molstar 3.8.2 → 3.9.0

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

@@ -93,11 +93,11 @@ var UnitRing;
     }
     UnitRing.elementFingerprint = elementFingerprint;
     var AromaticRingElements = new Set([
-        "B" /* B */, "C" /* C */, "N" /* N */, "O" /* O */,
-        "SI" /* SI */, "P" /* P */, "S" /* S */,
-        "GE" /* GE */, "AS" /* AS */,
-        "SN" /* SN */, "SB" /* SB */,
-        "BI" /* BI */
+        "B" /* Elements.B */, "C" /* Elements.C */, "N" /* Elements.N */, "O" /* Elements.O */,
+        "SI" /* Elements.SI */, "P" /* Elements.P */, "S" /* Elements.S */,
+        "GE" /* Elements.GE */, "AS" /* Elements.AS */,
+        "SN" /* Elements.SN */, "SB" /* Elements.SB */,
+        "BI" /* Elements.BI */
     ]);
     var AromaticRingPlanarityThreshold = 0.05;
     function isAromatic(unit, ring) {
@@ -115,7 +115,7 @@ var UnitRing;
             }
             for (var j = offset[aI], jl = offset[aI + 1]; j < jl; ++j) {
                 // comes e.g. from `chem_comp_bond.pdbx_aromatic_flag`
-                if (BondType.is(16 /* Aromatic */, flags[j])) {
+                if (BondType.is(16 /* BondType.Flag.Aromatic */, flags[j])) {
                     if (SortedArray.has(ring, b[j]))
                         aromaticBondCount += 1;
                 }

