molstar 3.0.0 → 3.0.1

package/lib/commonjs/mol-model/structure/structure/structure.js

@@ -1,1390 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2017-2021 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>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.Structure = void 0;
-var tslib_1 = require("tslib");
-var int_1 = require("../../../mol-data/int");
-var generic_1 = require("../../../mol-data/generic");
-var symmetry_operator_1 = require("../../../mol-math/geometry/symmetry-operator");
-var model_1 = require("../model");
-var util_1 = require("../../../mol-data/util");
-var element_1 = require("./element");
-var unit_1 = require("./unit");
-var lookup3d_1 = require("./util/lookup3d");
-var subset_builder_1 = require("./util/subset-builder");
-var bonds_1 = require("./unit/bonds");
-var symmetry_1 = require("./symmetry");
-var properties_1 = require("./properties");
-var compute_1 = require("./carbohydrates/compute");
-var linear_algebra_1 = require("../../../mol-math/linear-algebra");
-var id_factory_1 = require("../../../mol-util/id-factory");
-var geometry_1 = require("../../../mol-math/geometry");
-var custom_property_1 = require("../../custom-property");
-var atomic_1 = require("../model/properties/atomic");
-var selection_1 = require("../query/selection");
-var boundary_1 = require("../../../mol-math/geometry/boundary");
-var custom_structure_property_1 = require("../../../mol-model-props/common/custom-structure-property");
-var mol_task_1 = require("../../../mol-task");
-var boundary_2 = require("./util/boundary");
-var Structure = /** @class */ (function () {
-    /**
-     * @param units Array of all units in the structure, sorted by unit.id
-     * @param unitMap Maps unit.id to index of unit in units array
-     * @param unitIndexMap Array of all units in the structure, sorted by unit.id
-     */
-    function Structure(units, unitMap, unitIndexMap, state, asParent) {
-        this.units = units;
-        this.unitMap = unitMap;
-        this.unitIndexMap = unitIndexMap;
-        this.state = state;
-        // always assign to ensure object shape
-        this._child = asParent === null || asParent === void 0 ? void 0 : asParent.child;
-        this._target = asParent === null || asParent === void 0 ? void 0 : asParent.target;
-        this._proxy = undefined;
-    }
-    Structure.prototype.subsetBuilder = function (isSorted) {
-        return new subset_builder_1.StructureSubsetBuilder(this, isSorted);
-    };
-    Object.defineProperty(Structure.prototype, "elementCount", {
-        /** Count of all elements in the structure, i.e. the sum of the elements in the units */
-        get: function () {
-            return this.state.elementCount;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "bondCount", {
-        /** Count of all bonds (intra- and inter-unit) in the structure */
-        get: function () {
-            if (this.state.bondCount === -1) {
-                this.state.bondCount = this.interUnitBonds.edgeCount + bonds_1.Bond.getIntraUnitBondCount(this);
-            }
-            return this.state.bondCount;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "hasCustomProperties", {
-        get: function () {
-            return !!this.state.customProps && this.state.customProps.all.length > 0;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "customPropertyDescriptors", {
-        get: function () {
-            if (!this.state.customProps)
-                this.state.customProps = new custom_property_1.CustomProperties();
-            return this.state.customProps;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "currentPropertyData", {
-        /**
-         * Property data unique to this instance of the structure.
-         */
-        get: function () {
-            if (!this.state.propertyData)
-                this.state.propertyData = Object.create(null);
-            return this.state.propertyData;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "inheritedPropertyData", {
-        /**
-         * Property data of the parent structure if it exists, currentPropertyData otherwise.
-         */
-        get: function () {
-            return this.parent ? this.parent.currentPropertyData : this.currentPropertyData;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "polymerResidueCount", {
-        /** Count of all polymer residues in the structure */
-        get: function () {
-            if (this.state.polymerResidueCount === -1) {
-                this.state.polymerResidueCount = getPolymerResidueCount(this);
-            }
-            return this.state.polymerResidueCount;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "polymerGapCount", {
-        /** Count of all polymer gaps in the structure */
-        get: function () {
-            if (this.state.polymerGapCount === -1) {
-                this.state.polymerGapCount = getPolymerGapCount(this);
-            }
-            return this.state.polymerGapCount;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "polymerUnitCount", {
-        get: function () {
-            if (this.state.polymerUnitCount === -1) {
-                this.state.polymerUnitCount = getPolymerUnitCount(this);
-            }
-            return this.state.polymerUnitCount;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "uniqueElementCount", {
-        get: function () {
-            if (this.state.uniqueElementCount === -1) {
-                this.state.uniqueElementCount = getUniqueElementCount(this);
-            }
-            return this.state.uniqueElementCount;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "atomicResidueCount", {
-        get: function () {
-            if (this.state.atomicResidueCount === -1) {
-                this.state.atomicResidueCount = getAtomicResidueCount(this);
-            }
-            return this.state.atomicResidueCount;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "isCoarseGrained", {
-        /**
-         * True if any model the structure is based on is coarse grained.
-         * @see Model.isCoarseGrained
-         */
-        get: function () {
-            return this.models.some(function (m) { return model_1.Model.isCoarseGrained(m); });
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "isEmpty", {
-        get: function () {
-            return this.units.length === 0;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "hashCode", {
-        get: function () {
-            if (this.state.hashCode !== -1)
-                return this.state.hashCode;
-            return this.computeHash();
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "transformHash", {
-        /** Hash based on all unit.id values in the structure, reflecting the units transformation */
-        get: function () {
-            if (this.state.transformHash !== -1)
-                return this.state.transformHash;
-            this.state.transformHash = (0, util_1.hashFnv32a)(this.units.map(function (u) { return u.id; }));
-            return this.state.transformHash;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Structure.prototype.computeHash = function () {
-        var hash = 23;
-        for (var i = 0, _i = this.units.length; i < _i; i++) {
-            var u = this.units[i];
-            hash = (31 * hash + u.id) | 0;
-            hash = (31 * hash + int_1.SortedArray.hashCode(u.elements)) | 0;
-        }
-        hash = (31 * hash + this.elementCount) | 0;
-        hash = (0, util_1.hash1)(hash);
-        if (hash === -1)
-            hash = 0;
-        this.state.hashCode = hash;
-        return hash;
-    };
-    /** Returns a new element location iterator */
-    Structure.prototype.elementLocations = function () {
-        return new Structure.ElementLocationIterator(this);
-    };
-    Object.defineProperty(Structure.prototype, "root", {
-        /** The parent or itself in case this is the root */
-        get: function () {
-            var _a;
-            return (_a = this.state.parent) !== null && _a !== void 0 ? _a : this;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "parent", {
-        /** The root/top-most parent or `undefined` in case this is the root */
-        get: function () {
-            return this.state.parent;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "coordinateSystem", {
-        /**
-         * Conformation transformation that was applied to every unit of this structure.
