diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5f4fa6b8de5521de1aee1ac6f623327a730af463..c61b2edc7b422630067e84a15d566a92df7db931 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,10 @@ Note that since we don't clearly distinguish between a public and private interf
- Add ``includeResidueTest`` option to ``alignAndSuperposeWithSIFTSMapping``
- Add ``parentDisplay`` param for interactions representation.
- [Experimental] Add support for PyMOL, VMD, and Jmol atom expressions in selection scripts
+- Support for ``failIfMajorPerformanceCaveat`` webgl attribute. Add ``PluginConfig.General.AllowMajorPerformanceCaveat`` and ``allow-major-performance-caveat`` Viewer GET param.
+- Fix handling of PDB TER records (#549)
+- Add support for getting multiple loci from a representation (``.getAllLoci()``)
+- Add ``key`` property to intra- and inter-bonds for referencing source data
## [v3.16.0] - 2022-08-25
diff --git a/src/apps/viewer/app.ts b/src/apps/viewer/app.ts
index b5d18f401da78d1cfd6c77f75364f7987992d65f..6e2201f651601406247be2aded7f6bc210f727c7 100644
--- a/src/apps/viewer/app.ts
+++ b/src/apps/viewer/app.ts
@@ -89,6 +89,7 @@ const DefaultViewerOptions = {
pickPadding: PluginConfig.General.PickPadding.defaultValue,
enableWboit: PluginConfig.General.EnableWboit.defaultValue,
preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,
+ allowMajorPerformanceCaveat: PluginConfig.General.AllowMajorPerformanceCaveat.defaultValue,
viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
@@ -159,6 +160,7 @@ export class Viewer {
[PluginConfig.General.PickPadding, o.pickPadding],
[PluginConfig.General.EnableWboit, o.enableWboit],
[PluginConfig.General.PreferWebGl1, o.preferWebgl1],
+ [PluginConfig.General.AllowMajorPerformanceCaveat, o.allowMajorPerformanceCaveat],
[PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
[PluginConfig.Viewport.ShowControls, o.viewportShowControls],
[PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
diff --git a/src/apps/viewer/index.html b/src/apps/viewer/index.html
index c63978410e9ee354bfa5ac2d916dd2104d941b1d..aba056ce79dcf5327f99447a04a4cb3f5c9ac237 100644
--- a/src/apps/viewer/index.html
+++ b/src/apps/viewer/index.html
@@ -61,6 +61,7 @@
var pickPadding = getParam('pick-padding', '[^&]+').trim();
var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
+ var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
molstar.Viewer.create('app', {
layoutShowControls: !hideControls,
@@ -76,6 +77,7 @@
pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
enableWboit: disableWboit ? false : void 0, // use default value if disable-wboit is not set
preferWebgl1: preferWebgl1,
+ allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
}).then(viewer => {
var snapshotId = getParam('snapshot-id', '[^&]+').trim();
if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
diff --git a/src/extensions/geo-export/ui.tsx b/src/extensions/geo-export/ui.tsx
index 837c59021f5fb38fa342a315846ccd3eb8277466..78aa038e85dd6dcd5c6433940c2ea3f6a4e300c0 100644
--- a/src/extensions/geo-export/ui.tsx
+++ b/src/extensions/geo-export/ui.tsx
@@ -60,6 +60,8 @@ export class GeometryExporterUI extends CollapsableControls<{}, State> {
}
componentDidMount() {
+ if (!this.plugin.canvas3d) return;
+
const merged = merge(
this.controls.behaviors.params,
this.plugin.canvas3d!.reprCount
diff --git a/src/extensions/mp4-export/controls.ts b/src/extensions/mp4-export/controls.ts
index a8edd32816a919b64d0ce1337dc6e6084d2ed5bd..b6dadcc5e80f79a5f6a78201e6cde93c389e2012 100644
--- a/src/extensions/mp4-export/controls.ts
+++ b/src/extensions/mp4-export/controls.ts
@@ -118,11 +118,13 @@ export class Mp4Controls extends PluginComponent {
}
private init() {
+ if (!this.plugin.canvas3d) return;
+
this.subscribe(this.plugin.managers.animation.events.updated.pipe(debounceTime(16)), () => {
this.sync();
});
- this.subscribe(this.plugin.canvas3d?.resized!, () => this.syncInfo());
+ this.subscribe(this.plugin.canvas3d.resized, () => this.syncInfo());
this.subscribe(this.plugin.helpers.viewportScreenshot?.events.previewed!, () => this.syncInfo());
this.subscribe(this.plugin.behaviors.state.isBusy, b => this.updateCanApply(b));
diff --git a/src/mol-canvas3d/canvas3d.ts b/src/mol-canvas3d/canvas3d.ts
index e0c3335651cbb1cd19be7ea1f1417d3fa77a9d0e..e55c95a26bdd19be0b618dac28130cf37d0e5de0 100644
--- a/src/mol-canvas3d/canvas3d.ts
+++ b/src/mol-canvas3d/canvas3d.ts
@@ -117,6 +117,7 @@ interface Canvas3DContext {
namespace Canvas3DContext {
export const DefaultAttribs = {
+ failIfMajorPerformanceCaveat: false,
/** true by default to avoid issues with Safari (Jan 2021) */
antialias: true,
/** true to support multiple Canvas3D objects with a single context */
@@ -132,8 +133,9 @@ namespace Canvas3DContext {
