molstar 3.0.0 → 3.0.1

package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-index.js

@@ -1,229 +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.getAtomicIndex = void 0;
-var int_1 = require("../../../../../mol-data/int");
-var hierarchy_1 = require("../atomic/hierarchy");
-var util_1 = require("../../../../../mol-data/util");
-function getResidueId(seq_id, ins_code) {
-    if (!ins_code)
-        return seq_id;
-    if (ins_code.length === 1)
-        return (0, util_1.cantorPairing)(ins_code.charCodeAt(0), seq_id);
-    if (ins_code.length === 2)
-        return (0, util_1.cantorPairing)(ins_code.charCodeAt(0), (0, util_1.cantorPairing)(ins_code.charCodeAt(1), seq_id));
-    return "".concat(seq_id, " ").concat(ins_code);
-}
-function updateMapMapIndex(map, key0, key1, index) {
-    if (map.has(key0)) {
-        var submap = map.get(key0);
-        if (!submap.has(key1)) {
-            submap.set(key1, index);
-        }
-    }
-    else {
-        var submap = new Map();
-        map.set(key0, submap);
-        submap.set(key1, index);
-    }
-}
-function missingEntity(k) {
-    throw new Error("Missing entity entry for entity id '".concat(k, "'."));
-}
-function createMapping(entities, data, segments) {
-    return {
-        entities: entities,
-        segments: segments,
-        label_seq_id: int_1.SortedArray.ofSortedArray(data.residues.label_seq_id.toArray({ array: Int32Array })),
-        label_atom_id: data.atoms.label_atom_id,
-        auth_atom_id: data.atoms.auth_atom_id,
-        label_alt_id: data.atoms.label_alt_id,
-        type_symbol: data.atoms.type_symbol,
-        chain_index_entity_index: new Int32Array(data.chains._rowCount),
-        entity_index_label_asym_id: new Map(),
-        chain_index_label_seq_id: new Map(),
-        auth_asym_id_auth_seq_id: new Map(),
-        chain_index_auth_seq_id: new Map(),
-        label_asym_id: new Map(),
-    };
-}
-var _tempResidueKey = hierarchy_1.AtomicIndex.EmptyResidueKey();
-var Index = /** @class */ (function () {
-    function Index(map) {
-        this.map = map;
-        this.entityIndex = map.entities.getEntityIndex;
-        this.residueOffsets = this.map.segments.residueAtomSegments.offsets;
-    }
-    Index.prototype.getEntityFromChain = function (cI) {
-        return this.map.chain_index_entity_index[cI];
-    };
-    Index.prototype.findEntity = function (label_asym_id) {
-        var entityIndex = this.map.label_asym_id.get(label_asym_id);
-        return entityIndex !== undefined ? entityIndex : -1;
-    };
-    Index.prototype.findChainLabel = function (key) {
-        var eI = this.entityIndex(key.label_entity_id);
-        if (eI < 0 || !this.map.entity_index_label_asym_id.has(eI))
-            return -1;
-        var cm = this.map.entity_index_label_asym_id.get(eI);
-        if (!cm)
-            return -1;
-        return cm.has(key.label_asym_id) ? cm.get(key.label_asym_id) : -1;
-    };
-    Index.prototype.findChainAuth = function (key) {
-        if (!this.map.auth_asym_id_auth_seq_id.has(key.auth_asym_id))
-            return -1;
-        var rm = this.map.auth_asym_id_auth_seq_id.get(key.auth_asym_id);
-        return rm.has(key.auth_seq_id) ? rm.get(key.auth_seq_id) : -1;
-    };
-    Index.prototype.findResidue = function (label_entity_id_or_key, label_asym_id, auth_seq_id, pdbx_PDB_ins_code) {
-        var key;
-        if (arguments.length === 1) {
-            key = label_entity_id_or_key;
