molstar 3.2.0 → 3.4.0

package/lib/commonjs/mol-model-formats/structure/basic/coarse.js

@@ -31,8 +31,8 @@ function getCoarse(data, chemicalComponentMap) {
     return {
         hierarchy: {
             isDefined: true,
-            spheres: (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, sphereData), sphereKeys), sphereRanges),
-            gaussians: (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, gaussianData), gaussianKeys), gaussianRanges),
+            spheres: tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, sphereData), sphereKeys), sphereRanges),
+            gaussians: tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, gaussianData), gaussianKeys), gaussianRanges),
         },
         conformation: {
             id: mol_util_1.UUID.create22(),
@@ -79,6 +79,5 @@ function getSegments(asym_id, seq_id_begin, seq_id_end) {
 }
 function getData(data) {
     var entity_id = data.entity_id, seq_id_begin = data.seq_id_begin, seq_id_end = data.seq_id_end, asym_id = data.asym_id;
-    return (0, tslib_1.__assign)({ count: entity_id.rowCount, entity_id: entity_id, asym_id: asym_id, seq_id_begin: seq_id_begin, seq_id_end: seq_id_end }, getSegments(asym_id, seq_id_begin, seq_id_end));
+    return tslib_1.__assign({ count: entity_id.rowCount, entity_id: entity_id, asym_id: asym_id, seq_id_begin: seq_id_begin, seq_id_end: seq_id_end }, getSegments(asym_id, seq_id_begin, seq_id_end));
 }
-//# sourceMappingURL=coarse.js.map

package/lib/commonjs/mol-model-formats/structure/basic/entities.js

@@ -131,7 +131,6 @@ function getEntitiesWithPRD(data, entities, structAsymMap) {
         }
     }
     var prdIdColumn = db_1.Column.ofArray({ array: prdIds, schema: db_1.Column.Schema.str });
-    return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, entities), { prd_id: prdIdColumn });
+    return tslib_1.__assign(tslib_1.__assign({}, entities), { prd_id: prdIdColumn });
 }
 exports.getEntitiesWithPRD = getEntitiesWithPRD;
-//# sourceMappingURL=entities.js.map

package/lib/commonjs/mol-model-formats/structure/basic/parser.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>

