molstar 3.5.0 → 3.7.0

package/lib/commonjs/mol-io/reader/cif/schema/mmcif.js

@@ -1,8 +1,8 @@
 "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.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.356, IHM 1.17, MA 1.3.5.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.357, IHM 1.17, MA 1.3.6.
  *
  * @author molstar/ciftools package
  */
@@ -17,6 +17,7 @@ var coord = Schema.coord;
 var Aliased = Schema.Aliased;
 var Matrix = Schema.Matrix;
 var Vector = Schema.Vector;
+var lstr = Schema.lstr;
 var List = Schema.List;
 exports.mmCIF_Schema = {
     /**
@@ -511,7 +512,7 @@ exports.mmCIF_Schema = {
          * _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and
          * _chem_comp.mon_nstd_details data items.
          */
-        mon_nstd_flag: Aliased(str),
+        mon_nstd_flag: Aliased(lstr),
         /**
          * The full name of the component.
          */
@@ -522,7 +523,7 @@ exports.mmCIF_Schema = {
          * linking monomers, monomers with some type of N-terminal (or 5')
          * cap and monomers with some type of C-terminal (or 3') cap.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * Synonym list for the component.
          */
@@ -559,7 +560,7 @@ exports.mmCIF_Schema = {
          * bond associated with the specified atoms, expressed as a bond
          * order.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
         /**
          * Ordinal index for the component bond list.
          */
@@ -567,11 +568,11 @@ exports.mmCIF_Schema = {
         /**
          * Stereochemical configuration across a double bond.
          */
-        pdbx_stereo_config: Aliased(str),
+        pdbx_stereo_config: Aliased(lstr),
         /**
          * A flag indicating an aromatic bond.
          */
-        pdbx_aromatic_flag: Aliased(str),
+        pdbx_aromatic_flag: Aliased(lstr),
     },
     /**
      * Data items in the CITATION category record details about the
@@ -703,7 +704,7 @@ exports.mmCIF_Schema = {
         /**
          * An abbreviation that identifies the database.
          */
-        database_id: Aliased(str),
+        database_id: Aliased(lstr),
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.
@@ -766,7 +767,7 @@ exports.mmCIF_Schema = {
          * manipulated sources are expected to have further information in
          * the ENTITY_SRC_GEN category.
          */
-        src_method: Aliased(str),
+        src_method: Aliased(lstr),
         /**
          * Defines the type of the entity.
          *
@@ -779,7 +780,7 @@ exports.mmCIF_Schema = {
          * Water entities are not expected to have corresponding
          * entries in the ENTITY category.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * A description of the entity.
          *
@@ -819,12 +820,12 @@ exports.mmCIF_Schema = {
          * one monomer-to-monomer link different from that implied by
          * _entity_poly.type.
          */
-        nstd_linkage: Aliased(str),
+        nstd_linkage: Aliased(lstr),
         /**
          * A flag to indicate whether the polymer contains at least
          * one monomer that is not considered standard.
          */
-        nstd_monomer: Aliased(str),
+        nstd_monomer: Aliased(lstr),
         /**
          * The type of the polymer.
          */
@@ -893,6 +894,10 @@ exports.mmCIF_Schema = {
          * parent is not specified. Deoxynucleotides are
          * represented by their canonical one-letter codes of A,
          * C, G, or T.
+         *
+         * For modifications with several parent amino acids,
+         * all corresponding parent amino acid codes will be listed
+         * (ex. chromophores).
          */
         pdbx_seq_one_letter_code_can: str,
         /**
@@ -918,7 +923,7 @@ exports.mmCIF_Schema = {
          * A flag to indicate whether this monomer in the polymer is
          * heterogeneous in sequence.
          */
-        hetero: Aliased(str),
+        hetero: Aliased(lstr),
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -995,7 +1000,7 @@ exports.mmCIF_Schema = {
          * The classification of the software according to the most
          * common types.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * The version of the software.
          */
@@ -1118,7 +1123,7 @@ exports.mmCIF_Schema = {
          * This data item is a pointer to _struct_conf_type.id in the
          * STRUCT_CONF_TYPE category.
          */
-        conf_type_id: Aliased(str),
+        conf_type_id: Aliased(lstr),
         /**
          * A description of special aspects of the conformation assignment.
          */
@@ -1218,7 +1223,7 @@ exports.mmCIF_Schema = {
          * This data item is a pointer to _struct_conn_type.id in the
          * STRUCT_CONN_TYPE category.
          */
-        conn_type_id: Aliased(str),
+        conn_type_id: Aliased(lstr),
         /**
          * A description of special aspects of the connection.
          */
@@ -1438,7 +1443,7 @@ exports.mmCIF_Schema = {
          * The chemical bond order associated with the specified atoms in
          * this contact.
          */
-        pdbx_value_order: Aliased(str),
+        pdbx_value_order: Aliased(lstr),
     },
     /**
      * Data items in the STRUCT_CONN_TYPE category record details
@@ -1453,7 +1458,7 @@ exports.mmCIF_Schema = {
         /**
          * The chemical or structural type of the interaction.
          */
-        id: Aliased(str),
+        id: Aliased(lstr),
         /**
          * A reference that specifies the criteria used to define the
          * interaction.
@@ -1807,7 +1812,7 @@ exports.mmCIF_Schema = {
         /**
          * The cell settings for this space-group symmetry.
          */
-        cell_setting: Aliased(str),
+        cell_setting: Aliased(lstr),
         /**
          * Space-group number from International Tables for Crystallography
          * Vol. A (2002).