-        }
-        else {
-            _tempResidueKey.label_entity_id = label_entity_id_or_key;
-            _tempResidueKey.label_asym_id = label_asym_id;
-            _tempResidueKey.auth_seq_id = auth_seq_id;
-            _tempResidueKey.pdbx_PDB_ins_code = pdbx_PDB_ins_code;
-            key = _tempResidueKey;
-        }
-        var cI = this.findChainLabel(key);
-        if (cI < 0)
-            return -1;
-        var rm = this.map.chain_index_auth_seq_id.get(cI);
-        var id = getResidueId(key.auth_seq_id, key.pdbx_PDB_ins_code || '');
-        return rm.has(id) ? rm.get(id) : -1;
-    };
-    Index.prototype.findResidueAuth = function (key) {
-        var cI = this.findChainAuth(key);
-        if (cI < 0)
-            return -1;
-        var rm = this.map.chain_index_auth_seq_id.get(cI);
-        var id = getResidueId(key.auth_seq_id, key.pdbx_PDB_ins_code || '');
-        return rm.has(id) ? rm.get(id) : -1;
-    };
-    Index.prototype.findResidueInsertion = function (key) {
-        var cI = this.findChainLabel(key);
-        if (cI < 0)
-            return -1;
-        var rm = this.map.chain_index_label_seq_id.get(cI);
-        var id = getResidueId(key.label_seq_id, key.pdbx_PDB_ins_code || '');
-        if (rm.has(id))
-            return rm.get(id);
-        var idx = int_1.SortedArray.findPredecessorIndex(this.map.label_seq_id, key.label_seq_id);
-        var start = hierarchy_1.AtomicHierarchy.chainStartResidueIndex(this.map.segments, cI);
-        if (idx < start)
-            return start;
-        var end = hierarchy_1.AtomicHierarchy.chainEndResidueIndexExcl(this.map.segments, cI) - 1;
-        if (idx >= end)
-            return end;
-        return idx;
-    };
-    Index.prototype.findAtom = function (key) {
-        var rI = this.findResidue(key);
-        if (rI < 0)
-            return -1;
-        if (typeof key.label_alt_id === 'undefined') {
-            return findAtomByName(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.label_atom_id, key.label_atom_id);
-        }
-        return findAtomByNameAndAltLoc(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.label_atom_id, this.map.label_alt_id, key.label_atom_id, key.label_alt_id);
-    };
-    Index.prototype.findAtomAuth = function (key) {
-        var rI = this.findResidueAuth(key);
-        if (rI < 0)
-            return -1;
-        if (typeof key.label_alt_id === 'undefined') {
-            return findAtomByName(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.auth_atom_id, key.auth_atom_id);
-        }
-        return findAtomByNameAndAltLoc(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.auth_atom_id, this.map.label_alt_id, key.auth_atom_id, key.label_alt_id);
-    };
-    Index.prototype.findAtomOnResidue = function (rI, label_atom_id, label_alt_id) {
-        if (typeof label_alt_id === 'undefined') {
-            return findAtomByName(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.label_atom_id, label_atom_id);
-        }
-        return findAtomByNameAndAltLoc(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.label_atom_id, this.map.label_alt_id, label_atom_id, label_alt_id);
-    };
-    Index.prototype.findAtomsOnResidue = function (rI, label_atom_ids) {
-        return findAtomByNames(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.label_atom_id, label_atom_ids);
-    };
-    Index.prototype.findElementOnResidue = function (rI, type_symbol) {