package/lib/commonjs/mol-model-formats/structure/basic/parser.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
@@ -22,9 +22,9 @@ var entities_1 = require("./entities");
 var util_1 = require("./util");
 var trajectory_1 = require("../../../mol-model/structure/trajectory");
 function createModels(data, format, ctx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var properties, models, _a, i;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     properties = getCommonProperties(data, format);
@@ -60,7 +60,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
     var atomic = (0, atomic_1.getAtomicHierarchyAndConformation)(atom_site, sourceIndex, entities, properties.chemicalComponentMap, format, previous);
     var modelNum = atom_site.pdbx_PDB_model_num.value(0);
     if (previous && atomic.sameAsPrevious) {
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)({}, previous), { id: uuid_1.UUID.create22(), modelNum: modelNum, atomicConformation: atomic.conformation, _dynamicPropertyData: Object.create(null) });
+        return tslib_1.__assign(tslib_1.__assign({}, previous), { id: uuid_1.UUID.create22(), modelNum: modelNum, atomicConformation: atomic.conformation, _dynamicPropertyData: Object.create(null) });
     }
     var coarse = coarse_1.EmptyCoarse;
     var sequence = (0, sequence_1.getSequence)(data, entities, atomic.hierarchy, coarse.hierarchy);
@@ -89,7 +89,7 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
         atomicChainOperatorMappinng: atomic.chainOperatorMapping,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
-        properties: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, properties), { structAsymMap: structAsymMap }),
+        properties: tslib_1.__assign(tslib_1.__assign({}, properties), { structAsymMap: structAsymMap }),
         customProperties: new custom_property_1.CustomProperties(),
         _staticPropertyData: Object.create(null),
         _dynamicPropertyData: Object.create(null)
@@ -129,7 +129,7 @@ function createIntegrativeModel(data, ihm, properties, format) {
         atomicChainOperatorMappinng: atomic.chainOperatorMapping,
         coarseHierarchy: coarse.hierarchy,
         coarseConformation: coarse.conformation,
-        properties: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, properties), { structAsymMap: structAsymMap }),
+        properties: tslib_1.__assign(tslib_1.__assign({}, properties), { structAsymMap: structAsymMap }),
         customProperties: new custom_property_1.CustomProperties(),
         _staticPropertyData: Object.create(null),
         _dynamicPropertyData: Object.create(null)
@@ -145,9 +145,9 @@ function findModelEnd(num, startIndex) {
     return endIndex;
 }
 function readStandard(ctx, data, properties, format) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var models, atomCount, entities, modelStart, modelEnd, _a, atom_site, sourceIndex, model;
-        return (0, tslib_1.__generator)(this, function (_b) {
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     models = [];
@@ -188,9 +188,9 @@ function splitTable(table, col) {
     return ret;
 }
 function readIntegrative(ctx, data, properties, format) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var entities, atom_sites_modelColumn, atom_sites, sphere_sites, gauss_sites, models, _a, model_id, model_name, i, id, atom_site, atom_site_sourceIndex, e, _b, sorted, sourceIndex, ihm, model;
-        return (0, tslib_1.__generator)(this, function (_c) {
+        return tslib_1.__generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
                     entities = (0, entities_1.getEntityData)(data);
@@ -242,4 +242,3 @@ function readIntegrative(ctx, data, properties, format) {
         });
     });
 }
-//# sourceMappingURL=parser.js.map

package/lib/commonjs/mol-model-formats/structure/basic/properties.js

@@ -129,4 +129,3 @@ function getStructAsymMap(atomic, data) {
     return map;
 }
 exports.getStructAsymMap = getStructAsymMap;
-//# sourceMappingURL=properties.js.map

package/lib/commonjs/mol-model-formats/structure/basic/schema.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -196,4 +196,4 @@ export interface BasicData {
     pdbx_unobs_or_zero_occ_residues: UnobsOrZeroOccResidues;
     pdbx_molecule: Molecule;
 }
-export declare function createBasic(data: Partial<BasicData>): BasicData;
+export declare function createBasic(data: Partial<BasicData>, normalize?: boolean): BasicData;

package/lib/commonjs/mol-model-formats/structure/basic/schema.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -9,6 +9,7 @@ exports.createBasic = exports.BasicSchema = void 0;
 var mmcif_1 = require("../../../mol-io/reader/cif/schema/mmcif");
 var db_1 = require("../../../mol-data/db");
 var mmcif_extras_1 = require("../../../mol-io/reader/cif/schema/mmcif-extras");
+var util_1 = require("./util");
 exports.BasicSchema = {
     entry: mmcif_1.mmCIF_Schema.entry,
     struct: mmcif_1.mmCIF_Schema.struct,
@@ -28,7 +29,8 @@ exports.BasicSchema = {
     pdbx_unobs_or_zero_occ_residues: mmcif_1.mmCIF_Schema.pdbx_unobs_or_zero_occ_residues,
     pdbx_molecule: mmcif_1.mmCIF_Schema.pdbx_molecule,
 };
-function createBasic(data) {
+function createBasic(data, normalize) {
+    if (normalize === void 0) { normalize = false; }
     var basic = Object.create(null);
     for (var _i = 0, _a = Object.keys(exports.BasicSchema); _i < _a.length; _i++) {
         var name_1 = _a[_i];
@@ -39,7 +41,9 @@ function createBasic(data) {
             basic[name_1] = db_1.Table.ofUndefinedColumns(exports.BasicSchema[name_1], 0);
         }
     }
+    if (normalize) {
+        basic.atom_site = (0, util_1.getNormalizedAtomSite)(basic.atom_site);
+    }
     return basic;
 }
 exports.createBasic = createBasic;
-//# sourceMappingURL=schema.js.map

