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@@ -23,7 +23,7 @@ import { Carbohydrates } from './carbohydrates/data';
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import { computeCarbohydrates } from './carbohydrates/compute';
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import { Vec3, Mat4 } from '../../../mol-math/linear-algebra';
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import { idFactory } from '../../../mol-util/id-factory';
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-import { GridLookup3D } from '../../../mol-math/geometry';
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+import { Box3D, GridLookup3D } from '../../../mol-math/geometry';
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import { UUID } from '../../../mol-util';
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import { CustomProperties } from '../../custom-property';
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import { AtomicHierarchy } from '../model/properties/atomic';
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@@ -43,6 +43,8 @@ type State = {
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lookup3d?: StructureLookup3D,
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interUnitBonds?: InterUnitBonds,
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dynamicBonds: boolean,
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+ interBondsValidUnit?: (unit: Unit) => boolean,
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+ interBondsValidUnitPair?: (structure: Structure, unitA: Unit, unitB: Unit) => boolean,
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unitSymmetryGroups?: ReadonlyArray<Unit.SymmetryGroup>,
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unitSymmetryGroupsIndexMap?: IntMap<number>,
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unitsSortedByVolume?: ReadonlyArray<Unit>;
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@@ -241,6 +243,8 @@ class Structure {
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this.state.interUnitBonds = computeInterUnitBonds(this, {
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ignoreWater: !this.dynamicBonds,
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ignoreIon: !this.dynamicBonds,
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+ validUnit: this.state.interBondsValidUnit,
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+ validUnitPair: this.state.interBondsValidUnitPair,
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});
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}
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return this.state.interUnitBonds;
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@@ -250,6 +254,14 @@ class Structure {
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return this.state.dynamicBonds;
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}
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+ get interBondsValidUnit() {
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+ return this.state.interBondsValidUnit;
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+ }
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+
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+ get interBondsValidUnitPair() {
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+ return this.state.interBondsValidUnitPair;
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+ }
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+
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get unitSymmetryGroups(): ReadonlyArray<Unit.SymmetryGroup> {
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if (this.state.unitSymmetryGroups) return this.state.unitSymmetryGroups;
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this.state.unitSymmetryGroups = StructureSymmetry.computeTransformGroups(this);
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@@ -380,7 +392,12 @@ class Structure {
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parent: parent?.remapModel(m),
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label: this.label,
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interUnitBonds: dynamicBonds ? undefined : interUnitBonds,
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- dynamicBonds
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+ dynamicBonds,
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+ interBondsValidUnit: this.state.interBondsValidUnit,
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+ interBondsValidUnitPair: this.state.interBondsValidUnitPair,
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+ coordinateSystem: this.state.coordinateSystem,
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+ masterModel: this.state.masterModel,
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+ representativeModel: this.state.representativeModel,
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});
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}
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@@ -428,7 +445,6 @@ class Structure {
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function cmpUnits(units: ArrayLike<Unit>, i: number, j: number) {
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return units[i].id - units[j].id;
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-
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}
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function getModels(s: Structure) {
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@@ -634,6 +650,8 @@ namespace Structure {
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* Also enables calculation of inter-unit bonds in water molecules.
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*/
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dynamicBonds?: boolean,
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+ interBondsValidUnit?: (unit: Unit) => boolean,
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+ interBondsValidUnitPair?: (structure: Structure, unitA: Unit, unitB: Unit) => boolean,
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coordinateSystem?: SymmetryOperator
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label?: string
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/** Master model for structures of a protein model and multiple ligand models */
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@@ -722,6 +740,12 @@ namespace Structure {
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if (props.parent) state.parent = props.parent.parent || props.parent;
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if (props.interUnitBonds) state.interUnitBonds = props.interUnitBonds;
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+ if (props.interBondsValidUnit) state.interBondsValidUnit = props.interBondsValidUnit;
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+ else if (props.parent) state.interBondsValidUnit = props.parent.interBondsValidUnit;
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+
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+ if (props.interBondsValidUnitPair) state.interBondsValidUnitPair = props.interBondsValidUnitPair;
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+ else if (props.parent) state.interBondsValidUnitPair = props.parent.interBondsValidUnitPair;
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+
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if (props.dynamicBonds) state.dynamicBonds = props.dynamicBonds;
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else if (props.parent) state.dynamicBonds = props.parent.dynamicBonds;
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@@ -1180,7 +1204,7 @@ namespace Structure {
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/**
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* Iterate over all unit pairs of a structure and invokes callback for valid units
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- * and unit pairs if within a max distance.
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+ * and unit pairs if their boundaries are within a max distance.
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*/
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export function eachUnitPair(structure: Structure, callback: (unitA: Unit, unitB: Unit) => void, props: EachUnitPairProps) {
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const { maxRadius, validUnit, validUnitPair } = props;
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@@ -1188,15 +1212,19 @@ namespace Structure {
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const lookup = structure.lookup3d;
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const imageCenter = Vec3();
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+ const bbox = Box3D();
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+ const rvec = Vec3.create(maxRadius, maxRadius, maxRadius);
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for (const unit of structure.units) {
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if (!validUnit(unit)) continue;
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const bs = unit.boundary.sphere;
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+ Box3D.expand(bbox, unit.boundary.box, rvec);
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Vec3.transformMat4(imageCenter, bs.center, unit.conformation.operator.matrix);
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const closeUnits = lookup.findUnitIndices(imageCenter[0], imageCenter[1], imageCenter[2], bs.radius + maxRadius);
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for (let i = 0; i < closeUnits.count; i++) {
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const other = structure.units[closeUnits.indices[i]];
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+ if (!Box3D.overlaps(bbox, other.boundary.box)) continue;
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if (!validUnit(other) || unit.id >= other.id || !validUnitPair(unit, other)) continue;
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if (other.elements.length >= unit.elements.length) callback(unit, other);
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Alexander Rose