-        return findAtomByElement(this.residueOffsets[rI], this.residueOffsets[rI + 1], this.map.type_symbol, type_symbol);
-    };
-    return Index;
-}());
-function findAtomByName(start, end, data, atomName) {
-    for (var i = start; i < end; i++) {
-        if (data.value(i) === atomName)
-            return i;
-    }
-    return -1;
-}
-function findAtomByNames(start, end, data, atomNames) {
-    for (var i = start; i < end; i++) {
-        if (atomNames.has(data.value(i)))
-            return i;
-    }
-    return -1;
-}
-function findAtomByNameAndAltLoc(start, end, nameData, altLocData, atomName, altLoc) {
-    for (var i = start; i < end; i++) {
-        if (nameData.value(i) === atomName && altLocData.value(i) === altLoc)
-            return i;
-    }
-    return -1;
-}
-function findAtomByElement(start, end, data, typeSymbol) {
-    for (var i = start; i < end; i++) {
-        if (data.value(i) === typeSymbol)
-            return i;
-    }
-    return -1;
-}
-function getAtomicIndex(data, entities, segments) {
-    var map = createMapping(entities, data, segments);
-    var _a = data.residues, label_seq_id = _a.label_seq_id, auth_seq_id = _a.auth_seq_id, pdbx_PDB_ins_code = _a.pdbx_PDB_ins_code;
-    var _b = data.chains, label_entity_id = _b.label_entity_id, label_asym_id = _b.label_asym_id, auth_asym_id = _b.auth_asym_id;
-    var atomSet = int_1.Interval.ofBounds(0, data.atoms._rowCount);
-    var chainsIt = int_1.Segmentation.transientSegments(segments.chainAtomSegments, atomSet);
-    while (chainsIt.hasNext) {
-        var chainSegment = chainsIt.move();
-        var chainIndex = chainSegment.index;
-        var entityIndex = entities.getEntityIndex(label_entity_id.value(chainIndex));
-        if (entityIndex < 0)
-            missingEntity(label_entity_id.value(chainIndex));
-        map.chain_index_entity_index[chainIndex] = entityIndex;
-        var authAsymId = auth_asym_id.value(chainIndex);
-        var auth_asym_id_auth_seq_id = map.auth_asym_id_auth_seq_id.get(authAsymId);
-        if (!auth_asym_id_auth_seq_id) {
-            auth_asym_id_auth_seq_id = new Map();
-            map.auth_asym_id_auth_seq_id.set(authAsymId, auth_asym_id_auth_seq_id);
-        }
-        var labelAsymId = label_asym_id.value(chainIndex);
-        if (!map.label_asym_id.has(labelAsymId))
-            map.label_asym_id.set(labelAsymId, entityIndex);
-        updateMapMapIndex(map.entity_index_label_asym_id, entityIndex, labelAsymId, chainIndex);
-        var chain_index_label_seq_id = new Map();
-        var chain_index_auth_seq_id = new Map();
-        map.chain_index_label_seq_id.set(chainIndex, chain_index_label_seq_id);
-        map.chain_index_auth_seq_id.set(chainIndex, chain_index_auth_seq_id);
-        var residuesIt = int_1.Segmentation.transientSegments(segments.residueAtomSegments, atomSet, chainSegment);
-        while (residuesIt.hasNext) {
-            var residueSegment = residuesIt.move();
-            var rI = residueSegment.index;
-            var authSeqId = auth_seq_id.value(rI);
-            var insCode = pdbx_PDB_ins_code.value(rI);
-            chain_index_label_seq_id.set(getResidueId(label_seq_id.value(rI), insCode), rI);
-            chain_index_auth_seq_id.set(getResidueId(authSeqId, insCode), rI);
-            auth_asym_id_auth_seq_id.set(authSeqId, chainIndex);
-        }
-    }
-    return new Index(map);
-}
-exports.getAtomicIndex = getAtomicIndex;
-//# sourceMappingURL=atomic-index.js.map

