molstar 3.8.2 → 3.9.0

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

@@ -21,27 +21,27 @@ var Sequence;
         for (var i = 0, _i = Math.min(names.rowCount, 10); i < _i; i++) {
             var name_1 = names.value(i) || '';
             if ((0, constants_1.getProteinOneLetterCode)(name_1) !== 'X')
-                return "protein" /* Protein */;
+                return "protein" /* Kind.Protein */;
             if ((0, constants_1.getRnaOneLetterCode)(name_1) !== 'X')
-                return "RNA" /* RNA */;
+                return "RNA" /* Kind.RNA */;
             if ((0, constants_1.getDnaOneLetterCode)(name_1) !== 'X')
-                return "DNA" /* DNA */;
+                return "DNA" /* Kind.DNA */;
         }
-        return "generic" /* Generic */;
+        return "generic" /* Kind.Generic */;
     }
     function codeProvider(kind, map) {
         var code;
         switch (kind) {
-            case "protein" /* Protein */:
+            case "protein" /* Kind.Protein */:
                 code = constants_1.getProteinOneLetterCode;
                 break;
-            case "DNA" /* DNA */:
+            case "DNA" /* Kind.DNA */:
                 code = constants_1.getDnaOneLetterCode;
                 break;
-            case "RNA" /* RNA */:
+            case "RNA" /* Kind.RNA */:
                 code = constants_1.getRnaOneLetterCode;
                 break;
-            case "generic" /* Generic */:
+            case "generic" /* Kind.Generic */:
                 code = function () { return 'X'; };
                 break;
             default: (0, type_helpers_1.assertUnreachable)(kind);
@@ -122,7 +122,7 @@ var Sequence;
         return ResidueNamesImpl;
     }());
     function ofSequenceRanges(seqIdBegin, seqIdEnd) {
-        var kind = "generic" /* Generic */;
+        var kind = "generic" /* Kind.Generic */;
         return new SequenceRangesImpl(kind, seqIdBegin, seqIdEnd);
     }
     Sequence.ofSequenceRanges = ofSequenceRanges;

package/lib/commonjs/mol-model/structure/export/categories/atom_site_operator_mapping.js

@@ -34,8 +34,8 @@ exports.AtomSiteOperatorMappingSchema = {
         ncs_id: db_1.Column.Schema.Int(),
     }
 };
-var asmValueKind = function (i, xs) { return typeof xs[i].operator.assembly === 'undefined' ? 1 /* NotPresent */ : 0 /* Present */; };
-var symmetryValueKind = function (i, xs) { return xs[i].operator.spgrOp === -1 ? 1 /* NotPresent */ : 0 /* Present */; };
+var asmValueKind = function (i, xs) { return typeof xs[i].operator.assembly === 'undefined' ? 1 /* Column.ValueKind.NotPresent */ : 0 /* Column.ValueKind.Present */; };
+var symmetryValueKind = function (i, xs) { return xs[i].operator.spgrOp === -1 ? 1 /* Column.ValueKind.NotPresent */ : 0 /* Column.ValueKind.Present */; };
 var Fields = cif_1.CifWriter.fields()
     .str('label_asym_id', function (i, xs) { return xs[i].label_asym_id; })
     .str('auth_asym_id', function (i, xs) { return xs[i].auth_asym_id; })
@@ -66,7 +66,7 @@ function getEntries(ctx) {
         for (var _b = 0, _c = s.units; _b < _c.length; _b++) {
             var unit = _c[_b];
             var operator = unit.conformation.operator;
-            if (!operator.suffix || unit.kind !== 0 /* Atomic */)
+            if (!operator.suffix || unit.kind !== 0 /* Unit.Kind.Atomic */)
                 continue;
             l.unit = unit;
             var elements = unit.elements;

package/lib/commonjs/mol-model/structure/export/categories/secondary-structure.js

@@ -44,7 +44,7 @@ var struct_conf_fields = function () { return tslib_1.__spreadArray(tslib_1.__sp
 ], (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].start; }, { prefix: 'beg' }), true), (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].end; }, { prefix: 'end' }), true), [
     CifField.str('pdbx_PDB_helix_class', function (i, data) { return data[i].element.helix_class; }),
     CifField.str('details', function (i, data) { return data[i].element.details || ''; }, {
-        valueKind: function (i, d) { return !!d[i].element.details ? 0 /* Present */ : 2 /* Unknown */; }
+        valueKind: function (i, d) { return !!d[i].element.details ? 0 /* Column.ValueKind.Present */ : 2 /* Column.ValueKind.Unknown */; }
     }),
     CifField.int('pdbx_PDB_helix_length', function (i, data) { return data[i].length; })
 ], false); };
@@ -52,7 +52,7 @@ var struct_sheet_range_fields = function () { return tslib_1.__spreadArray(tslib
     CifField.str('sheet_id', function (i, data) { return data[i].element.sheet_id; }),
     CifField.index('id')
 ], (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].start; }, { prefix: 'beg' }), true), (0, atom_site_1.residueIdFields)(function (i, e) { return e[i].end; }, { prefix: 'end' }), true), [
-    CifField.str('symmetry', function (i, data) { return ''; }, { valueKind: function (i, d) { return 2 /* Unknown */; } })
+    CifField.str('symmetry', function (i, data) { return ''; }, { valueKind: function (i, d) { return 2 /* Column.ValueKind.Unknown */; } })
 ], false); };
 function findElements(ctx, kind) {
     // TODO: encode secondary structure for different models?

