molstar 3.3.1 → 3.6.0

package/lib/mol-model/structure/structure/carbohydrates/constants.js

@@ -1,11 +1,12 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 var _a, _b;
 import { ColorMap } from '../../../../mol-util/color';
+import { SaccharideNames } from '../../model/types/saccharides';
 export var SaccharideColors = ColorMap({
     Blue: 0x0090bc,
     Green: 0x00a651,
@@ -262,11 +263,6 @@ var CommonSaccharideNames = {
     Sor: ['SOE', 'UEA'],
     Psi: ['PSV', 'SF6', 'SF9', 'TTV'],
 };
-var UnknownSaccharideNames = [
-    'NGZ',
-    'LAT',
-    'PUF', 'GDA', '9WJ', // via updated CCD
-];
 /**
  * From http://glycam.org/docs/othertoolsservice/2016/06/09/3d-snfg-list-of-residue-names/#CHARMM
  */
@@ -309,8 +305,9 @@ export var SaccharideCompIdMap = (function () {
             }
         }
     }
-    for (var i = 0, il = UnknownSaccharideNames.length; i < il; ++i) {
-        map.set(UnknownSaccharideNames[i], UnknownSaccharideComponent);
-    }
+    SaccharideNames.forEach(function (name) {
+        if (!map.has(name))
+            map.set(name, UnknownSaccharideComponent);
+    });
     return map;
 })();

package/lib/mol-model/structure/structure/properties.d.ts

@@ -41,7 +41,7 @@ declare const StructureProperties: {
         microheterogeneityCompIds: StructureElement.Property<string[]>;
         secondary_structure_type: StructureElement.Property<SecondaryStructureType>;
         secondary_structure_key: StructureElement.Property<number>;
-        chem_comp_type: StructureElement.Property<"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">;
+        chem_comp_type: StructureElement.Property<"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">;
     };
     chain: {
         key: StructureElement.Property<import("../model").ChainIndex>;

package/lib/mol-model/structure/structure/unit/bonds/inter-compute.js

@@ -167,10 +167,8 @@ var DefaultInterBondComputationProps = __assign(__assign({}, DefaultBondComputat
 function findBonds(structure, props) {
     var builder = new InterUnitGraph.Builder();
     var hasIndexPairBonds = structure.models.some(function (m) { return IndexPairBonds.Provider.get(m); });
-    if (props.noCompute || (structure.isCoarseGrained && !hasIndexPairBonds)) {
-        // TODO add function that only adds bonds defined in structConn and avoids using
-        //      structure.lookup and unit.lookup (expensive for large structure and not
-        //      needed for archival files or files with an MD topology)
+    var hasExhaustiveStructConn = structure.models.some(function (m) { return StructConn.isExhaustive(m); });
+    if (props.noCompute || (structure.isCoarseGrained && !hasIndexPairBonds && !hasExhaustiveStructConn)) {
         return new InterUnitBonds(builder.getMap());
     }
     Structure.eachUnitPair(structure, function (unitA, unitB) {

package/lib/mol-model/structure/structure/unit/bonds/intra-compute.js

@@ -221,9 +221,7 @@ function findBonds(unit, props) {
 }
 function computeIntraUnitBonds(unit, props) {
     var p = __assign(__assign({}, DefaultBondComputationProps), props);
-    if (p.noCompute || Model.isCoarseGrained(unit.model)) {
-        // TODO add function that only adds bonds defined in structConn of chemCompBond
-        //      and avoid using unit.lookup
+    if (p.noCompute || (Model.isCoarseGrained(unit.model) && !IndexPairBonds.Provider.get(unit.model) && !StructConn.isExhaustive(unit.model))) {
         return IntraUnitBonds.Empty;
     }
     if (!p.forceCompute && IndexPairBonds.Provider.get(unit.model)) {

package/lib/mol-model/structure/structure/unit/rings.js

@@ -127,6 +127,9 @@ var UnitRing;
             return false;
         if (ring.length < 5)
             return false;
+        // no planarity-based aromaticity if any aromatic flags are present
+        if (aromaticBondCount > 0)
+            return false;
         var ma = PrincipalAxes.calculateMomentsAxes(getPositions(unit, ring));
         return Vec3.magnitude(ma.dirC) < AromaticRingPlanarityThreshold;
     }

package/lib/mol-model-formats/shape/ply.d.ts

@@ -30,6 +30,7 @@ export declare const PlyShapeParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -71,6 +72,7 @@ export declare function shapeFromPly(source: PlyFile, params?: {}): Task<ShapePr
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    allowTransparentBackfaces: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/mol-model-formats/structure/basic/atomic.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/mol-model-formats/structure/basic/atomic.js