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

@@ -23,19 +23,19 @@ import { ModelSymmetry } from '../../../mol-model-formats/structure/property/sym
 import { getResonance } from './unit/resonance';
 var Unit;
 (function (Unit) {
-    function isAtomic(u) { return u.kind === 0 /* Atomic */; }
+    function isAtomic(u) { return u.kind === 0 /* Kind.Atomic */; }
     Unit.isAtomic = isAtomic;
-    function isCoarse(u) { return u.kind === 1 /* Spheres */ || u.kind === 2 /* Gaussians */; }
+    function isCoarse(u) { return u.kind === 1 /* Kind.Spheres */ || u.kind === 2 /* Kind.Gaussians */; }
     Unit.isCoarse = isCoarse;
-    function isSpheres(u) { return u.kind === 1 /* Spheres */; }
+    function isSpheres(u) { return u.kind === 1 /* Kind.Spheres */; }
     Unit.isSpheres = isSpheres;
-    function isGaussians(u) { return u.kind === 2 /* Gaussians */; }
+    function isGaussians(u) { return u.kind === 2 /* Kind.Gaussians */; }
     Unit.isGaussians = isGaussians;
     function create(id, invariantId, chainGroupId, traits, kind, model, operator, elements, props) {
         switch (kind) {
-            case 0 /* Atomic */: return new Atomic(id, invariantId, chainGroupId, traits, model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation, void 0), props !== null && props !== void 0 ? props : AtomicProperties());
-            case 1 /* Spheres */: return createCoarse(id, invariantId, chainGroupId, traits, model, 1 /* Spheres */, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.spheres, getSphereRadiusFunc(model)), props !== null && props !== void 0 ? props : CoarseProperties());
-            case 2 /* Gaussians */: return createCoarse(id, invariantId, chainGroupId, traits, model, 2 /* Gaussians */, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians, getGaussianRadiusFunc(model)), props !== null && props !== void 0 ? props : CoarseProperties());
+            case 0 /* Kind.Atomic */: return new Atomic(id, invariantId, chainGroupId, traits, model, elements, SymmetryOperator.createMapping(operator, model.atomicConformation, void 0), props !== null && props !== void 0 ? props : AtomicProperties());
+            case 1 /* Kind.Spheres */: return createCoarse(id, invariantId, chainGroupId, traits, model, 1 /* Kind.Spheres */, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.spheres, getSphereRadiusFunc(model)), props !== null && props !== void 0 ? props : CoarseProperties());
+            case 2 /* Kind.Gaussians */: return createCoarse(id, invariantId, chainGroupId, traits, model, 2 /* Kind.Gaussians */, elements, SymmetryOperator.createMapping(operator, model.coarseConformation.gaussians, getGaussianRadiusFunc(model)), props !== null && props !== void 0 ? props : CoarseProperties());
         }
     }
     Unit.create = create;
@@ -123,7 +123,7 @@ var Unit;
      */
     var Atomic = /** @class */ (function () {
         function Atomic(id, invariantId, chainGroupId, traits, model, elements, conformation, props) {
-            this.kind = 0 /* Atomic */;
+            this.kind = 0 /* Kind.Atomic */;
             this.objectPrimitive = 'atomistic';
             this.id = id;
             this.invariantId = invariantId;
@@ -307,7 +307,7 @@ var Unit;
     var Coarse = /** @class */ (function () {
         function Coarse(id, invariantId, chainGroupId, traits, model, kind, elements, conformation, props) {
             this.kind = kind;
-            this.objectPrimitive = kind === 1 /* Spheres */ ? 'sphere' : 'gaussian';
+            this.objectPrimitive = kind === 1 /* Kind.Spheres */ ? 'sphere' : 'gaussian';
             this.id = id;
             this.invariantId = invariantId;
             this.chainGroupId = chainGroupId;
@@ -315,8 +315,8 @@ var Unit;
             this.model = model;
             this.elements = elements;
             this.conformation = conformation;
-            this.coarseElements = kind === 1 /* Spheres */ ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians;
-            this.coarseConformation = (kind === 1 /* Spheres */ ? model.coarseConformation.spheres : model.coarseConformation.gaussians);
+            this.coarseElements = kind === 1 /* Kind.Spheres */ ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians;
+            this.coarseConformation = (kind === 1 /* Kind.Spheres */ ? model.coarseConformation.spheres : model.coarseConformation.gaussians);
             this.props = props;
         }
         Coarse.prototype.getChild = function (elements) {
@@ -405,7 +405,7 @@ var Unit;
         return Coarse;
     }());
     function getCoarseConformation(kind, model) {
-        return kind === 1 /* Spheres */ ? model.coarseConformation.spheres : model.coarseConformation.gaussians;
+        return kind === 1 /* Kind.Spheres */ ? model.coarseConformation.spheres : model.coarseConformation.gaussians;
     }
     function CoarseProperties() {
         return BaseProperties();
@@ -479,8 +479,8 @@ var Unit;
     }
     Unit.isSameConformation = isSameConformation;
     function getModelConformationOfKind(kind, model) {
-        return kind === 0 /* Atomic */ ? model.atomicConformation :
-            kind === 1 /* Spheres */ ? model.coarseConformation.spheres :
+        return kind === 0 /* Kind.Atomic */ ? model.atomicConformation :
+            kind === 1 /* Kind.Spheres */ ? model.coarseConformation.spheres :
                 model.coarseConformation.gaussians;
     }
     Unit.getModelConformationOfKind = getModelConformationOfKind;
@@ -489,8 +489,8 @@ var Unit;
     }
     Unit.getConformation = getConformation;
     function getModelHierarchyOfKind(kind, model) {
-        return kind === 0 /* Atomic */ ? model.atomicHierarchy :
-            kind === 1 /* Spheres */ ? model.coarseHierarchy.spheres :
+        return kind === 0 /* Kind.Atomic */ ? model.atomicHierarchy :
+            kind === 1 /* Kind.Spheres */ ? model.coarseHierarchy.spheres :
                 model.coarseHierarchy.gaussians;
     }
     Unit.getModelHierarchyOfKind = getModelHierarchyOfKind;

package/lib/mol-model/structure/structure/util/superposition-sifts-mapping.js

@@ -105,7 +105,7 @@ function buildIndex(structure, index, sI, traceOnly) {
     var _a;
     for (var _i = 0, _b = structure.units; _i < _b.length; _i++) {
         var unit = _b[_i];
-        if (unit.kind !== 0 /* Atomic */)
+        if (unit.kind !== 0 /* Unit.Kind.Atomic */)
             continue;
         var elements = unit.elements, model = unit.model;
         var map = SIFTSMapping.Provider.get(model).value;