package/lib/commonjs/mol-model-formats/structure/basic/sequence.js

@@ -37,4 +37,3 @@ function getSequence(data, entities, atomicHierarchy, coarseHierarchy) {
     return { byEntityKey: byEntityKey, sequences: sequences };
 }
 exports.getSequence = getSequence;
-//# sourceMappingURL=sequence.js.map

package/lib/commonjs/mol-model-formats/structure/basic/sort.js

@@ -11,9 +11,9 @@ var util_1 = require("../../../mol-data/util");
 var db_1 = require("../../../mol-data/db");
 var array_1 = require("../../../mol-util/array");
 function sortAtomSite(ctx, atom_site, start, end) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
         var indices, label_entity_id, label_asym_id, label_seq_id, entityBuckets, ei, _eI, chainBuckets, cI, _cI, aI;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     indices = (0, util_1.createRangeArray)(start, end - 1);
@@ -69,4 +69,3 @@ function sortAtomSite(ctx, atom_site, start, end) {
     });
 }
 exports.sortAtomSite = sortAtomSite;
-//# sourceMappingURL=sort.js.map

package/lib/commonjs/mol-model-formats/structure/basic/util.d.ts

@@ -1,8 +1,39 @@
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
  */
-import { BasicData } from './schema';
+import { AtomSite, BasicData } from './schema';
+import { Column, Table } from '../../../mol-data/db';
 export declare function getModelGroupName(model_id: number, data: BasicData): string;
+/** Fix possibly missing auth_/label_ columns */
+export declare function getNormalizedAtomSite(atom_site: AtomSite): Table<{
+    auth_asym_id: Column.Schema.Str;
+    auth_atom_id: Column.Schema.Str;
+    auth_comp_id: Column.Schema.Str;
+    auth_seq_id: Column.Schema.Int;
+    B_iso_or_equiv: Column.Schema.Float;
+    Cartn_x: Column.Schema.Coordinate;
+    Cartn_y: Column.Schema.Coordinate;
+    Cartn_z: Column.Schema.Coordinate;
+    group_PDB: Column.Schema.Aliased<"ATOM" | "HETATM">;
+    id: Column.Schema.Int;
+    label_alt_id: Column.Schema.Str;
+    label_asym_id: Column.Schema.Str;
+    label_atom_id: Column.Schema.Str;
+    label_comp_id: Column.Schema.Str;
+    label_entity_id: Column.Schema.Str;
+    label_seq_id: Column.Schema.Int;
+    occupancy: Column.Schema.Float;
+    type_symbol: Column.Schema.Str;
+    pdbx_PDB_ins_code: Column.Schema.Str;
+    pdbx_PDB_model_num: Column.Schema.Int;
+    pdbx_formal_charge: Column.Schema.Int;
+    pdbx_label_index: Column.Schema.Int;
+    pdbx_sifts_xref_db_name: Column.Schema.Str;
+    pdbx_sifts_xref_db_acc: Column.Schema.Str;
+    pdbx_sifts_xref_db_num: Column.Schema.Str;
+    pdbx_sifts_xref_db_res: Column.Schema.Str;
+    ihm_model_id: Column.Schema.Int;
+}>;