package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-ranges.js

@@ -1,117 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2018-2019 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.getAtomicRanges = void 0;
-var int_1 = require("../../../../../mol-data/int");
-var sorted_ranges_1 = require("../../../../../mol-data/int/sorted-ranges");
-var types_1 = require("../../types");
-var util_1 = require("../../../util");
-var linear_algebra_1 = require("../../../../../mol-math/linear-algebra");
-function areBackboneConnected(riStart, riEnd, conformation, index, derived) {
-    var _a = derived.residue, polymerType = _a.polymerType, traceElementIndex = _a.traceElementIndex, directionFromElementIndex = _a.directionFromElementIndex, directionToElementIndex = _a.directionToElementIndex;
-    var ptStart = polymerType[riStart];
-    var ptEnd = polymerType[riEnd];
-    if (ptStart === 0 /* NA */ || ptEnd === 0 /* NA */)
-        return false;
-    if (traceElementIndex[riStart] === -1 || traceElementIndex[riEnd] === -1)
-        return false;
-    var eiStart = index.findAtomsOnResidue(riStart, (0, util_1.getAtomIdForAtomRole)(ptStart, 'backboneStart'));
-    var eiEnd = index.findAtomsOnResidue(riEnd, (0, util_1.getAtomIdForAtomRole)(ptEnd, 'backboneEnd'));
-    if (eiStart === -1 || eiEnd === -1) {
-        eiStart = index.findAtomsOnResidue(riStart, (0, util_1.getAtomIdForAtomRole)(ptStart, 'coarseBackbone'));
-        eiEnd = index.findAtomsOnResidue(riEnd, (0, util_1.getAtomIdForAtomRole)(ptEnd, 'coarseBackbone'));
-    }
-    var x = conformation.x, y = conformation.y, z = conformation.z;
-    var pStart = linear_algebra_1.Vec3.create(x[eiStart], y[eiStart], z[eiStart]);
-    var pEnd = linear_algebra_1.Vec3.create(x[eiEnd], y[eiEnd], z[eiEnd]);
-    var isCoarse = directionFromElementIndex[riStart] === -1 || directionToElementIndex[riStart] === -1 || directionFromElementIndex[riEnd] === -1 || directionToElementIndex[riEnd] === -1;
-    return linear_algebra_1.Vec3.distance(pStart, pEnd) < (isCoarse ? 10 : 3);
-}
-function getAtomicRanges(hierarchy, entities, conformation, sequence) {
-    var polymerRanges = [];
-    var gapRanges = [];
-    var cyclicPolymerMap = new Map();
-    var chainIt = int_1.Segmentation.transientSegments(hierarchy.chainAtomSegments, int_1.Interval.ofBounds(0, hierarchy.atoms._rowCount));
-    var residueIt = int_1.Segmentation.transientSegments(hierarchy.residueAtomSegments, int_1.Interval.ofBounds(0, hierarchy.atoms._rowCount));
-    var index = hierarchy.index, derived = hierarchy.derived;
-    var label_seq_id = hierarchy.residues.label_seq_id;
-    var label_entity_id = hierarchy.chains.label_entity_id;
-    var _a = derived.residue, moleculeType = _a.moleculeType, traceElementIndex = _a.traceElementIndex;
-    var prevSeqId;
-    var prevStart;
-    var prevEnd;
-    var startIndex;
-    while (chainIt.hasNext) {
-        var chainSegment = chainIt.move();
-        residueIt.setSegment(chainSegment);
-        prevSeqId = -1;
-        prevStart = -1;
-        prevEnd = -1;
-        startIndex = -1;
-        var eI = entities.getEntityIndex(label_entity_id.value(chainSegment.index));
-        var seq = sequence.byEntityKey[eI];
-        var maxSeqId = seq ? seq.sequence.seqId.value(seq.sequence.seqId.rowCount - 1) : -1;
-        // check cyclic peptides, seqIds and distance must be compatible
-        var riStart = hierarchy.residueAtomSegments.index[chainSegment.start];
-        var riEnd = hierarchy.residueAtomSegments.index[chainSegment.end - 1];
-        var seqIdStart = label_seq_id.value(riStart);
-        var seqIdEnd = label_seq_id.value(riEnd);
-        if (seqIdStart === 1 && seqIdEnd === maxSeqId && conformation.xyzDefined && areBackboneConnected(riStart, riEnd, conformation, index, derived)) {
-            cyclicPolymerMap.set(riStart, riEnd);
-            cyclicPolymerMap.set(riEnd, riStart);
-        }
-        while (residueIt.hasNext) {
-            var residueSegment = residueIt.move();
-            var residueIndex = residueSegment.index;
-            var seqId = label_seq_id.value(residueIndex);
-            // treat polymers residues that don't have a trace element resolved as gaps
-            if ((0, types_1.isPolymer)(moleculeType[residueIndex]) && traceElementIndex[residueIndex] !== -1) {
-                if (startIndex !== -1) {
-                    if (seqId !== prevSeqId + 1) {
-                        polymerRanges.push(startIndex, prevEnd - 1);
-                        gapRanges.push(prevStart, residueSegment.end - 1);
-                        startIndex = residueSegment.start;
-                    }
-                    else if (!residueIt.hasNext) {
-                        polymerRanges.push(startIndex, residueSegment.end - 1);
-                        // TODO store terminal gaps
-                    }
-                    else {
-                        var riStart_1 = hierarchy.residueAtomSegments.index[residueSegment.start];
-                        var riEnd_1 = hierarchy.residueAtomSegments.index[prevEnd - 1];
-                        if (conformation.xyzDefined && !areBackboneConnected(riStart_1, riEnd_1, conformation, hierarchy.index, derived)) {
-                            polymerRanges.push(startIndex, prevEnd - 1);
-                            // add gap even for consecutive residues if they are not connected
-                            gapRanges.push(prevStart, residueSegment.end - 1);
-                            startIndex = residueSegment.start;
-                        }
-                    }
-                }
-                else {
-                    startIndex = residueSegment.start; // start polymer
-                    // TODO store terminal gaps
-                }
-            }
-            else {
-                if (startIndex !== -1) {
-                    polymerRanges.push(startIndex, prevEnd - 1);
-                    startIndex = -1;
-                }
-            }
-            prevStart = residueSegment.start;
-            prevEnd = residueSegment.end;
-            prevSeqId = seqId;
-        }
-    }
-    return {
-        polymerRanges: sorted_ranges_1.SortedRanges.ofSortedRanges(polymerRanges),
-        gapRanges: sorted_ranges_1.SortedRanges.ofSortedRanges(gapRanges),
-        cyclicPolymerMap: cyclicPolymerMap
-    };
-}
-exports.getAtomicRanges = getAtomicRanges;
-//# sourceMappingURL=atomic-ranges.js.map