@@ -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>
@@ -37,14 +37,6 @@ function findHierarchyOffsets(atom_site) {
     }
     return { residues: residues, chains: chains };
 }
-function substUndefinedColumn(table, a, b) {
-    if (!table[a].isDefined) {
-        table[a] = table[b];
-    }
-    if (!table[b].isDefined) {
-        table[b] = table[a];
-    }
-}
 function createHierarchyData(atom_site, sourceIndex, offsets) {
     var atoms = Table.ofColumns(AtomsSchema, {
         type_symbol: Column.ofArray({ array: Column.mapToArray(atom_site.type_symbol, ElementSymbol), schema: Column.Schema.Aliased(Column.Schema.str) }),
@@ -74,11 +66,6 @@ function createHierarchyData(atom_site, sourceIndex, offsets) {
     // Optimize the numeric columns
     Table.columnToArray(residues, 'label_seq_id', Int32Array);
     Table.columnToArray(residues, 'auth_seq_id', Int32Array);
-    // Fix possibly missing auth_/label_ columns
-    substUndefinedColumn(atoms, 'label_atom_id', 'auth_atom_id');
-    substUndefinedColumn(atoms, 'label_comp_id', 'auth_comp_id');
-    substUndefinedColumn(residues, 'label_seq_id', 'auth_seq_id');
-    substUndefinedColumn(chains, 'label_asym_id', 'auth_asym_id');
     return { atoms: atoms, residues: residues, chains: chains, atomSourceIndex: sourceIndex };
 }
 function getConformation(atom_site) {

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

@@ -96,7 +96,7 @@ export function getEntityData(data) {
                 var entityId = label_entity_id.value(i);
                 if (!entityIds.has(entityId)) {
                     var compId = label_comp_id.value(i);
-                    var compType = chemCompType.get(compId) || '';
+                    var compType = chemCompType.get(compId) || 'other';
                     subtypes[getEntityIndex(entityId)] = getEntitySubtype(compId, compType);
                     entityIds.add(entityId);
                 }

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

@@ -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/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>
  */
@@ -88,7 +88,7 @@ export declare const BasicSchema: {
         type: import("../../../mol-data/db/column").Column.Schema.Aliased<"oligosaccharide">;
     };
     chem_comp: {
-        type: import("../../../mol-data/db/column").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">;
+        type: import("../../../mol-data/db/column").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: import("../../../mol-data/db/column").Column.Schema.Str;
         formula_weight: import("../../../mol-data/db/column").Column.Schema.Float;
         id: import("../../../mol-data/db/column").Column.Schema.Str;
@@ -160,7 +160,7 @@ export declare const BasicSchema: {
     };
     pdbx_unobs_or_zero_occ_residues: {
         id: import("../../../mol-data/db/column").Column.Schema.Int;
-        polymer_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"N" | "Y">;
+        polymer_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"y" | "n">;
         occupancy_flag: import("../../../mol-data/db/column").Column.Schema.Aliased<"1" | "0">;
         PDB_model_num: import("../../../mol-data/db/column").Column.Schema.Int;
         auth_asym_id: import("../../../mol-data/db/column").Column.Schema.Str;
@@ -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/mol-model-formats/structure/basic/schema.js

@@ -1,11 +1,12 @@
 /**
- * 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>
  */
 import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
 import { Table } from '../../../mol-data/db';
 import { mmCIF_chemComp_schema } from '../../../mol-io/reader/cif/schema/mmcif-extras';
+import { getNormalizedAtomSite } from './util';
 export var BasicSchema = {
     entry: mmCIF_Schema.entry,
     struct: mmCIF_Schema.struct,
@@ -25,7 +26,8 @@ export var BasicSchema = {
     pdbx_unobs_or_zero_occ_residues: mmCIF_Schema.pdbx_unobs_or_zero_occ_residues,
     pdbx_molecule: mmCIF_Schema.pdbx_molecule,
 };
-export function createBasic(data) {
+export function createBasic(data, normalize) {
+    if (normalize === void 0) { normalize = false; }
     var basic = Object.create(null);
     for (var _i = 0, _a = Object.keys(BasicSchema); _i < _a.length; _i++) {
         var name_1 = _a[_i];
@@ -36,5 +38,8 @@ export function createBasic(data) {
             basic[name_1] = Table.ofUndefinedColumns(BasicSchema[name_1], 0);
         }
     }
+    if (normalize) {
+        basic.atom_site = getNormalizedAtomSite(basic.atom_site);
+    }
     return basic;
 }

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

@@ -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>
@@ -15,3 +15,26 @@ export function getModelGroupName(model_id, data) {
     }
     return '';
 }
+//
+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 */
+export function getNormalizedAtomSite(atom_site) {
+    var normalized = 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;
+}