package/lib/commonjs/mol-model-formats/structure/basic/util.js

@@ -1,12 +1,12 @@
 "use strict";
 /**
- * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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.getModelGroupName = void 0;
+exports.getNormalizedAtomSite = exports.getModelGroupName = void 0;
 var db_1 = require("../../../mol-data/db");
 function getModelGroupName(model_id, data) {
     var ihm_model_group = data.ihm_model_group, ihm_model_group_link = data.ihm_model_group_link;
@@ -19,4 +19,27 @@ function getModelGroupName(model_id, data) {
     return '';
 }
 exports.getModelGroupName = getModelGroupName;
-//# sourceMappingURL=util.js.map
+//
+function hasPresentValues(column) {
+    for (var i = 0, il = column.rowCount; i < il; i++) {
+        if (column.valueKind(i) === 0 /* Present */)
+            return true;
+    }
+    return false;
+}
+function substUndefinedColumn(table, a, b) {
+    if (!table[a].isDefined || !hasPresentValues(table[a]))
+        table[a] = table[b];
+    if (!table[b].isDefined || !hasPresentValues(table[b]))
+        table[b] = table[a];
+}
+/** Fix possibly missing auth_/label_ columns */
+function getNormalizedAtomSite(atom_site) {
+    var normalized = db_1.Table.ofColumns(atom_site._schema, atom_site);
+    substUndefinedColumn(normalized, 'label_atom_id', 'auth_atom_id');
+    substUndefinedColumn(normalized, 'label_comp_id', 'auth_comp_id');
+    substUndefinedColumn(normalized, 'label_seq_id', 'auth_seq_id');
+    substUndefinedColumn(normalized, 'label_asym_id', 'auth_asym_id');
+    return normalized;
+}
+exports.getNormalizedAtomSite = getNormalizedAtomSite;

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

@@ -43,9 +43,9 @@ function getSymmetry(db) {
 }
 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) {
+    return 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, basic, 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 tslib_1.__generator(this, function (_e) {
             switch (_e.label) {
                 case 0:
                     atomCount = db.atom_site._rowCount;
@@ -99,7 +99,7 @@ function getModels(db, format, ctx) {
                         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));
+                            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);
@@ -135,12 +135,12 @@ function getModels(db, format, ctx) {
                     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)({
+                    basic = (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)];
+                    return [4 /*yield*/, (0, parser_1.createModels)(basic, format, ctx)];
                 case 1:
                     models = _e.sent();
                     if (models.frameCount > 0) {
@@ -255,4 +255,3 @@ function trajectoryFromCifCore(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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -10,6 +10,7 @@ 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 constants_1 = require("../../../mol-model/structure/structure/carbohydrates/constants");
 var ProteinAtomIdsList = [
     new Set(['CA']),
     new Set(['C']),
@@ -27,7 +28,7 @@ var DnaAtomIdsList = [
 ];
 /** Used to reduce false positives for atom name-based type guessing */
 var NonPolymerNames = new Set([
-    'FMN', 'NCN', 'FNS', 'FMA' // Mononucleotides
+    'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP', // Mononucleotides
 ]);
 var StandardComponents = (function () {
     var map = new Map();
@@ -151,9 +152,12 @@ var ComponentBuilder = /** @class */ (function () {
             else if (types_1.WaterNames.has(compId)) {
                 this.set({ id: compId, name: 'WATER', type: 'non-polymer' });
             }
-            else if (NonPolymerNames.has(compId)) {
+            else if (NonPolymerNames.has(compId.toUpperCase())) {
                 this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'non-polymer' });
             }
+            else if (constants_1.SaccharideCompIdMap.has(compId.toUpperCase())) {
+                this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'saccharide' });
+            }
             else {
                 var atomIds = this.getAtomIds(index);
                 if (atomIds.size === 1 && CharmmIonComponents.has(compId)) {
@@ -182,4 +186,3 @@ var ComponentBuilder = /** @class */ (function () {
     return ComponentBuilder;
 }());
 exports.ComponentBuilder = ComponentBuilder;
-//# sourceMappingURL=component.js.map

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

@@ -77,4 +77,3 @@ var EntityBuilder = /** @class */ (function () {
     return EntityBuilder;
 }());
 exports.EntityBuilder = EntityBuilder;
-//# sourceMappingURL=entity.js.map

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

@@ -75,4 +75,3 @@ var FormatPropertyProvider;
     FormatPropertyProvider.create = create;
 })(FormatPropertyProvider || (FormatPropertyProvider = {}));
 exports.FormatPropertyProvider = FormatPropertyProvider;
-//# sourceMappingURL=property.js.map