package/lib/commonjs/mol-model/structure/model/properties/utils/coarse-keys.js

@@ -1,97 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2017-2018 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.getCoarseKeys = void 0;
-var sorted_ranges_1 = require("../../../../../mol-data/int/sorted-ranges");
-var int_1 = require("../../../../../mol-data/int");
-function getElementKey(map, key, counter) {
-    if (map.has(key))
-        return map.get(key);
-    var ret = counter.index++;
-    map.set(key, ret);
-    return ret;
-}
-function getElementSubstructureKeyMap(map, key) {
-    if (map.has(key))
-        return map.get(key);
-    var ret = new Map();
-    map.set(key, ret);
-    return ret;
-}
-function createLookUp(entities, chain, seq) {
-    var getEntKey = entities.getEntityIndex;
-    var findChainKey = function (e, c) {
-        var eKey = getEntKey(e);
-        if (eKey < 0)
-            return -1;
-        var cm = chain.get(eKey);
-        if (!cm.has(c))
-            return -1;
-        return cm.get(c);
-    };
-    var findSequenceKey = function (e, c, s) {
-        var eKey = getEntKey(e);
-        if (eKey < 0)
-            return -1;
-        var cm = chain.get(eKey);
-        if (cm === undefined)
-            return -1;
-        var cKey = cm.get(c);
-        if (cKey === undefined)
-            return -1;
-        var sm = seq.get(cKey);
-        var elementIndices = sm.elementIndices, seqRanges = sm.seqRanges;
-        var idx = sorted_ranges_1.SortedRanges.firstIntersectionIndex(seqRanges, int_1.OrderedSet.ofSingleton(s));
-        return (idx !== -1 ? elementIndices[idx] : -1);
-    };
-    return { findChainKey: findChainKey, findSequenceKey: findSequenceKey };
-}
-function missingEntity(k) {
-    throw new Error("Missing entity entry for entity id '".concat(k, "'."));
-}
-function getCoarseKeys(data, entities) {
-    var entity_id = data.entity_id, asym_id = data.asym_id, seq_id_begin = data.seq_id_begin, seq_id_end = data.seq_id_end, count = data.count, chainElementSegments = data.chainElementSegments;
-    var seqMaps = new Map();
-    var chainMaps = new Map(), chainCounter = { index: 0 };
-    var chainKey = new Int32Array(count);
-    var entityKey = new Int32Array(count);
-    var chainToEntity = new Int32Array(chainElementSegments.count);
-    for (var i = 0; i < count; i++) {
-        entityKey[i] = entities.getEntityIndex(entity_id.value(i));
-        if (entityKey[i] < 0)
-            missingEntity(entity_id.value(i));
-    }
-    for (var cI = 0; cI < chainElementSegments.count; cI++) {
-        var start = chainElementSegments.offsets[cI];
-        var end = chainElementSegments.offsets[cI + 1];
-        var eK = entityKey[start];
-        chainToEntity[cI] = eK;
-        var map = getElementSubstructureKeyMap(chainMaps, eK);
-        var key = getElementKey(map, asym_id.value(start), chainCounter);
-        for (var i = start; i < end; i++)
-            chainKey[i] = key;
-        // create seq_id map for the ranges defined by seq_id_begin and seq_id_end
-        var elementIndices = [];
-        var seqRanges = [];
-        for (var i = start; i < end; i++) {
-            var seqStart = seq_id_begin.value(i);
-            var seqEnd = seq_id_end.value(i);
-            elementIndices.push(i);
-            seqRanges.push(seqStart, seqEnd);
-        }
-        var seqMap = { elementIndices: elementIndices, seqRanges: sorted_ranges_1.SortedRanges.ofSortedRanges(seqRanges) };
-        seqMaps.set(key, seqMap);
-    }
-    var _a = createLookUp(entities, chainMaps, seqMaps), findChainKey = _a.findChainKey, findSequenceKey = _a.findSequenceKey;
-    var getEntityFromChain = function (c) {
-        return chainToEntity[c];
-    };
-    return { chainKey: chainKey, entityKey: entityKey, findSequenceKey: findSequenceKey, findChainKey: findChainKey, getEntityFromChain: getEntityFromChain };
-}
-exports.getCoarseKeys = getCoarseKeys;
-//# sourceMappingURL=coarse-keys.js.map