export function fromCanvas(canvas: HTMLCanvasElement, assetManager: AssetManager, attribs: Partial<Attribs> = {}): Canvas3DContext {
const a = { ...DefaultAttribs, ...attribs };
- const { antialias, preserveDrawingBuffer, pixelScale, preferWebGl1 } = a;
+ const { failIfMajorPerformanceCaveat, antialias, preserveDrawingBuffer, pixelScale, preferWebGl1 } = a;
const gl = getGLContext(canvas, {
+ failIfMajorPerformanceCaveat,
antialias,
preserveDrawingBuffer,
alpha: true, // the renderer requires an alpha channel
diff --git a/src/mol-model-formats/structure/common/component.ts b/src/mol-model-formats/structure/common/component.ts
index 948a01fcb7df8a3b8942d5798a106a5c13588416..770a095cac67716d4bb64b82157b2a6a4a5af33b 100644
--- a/src/mol-model-formats/structure/common/component.ts
+++ b/src/mol-model-formats/structure/common/component.ts
@@ -32,6 +32,7 @@ const DnaAtomIdsList = [
/** Used to reduce false positives for atom name-based type guessing */
const NonPolymerNames = new Set([
'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP', // Mononucleotides
+ 'LIG'
]);
const StandardComponents = (function () {
diff --git a/src/mol-model-formats/structure/pdb/atom-site.ts b/src/mol-model-formats/structure/pdb/atom-site.ts
index 7de7aeed37eb9c36cd14b717f05b7b6b02f6b3f9..21d5364d6f546aa041e2992c94b84a156347cf52 100644
--- a/src/mol-model-formats/structure/pdb/atom-site.ts
+++ b/src/mol-model-formats/structure/pdb/atom-site.ts
@@ -39,7 +39,7 @@ export function getAtomSiteTemplate(data: string, count: number) {
};
}
-export function getAtomSite(sites: AtomSiteTemplate, hasTer: boolean): { [K in keyof mmCIF_Schema['atom_site'] | 'partial_charge']?: CifField } {
+export function getAtomSite(sites: AtomSiteTemplate, terIndices: Set<number>): { [K in keyof mmCIF_Schema['atom_site'] | 'partial_charge']?: CifField } {
const pdbx_PDB_model_num = CifField.ofStrings(sites.pdbx_PDB_model_num);
const auth_asym_id = CifField.ofTokens(sites.auth_asym_id);
const auth_seq_id = CifField.ofTokens(sites.auth_seq_id);
@@ -91,7 +91,7 @@ export function getAtomSite(sites: AtomSiteTemplate, hasTer: boolean): { [K in k
if (asymIdCounts.has(asymId)) {
// only change the chains name if there are TER records
// otherwise assume repeated chain name use is from interleaved chains
- if (hasTer && asymIdChanged) {
+ if (terIndices.has(i)) {
const asymIdCount = asymIdCounts.get(asymId)! + 1;
asymIdCounts.set(asymId, asymIdCount);
currLabelAsymId = `${asymId}_${asymIdCount}`;
diff --git a/src/mol-model-formats/structure/pdb/to-cif.ts b/src/mol-model-formats/structure/pdb/to-cif.ts
index 21a2a68f0593c6aeecf3d549600b0836290d167d..792d5a136d2c45388eba6ca8612803c890c7d32c 100644
--- a/src/mol-model-formats/structure/pdb/to-cif.ts
+++ b/src/mol-model-formats/structure/pdb/to-cif.ts
@@ -51,7 +51,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
let modelNum = 0, modelStr = '';
let conectRange: [number, number] | undefined = undefined;
- let hasTer = false;
+ const terIndices = new Set<number>();
for (let i = 0, _i = lines.count; i < _i; i++) {
let s = indices[2 * i], e = indices[2 * i + 1];
@@ -164,7 +164,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
break;
case 'T':
if (substringStartsWith(data, s, e, 'TER')) {
- hasTer = true;
+ terIndices.add(atomSite.index);
}
}
}
@@ -183,7 +183,7 @@ export async function pdbToMmCif(pdb: PdbFile): Promise<CifFrame> {
atomSite.label_entity_id[i] = entityBuilder.getEntityId(compId, moleculeType, asymIds.value(i));
}
- const atom_site = getAtomSite(atomSite, hasTer);
+ const atom_site = getAtomSite(atomSite, terIndices);
if (!isPdbqt) delete atom_site.partial_charge;
if (conectRange) {
diff --git a/src/mol-model-formats/structure/property/bonds/chem_comp.ts b/src/mol-model-formats/structure/property/bonds/chem_comp.ts
index b3f64adcff90adfd48410aa33035248c7f740ada..6ba2bc374891a16fff526ee3e8b7b96a3db37b70 100644
--- a/src/mol-model-formats/structure/property/bonds/chem_comp.ts
+++ b/src/mol-model-formats/structure/property/bonds/chem_comp.ts
@@ -65,7 +65,7 @@ export namespace ComponentBond {
return e;
}
- const { comp_id, atom_id_1, atom_id_2, value_order, pdbx_aromatic_flag, _rowCount } = data;
+ const { comp_id, atom_id_1, atom_id_2, value_order, pdbx_aromatic_flag, _rowCount, pdbx_ordinal } = data;
let entry = addEntry(comp_id.value(0)!);
for (let i = 0; i < _rowCount; i++) {
@@ -74,6 +74,7 @@ export namespace ComponentBond {
const nameB = atom_id_2.value(i)!;
const order = value_order.value(i)!;
const aromatic = pdbx_aromatic_flag.value(i) === 'y';
+ const key = pdbx_ordinal.value(i);
if (entry.id !== id) {
entry = addEntry(id);
@@ -89,29 +90,29 @@ export namespace ComponentBond {
case 'quad': ord = 4; break;
}
- entry.add(nameA, nameB, ord, flags);