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

@@ -13,17 +13,17 @@ export function getCoarseBegCompId(unit, element) {
 }
 export function getElementMoleculeType(unit, element) {
     switch (unit.kind) {
-        case 0 /* Atomic */:
+        case 0 /* Unit.Kind.Atomic */:
             return unit.model.atomicHierarchy.derived.residue.moleculeType[unit.residueIndex[element]];
-        case 1 /* Spheres */:
-        case 2 /* Gaussians */:
+        case 1 /* Unit.Kind.Spheres */:
+        case 2 /* Unit.Kind.Gaussians */:
             // TODO add unit.model.coarseHierarchy.derived.residue.moleculeType
             var compId = getCoarseBegCompId(unit, element);
             var cc = unit.model.properties.chemicalComponentMap.get(compId);
             if (cc)
                 return getMoleculeType(cc.type, compId);
     }
-    return 0 /* Unknown */;
+    return 0 /* MoleculeType.Unknown */;
 }
 export function getAtomicMoleculeType(model, rI) {
     return model.atomicHierarchy.derived.residue.moleculeType[rI];

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

@@ -95,12 +95,12 @@ function createChainOperatorMappingAndSubstituteNames(hierarchy, format) {
     var labelMap = new Map();
     var authMap = new Map();
     for (var i = 0; i < entries._rowCount; i++) {
-        var assembly = entries.assembly_operator_id.valueKind(i) === 0 /* Present */
+        var assembly = entries.assembly_operator_id.valueKind(i) === 0 /* Column.ValueKind.Present */
             ? { id: entries.assembly_id.value(i), operList: [], operId: entries.assembly_operator_id.value(i) }
             : void 0;
         var operator = SymmetryOperator.create(entries.operator_name.value(i), Mat4.identity(), {
             assembly: assembly,
-            spgrOp: entries.symmetry_operator_index.valueKind(i) === 0 /* Present */ ? entries.symmetry_operator_index.value(i) : void 0,
+            spgrOp: entries.symmetry_operator_index.valueKind(i) === 0 /* Column.ValueKind.Present */ ? entries.symmetry_operator_index.value(i) : void 0,
             hkl: Vec3.ofArray(entries.symmetry_hkl.value(i)),
             ncsId: entries.ncs_id.value(i)
         });

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

@@ -62,12 +62,12 @@ function createStandardModel(data, atom_site, sourceIndex, entities, properties,
     var sequence = getSequence(data, entities, atomic.hierarchy, coarse.hierarchy);
     var atomicRanges = getAtomicRanges(atomic.hierarchy, entities, atomic.conformation, sequence);
     var structAsymMap = getStructAsymMap(atomic.hierarchy);
-    var entry = data.entry.id.valueKind(0) === 0 /* Present */
+    var entry = data.entry.id.valueKind(0) === 0 /* Column.ValueKind.Present */
         ? data.entry.id.value(0) : format.name;
     var label = [];
     if (entry)
         label.push(entry);
-    if (data.struct.title.valueKind(0) === 0 /* Present */)
+    if (data.struct.title.valueKind(0) === 0 /* Column.ValueKind.Present */)
         label.push(data.struct.title.value(0));
     return {
         id: UUID.create22(),
@@ -97,12 +97,12 @@ function createIntegrativeModel(data, ihm, properties, format) {
     var coarse = getCoarse(ihm, properties.chemicalComponentMap);
     var sequence = getSequence(data, ihm.entities, atomic.hierarchy, coarse.hierarchy);
     var atomicRanges = getAtomicRanges(atomic.hierarchy, ihm.entities, atomic.conformation, sequence);
-    var entry = data.entry.id.valueKind(0) === 0 /* Present */
+    var entry = data.entry.id.valueKind(0) === 0 /* Column.ValueKind.Present */
         ? data.entry.id.value(0) : format.name;
     var label = [];
     if (entry)
         label.push(entry);
-    if (data.struct.title.valueKind(0) === 0 /* Present */)
+    if (data.struct.title.valueKind(0) === 0 /* Column.ValueKind.Present */)
         label.push(data.struct.title.value(0));
     if (ihm.model_name)
         label.push(ihm.model_name);