package/lib/commonjs/mol-model/structure/model/properties/utils/residue-set.js

@@ -1,98 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.ResidueSet = void 0;
-var properties_1 = require("../../../structure/properties");
-var ResidueSet = /** @class */ (function () {
-    function ResidueSet(options) {
-        var _a;
-        this.index = new Map();
-        this.checkOperator = false;
-        this.checkOperator = (_a = options === null || options === void 0 ? void 0 : options.checkOperator) !== null && _a !== void 0 ? _a : false;
-    }
-    ResidueSet.prototype.add = function (entry) {
-        var root = this.index.get(entry.label_asym_id);
-        if (!root) {
-            root = new Map();
-            this.index.set(entry.label_asym_id, root);
-        }
-        var entries = root.get(entry.label_seq_id);
-        if (!entries) {
-            entries = [];
-            root.set(entry.label_seq_id, entries);
-        }
-        var exists = this._find(entry, entries);
-        if (!exists) {
-            entries.push(entry);
-            return true;
-        }
-        return false;
-    };
-    ResidueSet.prototype.hasLabelAsymId = function (asym_id) {
-        return this.index.has(asym_id);
-    };
-    ResidueSet.prototype.has = function (loc) {
-        var _a, _b;
-        var asym_id = _asym_id(loc);
-        if (!this.index.has(asym_id))
-            return;
-        var root = this.index.get(asym_id);
-        var seq_id = _seq_id(loc);
-        if (!root.has(seq_id))
-            return;
-        var entries = root.get(seq_id);
-        var comp_id = _comp_id(loc);
-        var alt_id = _alt_id(loc);
-        var ins_code = _ins_code(loc);
-        var op_name = (_a = _op_name(loc)) !== null && _a !== void 0 ? _a : '1_555';
-        for (var _i = 0, entries_1 = entries; _i < entries_1.length; _i++) {
-            var e = entries_1[_i];
-            if (e.label_comp_id !== comp_id || e.label_alt_id !== alt_id || e.ins_code !== ins_code)
-                continue;
-            if (this.checkOperator && ((_b = e.operator_name) !== null && _b !== void 0 ? _b : '1_555') !== op_name)
-                continue;
-            return e;
-        }
-    };
-    ResidueSet.getLabel = function (entry, checkOperator) {
-        var _a;
-        if (checkOperator === void 0) { checkOperator = false; }
-        return "".concat(entry.label_asym_id, " ").concat(entry.label_comp_id, " ").concat(entry.label_seq_id, ":").concat(entry.ins_code, ":").concat(entry.label_alt_id).concat(checkOperator ? ' ' + ((_a = entry.operator_name) !== null && _a !== void 0 ? _a : '1_555') : '');
-    };
-    ResidueSet.getEntryFromLocation = function (loc) {
-        var _a;
-        return {
-            label_asym_id: _asym_id(loc),
-            label_comp_id: _comp_id(loc),
-            label_seq_id: _seq_id(loc),
-            label_alt_id: _alt_id(loc),
-            ins_code: _ins_code(loc),
-            operator_name: (_a = _op_name(loc)) !== null && _a !== void 0 ? _a : '1_555'
-        };
-    };
-    ResidueSet.prototype._find = function (entry, xs) {
-        var _a, _b;
-        for (var _i = 0, xs_1 = xs; _i < xs_1.length; _i++) {
-            var e = xs_1[_i];
-            if (e.label_comp_id !== entry.label_comp_id || e.label_alt_id !== entry.label_alt_id || e.ins_code !== entry.ins_code)
-                continue;
-            if (this.checkOperator && ((_a = e.operator_name) !== null && _a !== void 0 ? _a : '1_555') !== ((_b = entry.operator_name) !== null && _b !== void 0 ? _b : '1_555'))
-                continue;
-            return true;
-        }
-        return false;
-    };
-    return ResidueSet;
-}());
-exports.ResidueSet = ResidueSet;
-var _asym_id = properties_1.StructureProperties.chain.label_asym_id;
-var _seq_id = properties_1.StructureProperties.residue.label_seq_id;
-var _comp_id = properties_1.StructureProperties.atom.label_comp_id;
-var _alt_id = properties_1.StructureProperties.atom.label_alt_id;
-var _ins_code = properties_1.StructureProperties.residue.pdbx_PDB_ins_code;
-var _op_name = properties_1.StructureProperties.unit.operator_name;
-//# sourceMappingURL=residue-set.js.map