+ entry.add(nameA, nameB, ord, flags, key);
}
return entries;
}
export class Entry {
- readonly map: Map<string, Map<string, { order: number, flags: number }>> = new Map();
+ readonly map: Map<string, Map<string, { order: number, flags: number, key: number }>> = new Map();
- add(a: string, b: string, order: number, flags: number, swap = true) {
+ add(a: string, b: string, order: number, flags: number, key: number, swap = true) {
const e = this.map.get(a);
if (e !== void 0) {
const f = e.get(b);
if (f === void 0) {
- e.set(b, { order, flags });
+ e.set(b, { order, flags, key });
}
} else {
- const map = new Map<string, { order: number, flags: number }>();
- map.set(b, { order, flags });
+ const map = new Map<string, { order: number, flags: number, key: number }>();
+ map.set(b, { order, flags, key });
this.map.set(a, map);
}
- if (swap) this.add(b, a, order, flags, false);
+ if (swap) this.add(b, a, order, flags, key, false);
}
constructor(public readonly id: string) { }
diff --git a/src/mol-model/structure/query/context.ts b/src/mol-model/structure/query/context.ts
index 43b2538b98ba727032ab231948c203283e123f61..c51b441a77da6cfffd623877b0734df8e87fc757 100644
--- a/src/mol-model/structure/query/context.ts
+++ b/src/mol-model/structure/query/context.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2018 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>
*/
import { Structure, StructureElement, Unit } from '../structure';
@@ -113,6 +114,7 @@ class QueryContextBondInfo<U extends Unit = Unit> {
bIndex: StructureElement.UnitIndex = 0 as StructureElement.UnitIndex;
type: BondType = BondType.Flag.None;
order: number = 0;
+ key: number = -1;
private testFn: QueryPredicate = defaultBondTest;
diff --git a/src/mol-model/structure/query/queries/filters.ts b/src/mol-model/structure/query/queries/filters.ts
index 9f5db773754c98b824f7c7aa9a74256be90393da..00653ccf181d8217391e28a1cbddeb04865ffa30 100644
--- a/src/mol-model/structure/query/queries/filters.ts
+++ b/src/mol-model/structure/query/queries/filters.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2018 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>
*/
import { SetUtils } from '../../../../mol-util/set';
@@ -246,7 +247,7 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
const inputUnit = input.unitMap.get(unit.id) as Unit.Atomic;
- const { offset, b, edgeProps: { flags, order } } = inputUnit.bonds;
+ const { offset, b, edgeProps: { flags, order, key } } = inputUnit.bonds;
const bondedUnits = interBonds.getConnectedUnits(unit.id);
const buCount = bondedUnits.length;
@@ -271,6 +272,7 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
atomicBond.bIndex = b[l] as StructureElement.UnitIndex;
atomicBond.type = flags[l];
atomicBond.order = order[l];
+ atomicBond.key = key[l];
if (atomicBond.test(queryCtx, true)) return true;
}
@@ -293,6 +295,7 @@ function checkConnected(ctx: IsConnectedToCtx, structure: Structure) {
atomicBond.bIndex = bond.indexB;
atomicBond.type = bond.props.flag;
atomicBond.order = bond.props.order;
+ atomicBond.key = bond.props.key;
if (atomicBond.test(queryCtx, true)) return true;
}
}
diff --git a/src/mol-model/structure/query/queries/generators.ts b/src/mol-model/structure/query/queries/generators.ts
index e963dc2a5b2eb62f408ccde5f5bbfbf000c9510e..807114c5e2ccde81788992acb01c9719c19ec92e 100644
--- a/src/mol-model/structure/query/queries/generators.ts
+++ b/src/mol-model/structure/query/queries/generators.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
@@ -322,7 +322,7 @@ export function bondedAtomicPairs(bondTest?: QueryPredicate): StructureQuery {
for (const unit of structure.units) {
if (unit.kind !== Unit.Kind.Atomic) continue;
- const { offset: intraBondOffset, b: intraBondB, edgeProps: { flags, order } } = unit.bonds;
+ const { offset: intraBondOffset, b: intraBondB, edgeProps: { flags, order, key } } = unit.bonds;
atomicBond.a.unit = unit;
atomicBond.b.unit = unit;
for (let i = 0 as StructureElement.UnitIndex, _i = unit.elements.length; i < _i; i++) {
@@ -335,6 +335,7 @@ export function bondedAtomicPairs(bondTest?: QueryPredicate): StructureQuery {
atomicBond.b.element = unit.elements[intraBondB[lI]];
atomicBond.type = flags[lI];
atomicBond.order = order[lI];
+ atomicBond.key = key[lI];
// No need to "swap test" because each bond direction will be visited eventually.
if (atomicBond.test(ctx, false)) {
const b = structure.subsetBuilder(false);
@@ -358,6 +359,7 @@ export function bondedAtomicPairs(bondTest?: QueryPredicate): StructureQuery {
atomicBond.bIndex = bond.indexB;
atomicBond.order = bond.props.order;
atomicBond.type = bond.props.flag;
+ atomicBond.key = bond.props.key;
// No need to "swap test" because each bond direction will be visited eventually.
