molstar 3.0.0 → 3.0.1

package/lib/commonjs/mol-model-formats/structure/cif-core.js

@@ -1,258 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2020 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.trajectoryFromCifCore = exports.CifCoreFormat = void 0;
-var tslib_1 = require("tslib");
-var db_1 = require("../../mol-data/db");
-var mol_task_1 = require("../../mol-task");
-var parser_1 = require("./basic/parser");
-var schema_1 = require("./basic/schema");
-var component_1 = require("./common/component");
-var entity_1 = require("./common/entity");
-var cif_1 = require("../../mol-io/reader/cif");
-var geometry_1 = require("../../mol-math/geometry");
-var linear_algebra_1 = require("../../mol-math/linear-algebra");
-var symmetry_1 = require("./property/symmetry");
-var index_pair_1 = require("./property/bonds/index-pair");
-var anisotropic_1 = require("./property/anisotropic");
-var util_1 = require("./util");
-var util_2 = require("../../mol-data/util");
-function getSpacegroupNameOrNumber(space_group) {
-    var groupNumber = space_group.it_number.value(0);
-    var groupName = space_group['name_h-m_full'].value(0).replace('-', ' ');
-    if (!space_group.it_number.isDefined)
-        return groupName;
-    if (!space_group['name_h-m_full'].isDefined)
-        return groupNumber;
-    return groupNumber;
-}
-function getSymmetry(db) {
-    var cell = db.cell, space_group = db.space_group;
-    var nameOrNumber = getSpacegroupNameOrNumber(space_group);
-    var spaceCell = geometry_1.SpacegroupCell.create(nameOrNumber, linear_algebra_1.Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)), linear_algebra_1.Vec3.scale((0, linear_algebra_1.Vec3)(), linear_algebra_1.Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
-    return {
-        spacegroup: geometry_1.Spacegroup.create(spaceCell),
-        assemblies: [],
-        isNonStandardCrystalFrame: false,
-        ncsOperators: []
-    };
-}
-function getModels(db, format, ctx) {
-    var _a;
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var atomCount, MOL, A, seq_id, symmetry, m, _b, fract_x, fract_y, fract_z, x, y, z, v, i, _c, type_symbol, label, typeSymbol, formalCharge, element_symbol, formal_charge, i, ts, n, element_symbol, i, atom_site, name, entityBuilder, componentBuilder, basics, models, first, bondCount, labelIndexMap, label_1, i, il, bond_type, indexA, indexB, order, dist, flag, included, j, _d, atom_site_label_1, atom_site_label_2, valence, distance, i, iA, iB, id, t;
-        return (0, tslib_1.__generator)(this, function (_e) {
-            switch (_e.label) {
-                case 0:
-                    atomCount = db.atom_site._rowCount;
-                    MOL = db_1.Column.ofConst('MOL', atomCount, db_1.Column.Schema.str);
-                    A = db_1.Column.ofConst('A', atomCount, db_1.Column.Schema.str);
-                    seq_id = db_1.Column.ofConst(1, atomCount, db_1.Column.Schema.int);
-                    symmetry = getSymmetry(db);
-                    m = symmetry.spacegroup.cell.fromFractional;
-                    _b = db.atom_site, fract_x = _b.fract_x, fract_y = _b.fract_y, fract_z = _b.fract_z;
-                    x = new Float32Array(atomCount);
-                    y = new Float32Array(atomCount);
-                    z = new Float32Array(atomCount);
-                    v = (0, linear_algebra_1.Vec3)();
-                    for (i = 0; i < atomCount; ++i) {
-                        linear_algebra_1.Vec3.set(v, fract_x.value(i), fract_y.value(i), fract_z.value(i));
-                        linear_algebra_1.Vec3.transformMat4(v, v, m);
-                        x[i] = v[0], y[i] = v[1], z[i] = v[2];
-                    }
-                    _c = db.atom_site, type_symbol = _c.type_symbol, label = _c.label;
-                    if (type_symbol.isDefined) {
-                        element_symbol = new Array(atomCount);
-                        formal_charge = new Int8Array(atomCount);
-                        for (i = 0; i < atomCount; ++i) {
-                            ts = type_symbol.value(i);
-                            n = ts.length;
-                            if (ts[n - 1] === '+') {
-                                element_symbol[i] = ts.substring(0, n - 2);
-                                formal_charge[i] = parseInt(ts[n - 2]);
-                            }
-                            else if (ts[n - 2] === '+') {
-                                element_symbol[i] = ts.substring(0, n - 2);
-                                formal_charge[i] = parseInt(ts[n - 1]);
-                            }
-                            else if (ts[n - 1] === '-') {
-                                element_symbol[i] = ts.substring(0, n - 2);
-                                formal_charge[i] = -parseInt(ts[n - 2]);
-                            }
-                            else if (ts[n - 2] === '-') {
-                                element_symbol[i] = ts.substring(0, n - 2);
-                                formal_charge[i] = -parseInt(ts[n - 1]);
-                            }
-                            else {
-                                element_symbol[i] = ts;
-                                formal_charge[i] = 0;
-                            }
-                        }
-                        typeSymbol = db_1.Column.ofStringArray(element_symbol);
-                        formalCharge = db_1.Column.ofIntArray(formal_charge);
-                    }
-                    else {
-                        element_symbol = new Array(atomCount);
-                        for (i = 0; i < atomCount; ++i) {
-                            // TODO can take as is if type_symbol not given?