-         *
-         * Coordinate system applies to the *current* structure only.
-         * A parent structure can have a different coordinate system and thefore it has to be composed "manualy"
-         * by the consumer.
-         */
-        get: function () {
-            return this.state.coordinateSystem;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "label", {
-        get: function () {
-            return this.state.label;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "boundary", {
-        get: function () {
-            if (this.state.boundary)
-                return this.state.boundary;
-            this.state.boundary = (0, boundary_2.computeStructureBoundary)(this);
-            return this.state.boundary;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "lookup3d", {
-        get: function () {
-            if (this.state.lookup3d)
-                return this.state.lookup3d;
-            this.state.lookup3d = new lookup3d_1.StructureLookup3D(this);
-            return this.state.lookup3d;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "interUnitBonds", {
-        get: function () {
-            if (this.state.interUnitBonds)
-                return this.state.interUnitBonds;
-            this.state.interUnitBonds = (0, bonds_1.computeInterUnitBonds)(this, { ignoreWater: !this.dynamicBonds });
-            return this.state.interUnitBonds;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "dynamicBonds", {
-        get: function () {
-            return this.state.dynamicBonds;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "unitSymmetryGroups", {
-        get: function () {
-            if (this.state.unitSymmetryGroups)
-                return this.state.unitSymmetryGroups;
-            this.state.unitSymmetryGroups = symmetry_1.StructureSymmetry.computeTransformGroups(this);
-            return this.state.unitSymmetryGroups;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "unitSymmetryGroupsIndexMap", {
-        /** Maps unit.id to index of SymmetryGroup in unitSymmetryGroups array */
-        get: function () {
-            if (this.state.unitSymmetryGroupsIndexMap)
-                return this.state.unitSymmetryGroupsIndexMap;
-            this.state.unitSymmetryGroupsIndexMap = unit_1.Unit.SymmetryGroup.getUnitSymmetryGroupsIndexMap(this.unitSymmetryGroups);
-            return this.state.unitSymmetryGroupsIndexMap;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "carbohydrates", {
-        get: function () {
-            if (this.state.carbohydrates)
-                return this.state.carbohydrates;
-            this.state.carbohydrates = (0, compute_1.computeCarbohydrates)(this);
-            return this.state.carbohydrates;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "models", {
-        get: function () {
-            if (this.state.models)
-                return this.state.models;
-            this.state.models = getModels(this);
-            return this.state.models;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "uniqueResidueNames", {
-        get: function () {
-            return this.state.uniqueResidueNames
-                || (this.state.uniqueResidueNames = getUniqueResidueNames(this));
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "uniqueElementSymbols", {
-        get: function () {
-            return this.state.uniqueElementSymbols
-                || (this.state.uniqueElementSymbols = getUniqueElementSymbols(this));
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "entityIndices", {
-        get: function () {
-            return this.state.entityIndices
-                || (this.state.entityIndices = getEntityIndices(this));
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "uniqueAtomicResidueIndices", {
-        get: function () {
-            return this.state.uniqueAtomicResidueIndices
-                || (this.state.uniqueAtomicResidueIndices = getUniqueAtomicResidueIndices(this));
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "isAtomic", {
-        /** Contains only atomic units */
-        get: function () {
-            for (var _a = 0, _b = this.units; _a < _b.length; _a++) {
-                var u = _b[_a];
-                if (!unit_1.Unit.isAtomic(u))
-                    return false;
-            }
-            return true;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "hasAtomic", {
-        /** Contains some atomic units */
-        get: function () {
-            for (var _a = 0, _b = this.units; _a < _b.length; _a++) {
-                var u = _b[_a];
-                if (unit_1.Unit.isAtomic(u))
-                    return true;
-            }
-            return false;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "isCoarse", {
-        /** Contains only coarse units */
-        get: function () {
-            for (var _a = 0, _b = this.units; _a < _b.length; _a++) {
-                var u = _b[_a];
-                if (!unit_1.Unit.isCoarse(u))
-                    return false;
-            }
-            return true;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "hasCoarse", {
-        /** Contains some coarse units */
-        get: function () {
-            for (var _a = 0, _b = this.units; _a < _b.length; _a++) {
-                var u = _b[_a];
-                if (unit_1.Unit.isCoarse(u))
-                    return true;
-            }
-            return false;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "serialMapping", {
-        /**
-         * Provides mapping for serial element indices accross all units.
-         *
-         * Note that this is especially costly for structures with many units that are grouped
-         * into few symmetry groups. Use only when needed and prefer `StructureElement`
-         * to address elements in a structure.
-         */
-        get: function () {
-            return this.state.serialMapping || (this.state.serialMapping = getSerialMapping(this));
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "model", {
-        /**
-         * If the structure is based on a single model or has a master-/representative-model, return it.
-         * Otherwise throw an exception.
-         */
-        get: function () {
-            if (this.state.model)
-                return this.state.model;
-            if (this.state.representativeModel)
-                return this.state.representativeModel;
-            if (this.state.masterModel)
-                return this.state.masterModel;
-            var models = this.models;
-            if (models.length > 1) {
-                throw new Error('The structure is based on multiple models and has neither a master- nor a representative-model.');
-            }
-            this.state.model = models[0];
-            return this.state.model;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "masterModel", {
-        /** The master-model, other models can have bonds to it  */
-        get: function () {
-            return this.state.masterModel;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "representativeModel", {
-        /** A representative model, e.g. the first model of a trajectory */
-        get: function () {
-            return this.state.representativeModel;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Structure.prototype.hasElement = function (e) {
-        if (!this.unitMap.has(e.unit.id))
-            return false;
-        return int_1.SortedArray.has(this.unitMap.get(e.unit.id).elements, e.element);
-    };
-    Structure.prototype.getModelIndex = function (m) {
-        return this.models.indexOf(m);
-    };
-    Structure.prototype.remapModel = function (m) {
-        var _a = this.state, dynamicBonds = _a.dynamicBonds, interUnitBonds = _a.interUnitBonds, parent = _a.parent;
-        var units = [];
-        for (var _b = 0, _c = this.unitSymmetryGroups; _b < _c.length; _b++) {
-            var ug = _c[_b];
-            var unit = ug.units[0].remapModel(m, dynamicBonds);
-            units.push(unit);
-            for (var i = 1, il = ug.units.length; i < il; ++i) {
-                var u = ug.units[i];
-                units.push(u.remapModel(m, dynamicBonds, unit.props));
-            }
-        }
-        return Structure.create(units, {
-            parent: parent === null || parent === void 0 ? void 0 : parent.remapModel(m),
-            label: this.label,
-            interUnitBonds: dynamicBonds ? undefined : interUnitBonds,
-            dynamicBonds: dynamicBonds
-        });
-    };
-    /**
-     * For `structure` with `parent` this returns a proxy that
-     * targets `parent` and has `structure` attached as a child.