if (atomicBond.test(ctx, false)) {
diff --git a/src/mol-model/structure/query/queries/modifiers.ts b/src/mol-model/structure/query/queries/modifiers.ts
index c860695950b6b3430e8d6f8effa9843e4456b396..f10e9f7c7683243b6795c70e74c994d624678b5d 100644
--- a/src/mol-model/structure/query/queries/modifiers.ts
+++ b/src/mol-model/structure/query/queries/modifiers.ts
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
*/
import { Segmentation, SortedArray } from '../../../../mol-data/int';
@@ -370,7 +371,7 @@ function expandConnected(ctx: QueryContext, structure: Structure) {
}
const inputUnitA = inputStructure.unitMap.get(unit.id) as Unit.Atomic;
- const { offset: intraBondOffset, b: intraBondB, edgeProps: { flags, order } } = inputUnitA.bonds;
+ const { offset: intraBondOffset, b: intraBondB, edgeProps: { flags, order, key } } = inputUnitA.bonds;
atomicBond.setStructure(inputStructure);
@@ -397,6 +398,7 @@ function expandConnected(ctx: QueryContext, structure: Structure) {
atomicBond.b.element = bElement;
atomicBond.type = flags[lI];
atomicBond.order = order[lI];
+ atomicBond.key = key[lI];
if (atomicBond.test(ctx, true)) {
builder.addToUnit(unit.id, bElement);
@@ -427,6 +429,7 @@ function expandConnected(ctx: QueryContext, structure: Structure) {
atomicBond.b.element = bElement;
atomicBond.type = bond.props.flag;
atomicBond.order = bond.props.order;
+ atomicBond.key = bond.props.key;
if (atomicBond.test(ctx, true)) {
builder.addToUnit(bondedUnit.unitB, bElement);
diff --git a/src/mol-model/structure/structure/unit/bonds/data.ts b/src/mol-model/structure/structure/unit/bonds/data.ts
index b05df8ed1d0e27a6a5e1c4720741bcc6ae11d356..f2ab500a86fbb09a31bc4f4d72dc6ecd99cf195d 100644
--- a/src/mol-model/structure/structure/unit/bonds/data.ts
+++ b/src/mol-model/structure/structure/unit/bonds/data.ts
@@ -15,16 +15,17 @@ import { InterUnitGraph } from '../../../../../mol-math/graph/inter-unit-graph';
type IntraUnitBonds = IntAdjacencyGraph<StructureElement.UnitIndex, {
readonly order: ArrayLike<number>,
readonly flags: ArrayLike<BondType.Flag>
+ readonly key: ArrayLike<number>,
}, {
/** can remap even with dynamicBonds on, e.g., for water molecules */
readonly canRemap?: boolean
}>
namespace IntraUnitBonds {
- export const Empty: IntraUnitBonds = IntAdjacencyGraph.create([], [], [], 0, { flags: [], order: [] });
+ export const Empty: IntraUnitBonds = IntAdjacencyGraph.create([], [], [], 0, { flags: [], order: [], key: [] });
}
-type InterUnitEdgeProps = { readonly order: number, readonly flag: BondType.Flag }
+type InterUnitEdgeProps = { readonly order: number, readonly flag: BondType.Flag, readonly key: number }
class InterUnitBonds extends InterUnitGraph<number, StructureElement.UnitIndex, InterUnitEdgeProps> {
/** Get inter-unit bond given a bond-location */
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 ba0327c3fc2ffaecbc25b4abe2ed8b434a40373d..74f5127df14aabdc3ba3ec71e6ca40ba1c92804c 100644
--- a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
@@ -80,7 +80,7 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
if (!props.forceCompute && indexPairs) {
const { maxDistance } = indexPairs;
- const { offset, b, edgeProps: { order, distance, flag } } = indexPairs.bonds;
+ const { offset, b, edgeProps: { order, distance, flag, key } } = indexPairs.bonds;
const srcA = sourceIndex.value(aI);
const aeI = getElementIdx(type_symbolA.value(aI));
@@ -113,7 +113,7 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
}
if (add) {
- builder.add(_aI, _bI, { order: order[i], flag: flag[i] });
+ builder.add(_aI, _bI, { order: order[i], flag: flag[i], key: key[i] });
}
}
continue; // assume `indexPairs` supplies all bonds
@@ -131,7 +131,7 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
// check if the bond is within MAX_RADIUS for this pair of units
if (getDistance(unitA, aI, unitB, p.atomIndex) > maxRadius) continue;
- builder.add(_aI, _bI, { order: se.order, flag: se.flags });
+ builder.add(_aI, _bI, { order: se.order, flag: se.flags, key: se.rowIndex });
added = true;
}
// assume, for an atom, that if any inter unit bond is given
@@ -187,7 +187,8 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
const compIdB = label_comp_idB.value(residueIndexB[bI]);
builder.add(_aI, _bI, {
order: getInterBondOrderFromTable(compIdA, compIdB, atomIdA, atomIdB),
- flag: (isMetal ? BondType.Flag.MetallicCoordination : BondType.Flag.Covalent) | BondType.Flag.Computed
+ flag: (isMetal ? BondType.Flag.MetallicCoordination : BondType.Flag.Covalent) | BondType.Flag.Computed,
+ key: -1
});
}
}
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 a4be859321bf19f44ea5c7902fff9d373e7565d8..29fd505381b21fd4791c49718f3900b8eeb001cb 100644
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
@@ -24,17 +24,19 @@ 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 {
+function getGraph(atomA: StructureElement.UnitIndex[], atomB: StructureElement.UnitIndex[], _order: number[], _flags: number[], _key: number[], atomCount: number, canRemap: boolean): IntraUnitBonds {
const builder = new IntAdjacencyGraph.EdgeBuilder(atomCount, atomA, atomB);
const flags = new Uint16Array(builder.slotCount);
const order = new Int8Array(builder.slotCount);
+ const key = new Uint32Array(builder.slotCount);
for (let i = 0, _i = builder.edgeCount; i < _i; i++) {
builder.addNextEdge();
builder.assignProperty(flags, _flags[i]);
builder.assignProperty(order, _order[i]);
+ builder.assignProperty(key, _key[i]);
}
- return builder.createGraph({ flags, order }, { canRemap });
+ return builder.createGraph({ flags, order, key }, { canRemap });
}
const tmpDistVecA = Vec3();
@@ -53,7 +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 } } = indexPairs.bonds;
+ const { offset, b, edgeProps: { order, distance, flag, key } } = indexPairs.bonds;
const { atomSourceIndex: sourceIndex } = unit.model.atomicHierarchy;
const { invertedIndex } = Model.getInvertedAtomSourceIndex(unit.model);
@@ -62,6 +64,7 @@ function findIndexPairBonds(unit: Unit.Atomic) {