package/lib/commonjs/mol-model/structure/export/categories/utils.js

@@ -98,7 +98,7 @@ exports.copy_source_mmCifCategory = copy_source_mmCifCategory;
 function classifyField(name, field) {
     var type = (0, cif_2.getCifFieldType)(field);
     if (type['@type'] === 'str') {
-        return { name: name, type: 0 /* Str */, value: field.str, valueKind: field.valueKind };
+        return { name: name, type: 0 /* CifWriter.Field.Type.Str */, value: field.str, valueKind: field.valueKind };
     }
     else if (type['@type'] === 'float') {
         return cif_1.CifWriter.Field.float(name, field.float, { valueKind: field.valueKind, typedArray: Float64Array });

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

@@ -171,7 +171,7 @@ var Model;
             var polymerResidueCount = 0;
             var polymerType = model.atomicHierarchy.derived.residue.polymerType;
             for (var i = 0; i < polymerType.length; ++i) {
-                if (polymerType[i] !== 0 /* NA */)
+                if (polymerType[i] !== 0 /* PolymerType.NA */)
                     polymerResidueCount += 1;
             }
             // check for coarse grained atom names
@@ -340,7 +340,7 @@ var Model;
         // check if from pdb archive but missing relevant meta data
         hasPdbId(model) && (!db.exptl.method.isDefined ||
             (isFromXray(model) && (!db.pdbx_database_status.status_code_sf.isDefined ||
-                db.pdbx_database_status.status_code_sf.valueKind(0) === 2 /* Unknown */)) ||
+                db.pdbx_database_status.status_code_sf.valueKind(0) === 2 /* Column.ValueKind.Unknown */)) ||
             (isFromEm(model) && (!db.pdbx_database_related.db_name.isDefined))));
     }
     Model.probablyHasDensityMap = probablyHasDensityMap;

package/lib/commonjs/mol-model/structure/model/properties/custom/indexed.js

@@ -34,22 +34,22 @@ var IndexedCustomProperty;
     IndexedCustomProperty.fromAtomArray = fromAtomArray;
     var getResidueSegments = function (model) { return model.atomicHierarchy.residueAtomSegments; };
     function fromResidueMap(map) {
-        return new SegmentedMappedIndexedCustomProperty('residue', map, getResidueSegments, 0 /* Atomic */);
+        return new SegmentedMappedIndexedCustomProperty('residue', map, getResidueSegments, 0 /* Unit.Kind.Atomic */);
     }
     IndexedCustomProperty.fromResidueMap = fromResidueMap;
     function fromResidueArray(array) {
         // TODO: create "array based custom property" as optimization
-        return new SegmentedMappedIndexedCustomProperty('residue', arrayToMap(array), getResidueSegments, 0 /* Atomic */);
+        return new SegmentedMappedIndexedCustomProperty('residue', arrayToMap(array), getResidueSegments, 0 /* Unit.Kind.Atomic */);
     }
     IndexedCustomProperty.fromResidueArray = fromResidueArray;
     var getChainSegments = function (model) { return model.atomicHierarchy.chainAtomSegments; };
     function fromChainMap(map) {
-        return new SegmentedMappedIndexedCustomProperty('chain', map, getChainSegments, 0 /* Atomic */);
+        return new SegmentedMappedIndexedCustomProperty('chain', map, getChainSegments, 0 /* Unit.Kind.Atomic */);
     }
     IndexedCustomProperty.fromChainMap = fromChainMap;
     function fromChainArray(array) {
         // TODO: create "array based custom property" as optimization
-        return new SegmentedMappedIndexedCustomProperty('chain', arrayToMap(array), getChainSegments, 0 /* Atomic */);
+        return new SegmentedMappedIndexedCustomProperty('chain', arrayToMap(array), getChainSegments, 0 /* Unit.Kind.Atomic */);
     }
     IndexedCustomProperty.fromChainArray = fromChainArray;
     function fromEntityMap(map) {
@@ -112,7 +112,7 @@ var ElementMappedCustomProperty = /** @class */ (function () {
         this.map = map;
         this.id = mol_util_1.UUID.create22();
         this.level = 'atom';
-        this.kind = 0 /* Atomic */;
+        this.kind = 0 /* Unit.Kind.Atomic */;
     }
     ElementMappedCustomProperty.prototype.has = function (idx) { return this.map.has(idx); };
     ElementMappedCustomProperty.prototype.get = function (idx) { return this.map.get(idx); };
@@ -153,7 +153,7 @@ var EntityMappedCustomProperty = /** @class */ (function () {
         this.map = map;
         this.id = mol_util_1.UUID.create22();
         this.level = 'entity';
-        this.kind = 0 /* Atomic */;
+        this.kind = 0 /* Unit.Kind.Atomic */;
     }
     EntityMappedCustomProperty.prototype.has = function (idx) { return this.map.has(idx); };
     EntityMappedCustomProperty.prototype.get = function (idx) { return this.map.get(idx); };