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

@@ -76,7 +76,7 @@ export function getSaccharideComponentMap(data) {
             if (SaccharideCompIdMap.has(_id)) {
                 map.set(_id, SaccharideCompIdMap.get(_id));
             }
-            else if (getMoleculeType(_type, _id) === 9 /* Saccharide */) {
+            else if (getMoleculeType(_type, _id) === 9 /* MoleculeType.Saccharide */) {
                 map.set(_id, UnknownSaccharideComponent);
             }
         }

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

@@ -33,7 +33,7 @@ export function sortAtomSite(ctx, atom_site, start, end) {
                     if (!(cI < _cI)) return [3 /*break*/, 7];
                     aI = chainBuckets[cI];
                     // are we in HETATM territory?
-                    if (label_seq_id.valueKind(aI) !== 0 /* Present */)
+                    if (label_seq_id.valueKind(aI) !== 0 /* Column.ValueKind.Present */)
                         return [3 /*break*/, 6];
                     makeBuckets(indices, label_seq_id.value, { sort: true, start: aI, end: chainBuckets[cI + 1] });
                     if (!ctx.shouldUpdate) return [3 /*break*/, 6];

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

@@ -18,7 +18,7 @@ export function getModelGroupName(model_id, data) {
 //
 function hasPresentValues(column) {
     for (var i = 0, il = column.rowCount; i < il; i++) {
-        if (column.valueKind(i) === 0 /* Present */)
+        if (column.valueKind(i) === 0 /* Column.ValueKind.Present */)
             return true;
     }
     return false;

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

@@ -128,7 +128,7 @@ function getModels(db, format, ctx) {
                         db.chemical_formula.sum.value(0));
                     entityBuilder = new EntityBuilder();
                     entityBuilder.setNames([['MOL', name || 'Unknown Entity']]);
-                    entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
+                    entityBuilder.getEntityId('MOL', 0 /* MoleculeType.Unknown */, 'A');
                     componentBuilder = new ComponentBuilder(seq_id, db.atom_site.type_symbol);
                     componentBuilder.setNames([['MOL', name || 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);
@@ -173,23 +173,23 @@ function getModels(db, format, ctx) {
                                     t = bond_type.str(i);
                                     if (t === 'D') {
                                         order[j] = 2;
-                                        flag[j] = 1 /* Covalent */;
+                                        flag[j] = 1 /* BondType.Flag.Covalent */;
                                     }
                                     else if (t === 'A') {
                                         order[j] = 1;
-                                        flag[j] = 1 /* Covalent */ | 16 /* Aromatic */;
+                                        flag[j] = 1 /* BondType.Flag.Covalent */ | 16 /* BondType.Flag.Aromatic */;
                                     }
                                     else if (t === 'S') {
                                         order[j] = 1;
-                                        flag[j] = 1 /* Covalent */;
+                                        flag[j] = 1 /* BondType.Flag.Covalent */;
                                     }
                                     else {
                                         order[j] = 1;
-                                        flag[j] = 1 /* Covalent */;
+                                        flag[j] = 1 /* BondType.Flag.Covalent */;
                                     }
                                 }
                                 else {
-                                    flag[j] = 1 /* Covalent */;
+                                    flag[j] = 1 /* BondType.Flag.Covalent */;
                                     // TODO derive order from bond length if undefined
                                     order[j] = valence.isDefined ? valence.value(i) : 1;
                                 }