const atomB: StructureElement.UnitIndex[] = [];
const flags: number[] = [];
const orders: number[] = [];
+ const keys: number[] = [];
for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
const aI = atoms[_aI];
@@ -104,11 +107,12 @@ function findIndexPairBonds(unit: Unit.Atomic) {
atomB[atomB.length] = _bI;
orders[orders.length] = order[i];
flags[flags.length] = flag[i];
+ keys[keys.length] = key[i];
}
}
}
- return getGraph(atomA, atomB, orders, flags, atomCount, false);
+ return getGraph(atomA, atomB, orders, flags, keys, atomCount, false);
}
function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBonds {
@@ -132,9 +136,10 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
const atomB: StructureElement.UnitIndex[] = [];
const flags: number[] = [];
const order: number[] = [];
+ const key: number[] = [];
let lastResidue = -1;
- let componentMap: Map<string, Map<string, { flags: number, order: number }>> | undefined = void 0;
+ let componentMap: Map<string, Map<string, { flags: number, order: number, key: number }>> | undefined = void 0;
let isWatery = true, isDictionaryBased = true, isSequenced = true;
@@ -162,6 +167,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
atomB[atomB.length] = _bI;
flags[flags.length] = se.flags;
order[order.length] = se.order;
+ key[key.length] = se.rowIndex;
if (!hasStructConn) structConnAdded.clear();
hasStructConn = true;
@@ -230,6 +236,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
flag |= BondType.Flag.MetallicCoordination;
}
flags[flags.length] = flag;
+ key[key.length] = e.key;
}
continue;
}
@@ -243,6 +250,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
atomB[atomB.length] = _bI;
order[order.length] = getIntraBondOrderFromTable(compId, atomIdA, label_atom_id.value(bI));
flags[flags.length] = (isMetal ? BondType.Flag.MetallicCoordination : BondType.Flag.Covalent) | BondType.Flag.Computed;
+ key[key.length] = -1;
const seqIdB = label_seq_id.value(rbI);
@@ -253,7 +261,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
}
const canRemap = isWatery || (isDictionaryBased && isSequenced);
- return getGraph(atomA, atomB, order, flags, atomCount, canRemap);
+ return getGraph(atomA, atomB, order, flags, key, atomCount, canRemap);
}
function computeIntraUnitBonds(unit: Unit.Atomic, props?: Partial<BondComputationProps>) {
diff --git a/src/mol-plugin-ui/controls/screenshot.tsx b/src/mol-plugin-ui/controls/screenshot.tsx
index a90e0778da21ac8b193541c2f222d38275ebcdee..3d79a786f49152bb3ca050d02b244acb35dd9226 100644
--- a/src/mol-plugin-ui/controls/screenshot.tsx
+++ b/src/mol-plugin-ui/controls/screenshot.tsx
@@ -1,7 +1,8 @@
/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 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>
*/
import * as React from 'react';
@@ -25,7 +26,7 @@ export interface ScreenshotPreviewProps {
const _ScreenshotPreview = (props: ScreenshotPreviewProps) => {
const { plugin, cropFrameColor } = props;
- const helper = plugin.helpers.viewportScreenshot!;
+ const helper = plugin.helpers.viewportScreenshot;
const [currentCanvas, setCurrentCanvas] = useState<HTMLCanvasElement | null>(null);
const canvasRef = useRef<HTMLCanvasElement | null>(null);
const propsRef = useRef(props);
@@ -70,8 +71,8 @@ const _ScreenshotPreview = (props: ScreenshotPreviewProps) => {
subscribe(plugin.state.data.behaviors.isUpdating, v => {
if (!v) isDirty = true;
});
- subscribe(helper.behaviors.values, () => isDirty = true);
- subscribe(helper.behaviors.cropParams, () => isDirty = true);
+ subscribe(helper?.behaviors.values, () => isDirty = true);
+ subscribe(helper?.behaviors.cropParams, () => isDirty = true);
let resizeObserver: any = void 0;
if (typeof ResizeObserver !== 'undefined') {
@@ -108,7 +109,9 @@ export const ScreenshotPreview = React.memo(_ScreenshotPreview, (prev, next) =>
declare const ResizeObserver: any;
-function drawPreview(helper: ViewportScreenshotHelper, target: HTMLCanvasElement, customBackground?: string, borderColor?: string, borderWidth?: number) {
+function drawPreview(helper: ViewportScreenshotHelper | undefined, target: HTMLCanvasElement, customBackground?: string, borderColor?: string, borderWidth?: number) {
+ if (!helper) return;
+
const { canvas, width, height } = helper.getPreview()!;
const ctx = target.getContext('2d');
if (!ctx) return;
@@ -151,9 +154,9 @@ function drawPreview(helper: ViewportScreenshotHelper, target: HTMLCanvasElement
function ViewportFrame({ plugin, canvas, color = 'rgba(255, 87, 45, 0.75)' }: { plugin: PluginContext, canvas: HTMLCanvasElement | null, color?: string }) {
const helper = plugin.helpers.viewportScreenshot;
- const params = useBehavior(helper?.behaviors.values!);
- const cropParams = useBehavior(helper?.behaviors.cropParams!);
- const crop = useBehavior(helper?.behaviors.relativeCrop!);
+ const params = useBehavior(helper?.behaviors.values);
+ const cropParams = useBehavior(helper?.behaviors.cropParams);
+ const crop = useBehavior(helper?.behaviors.relativeCrop);
const cropFrameRef = useRef<Viewport>({ x: 0, y: 0, width: 0, height: 0 });
useBehavior(params?.resolution.name === 'viewport' ? plugin.canvas3d?.resized : void 0);
@@ -161,7 +164,7 @@ function ViewportFrame({ plugin, canvas, color = 'rgba(255, 87, 45, 0.75)' }: {
const [start, setStart] = useState([0, 0]);
const [current, setCurrent] = useState([0, 0]);
- if (!helper || !canvas) return null;
+ if (!helper || !canvas || !crop) return null;
const { width, height } = helper.getSizeAndViewport();
@@ -267,7 +270,7 @@ function ViewportFrame({ plugin, canvas, color = 'rgba(255, 87, 45, 0.75)' }: {
function finish() {
const cropFrame = cropFrameRef.current;
- if (cropParams.auto) {
+ if (cropParams?.auto) {
helper?.behaviors.cropParams.next({ ...cropParams, auto: false });
}
helper?.behaviors.relativeCrop.next({
diff --git a/src/mol-plugin-ui/left-panel.tsx b/src/mol-plugin-ui/left-panel.tsx
index 32477e580739e3388dbf0763db542fb97eb3c09c..62db9be7c613c82d0d1e8974d3523437aca376cf 100644
--- a/src/mol-plugin-ui/left-panel.tsx