@@ -1867,7 +1872,7 @@ exports.mmCIF_Schema = {
          * This code indicates whether the entry belongs to
          * Structural Genomics Project.
          */
-        SG_entry: Aliased(str),
+        SG_entry: Aliased(lstr),
         /**
          * The site where the file was deposited.
          */
@@ -1891,7 +1896,7 @@ exports.mmCIF_Schema = {
          * A value of 'N' indicates that the no PDB format data file is
          * corresponding to this entry is available in the PDB archive.
          */
-        pdb_format_compatible: Aliased(str),
+        pdb_format_compatible: Aliased(lstr),
     },
     /**
      * The PDBX_NONPOLY_SCHEME category provides residue level nomenclature
@@ -2044,7 +2049,7 @@ exports.mmCIF_Schema = {
          * The value of polymer flag indicates whether the unobserved or
          * zero occupancy residue is part of a polymer chain or not
          */
-        polymer_flag: Aliased(str),
+        polymer_flag: Aliased(lstr),
         /**
          * The value of occupancy flag indicates whether the residue
          * is unobserved (= 1) or the coordinates have an occupancy of zero (=0)
@@ -2297,7 +2302,7 @@ exports.mmCIF_Schema = {
         /**
          * Defines the polymer characteristic of the entity.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * Additional details about this entity.
          */
@@ -2392,7 +2397,7 @@ exports.mmCIF_Schema = {
         /**
          * The bond order target for the chemical linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
         /**
          * The entity component identifier for the first of two entities containing the linkage.
          */
@@ -2478,7 +2483,7 @@ exports.mmCIF_Schema = {
         /**
          * The bond order target for the non-standard linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
     },
     /**
      * Data items in the PDBX_MOLECULE category identify reference molecules
@@ -2513,11 +2518,11 @@ exports.mmCIF_Schema = {
         /**
          * Broadly defines the function of the molecule.
          */
-        class: Aliased(str),
+        class: Aliased(lstr),
         /**
          * Defines the structural classification of the molecule.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * A name of the molecule.
          */
@@ -2664,7 +2669,7 @@ exports.mmCIF_Schema = {
         /**
          * This data item contains the descriptor type.
          */
-        type: Aliased(str),
+        type: Aliased(lstr),
         /**
          * This data item contains the name of the program
          * or library used to compute the descriptor.
@@ -2739,7 +2744,7 @@ exports.mmCIF_Schema = {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Aliased(str),
+        hetero: Aliased(lstr),
         /**
          * This data item is a pointer to _chem_comp.id in the CHEM_COMP
          * category.
@@ -2811,7 +2816,7 @@ exports.mmCIF_Schema = {
         /**
          * The chiral configuration of the first atom making the linkage.
          */
-        atom_stereo_config_1: Aliased(str),
+        atom_stereo_config_1: Aliased(lstr),
         /**
          * The atom identifier/name for the second atom making the linkage.
          */
@@ -2823,11 +2828,11 @@ exports.mmCIF_Schema = {
         /**
          * The chiral configuration of the second atom making the linkage.
          */
-        atom_stereo_config_2: Aliased(str),
+        atom_stereo_config_2: Aliased(lstr),
         /**
          * The bond order target for the chemical linkage.
          */
-        value_order: Aliased(str),
+        value_order: Aliased(lstr),
     },
     /**
      * Data items in the PDBX_ENTITY_BRANCH category specify the list
@@ -2858,7 +2863,7 @@ exports.mmCIF_Schema = {
          * A flag to indicate whether this monomer in the entity is
          * heterogeneous in sequence.
          */
-        hetero: Aliased(str),
+        hetero: Aliased(lstr),
         /**
          * Pointer to _atom_site.label_asym_id.
          */
@@ -3331,15 +3336,15 @@ exports.mmCIF_Schema = {
         /**
          * A flag to indicate if the modeling is multi scale.
          */
-        multi_scale_flag: Aliased(str),
+        multi_scale_flag: Aliased(lstr),
         /**
          * A flag to indicate if the modeling is multi state.
          */
-        multi_state_flag: Aliased(str),
+        multi_state_flag: Aliased(lstr),
         /**
          * A flag to indicate if the modeling involves an ensemble ordered by time or other order.
          */
-        ordered_flag: Aliased(str),
+        ordered_flag: Aliased(lstr),
         /**
          * The file id corresponding to the script used in the modeling protocol step.
          * This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category.
@@ -3628,7 +3633,7 @@ exports.mmCIF_Schema = {
          * A flag that indicates whether the dataset is archived in
          * an IHM related database or elsewhere.
          */
-        database_hosted: Aliased(str),
+        database_hosted: Aliased(lstr),
     },
     /**
      * Category to define groups or collections of input datasets.
@@ -4235,7 +4240,7 @@ exports.mmCIF_Schema = {
          * whether the whole image is used or only a portion of it is used (by masking
          * or by other means) as restraint in the modeling.
          */
-        image_segment_flag: Aliased(str),
+        image_segment_flag: Aliased(lstr),
         /**
          * Number of 2D projections of the model used in the fitting.
          */
@@ -4388,7 +4393,7 @@ exports.mmCIF_Schema = {
          * whether the whole SAS profile is used or only a portion of it is used
          * (by masking or by other means) as restraint in the modeling.
          */
-        profile_segment_flag: Aliased(str),
+        profile_segment_flag: Aliased(lstr),
         /**
          * The type of atoms in the model fit to the SAS data.
          */