package/lib/commonjs/mol-model/structure/model/properties/utils/atomic-ranges.js

@@ -15,7 +15,7 @@ function areBackboneConnected(riStart, riEnd, conformation, index, derived) {
     var _a = derived.residue, polymerType = _a.polymerType, traceElementIndex = _a.traceElementIndex, directionFromElementIndex = _a.directionFromElementIndex, directionToElementIndex = _a.directionToElementIndex;
     var ptStart = polymerType[riStart];
     var ptEnd = polymerType[riEnd];
-    if (ptStart === 0 /* NA */ || ptEnd === 0 /* NA */)
+    if (ptStart === 0 /* PolymerType.NA */ || ptEnd === 0 /* PolymerType.NA */)
         return false;
     if (traceElementIndex[riStart] === -1 || traceElementIndex[riEnd] === -1)
         return false;

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

@@ -49,7 +49,7 @@ function getElementFromAtomicNumber(n) {
 }
 exports.getElementFromAtomicNumber = getElementFromAtomicNumber;
 exports.PolymerTypeAtomRoleId = (_a = {},
-    _a[0 /* NA */] = {
+    _a[0 /* PolymerType.NA */] = {
         trace: new Set(),
         directionFrom: new Set(),
         directionTo: new Set(),
@@ -57,7 +57,7 @@ exports.PolymerTypeAtomRoleId = (_a = {},
         backboneEnd: new Set(),
         coarseBackbone: new Set()
     },
-    _a[1 /* Protein */] = {
+    _a[1 /* PolymerType.Protein */] = {
         trace: new Set(['CA']),
         directionFrom: new Set(['C']),
         directionTo: new Set(['O', 'OC1', 'O1', 'OX1', 'OXT', 'OT1']),
@@ -67,7 +67,7 @@ exports.PolymerTypeAtomRoleId = (_a = {},
         // BB is often used for coarse grained models
         coarseBackbone: new Set(['CA', 'BB', 'CA1'])
     },
-    _a[2 /* GammaProtein */] = {
+    _a[2 /* PolymerType.GammaProtein */] = {
         trace: new Set(['CA']),
         directionFrom: new Set(['C']),
         directionTo: new Set(['O']),
@@ -75,7 +75,7 @@ exports.PolymerTypeAtomRoleId = (_a = {},
         backboneEnd: new Set(['CD']),
         coarseBackbone: new Set(['CA'])
     },
-    _a[3 /* BetaProtein */] = {
+    _a[3 /* PolymerType.BetaProtein */] = {
         trace: new Set(['CA']),
         directionFrom: new Set(['C']),
         directionTo: new Set(['O']),
@@ -83,7 +83,7 @@ exports.PolymerTypeAtomRoleId = (_a = {},
         backboneEnd: new Set(['CG']),
         coarseBackbone: new Set(['CA'])
     },
-    _a[4 /* RNA */] = {
+    _a[4 /* PolymerType.RNA */] = {
         trace: new Set(['O3\'', 'O3*']),
         directionFrom: new Set(['C4\'', 'C4*']),
         directionTo: new Set(['C3\'', 'C3*']),
@@ -91,7 +91,7 @@ exports.PolymerTypeAtomRoleId = (_a = {},
         backboneEnd: new Set(['O3\'', 'O3*']),
         coarseBackbone: new Set(['P'])
     },
-    _a[5 /* DNA */] = {
+    _a[5 /* PolymerType.DNA */] = {
         trace: new Set(['O3\'', 'O3*']),
         directionFrom: new Set(['C3\'', 'C3*']),
         directionTo: new Set(['C1\'', 'C1*']),
@@ -99,7 +99,7 @@ exports.PolymerTypeAtomRoleId = (_a = {},
         backboneEnd: new Set(['O3\'', 'O3*']),
         coarseBackbone: new Set(['P'])
     },
-    _a[6 /* PNA */] = {
+    _a[6 /* PolymerType.PNA */] = {
         trace: new Set(['N4\'', 'N4*']),
         directionFrom: new Set(['N4\'', 'N4*']),
         directionTo: new Set(['C7\'', 'C7*']),
@@ -241,78 +241,78 @@ exports.PolymerNames = set_1.SetUtils.unionMany(exports.AminoAcidNames, exports.
 function getMoleculeType(compType, compId) {
     compId = compId.toUpperCase();
     if (exports.PeptideBaseNames.has(compId)) {
-        return 8 /* PNA */;
+        return 8 /* MoleculeType.PNA */;
     }
     else if (exports.ProteinComponentTypeNames.has(compType)) {
-        return 5 /* Protein */;
+        return 5 /* MoleculeType.Protein */;
     }
     else if (exports.RNAComponentTypeNames.has(compType)) {
-        return 6 /* RNA */;
+        return 6 /* MoleculeType.RNA */;
     }
     else if (exports.DNAComponentTypeNames.has(compType)) {
-        return 7 /* DNA */;
+        return 7 /* MoleculeType.DNA */;
     }
     else if (exports.SaccharideComponentTypeNames.has(compType)) {
-        return 9 /* Saccharide */;
+        return 9 /* MoleculeType.Saccharide */;
     }