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

@@ -24,7 +24,7 @@ var EntityBuilder = /** @class */ (function () {
         this.descriptions.push([description]);
     };
     EntityBuilder.prototype.getEntityId = function (compId, moleculeType, chainId, options) {
-        if (moleculeType === 2 /* Water */) {
+        if (moleculeType === 2 /* MoleculeType.Water */) {
             if (this.waterId === undefined) {
                 this.set('water', (options === null || options === void 0 ? void 0 : options.customName) || 'Water');
                 this.waterId = "".concat(this.count);

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

@@ -42,7 +42,7 @@ function getModels(cube, ctx) {
                     }, atoms.count);
                     entityBuilder = new EntityBuilder();
                     entityBuilder.setNames([['MOL', 'Unknown Entity']]);
-                    entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
+                    entityBuilder.getEntityId('MOL', 0 /* MoleculeType.Unknown */, 'A');
                     componentBuilder = new ComponentBuilder(seq_id, type_symbol);
                     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);

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

@@ -28,7 +28,7 @@ function getBasic(atoms, modelNum) {
     var currentAsymIndex = 0;
     var currentAsymId = '';
     var currentSeqId = 0;
-    var prevMoleculeType = 0 /* Unknown */;
+    var prevMoleculeType = 0 /* MoleculeType.Unknown */;
     var prevResidueNumber = -1;
     for (var i = 0, il = atoms.count; i < il; ++i) {
         var residueNumber = atoms.residueNumber.value(i);

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

@@ -57,7 +57,7 @@ export function getMolModels(mol, format, ctx) {
                     }, atoms.count);
                     entityBuilder = new EntityBuilder();
                     entityBuilder.setNames([['MOL', 'Unknown Entity']]);
-                    entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
+                    entityBuilder.getEntityId('MOL', 0 /* MoleculeType.Unknown */, 'A');
                     componentBuilder = new ComponentBuilder(seq_id, type_symbol);
                     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
                     componentBuilder.add('MOL', 0);

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

@@ -63,7 +63,7 @@ function getModels(mol2, ctx) {
                     }, atoms.count);
                     entityBuilder = new EntityBuilder();
                     entityBuilder.setNames([['MOL', molecule.mol_name || 'Unknown Entity']]);
-                    entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
+                    entityBuilder.getEntityId('MOL', 0 /* MoleculeType.Unknown */, 'A');
                     componentBuilder = new ComponentBuilder(atoms.subst_id, atoms.atom_name);
                     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);
@@ -97,13 +97,13 @@ function getModels(mol2, ctx) {
                             switch (x) {
                                 case 'ar': // aromatic
                                 case 'am': // amide
-                                    return 16 /* Aromatic */ | 1 /* Covalent */;
+                                    return 16 /* BondType.Flag.Aromatic */ | 1 /* BondType.Flag.Covalent */;
                                 case 'du': // dummy
                                 case 'nc': // not connected
-                                    return 0 /* None */;
+                                    return 0 /* BondType.Flag.None */;
                                 case 'un': // unknown
                                 default:
-                                    return 1 /* Covalent */;
+                                    return 1 /* BondType.Flag.Covalent */;
                             }
                         }, Int8Array));
                         pairBonds = IndexPairBonds.fromData({ pairs: { key: key, indexA: indexA, indexB: indexB, order: order, flag: flag }, count: atoms.count });