-     */
-    Structure.prototype.asParent = function () {
-        if (this._proxy)
-            return this._proxy;
-        if (this.parent) {
-            var p = this.parent.coordinateSystem.isIdentity ? this.parent : Structure.transform(this.parent, this.parent.coordinateSystem.inverse);
-            var s = this.coordinateSystem.isIdentity ? p : Structure.transform(p, this.coordinateSystem.matrix);
-            this._proxy = new Structure(s.units, s.unitMap, s.unitIndexMap, (0, tslib_1.__assign)((0, tslib_1.__assign)({}, s.state), { dynamicBonds: this.dynamicBonds }), { child: this, target: this.parent });
-        }
-        else {
-            this._proxy = this;
-        }
-        return this._proxy;
-    };
-    Object.defineProperty(Structure.prototype, "child", {
-        get: function () {
-            return this._child;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    Object.defineProperty(Structure.prototype, "target", {
-        /** Get the proxy target. Usefull for equality checks. */
-        get: function () {
-            var _a;
-            return (_a = this._target) !== null && _a !== void 0 ? _a : this;
-        },
-        enumerable: false,
-        configurable: true
-    });
-    return Structure;
-}());
-exports.Structure = Structure;
-function cmpUnits(units, i, j) {
-    return units[i].id - units[j].id;
-}
-function getModels(s) {
-    var units = s.units;
-    var arr = generic_1.UniqueArray.create();
-    for (var _a = 0, units_1 = units; _a < units_1.length; _a++) {
-        var u = units_1[_a];
-        generic_1.UniqueArray.add(arr, u.model.id, u.model);
-    }
-    return arr.array;
-}
-function getUniqueResidueNames(s) {
-    var microheterogeneityCompIds = properties_1.StructureProperties.residue.microheterogeneityCompIds;
-    var names = new Set();
-    var loc = element_1.StructureElement.Location.create(s);
-    for (var _a = 0, _b = s.unitSymmetryGroups; _a < _b.length; _a++) {
-        var unitGroup = _b[_a];
-        var unit = unitGroup.units[0];
-        // TODO: support coarse unit?
-        if (!unit_1.Unit.isAtomic(unit))
-            continue;
-        var residues = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
-        loc.unit = unit;
-        while (residues.hasNext) {
-            var seg = residues.move();
-            loc.element = unit.elements[seg.start];
-            var compIds = microheterogeneityCompIds(loc);
-            for (var _c = 0, compIds_1 = compIds; _c < compIds_1.length; _c++) {
-                var compId = compIds_1[_c];
-                names.add(compId);
-            }
-        }
-    }
-    return names;
-}
-function getUniqueElementSymbols(s) {
-    var prop = properties_1.StructureProperties.atom.type_symbol;
-    var symbols = new Set();
-    var loc = element_1.StructureElement.Location.create(s);
-    for (var _a = 0, _b = s.unitSymmetryGroups; _a < _b.length; _a++) {
-        var unitGroup = _b[_a];
-        var unit = unitGroup.units[0];
-        if (!unit_1.Unit.isAtomic(unit))
-            continue;
-        loc.unit = unit;
-        for (var i = 0, il = unit.elements.length; i < il; ++i) {
-            loc.element = unit.elements[i];
-            symbols.add(prop(loc));
-        }
-    }
-    return symbols;
-}
-function getEntityIndices(structure) {
-    var units = structure.units;
-    var l = element_1.StructureElement.Location.create(structure);
-    var keys = generic_1.UniqueArray.create();
-    for (var _a = 0, units_2 = units; _a < units_2.length; _a++) {
-        var unit = units_2[_a];
-        var prop = unit.kind === 0 /* Atomic */ ? properties_1.StructureProperties.entity.key : properties_1.StructureProperties.coarse.entityKey;
-        l.unit = unit;
-        var elements = unit.elements;
-        var chainsIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
-        while (chainsIt.hasNext) {
-            var chainSegment = chainsIt.move();
-            l.element = elements[chainSegment.start];
-            var key = prop(l);
-            generic_1.UniqueArray.add(keys, key, key);
-        }
-    }
-    (0, util_1.sortArray)(keys.array);
-    return keys.array;
-}
-function getUniqueAtomicResidueIndices(structure) {
-    var map = new Map();
-    var modelIds = [];
-    var unitGroups = structure.unitSymmetryGroups;
-    for (var _a = 0, unitGroups_1 = unitGroups; _a < unitGroups_1.length; _a++) {
-        var unitGroup = unitGroups_1[_a];
-        var unit = unitGroup.units[0];
-        if (!unit_1.Unit.isAtomic(unit))
-            continue;
-        var uniqueResidues = void 0;
-        if (map.has(unit.model.id))
-            uniqueResidues = map.get(unit.model.id);
-        else {
-            uniqueResidues = generic_1.UniqueArray.create();
-            modelIds.push(unit.model.id);
-            map.set(unit.model.id, uniqueResidues);
-        }
-        var residues = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
-        while (residues.hasNext) {
-            var seg = residues.move();
-            generic_1.UniqueArray.add(uniqueResidues, seg.index, seg.index);
-        }
-    }
-    var ret = new Map();
-    for (var _b = 0, modelIds_1 = modelIds; _b < modelIds_1.length; _b++) {
-        var id = modelIds_1[_b];
-        var array = map.get(id).array;
-        (0, util_1.sortArray)(array);
-        ret.set(id, array);
-    }
-    return ret;
-}
-function getUniqueElementCount(structure) {
-    var unitSymmetryGroups = structure.unitSymmetryGroups;
-    var uniqueElementCount = 0;
-    for (var i = 0, _i = unitSymmetryGroups.length; i < _i; i++) {
-        uniqueElementCount += unitSymmetryGroups[i].elements.length;
-    }
-    return uniqueElementCount;
-}
-function getPolymerResidueCount(structure) {
-    var units = structure.units;
-    var polymerResidueCount = 0;
-    for (var i = 0, _i = units.length; i < _i; i++) {
-        polymerResidueCount += units[i].polymerElements.length;
-    }
-    return polymerResidueCount;
-}
-function getPolymerGapCount(structure) {
-    var units = structure.units;
-    var polymerGapCount = 0;
-    for (var i = 0, _i = units.length; i < _i; i++) {
-        polymerGapCount += units[i].gapElements.length / 2;
-    }
-    return polymerGapCount;
-}
-function getPolymerUnitCount(structure) {
-    var units = structure.units;
-    var polymerUnitCount = 0;
-    for (var i = 0, _i = units.length; i < _i; i++) {
-        if (units[i].polymerElements.length > 0)
-            polymerUnitCount += 1;
-    }
-    return polymerUnitCount;
-}
-function getAtomicResidueCount(structure) {
-    var units = structure.units;
-    var atomicResidueCount = 0;
-    for (var i = 0, _i = units.length; i < _i; i++) {
-        var unit = units[i];
-        if (!unit_1.Unit.isAtomic(unit))
-            continue;
-        var elements = unit.elements, residueIndex = unit.residueIndex;
-        var idx = -1;
-        var prevIdx = -1;
-        for (var j = 0, jl = elements.length; j < jl; ++j) {
-            idx = residueIndex[elements[j]];
-            if (idx !== prevIdx) {
-                atomicResidueCount += 1;
-                prevIdx = idx;
-            }
-        }