package/lib/commonjs/mol-io/reader/cif/schema.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2019 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-io/reader/cif/schema.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2017-2019 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>
@@ -48,13 +48,33 @@ function toTable(schema, category) {
 exports.toTable = toTable;
 function getColumnCtor(t) {
     switch (t.valueType) {
-        case 'str': return function (f, c, k) { return createColumn(t, f, f.str, f.toStringArray); };
+        case 'str': return function (f, c, k) { return createStringColumn(t, f, f.str, f.toStringArray); };
         case 'int': return function (f, c, k) { return createColumn(t, f, f.int, f.toIntArray); };
         case 'float': return function (f, c, k) { return createColumn(t, f, f.float, f.toFloatArray); };
         case 'list': throw new Error('Use createListColumn instead.');
         case 'tensor': throw new Error('Use createTensorColumn instead.');
     }
 }
+function createStringColumn(schema, field, value, toArray) {
+    return {
+        schema: schema,
+        __array: field.__array,
+        isDefined: field.isDefined,
+        rowCount: field.rowCount,
+        value: schema.transform === 'lowercase'
+            ? function (row) { return value(row).toLowerCase(); }
+            : schema.transform === 'uppercase'
+                ? function (row) { return value(row).toUpperCase(); }
+                : value,
+        valueKind: field.valueKind,
+        areValuesEqual: field.areValuesEqual,
+        toArray: schema.transform === 'lowercase'
+            ? function (p) { return Array.from(toArray(p)).map(function (x) { return x.toLowerCase(); }); }
+            : schema.transform === 'uppercase'
+                ? function (p) { return Array.from(toArray(p)).map(function (x) { return x.toUpperCase(); }); }
+                : toArray,
+    };
+}
 function createColumn(schema, field, value, toArray) {
     return {
         schema: schema,