package/lib/commonjs/mol-model/structure/model/types/ions.d.ts

@@ -1,8 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated ion names params file. Names extracted from CCD components.
- *
- * @author molstar/chem-comp-dict/create-table cli
- */
-export declare const IonNames: Set<string>;

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

@@ -1,12 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated ion names params file. Names extracted from CCD components.
- *
- * @author molstar/chem-comp-dict/create-table cli
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.IonNames = void 0;
-exports.IonNames = new Set(['118', '119', '543', '1AL', '1CU', '2FK', '2HP', '2OF', '3CO', '3MT', '3NI', '3OF', '3P8', '4MO', '4PU', '4TI', '6MO', 'ACT', 'AG', 'AL', 'ALF', 'AM', 'ATH', 'AU', 'AU3', 'AUC', 'AZI', 'BA', 'BCT', 'BEF', 'BF4', 'BO4', 'BR', 'BS3', 'BSY', 'CA', 'CAC', 'CD', 'CD1', 'CD3', 'CD5', 'CE', 'CF', 'CHT', 'CL', 'CO', 'CO3', 'CO5', 'CON', 'CR', 'CS', 'CSB', 'CU', 'CU1', 'CU3', 'CUA', 'CUZ', 'CYN', 'DME', 'DMI', 'DSC', 'DTI', 'DY', 'E4N', 'EDR', 'EMC', 'ER3', 'EU', 'EU3', 'F', 'FE', 'FE2', 'FPO', 'GA', 'GD3', 'GEP', 'HAI', 'HG', 'HGC', 'IN', 'IOD', 'IR', 'IR3', 'IRI', 'IUM', 'K', 'KO4', 'LA', 'LCO', 'LCP', 'LI', 'LU', 'MAC', 'MG', 'MH2', 'MH3', 'MLI', 'MMC', 'MN', 'MN3', 'MN5', 'MN6', 'MO1', 'MO2', 'MO3', 'MO4', 'MO5', 'MO6', 'MOO', 'MOS', 'MOW', 'MW1', 'MW2', 'MW3', 'NA', 'NA2', 'NA5', 'NA6', 'NAO', 'NAW', 'ND', 'NET', 'NH4', 'NI', 'NI1', 'NI2', 'NI3', 'NO2', 'NO3', 'NRU', 'O4M', 'OAA', 'OC1', 'OC2', 'OC3', 'OC4', 'OC5', 'OC6', 'OC7', 'OC8', 'OCL', 'OCM', 'OCN', 'OCO', 'OF1', 'OF2', 'OF3', 'OH', 'OS', 'OS4', 'OXL', 'PB', 'PBM', 'PD', 'PDV', 'PER', 'PI', 'PO3', 'PO4', 'PR', 'PT', 'PT4', 'PTN', 'RB', 'RH3', 'RHD', 'RU', 'SB', 'SCN', 'SE4', 'SEK', 'SM', 'SMO', 'SO3', 'SO4', 'SR', 'T1A', 'TB', 'TBA', 'TCN', 'TEA', 'TH', 'THE', 'TL', 'TMA', 'TRA', 'UNX', 'V', 'VN3', 'VO4', 'W', 'WO5', 'Y1', 'YB', 'YB2', 'YH', 'YT3', 'ZCM', 'ZN', 'ZN2', 'ZN3', 'ZNO', 'ZO3', 'ZR', 'NCO', 'OHX']);
-//# sourceMappingURL=ions.js.map