-                            element_symbol[i] = (0, util_1.guessElementSymbolString)(label.value(i));
-                        }
-                        typeSymbol = db_1.Column.ofStringArray(element_symbol);
-                        formalCharge = db_1.Column.Undefined(atomCount, db_1.Column.Schema.int);
-                    }
-                    atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
-                        auth_asym_id: A,
-                        auth_atom_id: label,
-                        auth_comp_id: MOL,
-                        auth_seq_id: seq_id,
-                        Cartn_x: db_1.Column.ofFloatArray(x),
-                        Cartn_y: db_1.Column.ofFloatArray(y),
-                        Cartn_z: db_1.Column.ofFloatArray(z),
-                        id: db_1.Column.range(0, atomCount - 1),
-                        label_asym_id: A,
-                        label_atom_id: label,
-                        label_comp_id: MOL,
-                        label_seq_id: seq_id,
-                        label_entity_id: db_1.Column.ofConst('1', atomCount, db_1.Column.Schema.str),
-                        occupancy: db.atom_site.occupancy.isDefined
-                            ? db.atom_site.occupancy
-                            : db_1.Column.ofConst(1, atomCount, db_1.Column.Schema.float),
-                        type_symbol: typeSymbol,
-                        pdbx_formal_charge: formalCharge,
-                        pdbx_PDB_model_num: db_1.Column.ofConst(1, atomCount, db_1.Column.Schema.int),
-                        B_iso_or_equiv: db.atom_site.u_iso_or_equiv,
-                    }, atomCount);
-                    name = (db.chemical.name_common.value(0) ||
-                        db.chemical.name_systematic.value(0) ||
-                        db.chemical_formula.sum.value(0));
-                    entityBuilder = new entity_1.EntityBuilder();
-                    entityBuilder.setNames([['MOL', name || 'Unknown Entity']]);
-                    entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
-                    componentBuilder = new component_1.ComponentBuilder(seq_id, db.atom_site.type_symbol);
-                    componentBuilder.setNames([['MOL', name || 'Unknown Molecule']]);
-                    componentBuilder.add('MOL', 0);
-                    basics = (0, schema_1.createBasic)({
-                        entity: entityBuilder.getEntityTable(),
-                        chem_comp: componentBuilder.getChemCompTable(),
-                        atom_site: atom_site
-                    });
-                    return [4 /*yield*/, (0, parser_1.createModels)(basics, format, ctx)];
-                case 1:
-                    models = _e.sent();
-                    if (models.frameCount > 0) {
-                        first = models.representative;
-                        symmetry_1.ModelSymmetry.Provider.set(first, symmetry);
-                        bondCount = db.geom_bond._rowCount;
-                        if (bondCount > 0) {
-                            labelIndexMap = {};
-                            label_1 = db.atom_site.label;
-                            for (i = 0, il = label_1.rowCount; i < il; ++i) {
-                                labelIndexMap[label_1.value(i)] = i;
-                            }
-                            bond_type = (_a = format.data.frame.categories.ccdc_geom_bond_type) === null || _a === void 0 ? void 0 : _a.getField('');
-                            indexA = [];
-                            indexB = [];
-                            order = [];
-                            dist = [];
-                            flag = [];
-                            included = new Set();
-                            j = 0;
-                            _d = db.geom_bond, atom_site_label_1 = _d.atom_site_label_1, atom_site_label_2 = _d.atom_site_label_2, valence = _d.valence, distance = _d.distance;
-                            for (i = 0; i < bondCount; ++i) {
-                                iA = labelIndexMap[atom_site_label_1.value(i)];