package/lib/commonjs/mol-io/writer/ligand-encoder.d.ts

@@ -8,11 +8,12 @@ import { Writer } from './writer';
 import { Encoder, Category } from './cif/encoder';
 import { ComponentAtom } from '../../mol-model-formats/structure/property/atoms/chem_comp';
 import { ComponentBond } from '../../mol-model-formats/structure/property/bonds/chem_comp';
+import { ElementSymbol } from '../../mol-model/structure/model/types';
 interface Atom {
     Cartn_x: number;
     Cartn_y: number;
     Cartn_z: number;
-    type_symbol: string;
+    type_symbol: ElementSymbol;
     index: number;
 }
 declare function Atom(partial: any): Atom;
@@ -39,7 +40,8 @@ export declare abstract class LigandEncoder implements Encoder<string> {
     getData(): string;
     protected getAtoms<Ctx>(instance: Category.Instance<Ctx>, source: any): Map<string, Atom>;
     private _getAtoms;
-    protected skipHydrogen(type_symbol: string): boolean;
+    protected skipHydrogen(type_symbol: ElementSymbol): boolean;
+    protected isHydrogen(type_symbol: ElementSymbol): boolean;
     private getSortedFields;
     private getField;
     protected getName<Ctx>(instance: Category.Instance<Ctx>, source: any): string;

package/lib/commonjs/mol-io/writer/ligand-encoder.js

@@ -8,6 +8,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.LigandEncoder = void 0;
 var tslib_1 = require("tslib");
 var mol_util_1 = require("../../mol-util");
+var common_1 = require("../../mol-model/structure/structure/unit/bonds/common");
 function Atom(partial) {
     return tslib_1.__assign({}, partial);
 }
@@ -80,11 +81,12 @@ var LigandEncoder = /** @class */ (function () {
             while (it_1.hasNext) {
                 var key = it_1.move();
                 var lai = label_atom_id.value(key, data, index);
+                // ignore all alternate locations after the first
+                if (atoms.has(lai))
+                    continue;
                 var ts = type_symbol.value(key, data, index);
-                if (this.skipHydrogen(ts)) {
-                    index++;
+                if (this.skipHydrogen(ts))
                     continue;
-                }
                 var a = {};
                 for (var _f = 0, _fl = fields.length; _f < _fl; _f++) {
                     var f = fields[_f];
@@ -102,7 +104,10 @@ var LigandEncoder = /** @class */ (function () {
         if (this.hydrogens) {
             return false;
         }
-        return type_symbol === 'H';
+        return this.isHydrogen(type_symbol);
+    };
+    LigandEncoder.prototype.isHydrogen = function (type_symbol) {
+        return (0, common_1.isHydrogen)((0, common_1.getElementIdx)(type_symbol));
     };
     LigandEncoder.prototype.getSortedFields = function (instance, names) {
         var _this = this;