     else if (exports.WaterNames.has(compId)) {
-        return 2 /* Water */;
+        return 2 /* MoleculeType.Water */;
     }
     else if (ions_1.IonNames.has(compId)) {
-        return 3 /* Ion */;
+        return 3 /* MoleculeType.Ion */;
     }
     else if (lipids_1.LipidNames.has(compId)) {
-        return 4 /* Lipid */;
+        return 4 /* MoleculeType.Lipid */;
     }
     else if (exports.OtherComponentTypeNames.has(compType)) {
         if (constants_1.SaccharideCompIdMap.has(compId)) {
             // trust our saccharide table more than given 'NON-POLYMER' or 'OTHER' component type
-            return 9 /* Saccharide */;
+            return 9 /* MoleculeType.Saccharide */;
         }
         else if (exports.AminoAcidNames.has(compId)) {
-            return 5 /* Protein */;
+            return 5 /* MoleculeType.Protein */;
         }
         else if (exports.RnaBaseNames.has(compId)) {
-            return 6 /* RNA */;
+            return 6 /* MoleculeType.RNA */;
         }
         else if (exports.DnaBaseNames.has(compId)) {
-            return 7 /* DNA */;
+            return 7 /* MoleculeType.DNA */;
         }
         else {
-            return 1 /* Other */;
+            return 1 /* MoleculeType.Other */;
         }
     }
     else {
-        return 0 /* Unknown */;
+        return 0 /* MoleculeType.Unknown */;
     }
 }
 exports.getMoleculeType = getMoleculeType;
 function getPolymerType(compType, molType) {
-    if (molType === 5 /* Protein */) {
+    if (molType === 5 /* MoleculeType.Protein */) {
         if (exports.GammaProteinComponentTypeNames.has(compType)) {
-            return 2 /* GammaProtein */;
+            return 2 /* PolymerType.GammaProtein */;
         }
         else if (exports.BetaProteinComponentTypeNames.has(compType)) {
-            return 3 /* BetaProtein */;
+            return 3 /* PolymerType.BetaProtein */;
         }
         else if (exports.ProteinTerminusComponentTypeNames.has(compType)) {
-            return 0 /* NA */;
+            return 0 /* PolymerType.NA */;
         }
         else {
-            return 1 /* Protein */;
+            return 1 /* PolymerType.Protein */;
         }
     }
-    else if (molType === 6 /* RNA */) {
-        return 4 /* RNA */;
+    else if (molType === 6 /* MoleculeType.RNA */) {
+        return 4 /* PolymerType.RNA */;
     }
-    else if (molType === 7 /* DNA */) {
-        return 5 /* DNA */;
+    else if (molType === 7 /* MoleculeType.DNA */) {
+        return 5 /* PolymerType.DNA */;
     }
-    else if (molType === 8 /* PNA */) {
-        return 6 /* PNA */;
+    else if (molType === 8 /* MoleculeType.PNA */) {
+        return 6 /* PolymerType.PNA */;
     }
     else {
-        return 0 /* NA */;
+        return 0 /* PolymerType.NA */;
     }
 }
 exports.getPolymerType = getPolymerType;
@@ -419,11 +419,11 @@ function isPolymer(moleculeType) {
 }
 exports.isPolymer = isPolymer;
 function isNucleic(moleculeType) {
-    return moleculeType === 7 /* DNA */ || moleculeType === 6 /* RNA */ || moleculeType === 8 /* PNA */;
+    return moleculeType === 7 /* MoleculeType.DNA */ || moleculeType === 6 /* MoleculeType.RNA */ || moleculeType === 8 /* MoleculeType.PNA */;
 }
 exports.isNucleic = isNucleic;
 function isProtein(moleculeType) {
-    return moleculeType === 5 /* Protein */;
+    return moleculeType === 5 /* MoleculeType.Protein */;
 }
 exports.isProtein = isProtein;
 var SecondaryStructureType;
@@ -431,79 +431,79 @@ var SecondaryStructureType;
     SecondaryStructureType.is = bit_flags_1.BitFlags.has;
     SecondaryStructureType.create = bit_flags_1.BitFlags.create;
     SecondaryStructureType.SecondaryStructureMmcif = {
-        helx_lh_27_p: 2 /* Helix */ | 32 /* LeftHanded */ | 1024 /* Helix27 */,
-        helx_lh_3t_p: 2 /* Helix */ | 32 /* LeftHanded */ | 2048 /* Helix3Ten */,
-        helx_lh_al_p: 2 /* Helix */ | 32 /* LeftHanded */ | 4096 /* HelixAlpha */,
-        helx_lh_a_n: 1 /* DoubleHelix */ | 32 /* LeftHanded */ | 524288 /* DoubleHelixA */,
-        helx_lh_b_n: 1 /* DoubleHelix */ | 32 /* LeftHanded */ | 1048576 /* DoubleHelixB */,