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

@@ -24,4 +24,3 @@ function _getChainId(index) {
     return chainId;
 }
 exports.getChainId = (0, memoize_1.memoize1)(_getChainId);
-//# sourceMappingURL=util.js.map

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

@@ -15,9 +15,9 @@ var schema_1 = require("./basic/schema");
 var component_1 = require("./common/component");
 var entity_1 = require("./common/entity");
 function getModels(cube, ctx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var atoms, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basics;
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var atoms, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basic;
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     atoms = cube.atoms;
@@ -49,12 +49,12 @@ function getModels(cube, ctx) {
                     componentBuilder = new component_1.ComponentBuilder(seq_id, type_symbol);
                     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);
-                    basics = (0, schema_1.createBasic)({
+                    basic = (0, schema_1.createBasic)({
                         entity: entityBuilder.getEntityTable(),
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, (0, parser_1.createModels)(basics, MolFormat.create(cube), ctx)];
+                    return [4 /*yield*/, (0, parser_1.createModels)(basic, MolFormat.create(cube), ctx)];
                 case 1: return [2 /*return*/, _a.sent()];
             }
         });
@@ -75,4 +75,3 @@ function trajectoryFromCube(cube) {
     return mol_task_1.Task.create('Parse Cube', function (ctx) { return getModels(cube, ctx); });
 }
 exports.trajectoryFromCube = trajectoryFromCube;
-//# sourceMappingURL=cube.js.map

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

@@ -16,9 +16,9 @@ var common_1 = require("../../mol-math/linear-algebra/3d/common");
 var charmmTimeUnitFactor = 20.45482949774598;
 function coordinatesFromDcd(dcdFile) {
     var _this = this;
-    return mol_task_1.Task.create('Parse DCD', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Parse DCD', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var header, deltaTime, offsetTime, frames, i, il, dcdFrame, frame, c;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0: return [4 /*yield*/, ctx.update('Converting to coordinates')];
                 case 1:
@@ -64,4 +64,3 @@ function coordinatesFromDcd(dcdFile) {
     }); });
 }
 exports.coordinatesFromDcd = coordinatesFromDcd;
-//# sourceMappingURL=dcd.js.map

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

@@ -24,6 +24,7 @@ function getBasic(atoms, modelNum) {
     var asymIds = new Array(atoms.count);
     var seqIds = new Uint32Array(atoms.count);
     var ids = new Uint32Array(atoms.count);
+    var typeSymbol = new Array(atoms.count);
     var entityBuilder = new entity_1.EntityBuilder();
     var componentBuilder = new component_1.ComponentBuilder(atoms.residueNumber, atoms.atomName);
     var currentEntityId = '';
@@ -53,6 +54,7 @@ function getBasic(atoms, modelNum) {
         asymIds[i] = currentAsymId;
         seqIds[i] = currentSeqId;
         ids[i] = i;
+        typeSymbol[i] = (0, util_1.guessElementSymbolString)(atoms.atomName.value(i), atoms.residueName.value(i));
     }
     var auth_asym_id = db_1.Column.ofStringArray(asymIds);
     var atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
@@ -70,7 +72,7 @@ function getBasic(atoms, modelNum) {
         label_seq_id: db_1.Column.ofIntArray(seqIds),
         label_entity_id: db_1.Column.ofStringArray(entityIds),
         occupancy: db_1.Column.ofConst(1, atoms.count, db_1.Column.Schema.float),
-        type_symbol: db_1.Column.ofStringArray(db_1.Column.mapToArray(atoms.atomName, function (s) { return (0, util_1.guessElementSymbolString)(s); })),
+        type_symbol: db_1.Column.ofStringArray(typeSymbol),
         pdbx_PDB_model_num: db_1.Column.ofConst(modelNum, atoms.count, db_1.Column.Schema.int),
     }, atoms.count);
     return (0, schema_1.createBasic)({
@@ -95,9 +97,9 @@ exports.GroFormat = GroFormat;
 //      need to pass all gro.structures as one table into createModels
 function trajectoryFromGRO(gro) {
     var _this = this;
-    return mol_task_1.Task.create('Parse GRO', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
+    return mol_task_1.Task.create('Parse GRO', function (ctx) { return tslib_1.__awaiter(_this, void 0, void 0, function () {
         var format, models, i, il, basic, m;
-        return (0, tslib_1.__generator)(this, function (_a) {
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     format = GroFormat.fromGro(gro);
@@ -123,4 +125,3 @@ function trajectoryFromGRO(gro) {
     }); });
 }
 exports.trajectoryFromGRO = trajectoryFromGRO;
-//# sourceMappingURL=gro.js.map

