molstar 3.8.2 → 3.9.0

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

@@ -31,22 +31,22 @@ export 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) {
@@ -109,7 +109,7 @@ var ElementMappedCustomProperty = /** @class */ (function () {
         this.map = map;
         this.id = 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); };
@@ -150,7 +150,7 @@ var EntityMappedCustomProperty = /** @class */ (function () {
         this.map = map;
         this.id = 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/mol-model/structure/model/properties/utils/atomic-ranges.js

@@ -12,7 +12,7 @@ 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/mol-model/structure/model/types.js

@@ -44,7 +44,7 @@ export function getElementFromAtomicNumber(n) {
     return ElementSymbol('H');
 }
 export var PolymerTypeAtomRoleId = (_a = {},
-    _a[0 /* NA */] = {
+    _a[0 /* PolymerType.NA */] = {
         trace: new Set(),
         directionFrom: new Set(),
         directionTo: new Set(),
@@ -52,7 +52,7 @@ export var 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']),
@@ -62,7 +62,7 @@ export var 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']),
@@ -70,7 +70,7 @@ export var 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']),
@@ -78,7 +78,7 @@ export var 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*']),
@@ -86,7 +86,7 @@ export var 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*']),
@@ -94,7 +94,7 @@ export var 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*']),
@@ -234,77 +234,77 @@ export var PolymerNames = SetUtils.unionMany(AminoAcidNames, BaseNames);
 export function getMoleculeType(compType, compId) {
     compId = compId.toUpperCase();
     if (PeptideBaseNames.has(compId)) {
-        return 8 /* PNA */;
+        return 8 /* MoleculeType.PNA */;
     }
     else if (ProteinComponentTypeNames.has(compType)) {
-        return 5 /* Protein */;
+        return 5 /* MoleculeType.Protein */;
     }
     else if (RNAComponentTypeNames.has(compType)) {
-        return 6 /* RNA */;
+        return 6 /* MoleculeType.RNA */;
     }
     else if (DNAComponentTypeNames.has(compType)) {
-        return 7 /* DNA */;
+        return 7 /* MoleculeType.DNA */;
     }
     else if (SaccharideComponentTypeNames.has(compType)) {
-        return 9 /* Saccharide */;
+        return 9 /* MoleculeType.Saccharide */;
     }
     else if (WaterNames.has(compId)) {
-        return 2 /* Water */;
+        return 2 /* MoleculeType.Water */;
     }
     else if (IonNames.has(compId)) {
-        return 3 /* Ion */;
+        return 3 /* MoleculeType.Ion */;
     }
     else if (LipidNames.has(compId)) {
-        return 4 /* Lipid */;
+        return 4 /* MoleculeType.Lipid */;
     }
     else if (OtherComponentTypeNames.has(compType)) {
         if (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 (AminoAcidNames.has(compId)) {
-            return 5 /* Protein */;
+            return 5 /* MoleculeType.Protein */;
         }
         else if (RnaBaseNames.has(compId)) {
-            return 6 /* RNA */;
+            return 6 /* MoleculeType.RNA */;
         }
         else if (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 */;
     }
 }
 export function getPolymerType(compType, molType) {
-    if (molType === 5 /* Protein */) {
+    if (molType === 5 /* MoleculeType.Protein */) {
         if (GammaProteinComponentTypeNames.has(compType)) {
-            return 2 /* GammaProtein */;
+            return 2 /* PolymerType.GammaProtein */;
         }
         else if (BetaProteinComponentTypeNames.has(compType)) {
-            return 3 /* BetaProtein */;
+            return 3 /* PolymerType.BetaProtein */;
         }
         else if (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 */;
     }
 }
 export function getComponentType(compId) {
@@ -405,89 +405,89 @@ export function isPolymer(moleculeType) {
     return isNucleic(moleculeType) || isProtein(moleculeType);
 }
 export 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 */;
 }
 export function isProtein(moleculeType) {
-    return moleculeType === 5 /* Protein */;
+    return moleculeType === 5 /* MoleculeType.Protein */;
 }
 export var SecondaryStructureType;
 (function (SecondaryStructureType) {
     SecondaryStructureType.is = BitFlags.has;
     SecondaryStructureType.create = 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 || (SecondaryStructureType = {}));
 /** Maximum accessible surface area observed for amino acids. Taken from: http://dx.doi.org/10.1371/journal.pone.0080635 */
@@ -526,7 +526,7 @@ export 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) {
@@ -534,12 +534,12 @@ export 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;
@@ -547,17 +547,17 @@ export 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/mol-model/structure/query/context.js