+++ b/src/mol-plugin-ui/left-panel.tsx
@@ -141,11 +141,13 @@ class FullSettings extends PluginUIComponent {
this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
this.subscribe(this.plugin.layout.events.updated, () => this.forceUpdate());
- this.subscribe(this.plugin.canvas3d!.camera.stateChanged, state => {
- if (state.radiusMax !== undefined || state.radius !== undefined) {
- this.forceUpdate();
- }
- });
+ if (this.plugin.canvas3d) {
+ this.subscribe(this.plugin.canvas3d.camera.stateChanged, state => {
+ if (state.radiusMax !== undefined || state.radius !== undefined) {
+ this.forceUpdate();
+ }
+ });
+ }
}
render() {
diff --git a/src/mol-plugin-ui/structure/measurements.tsx b/src/mol-plugin-ui/structure/measurements.tsx
index cd26069728850817262781ff669b27c229f9c573..f60269f9056abd696e2f4378d0f4313539f1966e 100644
--- a/src/mol-plugin-ui/structure/measurements.tsx
+++ b/src/mol-plugin-ui/structure/measurements.tsx
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
@@ -288,7 +288,12 @@ class MeasurementEntry extends PurePluginUIComponent<{ cell: StructureMeasuremen
for (const loci of this.lociArray) {
this.plugin.managers.interactivity.lociHighlights.highlight({ loci }, false);
}
- this.plugin.managers.interactivity.lociHighlights.highlight({ loci: this.props.cell.obj?.data.repr.getLoci()! }, false);
+ const reprLocis = this.props.cell.obj?.data.repr.getAllLoci();
+ if (reprLocis) {
+ for (const loci of reprLocis) {
+ this.plugin.managers.interactivity.lociHighlights.highlight({ loci }, false);
+ }
+ }
};
clearHighlight = () => {
diff --git a/src/mol-plugin-ui/viewport/canvas.tsx b/src/mol-plugin-ui/viewport/canvas.tsx
index 616c145d1bb5033e6ae956f125fe780863ff6f21..ab49d381a4e449ff238eea734d1b0f5def960e86 100644
--- a/src/mol-plugin-ui/viewport/canvas.tsx
+++ b/src/mol-plugin-ui/viewport/canvas.tsx
@@ -59,7 +59,7 @@ export class ViewportCanvas extends PluginUIComponent<ViewportCanvasParams, View
return <div className='msp-no-webgl'>
<div>
<p><b>WebGL does not seem to be available.</b></p>
- <p>This can be caused by an outdated browser, graphics card driver issue, or bad weather. Sometimes, just restarting the browser helps.</p>
+ <p>This can be caused by an outdated browser, graphics card driver issue, or bad weather. Sometimes, just restarting the browser helps. Also, make sure hardware acceleration is enabled in your browser.</p>
<p>For a list of supported browsers, refer to <a href='http://caniuse.com/#feat=webgl' target='_blank'>http://caniuse.com/#feat=webgl</a>.</p>
</div>
</div>;
diff --git a/src/mol-plugin-ui/viewport/screenshot.tsx b/src/mol-plugin-ui/viewport/screenshot.tsx
index 135beee19ae88e1204d2cda6eaa926e91b65eb8d..9158ef2b58961341f817a5bca89c5b663f28c477 100644
--- a/src/mol-plugin-ui/viewport/screenshot.tsx
+++ b/src/mol-plugin-ui/viewport/screenshot.tsx
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @author David Sehnal <david.sehnal@gmail.com>
@@ -96,18 +96,21 @@ export class DownloadScreenshotControls extends PluginUIComponent<{ close: () =>
}
function ScreenshotParams({ plugin, isDisabled }: { plugin: PluginContext, isDisabled: boolean }) {
- const helper = plugin.helpers.viewportScreenshot!;
- const values = useBehavior(helper.behaviors.values);
+ const helper = plugin.helpers.viewportScreenshot;
+
+ const values = useBehavior(helper?.behaviors.values);
+ if (!helper) return null;
return <ParameterControls params={helper.params} values={values} onChangeValues={v => helper.behaviors.values.next(v)} isDisabled={isDisabled} />;
}
function CropControls({ plugin }: { plugin: PluginContext }) {
const helper = plugin.helpers.viewportScreenshot;
- const cropParams = useBehavior(helper?.behaviors.cropParams!);
+
+ const cropParams = useBehavior(helper?.behaviors.cropParams);
useBehavior(helper?.behaviors.relativeCrop);
- if (!helper) return null;
+ if (!helper || !cropParams) return null;
return <div style={{ width: '100%', height: '24px', marginTop: '8px' }}>
<ToggleButton icon={CropOrginalSvg} title='Auto-crop' inline isSelected={cropParams.auto}
diff --git a/src/mol-plugin-ui/viewport/simple-settings.tsx b/src/mol-plugin-ui/viewport/simple-settings.tsx
index 122e11f8a64fa9d987db949223698ec55fc66771..77772e62b3047fbb12b8c3a77897456380b734ff 100644
--- a/src/mol-plugin-ui/viewport/simple-settings.tsx
+++ b/src/mol-plugin-ui/viewport/simple-settings.tsx
@@ -22,6 +22,8 @@ import { ViewportHelpContent } from './help';
export class SimpleSettingsControl extends PluginUIComponent {
componentDidMount() {
+ if (!this.plugin.canvas3d) return;
+
this.subscribe(this.plugin.events.canvas3d.settingsUpdated, () => this.forceUpdate());
this.subscribe(this.plugin.canvas3d!.camera.stateChanged, state => {
diff --git a/src/mol-plugin/behavior/static/state.ts b/src/mol-plugin/behavior/static/state.ts
index b02ae119a5e34ec6981c8437eb2668eeed021ec6..e4270736da5816cc6b6b5ce7287a6878169b5b24 100644
--- a/src/mol-plugin/behavior/static/state.ts
+++ b/src/mol-plugin/behavior/static/state.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>
@@ -119,7 +119,9 @@ export function Highlight(ctx: PluginContext) {
ctx.managers.interactivity.lociHighlights.highlight({ loci: Structure.Loci(cell.obj.data) }, false);
} else if (cell && SO.isRepresentation3D(cell.obj)) {
const { repr } = cell.obj.data;
- ctx.managers.interactivity.lociHighlights.highlight({ loci: repr.getLoci(), repr }, false);
+ for (const loci of repr.getAllLoci()) {
+ ctx.managers.interactivity.lociHighlights.highlight({ loci, repr }, false);
+ }
} else if (SO.Molecule.Structure.Selections.is(cell.obj)) {
for (const entry of cell.obj.data) {
ctx.managers.interactivity.lociHighlights.highlight({ loci: entry.loci }, false);
diff --git a/src/mol-plugin/config.ts b/src/mol-plugin/config.ts
index e087c3468e04b818d23357059b899aa9eb031db9..707dd37d0208d56c3080c6695a9046012fb663ad 100644
--- a/src/mol-plugin/config.ts
+++ b/src/mol-plugin/config.ts
@@ -35,6 +35,7 @@ export const PluginConfig = {
// as of Oct 1 2021, WebGL 2 doesn't work on iOS 15.