-        helx_lh_ga_p: 2 /* Helix */ | 32 /* LeftHanded */ | 8192 /* HelixGamma */,
-        helx_lh_n: 1 /* DoubleHelix */ | 32 /* LeftHanded */,
-        helx_lh_om_p: 2 /* Helix */ | 32 /* LeftHanded */ | 16384 /* HelixOmega */,
-        helx_lh_ot_n: 1 /* DoubleHelix */ | 32 /* LeftHanded */ | 131072 /* DoubleHelixOther */,
-        helx_lh_ot_p: 2 /* Helix */ | 32 /* LeftHanded */ | 512 /* HelixOther */,
-        helx_lh_p: 2 /* Helix */ | 32 /* LeftHanded */,
-        helx_lh_pi_p: 2 /* Helix */ | 32 /* LeftHanded */ | 32768 /* HelixPi */,
-        helx_lh_pp_p: 2 /* Helix */ | 32 /* LeftHanded */ | 65536 /* HelixPolyproline */,
-        helx_lh_z_n: 1 /* DoubleHelix */ | 32 /* LeftHanded */ | 262144 /* DoubleHelixZ */,
-        helx_n: 1 /* DoubleHelix */,
-        helx_ot_n: 1 /* DoubleHelix */,
-        helx_ot_p: 2 /* Helix */,
-        helx_p: 2 /* Helix */,
-        helx_rh_27_p: 2 /* Helix */ | 64 /* RightHanded */ | 1024 /* Helix27 */,
-        helx_rh_3t_p: 2 /* Helix */ | 64 /* RightHanded */ | 2048 /* Helix3Ten */,
-        helx_rh_al_p: 2 /* Helix */ | 64 /* RightHanded */ | 4096 /* HelixAlpha */,
-        helx_rh_a_n: 1 /* DoubleHelix */ | 64 /* RightHanded */ | 524288 /* DoubleHelixA */,
-        helx_rh_b_n: 1 /* DoubleHelix */ | 64 /* RightHanded */ | 1048576 /* DoubleHelixB */,
-        helx_rh_ga_p: 2 /* Helix */ | 64 /* RightHanded */ | 8192 /* HelixGamma */,
-        helx_rh_n: 1 /* DoubleHelix */ | 64 /* RightHanded */,
-        helx_rh_om_p: 2 /* Helix */ | 64 /* RightHanded */ | 16384 /* HelixOmega */,
-        helx_rh_ot_n: 1 /* DoubleHelix */ | 64 /* RightHanded */ | 131072 /* DoubleHelixOther */,
-        helx_rh_ot_p: 2 /* Helix */ | 64 /* RightHanded */ | 512 /* HelixOther */,
-        helx_rh_p: 2 /* Helix */ | 64 /* RightHanded */,
-        helx_rh_pi_p: 2 /* Helix */ | 64 /* RightHanded */ | 32768 /* HelixPi */,
-        helx_rh_pp_p: 2 /* Helix */ | 64 /* RightHanded */ | 65536 /* HelixPolyproline */,
-        helx_rh_z_n: 1 /* DoubleHelix */ | 64 /* RightHanded */ | 262144 /* DoubleHelixZ */,
-        strn: 4 /* Beta */ | 4194304 /* BetaStrand */,
-        turn_ot_p: 16 /* Turn */ | 33554432 /* TurnOther */,
-        turn_p: 16 /* Turn */,
-        turn_ty1p_p: 16 /* Turn */ | 256 /* InverseTurn */ | 67108864 /* Turn1 */,
-        turn_ty1_p: 16 /* Turn */ | 128 /* ClassicTurn */ | 67108864 /* Turn1 */,
-        turn_ty2p_p: 16 /* Turn */ | 256 /* InverseTurn */ | 134217728 /* Turn2 */,
-        turn_ty2_p: 16 /* Turn */ | 128 /* ClassicTurn */ | 134217728 /* Turn2 */,
-        turn_ty3p_p: 16 /* Turn */ | 256 /* InverseTurn */ | 268435456 /* Turn3 */,
-        turn_ty3_p: 16 /* Turn */ | 128 /* ClassicTurn */ | 268435456 /* Turn3 */,
-        bend: 8 /* Bend */,
-        other: 0 /* None */, // secondary structure type that does not conform to an accepted category, random coil (protein)
+        helx_lh_27_p: 2 /* Flag.Helix */ | 32 /* Flag.LeftHanded */ | 1024 /* Flag.Helix27 */,
+        helx_lh_3t_p: 2 /* Flag.Helix */ | 32 /* Flag.LeftHanded */ | 2048 /* Flag.Helix3Ten */,
+        helx_lh_al_p: 2 /* Flag.Helix */ | 32 /* Flag.LeftHanded */ | 4096 /* Flag.HelixAlpha */,
+        helx_lh_a_n: 1 /* Flag.DoubleHelix */ | 32 /* Flag.LeftHanded */ | 524288 /* Flag.DoubleHelixA */,
+        helx_lh_b_n: 1 /* Flag.DoubleHelix */ | 32 /* Flag.LeftHanded */ | 1048576 /* Flag.DoubleHelixB */,
+        helx_lh_ga_p: 2 /* Flag.Helix */ | 32 /* Flag.LeftHanded */ | 8192 /* Flag.HelixGamma */,
+        helx_lh_n: 1 /* Flag.DoubleHelix */ | 32 /* Flag.LeftHanded */,
+        helx_lh_om_p: 2 /* Flag.Helix */ | 32 /* Flag.LeftHanded */ | 16384 /* Flag.HelixOmega */,
+        helx_lh_ot_n: 1 /* Flag.DoubleHelix */ | 32 /* Flag.LeftHanded */ | 131072 /* Flag.DoubleHelixOther */,
+        helx_lh_ot_p: 2 /* Flag.Helix */ | 32 /* Flag.LeftHanded */ | 512 /* Flag.HelixOther */,
+        helx_lh_p: 2 /* Flag.Helix */ | 32 /* Flag.LeftHanded */,
+        helx_lh_pi_p: 2 /* Flag.Helix */ | 32 /* Flag.LeftHanded */ | 32768 /* Flag.HelixPi */,
+        helx_lh_pp_p: 2 /* Flag.Helix */ | 32 /* Flag.LeftHanded */ | 65536 /* Flag.HelixPolyproline */,