@@ -86,7 +86,7 @@ var QueryContextBondInfo = /** @class */ (function () {
         this.aIndex = 0;
         this.b = StructureElement.Location.create(void 0);
         this.bIndex = 0;
-        this.type = 0 /* None */;
+        this.type = 0 /* BondType.Flag.None */;
         this.order = 0;
         this.testFn = defaultBondTest;
     }

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

@@ -76,7 +76,7 @@ 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 = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
                 var residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
                 while (chainsIt.hasNext) {
@@ -111,7 +111,7 @@ 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 = Segmentation.transientSegments(chainElementSegments, elements);
                 while (chainsIt.hasNext) {
                     var chainSegment = chainsIt.move();
@@ -153,7 +153,7 @@ 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 = Segmentation.transientSegments(model.atomicHierarchy.chainAtomSegments, elements);
                 var residuesIt = Segmentation.transientSegments(model.atomicHierarchy.residueAtomSegments, elements);
                 while (chainsIt.hasNext) {
@@ -180,7 +180,7 @@ 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 = Segmentation.transientSegments(chainElementSegments, elements);
                 while (chainsIt.hasNext) {
                     var chainSegment = chainsIt.move();
@@ -288,7 +288,7 @@ export 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;

package/lib/mol-model/structure/query/queries/internal.js

@@ -20,7 +20,7 @@ export function atomicSequence() {
         var units = [];
         for (var _i = 0, _a = inputStructure.units; _i < _a.length; _i++) {
             var unit = _a[_i];
-            if (unit.kind !== 0 /* Atomic */)
+            if (unit.kind !== 0 /* Unit.Kind.Atomic */)
                 continue;
             l.unit = unit;
             var elements = unit.elements;
@@ -47,7 +47,7 @@ export function water() {
         var units = [];
         for (var _i = 0, _a = inputStructure.units; _i < _a.length; _i++) {
             var unit = _a[_i];
-            if (unit.kind !== 0 /* Atomic */)
+            if (unit.kind !== 0 /* Unit.Kind.Atomic */)
                 continue;
             l.unit = unit;
             var elements = unit.elements;
@@ -66,7 +66,7 @@ export function atomicHet() {
         var units = [];
         for (var _i = 0, _a = inputStructure.units; _i < _a.length; _i++) {
             var unit = _a[_i];
-            if (unit.kind !== 0 /* Atomic */)
+            if (unit.kind !== 0 /* Unit.Kind.Atomic */)
                 continue;
             l.unit = unit;
             var elements = unit.elements;
@@ -94,7 +94,7 @@ export function spheres() {
         var units = [];
         for (var _i = 0, _a = inputStructure.units; _i < _a.length; _i++) {
             var unit = _a[_i];
-            if (unit.kind !== 1 /* Spheres */)
+            if (unit.kind !== 1 /* Unit.Kind.Spheres */)
                 continue;
             units.push(unit);
         }