-                                iB = labelIndexMap[atom_site_label_2.value(i)];
-                                id = iA < iB ? (0, util_2.cantorPairing)(iA, iB) : (0, util_2.cantorPairing)(iB, iA);
-                                if (included.has(id))
-                                    continue;
-                                included.add(id);
-                                indexA[j] = iA;
-                                indexB[j] = iB;
-                                dist[j] = distance.value(i) || -1;
-                                if (bond_type) {
-                                    t = bond_type.str(i);
-                                    if (t === 'D') {
-                                        order[j] = 2;
-                                        flag[j] = 1 /* Covalent */;
-                                    }
-                                    else if (t === 'A') {
-                                        order[j] = 1;
-                                        flag[j] = 1 /* Covalent */ | 16 /* Aromatic */;
-                                    }
-                                    else if (t === 'S') {
-                                        order[j] = 1;
-                                        flag[j] = 1 /* Covalent */;
-                                    }
-                                    else {
-                                        order[j] = 1;
-                                        flag[j] = 1 /* Covalent */;
-                                    }
-                                }
-                                else {
-                                    flag[j] = 1 /* Covalent */;
-                                    // TODO derive order from bond length if undefined
-                                    order[j] = valence.isDefined ? valence.value(i) : 1;
-                                }
-                                j += 1;
-                            }
-                            index_pair_1.IndexPairBonds.Provider.set(first, index_pair_1.IndexPairBonds.fromData({ pairs: {
-                                    indexA: db_1.Column.ofIntArray(indexA),
-                                    indexB: db_1.Column.ofIntArray(indexB),
-                                    order: db_1.Column.ofIntArray(order),
-                                    distance: db_1.Column.ofFloatArray(dist),
-                                    flag: db_1.Column.ofIntArray(flag)
-                                }, count: atomCount }));
-                        }
-                    }
-                    return [2 /*return*/, models];
-            }
-        });
-    });
-}
-function atomSiteAnisotropFromCifCore(model) {
-    if (!CifCoreFormat.is(model.sourceData))
-        return;
-    var _a = model.sourceData.data.db, atom_site = _a.atom_site, atom_site_aniso = _a.atom_site_aniso;
-    var data = db_1.Table.ofPartialColumns(anisotropic_1.AtomSiteAnisotrop.Schema, {
-        U: atom_site_aniso.u,
-    }, atom_site_aniso._rowCount);
-    var elementToAnsiotrop = anisotropic_1.AtomSiteAnisotrop.getElementToAnsiotropFromLabel(atom_site.label, atom_site_aniso.label);
-    return { data: data, elementToAnsiotrop: elementToAnsiotrop };
-}
-function atomSiteAnisotropApplicableCifCore(model) {
-    if (!CifCoreFormat.is(model.sourceData))
-        return false;
-    return model.sourceData.data.db.atom_site_aniso.u.isDefined;
-}
-anisotropic_1.AtomSiteAnisotrop.Provider.formatRegistry.add('cifCore', atomSiteAnisotropFromCifCore, atomSiteAnisotropApplicableCifCore);
-var CifCoreFormat;
-(function (CifCoreFormat) {
-    function is(x) {
-        return (x === null || x === void 0 ? void 0 : x.kind) === 'cifCore';
-    }
-    CifCoreFormat.is = is;
-    function fromFrame(frame, db) {
-        if (!db)
-            db = cif_1.CIF.schema.cifCore(frame);
-        var name = (db.database_code.depnum_ccdc_archive.value(0) ||
-            db.database_code.depnum_ccdc_fiz.value(0) ||
-            db.database_code.icsd.value(0) ||
-            db.database_code.mdf.value(0) ||
-            db.database_code.nbs.value(0) ||
-            db.database_code.csd.value(0) ||
