diff --git a/CHANGELOG.md b/CHANGELOG.md
index 82c807e707b582f94f6a81fe3db30b971b48c9db..7cd972e722db61d82e2c96afd1052da04c358560 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,17 +8,18 @@ Note that since we don't clearly distinguish between a public and private interf
- Make `PluginContext.initContainer` checkered canvas background optional
- Store URL of downloaded assets to detect zip/gzip based on extension
+- Add optional `operator.key`; can be referenced in `IndexPairBonds`
## [v3.23.0] - 2022-10-19
- Add `PluginContext.initContainer/mount/unmount` methods; these should make it easier to reuse a plugin context with both custom and built-in UI
- Add `PluginContext.canvas3dInitialized`
- `createPluginUI` now resolves after the 3d canvas has been initialized
-- Change EM Volume Streaming default from `Whote Structure` to `Auto`
+- Change EM Volume Streaming default from `Whole Structure` to `Auto`
## [v3.22.0] - 2022-10-17
-- Replace `VolumeIsosurfaceParams.pickingGranularity` param with `Volume.PickingGranuality`
+- Replace `VolumeIsosurfaceParams.pickingGranularity` param with `Volume.PickingGranuality`
## [v3.21.0] - 2022-10-17
diff --git a/src/mol-model-formats/structure/property/bonds/index-pair.ts b/src/mol-model-formats/structure/property/bonds/index-pair.ts
index 99eb988e7e185d8297d2c71f66e4733dbdec5075..96e0945e91f7491d0743645e48dc5fee9f59c6ea 100644
--- a/src/mol-model-formats/structure/property/bonds/index-pair.ts
+++ b/src/mol-model-formats/structure/property/bonds/index-pair.ts
@@ -14,8 +14,8 @@ import { ElementIndex } from '../../../../mol-model/structure';
export type IndexPairsProps = {
readonly key: ArrayLike<number>
- /** Sorted contor-paired operator keys */
- readonly operator: ArrayLike<number>
+ readonly operatorA: ArrayLike<number>
+ readonly operatorB: ArrayLike<number>
readonly order: ArrayLike<number>
readonly distance: ArrayLike<number>
readonly flag: ArrayLike<BondType.Flag>
@@ -26,20 +26,22 @@ export type IndexPairBonds = { bonds: IndexPairs, maxDistance: number }
function getGraph(indexA: ArrayLike<ElementIndex>, indexB: ArrayLike<ElementIndex>, props: Partial<IndexPairsProps>, count: number): IndexPairs {
const builder = new IntAdjacencyGraph.EdgeBuilder(count, indexA, indexB);
const key = new Int32Array(builder.slotCount);
- const operator = new Array(builder.slotCount);
+ const operatorA = new Array(builder.slotCount);
+ const operatorB = new Array(builder.slotCount);
const order = new Int8Array(builder.slotCount);
const distance = new Array(builder.slotCount);
const flag = new Array(builder.slotCount);
for (let i = 0, _i = builder.edgeCount; i < _i; i++) {
builder.addNextEdge();
builder.assignProperty(key, props.key ? props.key[i] : -1);
- builder.assignProperty(operator, props.operator ? props.operator[i] : -1);
+ builder.assignProperty(operatorA, props.operatorA ? props.operatorA[i] : -1);
+ builder.assignProperty(operatorB, props.operatorB ? props.operatorB[i] : -1);
builder.assignProperty(order, props.order ? props.order[i] : 1);
builder.assignProperty(distance, props.distance ? props.distance[i] : -1);
builder.assignProperty(flag, props.flag ? props.flag[i] : BondType.Flag.Covalent);
}
- return builder.createGraph({ key, operator, order, distance, flag });
+ return builder.createGraph({ key, operatorA, operatorB, order, distance, flag });
}
export namespace IndexPairBonds {
@@ -54,10 +56,10 @@ export namespace IndexPairBonds {
indexA: Column<number>,
indexB: Column<number>,
key?: Column<number>,
- /**
- * Sorted contor-paired operator keys. Used in bond computation.