package/lib/commonjs/mol-model/structure/model/types/lipids.d.ts

@@ -1,8 +0,0 @@
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
- *
- * @author molstar/lipid-params cli
- */
-export declare const LipidNames: Set<string>;

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

@@ -1,12 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * Code-generated lipid params file. Names extracted from Martini FF lipids itp.
- *
- * @author molstar/lipid-params cli
- */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.LipidNames = void 0;
-exports.LipidNames = new Set(['DAPC', 'DBPC', 'DFPC', 'DGPC', 'DIPC', 'DLPC', 'DNPC', 'DOPC', 'DPPC', 'DRPC', 'DTPC', 'DVPC', 'DXPC', 'DYPC', 'LPPC', 'PAPC', 'PEPC', 'PGPC', 'PIPC', 'POPC', 'PRPC', 'PUPC', 'DAPE', 'DBPE', 'DFPE', 'DGPE', 'DIPE', 'DLPE', 'DNPE', 'DOPE', 'DPPE', 'DRPE', 'DTPE', 'DUPE', 'DVPE', 'DXPE', 'DYPE', 'LPPE', 'PAPE', 'PGPE', 'PIPE', 'POPE', 'PQPE', 'PRPE', 'PUPE', 'DAPS', 'DBPS', 'DFPS', 'DGPS', 'DIPS', 'DLPS', 'DNPS', 'DOPS', 'DPPS', 'DRPS', 'DTPS', 'DUPS', 'DVPS', 'DXPS', 'DYPS', 'LPPS', 'PAPS', 'PGPS', 'PIPS', 'POPS', 'PQPS', 'PRPS', 'PUPS', 'DAPG', 'DBPG', 'DFPG', 'DGPG', 'DIPG', 'DLPG', 'DNPG', 'DOPG', 'DPPG', 'DRPG', 'DTPG', 'DVPG', 'DXPG', 'DYPG', 'LPPG', 'PAPG', 'PGPG', 'PIPG', 'POPG', 'PRPG', 'DAPA', 'DBPA', 'DFPA', 'DGPA', 'DIPA', 'DLPA', 'DNPA', 'DOPA', 'DPPA', 'DRPA', 'DTPA', 'DVPA', 'DXPA', 'DYPA', 'LPPA', 'PAPA', 'PGPA', 'PIPA', 'POPA', 'PRPA', 'PUPA', 'DPP', 'DPPI', 'PAPI', 'PIPI', 'POP', 'POPI', 'PUPI', 'PVP', 'PVPI', 'PADG', 'PIDG', 'PODG', 'PUDG', 'PVDG', 'APC', 'CPC', 'IPC', 'LPC', 'OPC', 'PPC', 'TPC', 'UPC', 'VPC', 'BNSM', 'DBSM', 'DPSM', 'DXSM', 'PGSM', 'PNSM', 'POSM', 'PVSM', 'XNSM', 'DPCE', 'DXCE', 'PNCE', 'XNCE', 'DMPC']);
-//# sourceMappingURL=lipids.js.map