-            db.database_code.cod.value(0) ||
-            db._name);
-        return { kind: 'cifCore', name: name, data: { db: db, frame: frame } };
-    }
-    CifCoreFormat.fromFrame = fromFrame;
-})(CifCoreFormat || (CifCoreFormat = {}));
-exports.CifCoreFormat = CifCoreFormat;
-function trajectoryFromCifCore(frame) {
-    var format = CifCoreFormat.fromFrame(frame);
-    return mol_task_1.Task.create('Parse CIF Core', function (ctx) { return getModels(format.data.db, format, ctx); });
-}
-exports.trajectoryFromCifCore = trajectoryFromCifCore;
-//# sourceMappingURL=cif-core.js.map

package/lib/commonjs/mol-model-formats/structure/common/component.d.ts

@@ -1,50 +0,0 @@
-/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { Table, Column } from '../../../mol-data/db';
-export declare class ComponentBuilder {
-    private seqId;
-    private atomId;
-    private namesMap;
-    private comps;
-    private ids;
-    private names;
-    private types;
-    private mon_nstd_flags;
-    private set;
-    private getAtomIds;
-    private hasAtomIds;
-    private getType;
-    has(compId: string): boolean;
-    get(compId: string): Table.Row<Pick<{
-        type: Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
-        formula: Column.Schema.Str;
-        formula_weight: Column.Schema.Float;
-        id: Column.Schema.Str;
-        mon_nstd_flag: Column.Schema.Aliased<"y" | "yes" | "no" | "n">;
-        name: Column.Schema.Str;
-        pdbx_synonyms: Column.Schema.List<string>;
-    }, "name" | "id" | "type">> | undefined;
-    add(compId: string, index: number): Table.Row<Pick<{
-        type: Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
-        formula: Column.Schema.Str;
-        formula_weight: Column.Schema.Float;
-        id: Column.Schema.Str;
-        mon_nstd_flag: Column.Schema.Aliased<"y" | "yes" | "no" | "n">;
-        name: Column.Schema.Str;
-        pdbx_synonyms: Column.Schema.List<string>;
-    }, "name" | "id" | "type">>;
-    getChemCompTable(): Table<{
-        type: Column.Schema.Aliased<"other" | "D-peptide linking" | "L-peptide linking" | "D-peptide NH3 amino terminus" | "L-peptide NH3 amino terminus" | "D-peptide COOH carboxy terminus" | "L-peptide COOH carboxy terminus" | "DNA linking" | "RNA linking" | "L-RNA linking" | "L-DNA linking" | "DNA OH 5 prime terminus" | "RNA OH 5 prime terminus" | "DNA OH 3 prime terminus" | "RNA OH 3 prime terminus" | "D-saccharide, beta linking" | "D-saccharide, alpha linking" | "L-saccharide, beta linking" | "L-saccharide, alpha linking" | "L-saccharide" | "D-saccharide" | "saccharide" | "non-polymer" | "peptide linking" | "peptide-like" | "L-gamma-peptide, C-delta linking" | "D-gamma-peptide, C-delta linking" | "L-beta-peptide, C-gamma linking" | "D-beta-peptide, C-gamma linking" | "Ion" | "Lipid">;
-        formula: Column.Schema.Str;
-        formula_weight: Column.Schema.Float;
-        id: Column.Schema.Str;
-        mon_nstd_flag: Column.Schema.Aliased<"y" | "yes" | "no" | "n">;
-        name: Column.Schema.Str;
-        pdbx_synonyms: Column.Schema.List<string>;
-    }>;
-    setNames(names: [string, string][]): void;
-    constructor(seqId: Column<number>, atomId: Column<string>);
-}

package/lib/commonjs/mol-model-formats/structure/common/component.js

@@ -1,185 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019-2020 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.ComponentBuilder = void 0;
-var db_1 = require("../../../mol-data/db");
-var types_1 = require("../../../mol-model/structure/model/types");
-var set_1 = require("../../../mol-util/set");
-var schema_1 = require("../basic/schema");
-var ProteinAtomIdsList = [
-    new Set(['CA']),
-    new Set(['C']),
-    new Set(['N'])
-];
-var RnaAtomIdsList = [
-    new Set(['P', 'O3\'', 'O3*']),
-    new Set(['C4\'', 'C4*']),
-    new Set(['O2\'', 'O2*', 'F2\'', 'F2*'])
-];
-var DnaAtomIdsList = [
-    new Set(['P', 'O3\'', 'O3*']),
-    new Set(['C3\'', 'C3*']),
-    new Set(['O2\'', 'O2*', 'F2\'', 'F2*'])
-];
-/** Used to reduce false positives for atom name-based type guessing */
-var NonPolymerNames = new Set([