+        helx_lh_z_n: 1 /* Flag.DoubleHelix */ | 32 /* Flag.LeftHanded */ | 262144 /* Flag.DoubleHelixZ */,
+        helx_n: 1 /* Flag.DoubleHelix */,
+        helx_ot_n: 1 /* Flag.DoubleHelix */,
+        helx_ot_p: 2 /* Flag.Helix */,
+        helx_p: 2 /* Flag.Helix */,
+        helx_rh_27_p: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */ | 1024 /* Flag.Helix27 */,
+        helx_rh_3t_p: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */ | 2048 /* Flag.Helix3Ten */,
+        helx_rh_al_p: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */ | 4096 /* Flag.HelixAlpha */,
+        helx_rh_a_n: 1 /* Flag.DoubleHelix */ | 64 /* Flag.RightHanded */ | 524288 /* Flag.DoubleHelixA */,
+        helx_rh_b_n: 1 /* Flag.DoubleHelix */ | 64 /* Flag.RightHanded */ | 1048576 /* Flag.DoubleHelixB */,
+        helx_rh_ga_p: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */ | 8192 /* Flag.HelixGamma */,
+        helx_rh_n: 1 /* Flag.DoubleHelix */ | 64 /* Flag.RightHanded */,
+        helx_rh_om_p: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */ | 16384 /* Flag.HelixOmega */,
+        helx_rh_ot_n: 1 /* Flag.DoubleHelix */ | 64 /* Flag.RightHanded */ | 131072 /* Flag.DoubleHelixOther */,
+        helx_rh_ot_p: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */ | 512 /* Flag.HelixOther */,
+        helx_rh_p: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */,
+        helx_rh_pi_p: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */ | 32768 /* Flag.HelixPi */,
+        helx_rh_pp_p: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */ | 65536 /* Flag.HelixPolyproline */,
+        helx_rh_z_n: 1 /* Flag.DoubleHelix */ | 64 /* Flag.RightHanded */ | 262144 /* Flag.DoubleHelixZ */,
+        strn: 4 /* Flag.Beta */ | 4194304 /* Flag.BetaStrand */,
+        turn_ot_p: 16 /* Flag.Turn */ | 33554432 /* Flag.TurnOther */,
+        turn_p: 16 /* Flag.Turn */,
+        turn_ty1p_p: 16 /* Flag.Turn */ | 256 /* Flag.InverseTurn */ | 67108864 /* Flag.Turn1 */,
+        turn_ty1_p: 16 /* Flag.Turn */ | 128 /* Flag.ClassicTurn */ | 67108864 /* Flag.Turn1 */,
+        turn_ty2p_p: 16 /* Flag.Turn */ | 256 /* Flag.InverseTurn */ | 134217728 /* Flag.Turn2 */,
+        turn_ty2_p: 16 /* Flag.Turn */ | 128 /* Flag.ClassicTurn */ | 134217728 /* Flag.Turn2 */,
+        turn_ty3p_p: 16 /* Flag.Turn */ | 256 /* Flag.InverseTurn */ | 268435456 /* Flag.Turn3 */,
+        turn_ty3_p: 16 /* Flag.Turn */ | 128 /* Flag.ClassicTurn */ | 268435456 /* Flag.Turn3 */,
+        bend: 8 /* Flag.Bend */,
+        other: 0 /* Flag.None */, // secondary structure type that does not conform to an accepted category, random coil (protein)
     };
     SecondaryStructureType.SecondaryStructurePdb = {
-        1: 2 /* Helix */ | 64 /* RightHanded */ | 4096 /* HelixAlpha */,
-        2: 2 /* Helix */ | 64 /* RightHanded */ | 16384 /* HelixOmega */,
-        3: 2 /* Helix */ | 64 /* RightHanded */ | 32768 /* HelixPi */,
-        4: 2 /* Helix */ | 64 /* RightHanded */ | 8192 /* HelixGamma */,
-        5: 2 /* Helix */ | 64 /* RightHanded */ | 2048 /* Helix3Ten */,
-        6: 2 /* Helix */ | 32 /* LeftHanded */ | 4096 /* HelixAlpha */,
-        7: 2 /* Helix */ | 32 /* LeftHanded */ | 16384 /* HelixOmega */,
-        8: 2 /* Helix */ | 32 /* LeftHanded */ | 8192 /* HelixGamma */,
-        9: 2 /* Helix */ | 1024 /* Helix27 */,
-        10: 2 /* Helix */ | 65536 /* HelixPolyproline */, // Polyproline
+        1: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */ | 4096 /* Flag.HelixAlpha */,
+        2: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */ | 16384 /* Flag.HelixOmega */,
+        3: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */ | 32768 /* Flag.HelixPi */,
+        4: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */ | 8192 /* Flag.HelixGamma */,
+        5: 2 /* Flag.Helix */ | 64 /* Flag.RightHanded */ | 2048 /* Flag.Helix3Ten */,
+        6: 2 /* Flag.Helix */ | 32 /* Flag.LeftHanded */ | 4096 /* Flag.HelixAlpha */,
+        7: 2 /* Flag.Helix */ | 32 /* Flag.LeftHanded */ | 16384 /* Flag.HelixOmega */,
+        8: 2 /* Flag.Helix */ | 32 /* Flag.LeftHanded */ | 8192 /* Flag.HelixGamma */,