package/lib/mol-model/structure/query/queries/modifiers.js

@@ -19,7 +19,7 @@ function getWholeResidues(ctx, source, structure) {
     var builder = source.subsetBuilder(true);
     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 */) {
             // just copy non-atomic units.
             builder.setUnit(unit.id, unit.elements);
             continue;
@@ -318,7 +318,7 @@ function expandConnected(ctx, structure) {
     // 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 */) {
             // add the whole unit
             builder.beginUnit(unit.id);
             for (var i = 0, _i = unit.elements.length; i < _i; i++) {
@@ -403,7 +403,7 @@ export function surroundingLigands(_a) {
         var componentResidues = new ResidueSet({ checkOperator: true });
         for (var _a = 0, _b = surroundings.units; _a < _b.length; _a++) {
             var unit = _b[_a];
-            if (unit.kind !== 0 /* Atomic */)
+            if (unit.kind !== 0 /* Unit.Kind.Atomic */)
                 continue;
             l.unit = unit;
             var elements = unit.elements;
@@ -441,7 +441,7 @@ export function surroundingLigands(_a) {
         var builder = ctx.inputStructure.subsetBuilder(true);
         for (var _c = 0, _d = ctx.inputStructure.units; _c < _d.length; _c++) {
             var unit = _d[_c];
-            if (unit.kind !== 0 /* Atomic */)
+            if (unit.kind !== 0 /* Unit.Kind.Atomic */)
                 continue;
             l.unit = unit;
             var elements = unit.elements;

package/lib/mol-model/structure/query/utils/structure-distance.d.ts

@@ -10,60 +10,11 @@ export declare function checkStructureMinMaxDistance(ctx: QueryContext, a: Struc
 export declare function checkStructureMaxRadiusDistance(ctx: QueryContext, a: Structure, b: Structure, maxDist: number, elementRadius: QueryFn<number>): boolean | 0;
 declare namespace MinMaxDist {
     const enum Result {
-        BelowMin,
-        WithinMax,
-        Miss
-    }
-    const distVec = Vec3.zero();
-    function inUnit(ctx: QueryContext, unit: Unit, p: Vec3, eRadius: number, minDist: number, maxDist: number, elementRadius: QueryFn<number>) {
-        const { elements, conformation: { position } } = unit, dV = distVec;
-        ctx.element.unit = unit;
-        let withinRange = false;
-        for (let i = 0, _i = elements.length; i < _i; i++) {
-            const e = elements[i];
-            ctx.element.element = e;
-            const d = Math.max(0, Vec3.distance(p, position(e, dV)) - eRadius - elementRadius(ctx));
-            if (d < minDist)
-                return Result.BelowMin;
-            if (d < maxDist)
-                withinRange = true;
-        }
-        return withinRange ? Result.WithinMax : Result.Miss;
-    }
-    function toPoint(ctx: QueryContext, s: Structure, point: Vec3, radius: number, minDist: number, maxDist: number, elementRadius: QueryFn<number>) {
-        const { units } = s;
-        let withinRange = false;
-        for (let i = 0, _i = units.length; i < _i; i++) {
-            const iu = inUnit(ctx, units[i], point, radius, minDist, maxDist, elementRadius);
-            if (iu === Result.BelowMin)
-                return Result.BelowMin;
-            if (iu === Result.WithinMax)
-                withinRange = true;
-        }
-        return withinRange ? Result.WithinMax : Result.Miss;
-    }
-    const distPivot = Vec3.zero();
-    function check(ctx: QueryContext, a: Structure, b: Structure, minDist: number, maxDist: number, elementRadius: QueryFn<number>) {
-        if (a.elementCount === 0 || b.elementCount === 0)
-            return 0;
-        const { units } = a;
-        let withinRange = false;
-        ctx.element.structure = a;
-        for (let i = 0, _i = units.length; i < _i; i++) {
-            const unit = units[i];
-            const { elements, conformation: { position } } = unit;
-            ctx.element.unit = unit;
-            for (let i = 0, _i = elements.length; i < _i; i++) {
-                const e = elements[i];
-                ctx.element.element = e;
-                const tp = toPoint(ctx, b, position(e, distPivot), elementRadius(ctx), minDist, maxDist, elementRadius);
-                if (tp === Result.BelowMin)
-                    return Result.BelowMin;
-                if (tp === Result.WithinMax)
-                    withinRange = true;
-            }
-        }
-        return withinRange;
+        BelowMin = 0,
+        WithinMax = 1,
+        Miss = 2
     }
+    function toPoint(ctx: QueryContext, s: Structure, point: Vec3, radius: number, minDist: number, maxDist: number, elementRadius: QueryFn<number>): Result;
+    function check(ctx: QueryContext, a: Structure, b: Structure, minDist: number, maxDist: number, elementRadius: QueryFn<number>): boolean | 0 | Result.BelowMin;
 }
 export {};