-    'FMN', 'NCN', 'FNS', 'FMA' // Mononucleotides
-]);
-var StandardComponents = (function () {
-    var map = new Map();
-    var components = [
-        { id: 'HIS', name: 'HISTIDINE', type: 'L-peptide linking' },
-        { id: 'ARG', name: 'ARGININE', type: 'L-peptide linking' },
-        { id: 'LYS', name: 'LYSINE', type: 'L-peptide linking' },
-        { id: 'ILE', name: 'ISOLEUCINE', type: 'L-peptide linking' },
-        { id: 'PHE', name: 'PHENYLALANINE', type: 'L-peptide linking' },
-        { id: 'LEU', name: 'LEUCINE', type: 'L-peptide linking' },
-        { id: 'TRP', name: 'TRYPTOPHAN', type: 'L-peptide linking' },
-        { id: 'ALA', name: 'ALANINE', type: 'L-peptide linking' },
-        { id: 'MET', name: 'METHIONINE', type: 'L-peptide linking' },
-        { id: 'CYS', name: 'CYSTEINE', type: 'L-peptide linking' },
-        { id: 'ASN', name: 'ASPARAGINE', type: 'L-peptide linking' },
-        { id: 'VAL', name: 'VALINE', type: 'L-peptide linking' },
-        { id: 'GLY', name: 'GLYCINE', type: 'peptide linking' },
-        { id: 'SER', name: 'SERINE', type: 'L-peptide linking' },
-        { id: 'GLN', name: 'GLUTAMINE', type: 'L-peptide linking' },
-        { id: 'TYR', name: 'TYROSINE', type: 'L-peptide linking' },
-        { id: 'ASP', name: 'ASPARTIC ACID', type: 'L-peptide linking' },
-        { id: 'GLU', name: 'GLUTAMIC ACID', type: 'L-peptide linking' },
-        { id: 'THR', name: 'THREONINE', type: 'L-peptide linking' },
-        { id: 'PRO', name: 'PROLINE', type: 'L-peptide linking' },
-        { id: 'SEC', name: 'SELENOCYSTEINE', type: 'L-peptide linking' },
-        { id: 'PYL', name: 'PYRROLYSINE', type: 'L-peptide linking' },
-        { id: 'MSE', name: 'SELENOMETHIONINE', type: 'L-peptide linking' },
-        { id: 'SEP', name: 'PHOSPHOSERINE', type: 'L-peptide linking' },
-        { id: 'TPO', name: 'PHOSPHOTHREONINE', type: 'L-peptide linking' },
-        { id: 'PTR', name: 'O-PHOSPHOTYROSINE', type: 'L-peptide linking' },
-        { id: 'PCA', name: 'PYROGLUTAMIC ACID', type: 'L-peptide linking' },
-        { id: 'A', name: 'ADENOSINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
-        { id: 'C', name: 'CYTIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
-        { id: 'T', name: 'THYMIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
-        { id: 'G', name: 'GUANOSINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
-        { id: 'I', name: 'INOSINIC ACID', type: 'RNA linking' },
-        { id: 'U', name: 'URIDINE-5\'-MONOPHOSPHATE', type: 'RNA linking' },
-        { id: 'DA', name: '2\'-DEOXYADENOSINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
-        { id: 'DC', name: '2\'-DEOXYCYTIDINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
-        { id: 'DT', name: 'THYMIDINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
-        { id: 'DG', name: '2\'-DEOXYGUANOSINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
-        { id: 'DI', name: '2\'-DEOXYINOSINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
-        { id: 'DU', name: '2\'-DEOXYURIDINE-5\'-MONOPHOSPHATE', type: 'DNA linking' },
-    ];
-    components.forEach(function (c) { return map.set(c.id, c); });
-    return map;
-})();
-var CharmmIonComponents = (function () {
-    var map = new Map();
-    var components = [
-        { id: 'ZN2', name: 'ZINC ION', type: 'Ion' },
-        { id: 'SOD', name: 'SODIUM ION', type: 'Ion' },
-        { id: 'CES', name: 'CESIUM ION', type: 'Ion' },
-        { id: 'CLA', name: 'CHLORIDE ION', type: 'Ion' },
-        { id: 'CAL', name: 'CALCIUM ION', type: 'Ion' },
-        { id: 'POT', name: 'POTASSIUM ION', type: 'Ion' },
-    ];
-    components.forEach(function (c) { return map.set(c.id, c); });
-    return map;
-})();
-var ComponentBuilder = /** @class */ (function () {
-    function ComponentBuilder(seqId, atomId) {
-        this.seqId = seqId;
-        this.atomId = atomId;
-        this.namesMap = new Map();
-        this.comps = new Map();
-        this.ids = [];
-        this.names = [];
-        this.types = [];
-        this.mon_nstd_flags = [];
-    }