-    }
-    return atomicResidueCount;
-}
-function getSerialMapping(structure) {
-    var units = structure.units, elementCount = structure.elementCount, unitIndexMap = structure.unitIndexMap;
-    var cumulativeUnitElementCount = new Uint32Array(units.length);
-    var unitIndices = new Uint32Array(elementCount);
-    var elementIndices = new Uint32Array(elementCount);
-    for (var i = 0, m = 0, il = units.length; i < il; ++i) {
-        cumulativeUnitElementCount[i] = m;
-        var elements = units[i].elements;
-        for (var j = 0, jl = elements.length; j < jl; ++j) {
-            var mj = m + j;
-            unitIndices[mj] = i;
-            elementIndices[mj] = elements[j];
-        }
-        m += elements.length;
-    }
-    return {
-        cumulativeUnitElementCount: cumulativeUnitElementCount,
-        unitIndices: unitIndices,
-        elementIndices: elementIndices,
-        getSerialIndex: function (unit, element) { return cumulativeUnitElementCount[unitIndexMap.get(unit.id)] + int_1.OrderedSet.indexOf(unit.elements, element); }
-    };
-}
-(function (Structure) {
-    Structure.Empty = create([]);
-    function Loci(structure) {
-        return { kind: 'structure-loci', structure: structure };
-    }
-    Structure.Loci = Loci;
-    function toStructureElementLoci(structure) {
-        var elements = [];
-        for (var _a = 0, _b = structure.units; _a < _b.length; _a++) {
-            var unit = _b[_a];
-            elements.push({ unit: unit, indices: int_1.Interval.ofBounds(0, unit.elements.length) });
-        }
-        return element_1.StructureElement.Loci(structure, elements);
-    }
-    Structure.toStructureElementLoci = toStructureElementLoci;
-    function toSubStructureElementLoci(parent, structure) {
-        return selection_1.StructureSelection.toLociWithSourceUnits(selection_1.StructureSelection.Singletons(parent, structure));
-    }
-    Structure.toSubStructureElementLoci = toSubStructureElementLoci;
-    function isLoci(x) {
-        return !!x && x.kind === 'structure-loci';
-    }
-    Structure.isLoci = isLoci;
-    function areLociEqual(a, b) {
-        return a.structure === b.structure;
-    }
-    Structure.areLociEqual = areLociEqual;
-    function isLociEmpty(loci) {
-        return loci.structure.isEmpty;
-    }
-    Structure.isLociEmpty = isLociEmpty;
-    function remapLoci(loci, structure) {
-        if (structure === loci.structure)
-            return loci;
-        return Loci(structure);
-    }
-    Structure.remapLoci = remapLoci;
-    function create(units, props) {
-        if (props === void 0) { props = {}; }
-        // init units
-        var unitMap = int_1.IntMap.Mutable();
-        var unitIndexMap = int_1.IntMap.Mutable();
-        var elementCount = 0;
-        var isSorted = true;
-        var lastId = units.length > 0 ? units[0].id : 0;
-        for (var i = 0, _i = units.length; i < _i; i++) {
-            var u = units[i];
-            unitMap.set(u.id, u);
-            elementCount += u.elements.length;
-            if (u.id < lastId)
-                isSorted = false;
-            lastId = u.id;
-        }
-        if (!isSorted)
-            (0, util_1.sort)(units, 0, units.length, cmpUnits, util_1.arraySwap);
-        for (var i = 0, _i = units.length; i < _i; i++) {
-            unitIndexMap.set(units[i].id, i);
-        }
-        // initial state
-        var state = {
-            hashCode: -1,
-            transformHash: -1,
-            elementCount: elementCount,
-            bondCount: -1,
-            uniqueElementCount: -1,
-            atomicResidueCount: -1,
-            polymerResidueCount: -1,
-            polymerGapCount: -1,
-            polymerUnitCount: -1,
-            dynamicBonds: false,
-            coordinateSystem: symmetry_operator_1.SymmetryOperator.Default,
-            label: ''
-        };
-        // handle props
-        if (props.parent)
-            state.parent = props.parent.parent || props.parent;
-        if (props.interUnitBonds)
-            state.interUnitBonds = props.interUnitBonds;
-        if (props.dynamicBonds)
-            state.dynamicBonds = props.dynamicBonds;
-        else if (props.parent)
-            state.dynamicBonds = props.parent.dynamicBonds;
-        if (props.coordinateSystem)
-            state.coordinateSystem = props.coordinateSystem;
-        else if (props.parent)
-            state.coordinateSystem = props.parent.coordinateSystem;
-        if (props.label)
-            state.label = props.label;
-        else if (props.parent)
-            state.label = props.parent.label;
-        if (props.masterModel)
-            state.masterModel = props.masterModel;
-        else if (props.parent)
-            state.masterModel = props.parent.masterModel;
-        if (props.representativeModel)
-            state.representativeModel = props.representativeModel;
-        else if (props.parent)
-            state.representativeModel = props.parent.representativeModel;
-        return new Structure(units, unitMap, unitIndexMap, state);
-    }
-    Structure.create = create;
-    function ofTrajectory(trajectory, ctx) {
-        return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var units, first, count, i, il, frame, structure, j, jl, u, invariantId, chainGroupId, newUnit;
-            return (0, tslib_1.__generator)(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        if (trajectory.frameCount === 0)
-                            return [2 /*return*/, Structure.Empty];
-                        units = [];
-                        first = void 0;
-                        count = 0;
-                        i = 0, il = trajectory.frameCount;
-                        _a.label = 1;
-                    case 1:
-                        if (!(i < il)) return [3 /*break*/, 4];
-                        return [4 /*yield*/, mol_task_1.Task.resolveInContext(trajectory.getFrameAtIndex(i), ctx)];
-                    case 2:
-                        frame = _a.sent();
-                        if (!first)
-                            first = frame;
-                        structure = ofModel(frame);
-                        for (j = 0, jl = structure.units.length; j < jl; ++j) {
-                            u = structure.units[j];
-                            invariantId = u.invariantId + count;
-                            chainGroupId = u.chainGroupId + count;
-                            newUnit = unit_1.Unit.create(units.length, invariantId, chainGroupId, u.traits, u.kind, u.model, u.conformation.operator, u.elements);
-                            units.push(newUnit);
-                        }
-                        count = units.length;
-                        _a.label = 3;
-                    case 3:
-                        ++i;
-                        return [3 /*break*/, 1];
-                    case 4: return [2 /*return*/, create(units, { representativeModel: first, label: first.label })];
-                }
-            });
-        });
-    }
-    Structure.ofTrajectory = ofTrajectory;
-    var PARTITION = false;
-    /**
-     * Construct a Structure from a model.