package/lib/commonjs/mol-io/writer/mol/encoder.js

@@ -36,13 +36,25 @@ var MolEncoder = /** @class */ (function (_super) {
         mol_util_1.StringBuilder.writeSafe(this.builder, "".concat(name, "\n  ").concat(this.encoder, "\n\n"));
         var atomMap = this.componentAtomData.entries.get(name);
         var bondMap = this.componentBondData.entries.get(name);
+        // happens for the unknown ligands (UNL)
+        if (!atomMap)
+            throw Error("The Chemical Component Dictionary doesn't hold any atom data for ".concat(name));
         var bondCount = 0;
         var chiral = false;
         // traverse once to determine all actually present atoms
         var atoms = this.getAtoms(instance, source);
         atoms.forEach(function (atom1, label_atom_id1) {
-            var i1 = atom1.index;
-            var _a = atomMap.map.get(label_atom_id1), charge = _a.charge, stereo_config = _a.stereo_config;
+            var i1 = atom1.index, type_symbol1 = atom1.type_symbol;
+            var atomMapData1 = atomMap.map.get(label_atom_id1);
+            if (!atomMapData1) {
+                if (_this.isHydrogen(type_symbol1)) {
+                    return;
+                }
+                else {
+                    throw Error("Unknown atom ".concat(label_atom_id1, " for component ").concat(name));
+                }
+            }
+            var charge = atomMapData1.charge, stereo_config = atomMapData1.stereo_config;
             mol_util_1.StringBuilder.writePadLeft(ctab, atom1.Cartn_x.toFixed(4), 10);
             mol_util_1.StringBuilder.writePadLeft(ctab, atom1.Cartn_y.toFixed(4), 10);
             mol_util_1.StringBuilder.writePadLeft(ctab, atom1.Cartn_z.toFixed(4), 10);
@@ -51,7 +63,7 @@ var MolEncoder = /** @class */ (function (_super) {
             mol_util_1.StringBuilder.writeSafe(ctab, '  0');
             mol_util_1.StringBuilder.writeIntegerPadLeft(ctab, _this.mapCharge(charge), 3);
             mol_util_1.StringBuilder.writeSafe(ctab, '  0  0  0  0  0  0  0  0  0  0\n');
-            if (stereo_config !== 'N')
+            if (stereo_config !== 'n')
                 chiral = true;
             // no data for metal ions
             if (!(bondMap === null || bondMap === void 0 ? void 0 : bondMap.map))
@@ -60,8 +72,8 @@ var MolEncoder = /** @class */ (function (_super) {
                 var atom2 = atoms.get(label_atom_id2);
                 if (!atom2)
                     return;
-                var i2 = atom2.index, type_symbol2 = atom2.type_symbol;
-                if (i1 < i2 && !_this.skipHydrogen(type_symbol2)) {
+                var i2 = atom2.index;
+                if (i1 < i2) {
                     var order = bond.order;
                     mol_util_1.StringBuilder.writeIntegerPadLeft(bonds, i1 + 1, 3);
                     mol_util_1.StringBuilder.writeIntegerPadLeft(bonds, i2 + 1, 3);

package/lib/commonjs/mol-io/writer/mol2/encoder.js

@@ -30,20 +30,33 @@ var Mol2Encoder = /** @class */ (function (_super) {
         // write header
         var name = this.getName(instance, source);
         mol_util_1.StringBuilder.writeSafe(this.builder, "# Name: ".concat(name, "\n# Created by ").concat(this.encoder, "\n\n"));
+        var atomMap = this.componentAtomData.entries.get(name);
         var bondMap = this.componentBondData.entries.get(name);
+        // happens for the unknown ligands (UNL)
+        if (!atomMap)
+            throw Error("The Chemical Component Dictionary doesn't hold any atom data for ".concat(name));
         var bondCount = 0;
         var atoms = this.getAtoms(instance, source);
         mol_util_1.StringBuilder.writeSafe(a, '@<TRIPOS>ATOM\n');
         mol_util_1.StringBuilder.writeSafe(b, '@<TRIPOS>BOND\n');
         atoms.forEach(function (atom1, label_atom_id1) {
-            var i1 = atom1.index;
+            var i1 = atom1.index, type_symbol1 = atom1.type_symbol;
+            var atomMapData1 = atomMap.map.get(label_atom_id1);
+            if (!atomMapData1) {
+                if (_this.isHydrogen(type_symbol1)) {
+                    return;
+                }
+                else {
+                    throw Error("Unknown atom ".concat(label_atom_id1, " for component ").concat(name));
+                }
+            }
             if (bondMap === null || bondMap === void 0 ? void 0 : bondMap.map) {
                 bondMap.map.get(label_atom_id1).forEach(function (bond, label_atom_id2) {
                     var atom2 = atoms.get(label_atom_id2);
                     if (!atom2)
                         return;
-                    var i2 = atom2.index, type_symbol2 = atom2.type_symbol;
-                    if (i1 < i2 && !_this.skipHydrogen(type_symbol2)) {
+                    var i2 = atom2.index;
+                    if (i1 < i2) {
                         var order = bond.order, flags = bond.flags;
                         var ar = types_1.BondType.is(16 /* Aromatic */, flags);
                         mol_util_1.StringBuilder.writeSafe(b, "".concat(++bondCount, " ").concat(i1 + 1, " ").concat(i2 + 1, " ").concat(ar ? 'ar' : order));
@@ -51,7 +64,7 @@ var Mol2Encoder = /** @class */ (function (_super) {
                     }
                 });
             }
-            var sybyl = (bondMap === null || bondMap === void 0 ? void 0 : bondMap.map) ? _this.mapToSybyl(label_atom_id1, atom1.type_symbol, bondMap) : atom1.type_symbol;
+            var sybyl = (bondMap === null || bondMap === void 0 ? void 0 : bondMap.map) ? _this.mapToSybyl(label_atom_id1, type_symbol1, bondMap) : type_symbol1;
             mol_util_1.StringBuilder.writeSafe(a, "".concat(i1 + 1, " ").concat(label_atom_id1, " ").concat(atom1.Cartn_x.toFixed(3), " ").concat(atom1.Cartn_y.toFixed(3), " ").concat(atom1.Cartn_z.toFixed(3), " ").concat(sybyl, " 1 ").concat(name, " 0.000\n"));
         });
         // could write something like 'SMALL\nNO_CHARGES', for now let's write **** indicating non-optional, yet missing, string values

