diff --git a/CHANGELOG.md b/CHANGELOG.md
index a9bf194729db03f2118718ea4e2d54445edfc936..ce195bc72bfe53f3c7e1ca532f13527181771e00 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ Note that since we don't clearly distinguish between a public and private interf
- [Fix] Clone ``Canvas3DParams`` when creating a ``Canvas3D`` instance to prevent shared state between multiple instances
- Add ``includeResidueTest`` option to ``alignAndSuperposeWithSIFTSMapping``
- Add ``parentDisplay`` param for interactions representation.
+- Add ``key`` property to intra- and inter-bonds for referencing source data
## [v3.16.0] - 2022-08-25
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 128f9b4fa7d0b698d88a7f939140d5737c3f8e21..81e698f1649ada29eafa19194f1d2af23c5ab1a1 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';
@@ -248,7 +249,7 @@ 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;
@@ -273,6 +274,7 @@ 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;
}
@@ -295,6 +297,7 @@ 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-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 dc32f889628e0958a518ed074a31cbb8390d4780..dcb18e9fef74f4744f7d7e92625e29943a1ca0e4 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>
@@ -356,6 +356,7 @@ 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),