-     *
-     * Generally, a single unit corresponds to a single chain, with the exception
-     * of consecutive "single atom chains" with same entity_id and same auth_asym_id.
-     */
-    function ofModel(model, props) {
-        if (props === void 0) { props = {}; }
-        var chains = model.atomicHierarchy.chainAtomSegments;
-        var index = model.atomicHierarchy.index;
-        var auth_asym_id = model.atomicHierarchy.chains.auth_asym_id;
-        var atomicChainOperatorMappinng = model.atomicChainOperatorMappinng;
-        var builder = new StructureBuilder((0, tslib_1.__assign)({ label: model.label }, props));
-        for (var c = 0; c < chains.count; c++) {
-            var operator = atomicChainOperatorMappinng.get(c) || symmetry_operator_1.SymmetryOperator.Default;
-            var start = chains.offsets[c];
-            // set to true for chains that consist of "single atom residues",
-            // note that it assumes there are no "zero atom residues"
-            var singleAtomResidues = atomic_1.AtomicHierarchy.chainResidueCount(model.atomicHierarchy, c) === chains.offsets[c + 1] - chains.offsets[c];
-            var multiChain = false;
-            if (isWaterChain(model, c)) {
-                // merge consecutive water chains
-                while (c + 1 < chains.count && isWaterChain(model, c + 1)) {
-                    var op1 = atomicChainOperatorMappinng.get(c);
-                    var op2 = atomicChainOperatorMappinng.get(c + 1);
-                    if (op1 !== op2)
-                        break;
-                    multiChain = true;
-                    c++;
-                }
-            }
-            else {
-                // merge consecutive "single atom chains" with same entity_id and auth_asym_id
-                while (c + 1 < chains.count
-                    && chains.offsets[c + 1] - chains.offsets[c] === 1
-                    && chains.offsets[c + 2] - chains.offsets[c + 1] === 1) {
-                    singleAtomResidues = true;
-                    var e1 = index.getEntityFromChain(c);
-                    var e2 = index.getEntityFromChain(c + 1);
-                    if (e1 !== e2)
-                        break;
-                    var a1 = auth_asym_id.value(c);
-                    var a2 = auth_asym_id.value(c + 1);
-                    if (a1 !== a2)
-                        break;
-                    var op1 = atomicChainOperatorMappinng.get(c);
-                    var op2 = atomicChainOperatorMappinng.get(c + 1);
-                    if (op1 !== op2)
-                        break;
-                    multiChain = true;
-                    c++;
-                }
-            }
-            var elements = int_1.SortedArray.ofBounds(start, chains.offsets[c + 1]);
-            if (PARTITION) {
-                // check for polymer to exclude CA/P-only models
-                if (singleAtomResidues && !isPolymerChain(model, c)) {
-                    partitionAtomicUnitByAtom(model, elements, builder, multiChain, operator);
-                }
-                else if (elements.length > 200000 || isWaterChain(model, c)) {
-                    // split up very large chains e.g. lipid bilayers, micelles or water with explicit H
-                    partitionAtomicUnitByResidue(model, elements, builder, multiChain, operator);
-                }
-                else {
-                    builder.addUnit(0 /* Atomic */, model, operator, elements, multiChain ? 1 /* MultiChain */ : 0 /* None */);
-                }
-            }
-            else {
-                builder.addUnit(0 /* Atomic */, model, operator, elements, multiChain ? 1 /* MultiChain */ : 0 /* None */);
-            }
-        }
-        var cs = model.coarseHierarchy;
-        if (cs.isDefined) {
-            if (cs.spheres.count > 0) {
-                addCoarseUnits(builder, model, model.coarseHierarchy.spheres, 1 /* Spheres */);
-            }
-            if (cs.gaussians.count > 0) {
-                addCoarseUnits(builder, model, model.coarseHierarchy.gaussians, 2 /* Gaussians */);
-            }
-        }
-        return builder.getStructure();
-    }
-    Structure.ofModel = ofModel;
-    function isWaterChain(model, chainIndex) {
-        var e = model.atomicHierarchy.index.getEntityFromChain(chainIndex);
-        return model.entities.data.type.value(e) === 'water';
-    }
-    function isPolymerChain(model, chainIndex) {
-        var e = model.atomicHierarchy.index.getEntityFromChain(chainIndex);
-        return model.entities.data.type.value(e) === 'polymer';
-    }
-    function partitionAtomicUnitByAtom(model, indices, builder, multiChain, operator) {
-        var _a = model.atomicConformation, x = _a.x, y = _a.y, z = _a.z;
-        var position = { x: x, y: y, z: z, indices: indices };
-        var lookup = (0, geometry_1.GridLookup3D)(position, (0, boundary_1.getBoundary)(position), 8192);
-        var _b = lookup.buckets, offset = _b.offset, count = _b.count, array = _b.array;
-        var traits = (multiChain ? 1 /* MultiChain */ : 0 /* None */) | (offset.length > 1 ? 2 /* Partitioned */ : 0 /* None */);
-        builder.beginChainGroup();
-        for (var i = 0, _i = offset.length; i < _i; i++) {
-            var start = offset[i];
-            var set = new Int32Array(count[i]);
-            for (var j = 0, _j = count[i]; j < _j; j++) {
-                set[j] = indices[array[start + j]];
-            }
-            builder.addUnit(0 /* Atomic */, model, operator, int_1.SortedArray.ofSortedArray(set), traits);
-        }
-        builder.endChainGroup();
-    }
-    // keeps atoms of residues together
-    function partitionAtomicUnitByResidue(model, indices, builder, multiChain, operator) {
-        var residueAtomSegments = model.atomicHierarchy.residueAtomSegments;
-        var startIndices = [];
-        var endIndices = [];
-        var residueIt = int_1.Segmentation.transientSegments(residueAtomSegments, indices);
-        while (residueIt.hasNext) {
-            var residueSegment = residueIt.move();
-            startIndices[startIndices.length] = indices[residueSegment.start];