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

@@ -41,7 +41,7 @@ function getSymmetry(db) {
 function getModels(db, format, ctx) {
     var _a;
     return __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;
+        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 __generator(this, function (_e) {
             switch (_e.label) {
                 case 0:
@@ -96,7 +96,7 @@ 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] = guessElementSymbolString(label.value(i));
+                            element_symbol[i] = guessElementSymbolString(label.value(i), '');
                         }
                         typeSymbol = Column.ofStringArray(element_symbol);
                         formalCharge = Column.Undefined(atomCount, Column.Schema.int);
@@ -132,12 +132,12 @@ function getModels(db, format, ctx) {
                     componentBuilder = new ComponentBuilder(seq_id, db.atom_site.type_symbol);
                     componentBuilder.setNames([['MOL', name || 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);
-                    basics = createBasic({
+                    basic = createBasic({
                         entity: entityBuilder.getEntityTable(),
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, createModels(basics, format, ctx)];
+                    return [4 /*yield*/, createModels(basic, format, ctx)];
                 case 1:
                     models = _e.sent();
                     if (models.frameCount > 0) {

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

@@ -19,7 +19,7 @@ export declare class ComponentBuilder {
     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">;
+        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;
@@ -28,7 +28,7 @@ export declare class ComponentBuilder {
         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">;
+        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;
@@ -37,7 +37,7 @@ export declare class ComponentBuilder {
         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">;
+        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;

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

@@ -7,6 +7,7 @@ import { Table, Column } from '../../../mol-data/db';
 import { WaterNames, PolymerNames } from '../../../mol-model/structure/model/types';
 import { SetUtils } from '../../../mol-util/set';
 import { BasicSchema } from '../basic/schema';
+import { SaccharideCompIdMap } from '../../../mol-model/structure/structure/carbohydrates/constants';
 var ProteinAtomIdsList = [
     new Set(['CA']),
     new Set(['C']),
@@ -24,50 +25,50 @@ var DnaAtomIdsList = [
 ];
 /** Used to reduce false positives for atom name-based type guessing */
 var NonPolymerNames = new Set([
-    'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP' // Mononucleotides
+    'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP', // 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: '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' },
+        { 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;
@@ -75,12 +76,12 @@ var StandardComponents = (function () {
 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' },
+        { 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;
@@ -129,10 +130,10 @@ var ComponentBuilder = /** @class */ (function () {
             return 'peptide linking';
         }
         else if (this.hasAtomIds(atomIds, RnaAtomIdsList)) {
-            return 'RNA linking';
+            return 'rna linking';
         }
         else if (this.hasAtomIds(atomIds, DnaAtomIdsList)) {
-            return 'DNA linking';
+            return 'dna linking';
         }
         else {
             return 'other';
@@ -151,6 +152,9 @@ var ComponentBuilder = /** @class */ (function () {
             else if (NonPolymerNames.has(compId.toUpperCase())) {
                 this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'non-polymer' });
             }
+            else if (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)) {

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

@@ -13,7 +13,7 @@ import { ComponentBuilder } from './common/component';
 import { EntityBuilder } from './common/entity';
 function getModels(cube, ctx) {
     return __awaiter(this, void 0, void 0, function () {
-        var atoms, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basics;
+        var atoms, MOL, A, type_symbol, seq_id, atom_site, entityBuilder, componentBuilder, basic;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -46,12 +46,12 @@ function getModels(cube, ctx) {
                     componentBuilder = new ComponentBuilder(seq_id, type_symbol);
                     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);
-                    basics = createBasic({
+                    basic = createBasic({
                         entity: entityBuilder.getEntityTable(),
                         chem_comp: componentBuilder.getChemCompTable(),
                         atom_site: atom_site
                     });
-                    return [4 /*yield*/, createModels(basics, MolFormat.create(cube), ctx)];
+                    return [4 /*yield*/, createModels(basic, MolFormat.create(cube), ctx)];
                 case 1: return [2 /*return*/, _a.sent()];
             }
         });

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

@@ -21,6 +21,7 @@ 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 EntityBuilder();
     var componentBuilder = new ComponentBuilder(atoms.residueNumber, atoms.atomName);
     var currentEntityId = '';
@@ -50,6 +51,7 @@ function getBasic(atoms, modelNum) {
         asymIds[i] = currentAsymId;
         seqIds[i] = currentSeqId;
         ids[i] = i;
+        typeSymbol[i] = guessElementSymbolString(atoms.atomName.value(i), atoms.residueName.value(i));
     }
     var auth_asym_id = Column.ofStringArray(asymIds);
     var atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
@@ -67,7 +69,7 @@ function getBasic(atoms, modelNum) {
         label_seq_id: Column.ofIntArray(seqIds),
         label_entity_id: Column.ofStringArray(entityIds),
         occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
-        type_symbol: Column.ofStringArray(Column.mapToArray(atoms.atomName, function (s) { return guessElementSymbolString(s); })),
+        type_symbol: Column.ofStringArray(typeSymbol),
         pdbx_PDB_model_num: Column.ofConst(modelNum, atoms.count, Column.Schema.int),
     }, atoms.count);
     return createBasic({

package/lib/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>