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

@@ -44,7 +44,7 @@ function getBasic(prmtop) {
     var currentAsymIndex = 0;
     var currentAsymId = '';
     var currentSeqId = 0;
-    var prevMoleculeType = 0 /* Unknown */;
+    var prevMoleculeType = 0 /* MoleculeType.Unknown */;
     var prevResidueNumber = -1;
     for (var i = 0, il = atomCount; i < il; ++i) {
         var residueNumber = residueId.value(i);

package/lib/mol-model-formats/structure/property/bonds/chem_comp.js

@@ -64,13 +64,13 @@ export var ComponentBond;
             if (entry.id !== id) {
                 entry = addEntry(id);
             }
-            var flags = 1 /* Covalent */;
+            var flags = 1 /* BondType.Flag.Covalent */;
             var ord = 1;
             if (aromatic)
-                flags |= 16 /* Aromatic */;
+                flags |= 16 /* BondType.Flag.Aromatic */;
             switch (order.toLowerCase()) {
                 case 'delo':
-                    flags |= 16 /* Aromatic */;
+                    flags |= 16 /* BondType.Flag.Aromatic */;
                     break;
                 case 'doub':
                     ord = 2;

package/lib/mol-model-formats/structure/property/bonds/index-pair.js

@@ -18,7 +18,7 @@ function getGraph(indexA, indexB, props, count) {
         builder.assignProperty(key, props.key ? props.key[i] : -1);
         builder.assignProperty(order, props.order ? props.order[i] : 1);
         builder.assignProperty(distance, props.distance ? props.distance[i] : -1);
-        builder.assignProperty(flag, props.flag ? props.flag[i] : 1 /* Covalent */);
+        builder.assignProperty(flag, props.flag ? props.flag[i] : 1 /* BondType.Flag.Covalent */);
     }
     return builder.createGraph({ key: key, order: order, distance: distance, flag: flag });
 }

package/lib/mol-model-formats/structure/property/bonds/struct_conn.js

@@ -90,7 +90,7 @@ export var StructConn;
             symmetry: struct_conn.ptnr2_symmetry
         };
         var _p = function (row, ps) {
-            if (ps.label_asym_id.valueKind(row) !== 0 /* Present */)
+            if (ps.label_asym_id.valueKind(row) !== 0 /* Column.ValueKind.Present */)
                 return void 0;
             var asymId = ps.label_asym_id.value(row);
             var entityIndex = model.atomicHierarchy.index.findEntity(asymId);
@@ -116,7 +116,7 @@ export var StructConn;
                 continue;
             var type = conn_type_id.value(i);
             var orderType = (pdbx_value_order.value(i) || '');
-            var flags = 0 /* None */;
+            var flags = 0 /* BondType.Flag.None */;
             var order = 1;
             switch (orderType) {
                 case 'sing':
@@ -136,16 +136,16 @@ export var StructConn;
             }
             switch (type) {
                 case 'covale':
-                    flags = 1 /* Covalent */;
+                    flags = 1 /* BondType.Flag.Covalent */;
                     break;
                 case 'disulf':
-                    flags = 1 /* Covalent */ | 8 /* Disulfide */;
+                    flags = 1 /* BondType.Flag.Covalent */ | 8 /* BondType.Flag.Disulfide */;
                     break;
                 case 'hydrog':
-                    flags = 4 /* HydrogenBond */;
+                    flags = 4 /* BondType.Flag.HydrogenBond */;
                     break;
                 case 'metalc':
-                    flags = 2 /* MetallicCoordination */;
+                    flags = 2 /* BondType.Flag.MetallicCoordination */;
                     break;
             }
             entries.push({