-            endIndices[endIndices.length] = indices[residueSegment.end];
-        }
-        var firstResidueAtomCount = endIndices[0] - startIndices[0];
-        var gridCellCount = 512 * firstResidueAtomCount;
-        var _a = model.atomicConformation, x = _a.x, y = _a.y, z = _a.z;
-        var position = { x: x, y: y, z: z, indices: int_1.SortedArray.ofSortedArray(startIndices) };
-        var lookup = (0, geometry_1.GridLookup3D)(position, (0, boundary_1.getBoundary)(position), gridCellCount);
-        var _b = lookup.buckets, offset = _b.offset, count = _b.count, array = _b.array;
-        var traits = (multiChain ? 1 /* MultiChain */ : 0 /* None */) | (offset.length > 1 ? 2 /* Partitioned */ : 0 /* None */);
-        builder.beginChainGroup();
-        for (var i = 0, _i = offset.length; i < _i; i++) {
-            var start = offset[i];
-            var set = [];
-            for (var j = 0, _j = count[i]; j < _j; j++) {
-                var k = array[start + j];
-                for (var l = startIndices[k], _l = endIndices[k]; l < _l; l++) {
-                    set[set.length] = l;
-                }
-            }
-            builder.addUnit(0 /* Atomic */, model, operator, int_1.SortedArray.ofSortedArray(new Int32Array(set)), traits);
-        }
-        builder.endChainGroup();
-    }
-    function addCoarseUnits(builder, model, elements, kind) {
-        var chainElementSegments = elements.chainElementSegments;
-        for (var cI = 0; cI < chainElementSegments.count; cI++) {
-            var elements_1 = int_1.SortedArray.ofBounds(chainElementSegments.offsets[cI], chainElementSegments.offsets[cI + 1]);
-            builder.addUnit(kind, model, symmetry_operator_1.SymmetryOperator.Default, elements_1, 0 /* None */);
-        }
-    }
-    function transform(s, transform) {
-        if (linear_algebra_1.Mat4.isIdentity(transform))
-            return s;
-        if (!linear_algebra_1.Mat4.isRotationAndTranslation(transform, symmetry_operator_1.SymmetryOperator.RotationTranslationEpsilon))
-            throw new Error('Only rotation/translation combination can be applied.');
-        var units = [];
-        for (var _a = 0, _b = s.units; _a < _b.length; _a++) {
-            var u = _b[_a];
-            var old = u.conformation.operator;
-            var op = symmetry_operator_1.SymmetryOperator.create(old.name, transform, old);
-            units.push(u.applyOperator(u.id, op));
-        }
-        var cs = s.coordinateSystem;
-        var newCS = symmetry_operator_1.SymmetryOperator.compose(symmetry_operator_1.SymmetryOperator.create(cs.name, transform, cs), cs);
-        return create(units, { parent: s, coordinateSystem: newCS });
-    }
-    Structure.transform = transform;
-    var StructureBuilder = /** @class */ (function () {
-        function StructureBuilder(props) {
-            if (props === void 0) { props = {}; }
-            this.props = props;
-            this.units = [];
-            this.invariantId = (0, id_factory_1.idFactory)();
-            this.chainGroupId = -1;
-            this.inChainGroup = false;
-            this.p = (0, linear_algebra_1.Vec3)();
-            this.singleElementUnits = new Map();
-        }
-        StructureBuilder.prototype.beginChainGroup = function () {
-            this.chainGroupId++;
-            this.inChainGroup = true;
-        };
-        StructureBuilder.prototype.endChainGroup = function () {
-            this.inChainGroup = false;
-        };
-        StructureBuilder.prototype.addUnit = function (kind, model, operator, elements, traits, invariantId) {
-            if (invariantId === undefined)
-                invariantId = this.invariantId();
-            var chainGroupId = this.inChainGroup ? this.chainGroupId : ++this.chainGroupId;
-            var unit = unit_1.Unit.create(this.units.length, invariantId, chainGroupId, traits, kind, model, operator, elements);
-            return this.add(unit);
-        };
-        StructureBuilder.prototype.add = function (unit) {
-            // this is to avoid adding many identical single atom units,
-            // for example, from 'degenerate' spacegroups
-            // - Diamond (COD 9008564)
-            if (unit.elements.length === 1) {
-                unit.conformation.position(unit.elements[0], this.p);
-                var hash = [unit.invariantId, this.p[0], this.p[1], this.p[2]].join('|');
-                if (this.singleElementUnits.has(hash)) {
-                    return this.singleElementUnits.get(hash);
-                }
-                else {
-                    this.singleElementUnits.set(hash, unit);
-                }
-            }
-            this.units.push(unit);
-            return unit;
-        };
-        StructureBuilder.prototype.addWithOperator = function (unit, operator, dontCompose) {
-            if (dontCompose === void 0) { dontCompose = false; }
-            return this.add(unit.applyOperator(this.units.length, operator, dontCompose));
-        };
-        StructureBuilder.prototype.getStructure = function () {
-            return create(this.units, this.props);
-        };
-        Object.defineProperty(StructureBuilder.prototype, "isEmpty", {
-            get: function () {
-                return this.units.length === 0;
-            },
-            enumerable: false,
-            configurable: true
-        });
-        return StructureBuilder;
-    }());
-    Structure.StructureBuilder = StructureBuilder;
-    function Builder(props) {
-        if (props === void 0) { props = {}; }
-        return new StructureBuilder(props);
-    }
-    Structure.Builder = Builder;
-    function hashCode(s) {
-        return s.hashCode;
-    }
-    Structure.hashCode = hashCode;
-    /** Hash based on all unit.model conformation values in the structure */
-    function conformationHash(s) {
-        return (0, util_1.hashString)(s.units.map(function (u) { return unit_1.Unit.conformationId(u); }).join('|'));
-    }
-    Structure.conformationHash = conformationHash;
-    // TODO: there should be a version that properly supports partitioned units
