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molstar

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A comprehensive macromolecular library.

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"use strict"; /** * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info. * * @author Alexander Rose <alexander.rose@weirdbyte.de> */ Object.defineProperty(exports, "__esModule", { value: true }); exports.CoarsePolymerGapIterator = exports.AtomicPolymerGapIterator = void 0; exports.PolymerGapIterator = PolymerGapIterator; const structure_1 = require("../../../../../mol-model/structure"); const sorted_ranges_1 = require("../../../../../mol-data/int/sorted-ranges"); const polymer_1 = require("../polymer"); /** Iterates over gaps, i.e. the stem residues/coarse elements adjacent to gaps */ function PolymerGapIterator(structure, unit) { switch (unit.kind) { case 0 /* Unit.Kind.Atomic */: return new AtomicPolymerGapIterator(structure, unit); case 1 /* Unit.Kind.Spheres */: case 2 /* Unit.Kind.Gaussians */: return new CoarsePolymerGapIterator(structure, unit); } } function createPolymerGapPair(structure, unit) { return { centerA: structure_1.StructureElement.Location.create(structure, unit), centerB: structure_1.StructureElement.Location.create(structure, unit), }; } class AtomicPolymerGapIterator { move() { const { elements, residueIndex } = this.unit; const gapSegment = this.gapIt.move(); this.value.centerA.element = this.traceElementIndex[residueIndex[elements[gapSegment.start]]]; this.value.centerB.element = this.traceElementIndex[residueIndex[elements[gapSegment.end - 1]]]; this.hasNext = this.gapIt.hasNext; return this.value; } constructor(structure, unit) { this.unit = unit; this.hasNext = false; this.traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex; // can assume it won't be -1 for polymer residues this.gapIt = sorted_ranges_1.SortedRanges.transientSegments((0, polymer_1.getGapRanges)(unit), unit.elements); this.value = createPolymerGapPair(structure, unit); this.hasNext = this.gapIt.hasNext; } } exports.AtomicPolymerGapIterator = AtomicPolymerGapIterator; class CoarsePolymerGapIterator { move() { const gapSegment = this.gapIt.move(); this.value.centerA.element = this.unit.elements[gapSegment.start]; this.value.centerB.element = this.unit.elements[gapSegment.end - 1]; this.hasNext = this.gapIt.hasNext; return this.value; } constructor(structure, unit) { this.unit = unit; this.hasNext = false; this.gapIt = sorted_ranges_1.SortedRanges.transientSegments((0, polymer_1.getGapRanges)(unit), unit.elements); this.value = createPolymerGapPair(structure, unit); this.hasNext = this.gapIt.hasNext; } } exports.CoarsePolymerGapIterator = CoarsePolymerGapIterator;