-    ComponentBuilder.prototype.set = function (c) {
-        this.comps.set(c.id, c);
-        this.ids.push(c.id);
-        this.names.push(c.name);
-        this.types.push(c.type);
-        this.mon_nstd_flags.push(types_1.PolymerNames.has(c.id) ? 'y' : 'n');
-    };
-    ComponentBuilder.prototype.getAtomIds = function (index) {
-        var atomIds = new Set();
-        var prevSeqId = this.seqId.value(index);
-        while (index < this.seqId.rowCount) {
-            var seqId = this.seqId.value(index);
-            if (seqId !== prevSeqId)
-                break;
-            atomIds.add(this.atomId.value(index));
-            prevSeqId - seqId;
-            index += 1;
-        }
-        return atomIds;
-    };
-    ComponentBuilder.prototype.hasAtomIds = function (atomIds, atomIdsList) {
-        for (var i = 0, il = atomIdsList.length; i < il; ++i) {
-            if (!set_1.SetUtils.areIntersecting(atomIds, atomIdsList[i])) {
-                return false;
-            }
-        }
-        return true;
-    };
-    ComponentBuilder.prototype.getType = function (atomIds) {
-        if (this.hasAtomIds(atomIds, ProteinAtomIdsList)) {
-            return 'peptide linking';
-        }
-        else if (this.hasAtomIds(atomIds, RnaAtomIdsList)) {
-            return 'RNA linking';
-        }
-        else if (this.hasAtomIds(atomIds, DnaAtomIdsList)) {
-            return 'DNA linking';
-        }
-        else {
-            return 'other';
-        }
-    };
-    ComponentBuilder.prototype.has = function (compId) { return this.comps.has(compId); };
-    ComponentBuilder.prototype.get = function (compId) { return this.comps.get(compId); };
-    ComponentBuilder.prototype.add = function (compId, index) {
-        if (!this.has(compId)) {
-            if (StandardComponents.has(compId)) {
-                this.set(StandardComponents.get(compId));
-            }
-            else if (types_1.WaterNames.has(compId)) {
-                this.set({ id: compId, name: 'WATER', type: 'non-polymer' });
-            }
-            else if (NonPolymerNames.has(compId)) {
-                this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'non-polymer' });
-            }
-            else {
-                var atomIds = this.getAtomIds(index);
-                if (atomIds.size === 1 && CharmmIonComponents.has(compId)) {
-                    this.set(CharmmIonComponents.get(compId));
-                }
-                else {
-                    var type = this.getType(atomIds);
-                    this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: type });
-                }
-            }
-        }
-        return this.get(compId);
-    };
-    ComponentBuilder.prototype.getChemCompTable = function () {
-        return db_1.Table.ofPartialColumns(schema_1.BasicSchema.chem_comp, {
-            id: db_1.Column.ofStringArray(this.ids),
-            name: db_1.Column.ofStringArray(this.names),
-            type: db_1.Column.ofStringAliasArray(this.types),
-            mon_nstd_flag: db_1.Column.ofStringAliasArray(this.mon_nstd_flags),
-        }, this.ids.length);
-    };
-    ComponentBuilder.prototype.setNames = function (names) {
-        var _this = this;
-        names.forEach(function (n) { return _this.namesMap.set(n[0], n[1]); });
-    };
-    return ComponentBuilder;
-}());
-exports.ComponentBuilder = ComponentBuilder;
-//# sourceMappingURL=component.js.map

package/lib/commonjs/mol-model-formats/structure/common/entity.d.ts

@@ -1,40 +0,0 @@
-/**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-import { MoleculeType } from '../../../mol-model/structure/model/types';
-import { Column, Table } from '../../../mol-data/db';
-export declare type EntityCompound = {
-    chains: string[];
-    description: string;
-};
-export declare class EntityBuilder {
-    private count;
-    private ids;
-    private types;
-    private descriptions;
-    private compoundsMap;
-    private namesMap;
-    private heteroMap;
-    private chainMap;
-    private waterId?;
-    private set;
-    getEntityId(compId: string, moleculeType: MoleculeType, chainId: string, options?: {