+        9: 2 /* Flag.Helix */ | 1024 /* Flag.Helix27 */,
+        10: 2 /* Flag.Helix */ | 65536 /* Flag.HelixPolyproline */, // Polyproline
     };
     SecondaryStructureType.SecondaryStructureStride = {
-        H: 2 /* Helix */ | 4096 /* HelixAlpha */,
-        G: 2 /* Helix */ | 2048 /* Helix3Ten */,
-        I: 2 /* Helix */ | 32768 /* HelixPi */,
-        E: 4 /* Beta */ | 8388608 /* BetaSheet */,
-        B: 4 /* Beta */ | 4194304 /* BetaStrand */,
-        T: 16 /* Turn */,
-        C: 536870912 /* NA */, // Coil (none of the above)
+        H: 2 /* Flag.Helix */ | 4096 /* Flag.HelixAlpha */,
+        G: 2 /* Flag.Helix */ | 2048 /* Flag.Helix3Ten */,
+        I: 2 /* Flag.Helix */ | 32768 /* Flag.HelixPi */,
+        E: 4 /* Flag.Beta */ | 8388608 /* Flag.BetaSheet */,
+        B: 4 /* Flag.Beta */ | 4194304 /* Flag.BetaStrand */,
+        T: 16 /* Flag.Turn */,
+        C: 536870912 /* Flag.NA */, // Coil (none of the above)
     };
     SecondaryStructureType.SecondaryStructureDssp = {
-        H: 2 /* Helix */ | 4096 /* HelixAlpha */,
-        B: 4 /* Beta */ | 4194304 /* BetaStrand */,
-        E: 4 /* Beta */ | 8388608 /* BetaSheet */,
-        G: 2 /* Helix */ | 2048 /* Helix3Ten */,
-        I: 2 /* Helix */ | 32768 /* HelixPi */,
-        T: 16 /* Turn */,
-        S: 8 /* Bend */, // bend
+        H: 2 /* Flag.Helix */ | 4096 /* Flag.HelixAlpha */,
+        B: 4 /* Flag.Beta */ | 4194304 /* Flag.BetaStrand */,
+        E: 4 /* Flag.Beta */ | 8388608 /* Flag.BetaSheet */,
+        G: 2 /* Flag.Helix */ | 2048 /* Flag.Helix3Ten */,
+        I: 2 /* Flag.Helix */ | 32768 /* Flag.HelixPi */,
+        T: 16 /* Flag.Turn */,
+        S: 8 /* Flag.Bend */, // bend
     };
 })(SecondaryStructureType = exports.SecondaryStructureType || (exports.SecondaryStructureType = {}));
 /** Maximum accessible surface area observed for amino acids. Taken from: http://dx.doi.org/10.1371/journal.pone.0080635 */
@@ -542,7 +542,7 @@ var BondType;
     }
     BondType.create = create;
     function isCovalent(flags) {
-        return (flags & 1 /* Covalent */) !== 0;
+        return (flags & 1 /* BondType.Flag.Covalent */) !== 0;
     }
     BondType.isCovalent = isCovalent;
     function isAll(flags) {
@@ -550,12 +550,12 @@ var BondType;
     }
     BondType.isAll = isAll;
     BondType.Names = {
-        'covalent': 1 /* Covalent */,
-        'metal-coordination': 2 /* MetallicCoordination */,
-        'hydrogen-bond': 4 /* HydrogenBond */,
-        'disulfide': 8 /* Disulfide */,
-        'aromatic': 16 /* Aromatic */,
-        'computed': 32 /* Computed */,
+        'covalent': 1 /* Flag.Covalent */,
+        'metal-coordination': 2 /* Flag.MetallicCoordination */,
+        'hydrogen-bond': 4 /* Flag.HydrogenBond */,
+        'disulfide': 8 /* Flag.Disulfide */,
+        'aromatic': 16 /* Flag.Aromatic */,
+        'computed': 32 /* Flag.Computed */,
     };
     function isName(name) {
         return name in BondType.Names;
@@ -563,17 +563,17 @@ var BondType;
     BondType.isName = isName;
     function fromName(name) {
         switch (name) {
-            case 'covalent': return 1 /* Covalent */;
-            case 'metal-coordination': return 2 /* MetallicCoordination */;
-            case 'hydrogen-bond': return 4 /* HydrogenBond */;
-            case 'disulfide': return 8 /* Disulfide */;
-            case 'aromatic': return 16 /* Aromatic */;
-            case 'computed': return 32 /* Computed */;
+            case 'covalent': return 1 /* Flag.Covalent */;
+            case 'metal-coordination': return 2 /* Flag.MetallicCoordination */;
+            case 'hydrogen-bond': return 4 /* Flag.HydrogenBond */;
+            case 'disulfide': return 8 /* Flag.Disulfide */;
+            case 'aromatic': return 16 /* Flag.Aromatic */;
+            case 'computed': return 32 /* Flag.Computed */;
         }
     }
     BondType.fromName = fromName;
     function fromNames(names) {
-        var f = 0 /* None */;
+        var f = 0 /* Flag.None */;
         for (var i = 0, il = names.length; i < il; ++i) {
             f |= fromName(names[i]);
         }

