if (Vec3.squaredDistance(_imageA, bCenter) > testDistanceSq) continue;
+ v3set(_imageA, xA[aI], yA[aI], zA[aI]);
+ if (isNotIdentity) v3transformMat4(_imageA, _imageA, imageTransform);
+ if (v3squaredDistance(_imageA, bCenter) > testDistanceSq) continue;
if (!props.forceCompute && indexPairs) {
const { maxDistance } = indexPairs;
const { offset, b, edgeProps: { order, distance, flag } } = indexPairs.bonds;
const srcA = sourceIndex.value(aI);
+ const aeI = getElementIdx(type_symbolA.value(aI));
for (let i = offset[srcA], il = offset[srcA + 1]; i < il; ++i) {
const bI = invertedIndex![b[i]];
const _bI = SortedArray.indexOf(unitB.elements, bI) as StructureElement.UnitIndex;
if (_bI < 0) continue;
- const aeI = getElementIdx(type_symbolA.value(aI));
const beI = getElementIdx(type_symbolA.value(bI));
const d = distance[i];
@@ -191,6 +197,7 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
}
export interface InterBondComputationProps extends BondComputationProps {
+ validUnit: (unit: Unit) => boolean
validUnitPair: (structure: Structure, unitA: Unit, unitB: Unit) => boolean
ignoreWater: boolean
ignoreIon: boolean
@@ -215,7 +222,7 @@ function findBonds(structure: Structure, props: InterBondComputationProps) {
findPairBonds(unitA as Unit.Atomic, unitB as Unit.Atomic, props, builder);
}, {
maxRadius: props.maxRadius,
- validUnit: (unit: Unit) => Unit.isAtomic(unit),
+ validUnit: (unit: Unit) => props.validUnit(unit),
validUnitPair: (unitA: Unit, unitB: Unit) => props.validUnitPair(structure, unitA, unitB)
});
@@ -226,6 +233,7 @@ function computeInterUnitBonds(structure: Structure, props?: Partial<InterBondCo
const p = { ...DefaultInterBondComputationProps, ...props };
return findBonds(structure, {
...p,
+ validUnit: (props && props.validUnit) || (u => Unit.isAtomic(u)),
validUnitPair: (props && props.validUnitPair) || ((s, a, b) => {
const mtA = a.model.atomicHierarchy.derived.residue.moleculeType;
const mtB = b.model.atomicHierarchy.derived.residue.moleculeType;
diff --git a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
index 105347895b27c9080d7e5daeca079c975cbb6261..a4be859321bf19f44ea5c7902fff9d373e7565d8 100644
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
@@ -21,6 +21,9 @@ import { ElementIndex } from '../../../model/indexing';
import { equalEps } from '../../../../../mol-math/linear-algebra/3d/common';
import { Model } from '../../../model/model';
+// avoiding namespace lookup improved performance in Chrome (Aug 2020)
+const v3distance = Vec3.distance;
+
function getGraph(atomA: StructureElement.UnitIndex[], atomB: StructureElement.UnitIndex[], _order: number[], _flags: number[], atomCount: number, canRemap: boolean): IntraUnitBonds {
const builder = new IntAdjacencyGraph.EdgeBuilder(atomCount, atomA, atomB);
const flags = new Uint16Array(builder.slotCount);
@@ -39,7 +42,7 @@ const tmpDistVecB = Vec3();
function getDistance(unit: Unit.Atomic, indexA: ElementIndex, indexB: ElementIndex) {
unit.conformation.position(indexA, tmpDistVecA);
unit.conformation.position(indexB, tmpDistVecB);
- return Vec3.distance(tmpDistVecA, tmpDistVecB);
+ return v3distance(tmpDistVecA, tmpDistVecB);
}
const __structConnAdded = new Set<StructureElement.UnitIndex>();
diff --git a/src/mol-plugin/features.ts b/src/mol-plugin/features.ts
index ad04c71c6287bbae2ca4f8439632503403ea3b71..df2c7f2e3371cfd5a82ce5c71dfc7230e98838f7 100644
--- a/src/mol-plugin/features.ts
+++ b/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;