-        customName?: string;
-    }): string;
-    getEntityTable(): Table<{
-        details: Column.Schema.Str;
-        formula_weight: Column.Schema.Float;
-        id: Column.Schema.Str;
-        src_method: Column.Schema.Aliased<"nat" | "man" | "syn">;
-        type: Column.Schema.Aliased<"non-polymer" | "polymer" | "macrolide" | "water" | "branched">;
-        pdbx_description: Column.Schema.List<string>;
-        pdbx_number_of_molecules: Column.Schema.Int;
-        pdbx_mutation: Column.Schema.Str;
-        pdbx_fragment: Column.Schema.Str;
-        pdbx_ec: Column.Schema.List<string>;
-    }>;
-    setCompounds(compounds: EntityCompound[]): void;
-    setNames(names: [string, string][]): void;
-}

package/lib/commonjs/mol-model-formats/structure/common/entity.js

@@ -1,80 +0,0 @@
-"use strict";
-/**
- * Copyright (c) 2019-2020 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.EntityBuilder = void 0;
-var types_1 = require("../../../mol-model/structure/model/types");
-var db_1 = require("../../../mol-data/db");
-var schema_1 = require("../basic/schema");
-var EntityBuilder = /** @class */ (function () {
-    function EntityBuilder() {
-        this.count = 0;
-        this.ids = [];
-        this.types = [];
-        this.descriptions = [];
-        this.compoundsMap = new Map();
-        this.namesMap = new Map();
-        this.heteroMap = new Map();
-        this.chainMap = new Map();
-    }
-    EntityBuilder.prototype.set = function (type, description) {
-        this.count += 1;
-        this.ids.push("".concat(this.count));
-        this.types.push(type);
-        this.descriptions.push([description]);
-    };
-    EntityBuilder.prototype.getEntityId = function (compId, moleculeType, chainId, options) {
-        if (moleculeType === 2 /* Water */) {
-            if (this.waterId === undefined) {
-                this.set('water', (options === null || options === void 0 ? void 0 : options.customName) || 'Water');
-                this.waterId = "".concat(this.count);
-            }
-            return this.waterId;
-        }
-        else if ((0, types_1.isPolymer)(moleculeType)) {
-            if (this.compoundsMap.has(chainId)) {
-                return this.compoundsMap.get(chainId);
-            }
-            else {
-                if (!this.chainMap.has(chainId)) {
-                    this.set('polymer', (options === null || options === void 0 ? void 0 : options.customName) || "Polymer ".concat(this.chainMap.size + 1));
-                    this.chainMap.set(chainId, "".concat(this.count));
-                }
-                return this.chainMap.get(chainId);
-            }
-        }
-        else {
-            if (!this.heteroMap.has(compId)) {
-                this.set('non-polymer', (options === null || options === void 0 ? void 0 : options.customName) || this.namesMap.get(compId) || compId);
-                this.heteroMap.set(compId, "".concat(this.count));
-            }
-            return this.heteroMap.get(compId);
-        }
-    };
-    EntityBuilder.prototype.getEntityTable = function () {
-        return db_1.Table.ofPartialColumns(schema_1.BasicSchema.entity, {
-            id: db_1.Column.ofStringArray(this.ids),
-            type: db_1.Column.ofStringAliasArray(this.types),
-            pdbx_description: db_1.Column.ofStringListArray(this.descriptions),
-        }, this.count);
-    };
-    EntityBuilder.prototype.setCompounds = function (compounds) {
-        for (var i = 0, il = compounds.length; i < il; ++i) {
-            var _a = compounds[i], chains = _a.chains, description = _a.description;
-            this.set('polymer', description);
-            for (var j = 0, jl = chains.length; j < jl; ++j) {
-                this.compoundsMap.set(chains[j], "".concat(this.count));
-            }
-        }
-    };
-    EntityBuilder.prototype.setNames = function (names) {
-        var _this = this;
-        names.forEach(function (n) { return _this.namesMap.set(n[0], n[1]); });
-    };
-    return EntityBuilder;
-}());
-exports.EntityBuilder = EntityBuilder;
-//# sourceMappingURL=entity.js.map