-    function areUnitIdsEqual(a, b) {
-        if (a === b)
-            return true;
-        if (a.elementCount !== b.elementCount)
-            return false;
-        var len = a.units.length;
-        if (len !== b.units.length)
-            return false;
-        for (var i = 0; i < len; i++) {
-            if (a.units[i].id !== b.units[i].id)
-                return false;
-        }
-        return true;
-    }
-    Structure.areUnitIdsEqual = areUnitIdsEqual;
-    function areUnitIdsAndIndicesEqual(a, b) {
-        if (!areUnitIdsEqual(a, b))
-            return false;
-        for (var i = 0, il = a.units.length; i < il; i++) {
-            if (!int_1.SortedArray.areEqual(a.units[i].elements, b.units[i].elements))
-                return false;
-        }
-        return true;
-    }
-    Structure.areUnitIdsAndIndicesEqual = areUnitIdsAndIndicesEqual;
-    function areHierarchiesEqual(a, b) {
-        if (a.hashCode !== b.hashCode)
-            return false;
-        var len = a.models.length;
-        if (len !== b.models.length)
-            return false;
-        for (var i = 0; i < len; i++) {
-            if (!model_1.Model.areHierarchiesEqual(a.models[i], b.models[i]))
-                return false;
-        }
-        return true;
-    }
-    Structure.areHierarchiesEqual = areHierarchiesEqual;
-    function areEquivalent(a, b) {
-        return a === b || (a.hashCode === b.hashCode &&
-            symmetry_1.StructureSymmetry.areTransformGroupsEquivalent(a.unitSymmetryGroups, b.unitSymmetryGroups));
-    }
-    Structure.areEquivalent = areEquivalent;
-    /** Check if the structures or their parents are equivalent */
-    function areRootsEquivalent(a, b) {
-        return areEquivalent(a.root, b.root);
-    }
-    Structure.areRootsEquivalent = areRootsEquivalent;
-    /** Check if the structures or their parents are equal */
-    function areRootsEqual(a, b) {
-        return a.root === b.root;
-    }
-    Structure.areRootsEqual = areRootsEqual;
-    var ElementLocationIterator = /** @class */ (function () {
-        function ElementLocationIterator(structure) {
-            this.structure = structure;
-            this.unitIndex = 0;
-            this.maxIdx = 0;
-            this.idx = -1;
-            this.current = element_1.StructureElement.Location.create(structure);
-            this.hasNext = structure.elementCount > 0;
-            if (this.hasNext) {
-                this.elements = structure.units[0].elements;
-                this.maxIdx = this.elements.length - 1;
-                this.current.unit = structure.units[0];
-            }
-        }
-        ElementLocationIterator.prototype.move = function () {
-            this.advance();
-            this.current.element = this.elements[this.idx];
-            return this.current;
-        };
-        ElementLocationIterator.prototype.advance = function () {
-            if (this.idx < this.maxIdx) {
-                this.idx++;
-                if (this.idx === this.maxIdx)
-                    this.hasNext = this.unitIndex + 1 < this.structure.units.length;
-                return;
-            }
-            this.idx = 0;
-            this.unitIndex++;
-            if (this.unitIndex >= this.structure.units.length) {
-                this.hasNext = false;
-                return;
-            }
-            this.current.unit = this.structure.units[this.unitIndex];
-            this.elements = this.current.unit.elements;
-            this.maxIdx = this.elements.length - 1;
-            if (this.maxIdx === 0) {
-                this.hasNext = this.unitIndex + 1 < this.structure.units.length;
-            }
-        };
-        return ElementLocationIterator;
-    }());
-    Structure.ElementLocationIterator = ElementLocationIterator;
-    var distVec = (0, linear_algebra_1.Vec3)();
-    function unitElementMinDistance(unit, p, eRadius) {
-        var elements = unit.elements, _a = unit.conformation, position = _a.position, r = _a.r, dV = distVec;
-        var minD = Number.MAX_VALUE;
-        for (var i = 0, _i = elements.length; i < _i; i++) {
-            var e = elements[i];
-            var d = linear_algebra_1.Vec3.distance(p, position(e, dV)) - eRadius - r(e);
-            if (d < minD)
-                minD = d;
-        }
-        return minD;
-    }
-    function minDistanceToPoint(s, point, radius) {
-        var units = s.units;
-        var minD = Number.MAX_VALUE;
-        for (var i = 0, _i = units.length; i < _i; i++) {
-            var unit = units[i];
-            var d = unitElementMinDistance(unit, point, radius);
-            if (d < minD)
-                minD = d;
-        }
-        return minD;
-    }
-    Structure.minDistanceToPoint = minDistanceToPoint;
-    var distPivot = (0, linear_algebra_1.Vec3)();
-    function distance(a, b) {
-        if (a.elementCount === 0 || b.elementCount === 0)
-            return 0;
-        var units = a.units;
-        var minD = Number.MAX_VALUE;
-        for (var i = 0, _i = units.length; i < _i; i++) {
-            var unit = units[i];
-            var elements = unit.elements, _a = unit.conformation, position = _a.position, r = _a.r;
-            for (var i_1 = 0, _i_1 = elements.length; i_1 < _i_1; i_1++) {
-                var e = elements[i_1];
-                var d = minDistanceToPoint(b, position(e, distPivot), r(e));
-                if (d < minD)
-                    minD = d;
-            }
-        }
-        return minD;
-    }
-    Structure.distance = distance;
-    function elementDescription(s) {
-        return s.elementCount === 1 ? '1 element' : "".concat(s.elementCount, " elements");
-    }
-    Structure.elementDescription = elementDescription;
-    function validUnitPair(s, a, b) {
-        return s.masterModel
-            ? a.model === b.model || a.model === s.masterModel || b.model === s.masterModel
-            : a.model === b.model;
-    }
-    Structure.validUnitPair = validUnitPair;
-    /**
-     * Iterate over all unit pairs of a structure and invokes callback for valid units
-     * and unit pairs if within a max distance.