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 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>
@@ -17,6 +17,7 @@ var anisotropic_1 = require("./property/anisotropic");
 var chem_comp_1 = require("./property/bonds/chem_comp");
 var struct_conn_1 = require("./property/bonds/struct_conn");
 var global_transform_1 = require("../../mol-model/structure/model/properties/global-transform");
+var schema_1 = require("./basic/schema");
 function modelSymmetryFromMmcif(model) {
     if (!MmcifFormat.is(model.sourceData))
         return;
@@ -87,7 +88,7 @@ var MmcifFormat;
 exports.MmcifFormat = MmcifFormat;
 function trajectoryFromMmCIF(frame) {
     var format = MmcifFormat.fromFrame(frame);
-    return mol_task_1.Task.create('Create mmCIF Model', function (ctx) { return (0, parser_1.createModels)(format.data.db, format, ctx); });
+    var basic = (0, schema_1.createBasic)(format.data.db, true);
+    return mol_task_1.Task.create('Create mmCIF Model', function (ctx) { return (0, parser_1.createModels)(basic, format, ctx); });
 }
 exports.trajectoryFromMmCIF = trajectoryFromMmCIF;
-//# sourceMappingURL=mmcif.js.map

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

@@ -18,9 +18,9 @@ var component_1 = require("./common/component");
 var entity_1 = require("./common/entity");
 var index_pair_1 = require("./property/bonds/index-pair");
 function getMolModels(mol, format, ctx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var atoms, bonds, formalCharges, MOL, A, type_symbol, seq_id, computedFormalCharges, i, i, atom_site, entityBuilder, componentBuilder, basics, models, indexA, indexB, order, pairBonds;
-        return (0, tslib_1.__generator)(this, function (_a) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var atoms, bonds, formalCharges, MOL, A, type_symbol, seq_id, computedFormalCharges, i, i, atom_site, entityBuilder, componentBuilder, basic, models, indexA, indexB, order, pairBonds;
+        return tslib_1.__generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
                     atoms = mol.atoms, bonds = mol.bonds, formalCharges = mol.formalCharges;
@@ -64,12 +64,12 @@ function getMolModels(mol, format, ctx) {
                     componentBuilder = new component_1.ComponentBuilder(seq_id, type_symbol);
                     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);
-                    basics = (0, schema_1.createBasic)({
+                    basic = (0, schema_1.createBasic)({
                         entity: entityBuilder.getEntityTable(),
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, (0, parser_2.createModels)(basics, format !== null && format !== void 0 ? format : MolFormat.create(mol), ctx)];
+                    return [4 /*yield*/, (0, parser_2.createModels)(basic, format !== null && format !== void 0 ? format : MolFormat.create(mol), ctx)];
                 case 1:
                     models = _a.sent();
                     if (models.frameCount > 0) {
@@ -101,4 +101,3 @@ function trajectoryFromMol(mol) {
     return mol_task_1.Task.create('Parse MOL', function (ctx) { return getMolModels(mol, void 0, ctx); });
 }
 exports.trajectoryFromMol = trajectoryFromMol;
-//# sourceMappingURL=mol.js.map