// TODO: check back in a few weeks to see if it was fixed
PreferWebGl1: item('plugin-config.prefer-webgl1', PluginFeatureDetection.preferWebGl1),
+ AllowMajorPerformanceCaveat: item('plugin-config.allow-major-performance-caveat', false),
},
State: {
DefaultServer: item('plugin-state.server', 'https://webchem.ncbr.muni.cz/molstar-state'),
diff --git a/src/mol-plugin/context.ts b/src/mol-plugin/context.ts
index 405087080f0c118dece7b9c2ec541134ddcf23d0..4db484ae17be78415b1bba5e237e019c2b93b019 100644
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -201,7 +201,8 @@ export class PluginContext {
const pickPadding = this.config.get(PluginConfig.General.PickPadding) ?? 1;
const enableWboit = this.config.get(PluginConfig.General.EnableWboit) || false;
const preferWebGl1 = this.config.get(PluginConfig.General.PreferWebGl1) || false;
- (this.canvas3dContext as Canvas3DContext) = Canvas3DContext.fromCanvas(canvas, this.managers.asset, { antialias, preserveDrawingBuffer, pixelScale, pickScale, pickPadding, enableWboit, preferWebGl1 });
+ const failIfMajorPerformanceCaveat = !(this.config.get(PluginConfig.General.AllowMajorPerformanceCaveat) ?? false);
+ (this.canvas3dContext as Canvas3DContext) = Canvas3DContext.fromCanvas(canvas, this.managers.asset, { antialias, preserveDrawingBuffer, pixelScale, pickScale, pickPadding, enableWboit, preferWebGl1, failIfMajorPerformanceCaveat });
}
(this.canvas3d as Canvas3D) = Canvas3D.create(this.canvas3dContext!);
this.canvas3dInit.next(true);
diff --git a/src/mol-repr/representation.ts b/src/mol-repr/representation.ts
index 246e34eb625d176da85f0221531742c4c93ca499..17da5156448dd9e75ff88ae586a1106c9386825d 100644
--- a/src/mol-repr/representation.ts
+++ b/src/mol-repr/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>
*/
@@ -154,8 +154,8 @@ interface Representation<D, P extends PD.Params = {}, S extends Representation.S
createOrUpdate: (props?: Partial<PD.Values<P>>, data?: D) => Task<void>
setState: (state: Partial<S>) => void
setTheme: (theme: Theme) => void
- /** If no pickingId is given, returns a Loci for the whole representation */
- getLoci: (pickingId?: PickingId) => ModelLoci
+ getLoci: (pickingId: PickingId) => ModelLoci
+ getAllLoci: () => ModelLoci[]
mark: (loci: ModelLoci, action: MarkerAction) => boolean
destroy: () => void
}
@@ -227,6 +227,7 @@ namespace Representation {
setState: () => {},
setTheme: () => {},
getLoci: () => EmptyLoci,
+ getAllLoci: () => [],
mark: () => false,
destroy: () => {}
};
@@ -327,7 +328,7 @@ namespace Representation {
},
get state() { return currentState; },
get theme() { return currentTheme; },
- getLoci: (pickingId?: PickingId) => {
+ getLoci: (pickingId: PickingId) => {
const { visuals } = currentProps;
for (let i = 0, il = reprList.length; i < il; ++i) {
if (!visuals || visuals.includes(reprMap[i])) {
@@ -337,6 +338,16 @@ namespace Representation {
}
return EmptyLoci;
},
+ getAllLoci: () => {
+ const loci: ModelLoci[] = [];
+ const { visuals } = currentProps;
+ for (let i = 0, il = reprList.length; i < il; ++i) {
+ if (!visuals || visuals.includes(reprMap[i])) {
+ loci.push(...reprList[i].getAllLoci());
+ }
+ }
+ return loci;
+ },
mark: (loci: ModelLoci, action: MarkerAction) => {
let marked = false;
for (let i = 0, il = reprList.length; i < il; ++i) {
@@ -399,6 +410,10 @@ namespace Representation {
// TODO
return EmptyLoci;
},
+ getAllLoci: () => {
+ // TODO
+ return [];
+ },
mark: (loci: ModelLoci, action: MarkerAction) => {
// TODO
return false;
diff --git a/src/mol-repr/shape/representation.ts b/src/mol-repr/shape/representation.ts
index 803199b180ff825601d3c1c88b2d5c69eef1f6c7..45c4c68776db007b38a7e0568bd9c0f3c1581095 100644
--- a/src/mol-repr/shape/representation.ts
+++ b/src/mol-repr/shape/representation.ts
@@ -213,14 +213,16 @@ export function ShapeRepresentation<D, G extends Geometry, P extends Geometry.Pa
get geometryVersion() { return geometryVersion; },
updated,
createOrUpdate,
- getLoci(pickingId?: PickingId) {
- if (pickingId === undefined) return Shape.Loci(_shape);
+ getLoci(pickingId: PickingId) {
const { objectId, groupId, instanceId } = pickingId;
if (_renderObject && _renderObject.id === objectId) {
return ShapeGroup.Loci(_shape, [{ ids: OrderedSet.ofSingleton(groupId), instance: instanceId }]);
}
return EmptyLoci;
},
+ getAllLoci() {
+ return [Shape.Loci(_shape)];
+ },
mark(loci: Loci, action: MarkerAction) {
if (!MarkerActions.is(_state.markerActions, action)) return false;
if (ShapeGroup.isLoci(loci) || Shape.isLoci(loci)) {
diff --git a/src/mol-repr/structure/complex-representation.ts b/src/mol-repr/structure/complex-representation.ts