- */
- operator?: Column<number>,
+ /** Operator key for indexA. Used in bond computation. */
+ operatorA?: Column<number>,
+ /** Operator key for indexB. Used in bond computation. */
+ operatorB?: Column<number>,
order?: Column<number>,
/**
* Useful for bonds in periodic cells. That is, only bonds within the given
@@ -91,12 +93,13 @@ export namespace IndexPairBonds {
const indexA = pairs.indexA.toArray() as ArrayLike<ElementIndex>;
const indexB = pairs.indexB.toArray() as ArrayLike<ElementIndex>;
const key = pairs.key && pairs.key.toArray();
- const operator = pairs.operator && pairs.operator.toArray();
+ const operatorA = pairs.operatorA && pairs.operatorA.toArray();
+ const operatorB = pairs.operatorB && pairs.operatorB.toArray();
const order = pairs.order && pairs.order.toArray();
const distance = pairs.distance && pairs.distance.toArray();
const flag = pairs.flag && pairs.flag.toArray();
return {
- bonds: getGraph(indexA, indexB, { key, operator, order, distance, flag }, count),
+ bonds: getGraph(indexA, indexB, { key, operatorA, operatorB, order, distance, flag }, count),
maxDistance: p.maxDistance
};
}
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 2585e4c850423cf0558aeba61d46ce7956e30b80..c8d34230db378656cc0aa60007a77be463292b83 100644
--- a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
@@ -20,7 +20,6 @@ import { InterUnitGraph } from '../../../../../mol-math/graph/inter-unit-graph';
import { StructConn } from '../../../../../mol-model-formats/structure/property/bonds/struct_conn';
import { equalEps } from '../../../../../mol-math/linear-algebra/3d/common';
import { Model } from '../../../model';
-import { sortedCantorPairing } from '../../../../../mol-data/util';
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
const v3distance = Vec3.distance;
@@ -72,7 +71,8 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
const testDistanceSq = (bRadius + maxRadius) * (bRadius + maxRadius);
builder.startUnitPair(unitA.id, unitB.id);
- const opPairKey = sortedCantorPairing(unitA.conformation.operator.key, unitB.conformation.operator.key);
+ const opKeyA = unitA.conformation.operator.key;
+ const opKeyB = unitB.conformation.operator.key;
for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
const aI = atomsA[_aI];
@@ -82,7 +82,7 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
if (!props.forceCompute && indexPairs) {
const { maxDistance } = indexPairs;
- const { offset, b, edgeProps: { order, distance, flag, key, operator } } = indexPairs.bonds;
+ const { offset, b, edgeProps: { order, distance, flag, key, operatorA, operatorB } } = indexPairs.bonds;
const srcA = sourceIndex.value(aI);
const aeI = getElementIdx(type_symbolA.value(aI));
@@ -92,8 +92,9 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
const _bI = SortedArray.indexOf(unitB.elements, bI) as StructureElement.UnitIndex;
if (_bI < 0) continue;
- const op = operator[i];
- if (op >= 0 && opPairKey !== op) continue;
+ const opA = operatorA[i];
+ const opB = operatorB[i];
+ if ((opA >= 0 && opA !== opKeyA) || (opB >= 0 && opB !== opKeyB)) continue;
const beI = getElementIdx(type_symbolA.value(bI));
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 67d89caac6753787379ea4bb84b6fe1860634f29..71bef526e5b8e7c850c46e1c84f180fe907ea976 100644
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
@@ -20,7 +20,6 @@ import { Vec3 } from '../../../../../mol-math/linear-algebra';
import { ElementIndex } from '../../../model/indexing';
import { equalEps } from '../../../../../mol-math/linear-algebra/3d/common';
import { Model } from '../../../model/model';
-import { sortedCantorPairing } from '../../../../../mol-data/util';
// avoiding namespace lookup improved performance in Chrome (Aug 2020)
const v3distance = Vec3.distance;
@@ -56,7 +55,7 @@ function findIndexPairBonds(unit: Unit.Atomic) {
const { type_symbol } = unit.model.atomicHierarchy.atoms;
const atomCount = unit.elements.length;
const { maxDistance } = indexPairs;
- const { offset, b, edgeProps: { order, distance, flag, key, operator } } = indexPairs.bonds;
+ const { offset, b, edgeProps: { order, distance, flag, key, operatorA, operatorB } } = indexPairs.bonds;
const { atomSourceIndex: sourceIndex } = unit.model.atomicHierarchy;
const { invertedIndex } = Model.getInvertedAtomSourceIndex(unit.model);
@@ -67,7 +66,7 @@ function findIndexPairBonds(unit: Unit.Atomic) {
const orders: number[] = [];
const keys: number[] = [];
- const opPairKey = sortedCantorPairing(unit.conformation.operator.key, unit.conformation.operator.key);
+ const opKey = unit.conformation.operator.key;
for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
const aI = atoms[_aI];
@@ -83,8 +82,9 @@ function findIndexPairBonds(unit: Unit.Atomic) {
const _bI = SortedArray.indexOf(unit.elements, bI) as StructureElement.UnitIndex;
if (_bI < 0) continue;
- const op = operator[i];
- if (op >= 0 && opPairKey !== op) continue;
+ const opA = operatorA[i];
+ const opB = operatorB[i];
+ if ((opA >= 0 && opA !== opKey) || (opB >= 0 && opB !== opKey)) continue;
const beI = getElementIdx(type_symbol.value(bI));