-     */
-    function eachUnitPair(structure, callback, props) {
-        var maxRadius = props.maxRadius, validUnit = props.validUnit, validUnitPair = props.validUnitPair;
-        if (!structure.units.some(function (u) { return validUnit(u); }))
-            return;
-        var lookup = structure.lookup3d;
-        var imageCenter = (0, linear_algebra_1.Vec3)();
-        for (var _a = 0, _b = structure.units; _a < _b.length; _a++) {
-            var unit = _b[_a];
-            if (!validUnit(unit))
-                continue;
-            var bs = unit.boundary.sphere;
-            linear_algebra_1.Vec3.transformMat4(imageCenter, bs.center, unit.conformation.operator.matrix);
-            var closeUnits = lookup.findUnitIndices(imageCenter[0], imageCenter[1], imageCenter[2], bs.radius + maxRadius);
-            for (var i = 0; i < closeUnits.count; i++) {
-                var other = structure.units[closeUnits.indices[i]];
-                if (!validUnit(other) || unit.id >= other.id || !validUnitPair(unit, other))
-                    continue;
-                if (other.elements.length >= unit.elements.length)
-                    callback(unit, other);
-                else
-                    callback(other, unit);
-            }
-        }
-    }
-    Structure.eachUnitPair = eachUnitPair;
-    ;
-    function eachAtomicHierarchyElement(structure, _a) {
-        var chain = _a.chain, residue = _a.residue, atom = _a.atom;
-        var l = element_1.StructureElement.Location.create(structure);
-        for (var _b = 0, _c = structure.units; _b < _c.length; _b++) {
-            var unit = _c[_b];
-            if (unit.kind !== 0 /* Atomic */)
-                continue;
-            l.unit = unit;
-            var elements = unit.elements;
-            var chainsIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
-            var residuesIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
-            while (chainsIt.hasNext) {
-                var chainSegment = chainsIt.move();
-                if (chain) {
-                    l.element = elements[chainSegment.start];
-                    chain(l);
-                }
-                if (!residue && !atom)
-                    continue;
-                residuesIt.setSegment(chainSegment);
-                while (residuesIt.hasNext) {
-                    var residueSegment = residuesIt.move();
-                    if (residue) {
-                        l.element = elements[residueSegment.start];
-                        residue(l);
-                    }
-                    if (!atom)
-                        continue;
-                    for (var j = residueSegment.start, _j = residueSegment.end; j < _j; j++) {
-                        l.element = elements[j];
-                        atom(l);
-                    }
-                }
-            }
-        }
-    }
-    Structure.eachAtomicHierarchyElement = eachAtomicHierarchyElement;
-    //
-    Structure.DefaultSizeThresholds = {
-        /** Must be lower to be small */
-        smallResidueCount: 10,
-        /** Must be lower to be medium */
-        mediumResidueCount: 5000,
-        /** Must be lower to be large (big ribosomes like 4UG0 should still be `large`) */
-        largeResidueCount: 30000,
-        /**
-         * Structures above `largeResidueCount` are consider huge when they have
-         * a `highSymmetryUnitCount` or gigantic when not
-         */
-        highSymmetryUnitCount: 10,
-        /** Fiber-like structure are consider small when below this */
-        fiberResidueCount: 15,
-    };
-    function getPolymerSymmetryGroups(structure) {
-        return structure.unitSymmetryGroups.filter(function (ug) { return ug.units[0].polymerElements.length > 0; });
-    }
-    /**
-     * Try to match fiber-like structures like 6nk4
-     */
-    function isFiberLike(structure, thresholds) {
-        var polymerSymmetryGroups = getPolymerSymmetryGroups(structure);
-        return (polymerSymmetryGroups.length === 1 &&
-            polymerSymmetryGroups[0].units.length > 2 &&
-            polymerSymmetryGroups[0].units[0].polymerElements.length < thresholds.fiberResidueCount);
-    }
-    function hasHighSymmetry(structure, thresholds) {
-        var polymerSymmetryGroups = getPolymerSymmetryGroups(structure);
-        return (polymerSymmetryGroups.length >= 1 &&
-            polymerSymmetryGroups[0].units.length > thresholds.highSymmetryUnitCount);
-    }
-    var Size;
-    (function (Size) {
-        Size[Size["Small"] = 0] = "Small";
-        Size[Size["Medium"] = 1] = "Medium";
-        Size[Size["Large"] = 2] = "Large";
-        Size[Size["Huge"] = 3] = "Huge";
-        Size[Size["Gigantic"] = 4] = "Gigantic";
-    })(Size = Structure.Size || (Structure.Size = {}));
-    /**
-     * @param residueCountFactor - modifies the threshold counts, useful when estimating
-     *                             the size of a structure comprised of multiple models
-     */
-    function getSize(structure, thresholds, residueCountFactor) {
-        if (thresholds === void 0) { thresholds = {}; }
-        if (residueCountFactor === void 0) { residueCountFactor = 1; }
-        var t = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, Structure.DefaultSizeThresholds), thresholds);
-        if (structure.polymerResidueCount >= t.largeResidueCount * residueCountFactor) {
-            if (hasHighSymmetry(structure, t)) {
-                return Size.Huge;
-            }
-            else {
-                return Size.Gigantic;
-            }
-        }
-        else if (isFiberLike(structure, t)) {
-            return Size.Small;
-        }
-        else if (structure.polymerResidueCount < t.smallResidueCount * residueCountFactor) {
-            return Size.Small;
-        }
-        else if (structure.polymerResidueCount < t.mediumResidueCount * residueCountFactor) {
-            return Size.Medium;
-        }
-        else {
-            return Size.Large;
-        }
-    }
-    Structure.getSize = getSize;
-    Structure.Index = custom_structure_property_1.CustomStructureProperty.createSimple('index', 'root');
-    var PrincipalAxesProp = '__PrincipalAxes__';
-    function getPrincipalAxes(structure) {
-        if (structure.currentPropertyData[PrincipalAxesProp])
-            return structure.currentPropertyData[PrincipalAxesProp];
-        var principalAxes = element_1.StructureElement.Loci.getPrincipalAxes(Structure.toStructureElementLoci(structure));
-        structure.currentPropertyData[PrincipalAxesProp] = principalAxes;
-        return principalAxes;
-    }
-    Structure.getPrincipalAxes = getPrincipalAxes;
-})(Structure || (Structure = {}));
-exports.Structure = Structure;
-//# sourceMappingURL=structure.js.map