index f1edcbae4f58c5fe4938f2c4e2f2923ecf27b7a3..a50d04ae0c47bda3e592bfd93e2aa2b25dcc4de3 100644
--- a/src/mol-repr/structure/complex-representation.ts
+++ b/src/mol-repr/structure/complex-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>
* @author David Sehnal <david.sehnal@gmail.com>
@@ -72,11 +72,14 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
});
}
- function getLoci(pickingId?: PickingId) {
- if (pickingId === undefined) return Structure.Loci(_structure.target);
+ function getLoci(pickingId: PickingId) {
return visual ? visual.getLoci(pickingId) : EmptyLoci;
}
+ function getAllLoci() {
+ return [Structure.Loci(_structure.target)];
+ }
+
function mark(loci: Loci, action: MarkerAction) {
if (!_structure) return false;
if (!MarkerActions.is(_state.markerActions, action)) return false;
@@ -157,6 +160,7 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
setState,
setTheme,
getLoci,
+ getAllLoci,
mark,
destroy
};
diff --git a/src/mol-repr/structure/units-representation.ts b/src/mol-repr/structure/units-representation.ts
index bc3130700ca2fe75673b471f9b4a3aa4ff634369..d7a2b6e0634e71156342aff34217ec67b23ac55b 100644
--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-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>
* @author David Sehnal <david.sehnal@gmail.com>
@@ -185,8 +185,7 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
});
}
- function getLoci(pickingId?: PickingId) {
- if (pickingId === undefined) return Structure.Loci(_structure.target);
+ function getLoci(pickingId: PickingId) {
let loci: Loci = EmptyLoci;
visuals.forEach(({ visual }) => {
const _loci = visual.getLoci(pickingId);
@@ -195,6 +194,10 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
return loci;
}
+ function getAllLoci() {
+ return [Structure.Loci(_structure.target)];
+ }
+
function mark(loci: Loci, action: MarkerAction) {
if (!_structure) return false;
if (!MarkerActions.is(_state.markerActions, action)) return false;
@@ -302,6 +305,7 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
setState,
setTheme,
getLoci,
+ getAllLoci,
mark,
destroy
};
diff --git a/src/mol-repr/volume/representation.ts b/src/mol-repr/volume/representation.ts
index fae57da2554529ff0eee4d13a229d8cc6c956271..c6de383731b5f36a097cd321d19660c7e4502651 100644
--- a/src/mol-repr/volume/representation.ts
+++ b/src/mol-repr/volume/representation.ts
@@ -358,10 +358,12 @@ export function VolumeRepresentation<P extends VolumeParams>(label: string, ctx:
createOrUpdate,
setState,
setTheme,
- getLoci: (pickingId?: PickingId): Loci => {
- if (pickingId === undefined) return getLoci(_volume, _props);
+ getLoci: (pickingId: PickingId): Loci => {
return visual ? visual.getLoci(pickingId) : EmptyLoci;
},
+ getAllLoci: (): Loci[] => {
+ return [getLoci(_volume, _props)];
+ },
mark,
destroy
};
diff --git a/src/mol-script/language/symbol-table/structure-query.ts b/src/mol-script/language/symbol-table/structure-query.ts
index 9e765f41649288a054b01a69b4a6a7d06b1c2bf6..209da4376e81c413caada96b2a2b544146e3de48 100644
--- a/src/mol-script/language/symbol-table/structure-query.ts
+++ b/src/mol-script/language/symbol-table/structure-query.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2019 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>
@@ -333,6 +333,7 @@ const bondProperty = {
flags: bondProp(Types.BondFlags),
order: bondProp(Type.Num),
+ key: bondProp(Type.Num),
length: bondProp(Type.Num),
atomA: bondProp(Types.ElementReference),
atomB: bondProp(Types.ElementReference)
@@ -356,5 +357,5 @@ export const structureQuery = {
combinator,
atomSet,
atomProperty,
- bondProperty: bondProperty
+ bondProperty
};
\ No newline at end of file
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index 0ad2bec0c74a438d242cd4fba125bd1e4d48c3c8..deab2d4baa0c10ab7fc3641b258ef8a1c7a0cce2 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -1,5 +1,5 @@
/**
- * Copyright (c) 2018-2019 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>
@@ -377,6 +377,7 @@ const symbols = [
// ============= BOND PROPERTIES ================
D(MolScript.structureQuery.bondProperty.order, (ctx, xs) => ctx.atomicBond.order),
D(MolScript.structureQuery.bondProperty.flags, (ctx, xs) => ctx.atomicBond.type),
+ D(MolScript.structureQuery.bondProperty.key, (ctx, xs) => ctx.atomicBond.key),
D(MolScript.structureQuery.bondProperty.atomA, (ctx, xs) => ctx.atomicBond.a),
D(MolScript.structureQuery.bondProperty.atomB, (ctx, xs) => ctx.atomicBond.b),
D(MolScript.structureQuery.bondProperty.length, (ctx, xs) => ctx.atomicBond.length),