package/lib/mol-model-formats/structure/property/secondary-structure.js

@@ -37,11 +37,11 @@ var ModelSecondaryStructure;
 })(ModelSecondaryStructure || (ModelSecondaryStructure = {}));
 function getCoordinateType(conf, sheetRange) {
     if (conf._rowCount > 0) {
-        if (conf.beg_label_seq_id.valueKind(0) !== 0 /* Present */ || conf.end_label_seq_id.valueKind(0) !== 0 /* Present */)
+        if (conf.beg_label_seq_id.valueKind(0) !== 0 /* Column.ValueKind.Present */ || conf.end_label_seq_id.valueKind(0) !== 0 /* Column.ValueKind.Present */)
             return 'auth';
     }
     else if (sheetRange) {
-        if (sheetRange.beg_label_seq_id.valueKind(0) !== 0 /* Present */ || sheetRange.end_label_seq_id.valueKind(0) !== 0 /* Present */)
+        if (sheetRange.beg_label_seq_id.valueKind(0) !== 0 /* Column.ValueKind.Present */ || sheetRange.end_label_seq_id.valueKind(0) !== 0 /* Column.ValueKind.Present */)
             return 'auth';
     }
     return 'label';
@@ -55,17 +55,17 @@ function addHelices(cat, coordinates, map, elements) {
     var beg_seq_id = coordinates === 'label' ? beg_label_seq_id : beg_auth_seq_id;
     var end_seq_id = coordinates === 'label' ? end_label_seq_id : end_auth_seq_id;
     for (var i = 0, _i = cat._rowCount; i < _i; i++) {
-        var type = SecondaryStructureType.create(pdbx_PDB_helix_class.valueKind(i) === 0 /* Present */
+        var type = SecondaryStructureType.create(pdbx_PDB_helix_class.valueKind(i) === 0 /* Column.ValueKind.Present */
             ? SecondaryStructureType.SecondaryStructurePdb[pdbx_PDB_helix_class.value(i)]
-            : conf_type_id.valueKind(i) === 0 /* Present */
+            : conf_type_id.valueKind(i) === 0 /* Column.ValueKind.Present */
                 ? SecondaryStructureType.SecondaryStructureMmcif[conf_type_id.value(i)]
-                : 536870912 /* NA */);
+                : 536870912 /* SecondaryStructureType.Flag.NA */);
         var element = {
             kind: 'helix',
             flags: type,
-            type_id: conf_type_id.valueKind(i) === 0 /* Present */ ? conf_type_id.value(i) : 'helx_p',
+            type_id: conf_type_id.valueKind(i) === 0 /* Column.ValueKind.Present */ ? conf_type_id.value(i) : 'helx_p',
             helix_class: pdbx_PDB_helix_class.value(i),
-            details: details.valueKind(i) === 0 /* Present */ ? details.value(i) : void 0
+            details: details.valueKind(i) === 0 /* Column.ValueKind.Present */ ? details.value(i) : void 0
         };
         var entry = {
             startSeqId: beg_seq_id.value(i),
@@ -110,7 +110,7 @@ function addSheets(cat, coordinates, map, sheetCount, elements) {
             key = currentKey++;
             sheet_id_key.set(id, key);
         }
-        var type = SecondaryStructureType.create(4 /* Beta */ | 8388608 /* BetaSheet */);
+        var type = SecondaryStructureType.create(4 /* SecondaryStructureType.Flag.Beta */ | 8388608 /* SecondaryStructureType.Flag.BetaSheet */);
         var element = {
             kind: 'sheet',
             flags: type,

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

@@ -26,7 +26,7 @@ function getBasic(atoms) {
     var currentAsymId = '';
     var currentSeqId = 0;
     var currentSegmentName = atoms.segmentName.value(0), segmentChanged = false;
-    var prevMoleculeType = 0 /* Unknown */;
+    var prevMoleculeType = 0 /* MoleculeType.Unknown */;
     var prevResidueNumber = -1;
     for (var i = 0, il = atoms.count; i < il; ++i) {
         var residueNumber = atoms.residueId.value(i);

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

@@ -71,7 +71,7 @@ function getBasic(top) {
     var currentAsymIndex = 0;
     var currentAsymId = '';
     var currentSeqId = 0;
-    var prevMoleculeType = 0 /* Unknown */;
+    var prevMoleculeType = 0 /* MoleculeType.Unknown */;
     var prevResidueNumber = -1;
     for (var i = 0, il = atomCount; i < il; ++i) {
         var residueNumber = residueId.value(i);