package/lib/commonjs/mol-model-formats/structure/mol2.js

@@ -21,9 +21,9 @@ var symmetry_1 = require("./property/symmetry");
 var geometry_1 = require("../../mol-math/geometry");
 var linear_algebra_1 = require("../../mol-math/linear-algebra");
 function getModels(mol2, ctx) {
-    return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var models, i, il, _a, molecule, atoms, bonds, crysin, A, type_symbol, hasAtomType, i_1, i_2, atom_site, entityBuilder, componentBuilder, i_3, il_1, basics, _models, indexA, indexB, key, order, flag, pairBonds, first, symmetry;
-        return (0, tslib_1.__generator)(this, function (_b) {
+    return tslib_1.__awaiter(this, void 0, void 0, function () {
+        var models, i, il, _a, molecule, atoms, bonds, crysin, A, type_symbol, hasAtomType, i_1, i_2, atom_site, entityBuilder, componentBuilder, i_3, il_1, basic, _models, indexA, indexB, key, order, flag, pairBonds, first, symmetry;
+        return tslib_1.__generator(this, function (_b) {
             switch (_b.label) {
                 case 0:
                     models = [];
@@ -44,7 +44,7 @@ function getModels(mol2, ctx) {
                     for (i_2 = 0; i_2 < atoms.count; ++i_2) {
                         type_symbol[i_2] = hasAtomType
                             ? atoms.atom_type.value(i_2).split('.')[0].toUpperCase()
-                            : (0, util_1.guessElementSymbolString)(atoms.atom_name.value(i_2));
+                            : (0, util_1.guessElementSymbolString)(atoms.atom_name.value(i_2), atoms.subst_name.value(i_2));
                     }
                     atom_site = db_1.Table.ofPartialColumns(schema_1.BasicSchema.atom_site, {
                         auth_asym_id: A,
@@ -71,12 +71,12 @@ function getModels(mol2, ctx) {
                     for (i_3 = 0, il_1 = atoms.subst_name.rowCount; i_3 < il_1; ++i_3) {
                         componentBuilder.add(atoms.subst_name.value(i_3), i_3);
                     }
-                    basics = (0, schema_1.createBasic)({
+                    basic = (0, schema_1.createBasic)({
                         entity: entityBuilder.getEntityTable(),
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, (0, parser_1.createModels)(basics, Mol2Format.create(mol2), ctx)];
+                    return [4 /*yield*/, (0, parser_1.createModels)(basic, Mol2Format.create(mol2), ctx)];
                 case 2:
                     _models = _b.sent();
                     if (_models.frameCount > 0) {
@@ -99,11 +99,11 @@ function getModels(mol2, ctx) {
                         flag = db_1.Column.ofIntArray(db_1.Column.mapToArray(bonds.bond_type, function (x) {
                             switch (x) {
                                 case 'ar': // aromatic
+                                case 'am': // amide
                                     return 16 /* Aromatic */ | 1 /* Covalent */;
                                 case 'du': // dummy
                                 case 'nc': // not connected
                                     return 0 /* None */;
-                                case 'am': // amide
                                 case 'un': // unknown
                                 default:
                                     return 1 /* Covalent */;
@@ -160,4 +160,3 @@ function trajectoryFromMol2(mol2) {
     return mol_task_1.Task.create('Parse MOL2', function (ctx) { return getModels(mol2, ctx); });
 }
 exports.trajectoryFromMol2 = trajectoryFromMol2;
-//# sourceMappingURL=mol2.js.map

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

@@ -0,0 +1,9 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { Task } from '../../mol-task';
+import { NctrajFile } from '../../mol-io/reader/nctraj/parser';
+import { Coordinates } from '../../mol-model/structure/coordinates';
+export declare function coordinatesFromNctraj(file: NctrajFile): Task<Coordinates>;