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

@@ -89,7 +89,7 @@ var QueryContextBondInfo = /** @class */ (function () {
         this.aIndex = 0;
         this.b = structure_1.StructureElement.Location.create(void 0);
         this.bIndex = 0;
-        this.type = 0 /* None */;
+        this.type = 0 /* BondType.Flag.None */;
         this.order = 0;
         this.testFn = internal_1.defaultBondTest;
     }

package/lib/commonjs/mol-model/structure/query/queries/generators.js

@@ -84,7 +84,7 @@ function atomGroupsSegmented(_a) {
                 continue;
             var elements = unit.elements, model = unit.model;
             builder.beginUnit(unit.id);
-            if (unit.kind === 0 /* Atomic */) {
+            if (unit.kind === 0 /* Unit.Kind.Atomic */) {
                 var chainsIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
                 var residuesIt = int_1.Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
                 while (chainsIt.hasNext) {
@@ -119,7 +119,7 @@ function atomGroupsSegmented(_a) {
                 }
             }
             else {
-                var chainElementSegments = (1 /* Spheres */ ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians).chainElementSegments;
+                var chainElementSegments = (1 /* Unit.Kind.Spheres */ ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians).chainElementSegments;
                 var chainsIt = int_1.Segmentation.transientSegments(chainElementSegments, elements);
                 while (chainsIt.hasNext) {
                     var chainSegment = chainsIt.move();
@@ -161,7 +161,7 @@ function atomGroupsGrouped(_a) {
             if (!unitTest(ctx))
                 continue;
             var elements = unit.elements, model = unit.model;
-            if (unit.kind === 0 /* Atomic */) {
+            if (unit.kind === 0 /* Unit.Kind.Atomic */) {
                 var chainsIt = int_1.Segmentation.transientSegments(model.atomicHierarchy.chainAtomSegments, elements);
                 var residuesIt = int_1.Segmentation.transientSegments(model.atomicHierarchy.residueAtomSegments, elements);
                 while (chainsIt.hasNext) {
@@ -188,7 +188,7 @@ function atomGroupsGrouped(_a) {
                 }
             }
             else {
-                var chainElementSegments = (1 /* Spheres */ ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians).chainElementSegments;
+                var chainElementSegments = (1 /* Unit.Kind.Spheres */ ? model.coarseHierarchy.spheres : model.coarseHierarchy.gaussians).chainElementSegments;
                 var chainsIt = int_1.Segmentation.transientSegments(chainElementSegments, elements);
                 while (chainsIt.hasNext) {
                     var chainSegment = chainsIt.move();
@@ -298,7 +298,7 @@ function bondedAtomicPairs(bondTest) {
         // Process intra unit bonds
         for (var _a = 0, _b = structure.units; _a < _b.length; _a++) {
             var unit = _b[_a];
-            if (unit.kind !== 0 /* Atomic */)
+            if (unit.kind !== 0 /* Unit.Kind.Atomic */)
                 continue;
             var _c = unit.bonds, intraBondOffset = _c.offset, intraBondB = _c.b, _d = _c.edgeProps, flags = _d.flags, order = _d.order;
             atomicBond.a.unit = unit;