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

@@ -59,7 +59,7 @@ function getModels(mol, ctx) {
     }, count);
     var entityBuilder = new EntityBuilder();
     entityBuilder.setNames([['MOL', 'Unknown Entity']]);
-    entityBuilder.getEntityId('MOL', 0 /* Unknown */, 'A');
+    entityBuilder.getEntityId('MOL', 0 /* MoleculeType.Unknown */, 'A');
     var componentBuilder = new ComponentBuilder(seq_id, type_symbol);
     componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
     componentBuilder.add('MOL', 0);

package/lib/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.js

@@ -43,7 +43,7 @@ export function assignRadiusForHeavyAtoms(ctx) {
             var atomId = label_atom_id(l);
             var moleculeType = getElementMoleculeType(unit, eI);
             // skip water and optionally non-polymer groups
-            if (moleculeType === 2 /* Water */ || (!ctx.nonPolymer && !isPolymer(moleculeType))) {
+            if (moleculeType === 2 /* MoleculeType.Water */ || (!ctx.nonPolymer && !isPolymer(moleculeType))) {
                 atomRadiusType[mj] = 0;
                 serialResidueIndex[mj] = -1;
                 continue;
@@ -57,7 +57,7 @@ export function assignRadiusForHeavyAtoms(ctx) {
             if (isNucleic(moleculeType)) {
                 atomRadiusType[mj] = determineRadiusNucl(atomId, element, compId);
             }
-            else if (moleculeType === 5 /* Protein */) {
+            else if (moleculeType === 5 /* MoleculeType.Protein */) {
                 atomRadiusType[mj] = determineRadiusAmino(atomId, element, compId);
             }
             else {

package/lib/mol-model-props/computed/accessible-surface-area/shrake-rupley.js

@@ -111,9 +111,9 @@ var AccessibleSurfaceArea;
     AccessibleSurfaceArea.getNormalizedValue = getNormalizedValue;
     function getFlag(location, accessibleSurfaceArea) {
         var value = getNormalizedValue(location, accessibleSurfaceArea);
-        return value === -1 ? 0 /* NA */ :
-            value < 0.16 ? 1 /* Buried */ :
-                2 /* Accessible */;
+        return value === -1 ? 0 /* Flag.NA */ :
+            value < 0.16 ? 1 /* Flag.Buried */ :
+                2 /* Flag.Accessible */;
     }
     AccessibleSurfaceArea.getFlag = getFlag;
 })(AccessibleSurfaceArea || (AccessibleSurfaceArea = {}));

package/lib/mol-model-props/computed/accessible-surface-area.js

@@ -21,7 +21,7 @@ export var AccessibleSurfaceAreaSymbols = {
         var accessibleSurfaceArea = AccessibleSurfaceAreaProvider.get(ctx.element.structure).value;
         if (!accessibleSurfaceArea)
             return false;
-        return AccessibleSurfaceArea.getFlag(ctx.element, accessibleSurfaceArea) === 1 /* Buried */;
+        return AccessibleSurfaceArea.getFlag(ctx.element, accessibleSurfaceArea) === 1 /* AccessibleSurfaceArea.Flag.Buried */;
     }),
     isAccessible: QuerySymbolRuntime.Dynamic(CustomPropSymbol('computed', 'accessible-surface-area.is-accessible', Type.Bool), function (ctx) {
         if (!Unit.isAtomic(ctx.element.unit))
@@ -29,7 +29,7 @@ export var AccessibleSurfaceAreaSymbols = {
         var accessibleSurfaceArea = AccessibleSurfaceAreaProvider.get(ctx.element.structure).value;
         if (!accessibleSurfaceArea)
             return false;
-        return AccessibleSurfaceArea.getFlag(ctx.element, accessibleSurfaceArea) === 2 /* Accessible */;
+        return AccessibleSurfaceArea.getFlag(ctx.element, accessibleSurfaceArea) === 2 /* AccessibleSurfaceArea.Flag.Accessible */;
     }),
 };
 export var AccessibleSurfaceAreaProvider = CustomStructureProperty.createProvider({