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

@@ -21,6 +21,7 @@ var symmetry_1 = require("../../../mol-model-formats/structure/property/symmetry
 var db_1 = require("../../../mol-data/db");
 var custom_model_property_1 = require("../../../mol-model-props/common/custom-model-property");
 var trajectory_1 = require("../trajectory");
+var secondary_structure_1 = require("../../../mol-model-formats/structure/property/secondary-structure");
 { }
 var Model;
 (function (Model) {
@@ -31,8 +32,12 @@ var Model;
         var isIdentity = db_1.Column.isIdentity(srcIndex);
         var srcIndexArray = isIdentity ? void 0 : srcIndex.toArray({ array: Int32Array });
         var coarseGrained = isCoarseGrained(model);
+        var elementCount = model.atomicHierarchy.atoms._rowCount;
         for (var i = 0, il = frames.length; i < il; ++i) {
             var f = frames[i];
+            if (f.elementCount !== elementCount) {
+                throw new Error("Frame element count mismatch, got ".concat(f.elementCount, " but expected ").concat(elementCount, "."));
+            }
             var m = tslib_1.__assign(tslib_1.__assign({}, model), { id: uuid_1.UUID.create22(), modelNum: i, atomicConformation: coordinates_1.Coordinates.getAtomicConformation(f, model.atomicConformation.atomId, srcIndexArray), 
                 // TODO: add support for supplying sphere and gaussian coordinates in addition to atomic coordinates?
                 // coarseConformation: coarse.conformation,
@@ -218,7 +223,7 @@ var Model;
             return false;
         var db = model.sourceData.data.db;
         for (var i = 0, il = db.database_2.database_id.rowCount; i < il; ++i) {
-            if (db.database_2.database_id.value(i) === 'PDB')
+            if (db.database_2.database_id.value(i) === 'pdb')
                 return true;
         }
         return false;
@@ -235,11 +240,14 @@ var Model;
     }
     Model.hasPdbId = hasPdbId;
     function hasSecondaryStructure(model) {
-        if (!mmcif_1.MmcifFormat.is(model.sourceData))
-            return false;
-        var db = model.sourceData.data.db;
-        return (db.struct_conf.id.isDefined ||
-            db.struct_sheet_range.id.isDefined);
+        if (mmcif_1.MmcifFormat.is(model.sourceData)) {
+            var db = model.sourceData.data.db;
+            return (db.struct_conf.id.isDefined ||
+                db.struct_sheet_range.id.isDefined);
+        }
+        else {
+            return secondary_structure_1.ModelSecondaryStructure.Provider.isApplicable(model);
+        }
     }
     Model.hasSecondaryStructure = hasSecondaryStructure;
     var tmpAngles90 = linear_algebra_1.Vec3.create(1.5707963, 1.5707963, 1.5707963); // in radians

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

@@ -8,4 +8,4 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.EntitySubtype = void 0;
 var db_1 = require("../../../../mol-data/db");
-exports.EntitySubtype = db_1.Column.Schema.Aliased(db_1.Column.Schema.Str(''));
+exports.EntitySubtype = db_1.Column.Schema.Aliased(db_1.Column.Schema.Str());