molstar 3.8.2 → 3.9.0

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

@@ -24,7 +24,7 @@ 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;
@@ -52,7 +52,7 @@ 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;
@@ -72,7 +72,7 @@ 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;
@@ -101,7 +101,7 @@ 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/commonjs/mol-model/structure/query/queries/modifiers.js

@@ -22,7 +22,7 @@ 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;
@@ -329,7 +329,7 @@ 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++) {
@@ -414,7 +414,7 @@ function surroundingLigands(_a) {
         var componentResidues = new residue_set_1.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;
@@ -452,7 +452,7 @@ 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/commonjs/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 {};

package/lib/commonjs/mol-model/structure/query/utils/structure-distance.js

@@ -35,23 +35,23 @@ var MinMaxDist;
             ctx.element.element = e;
             var d = Math.max(0, linear_algebra_1.Vec3.distance(p, position(e, dV)) - eRadius - elementRadius(ctx));
             if (d < minDist)
-                return 0 /* BelowMin */;
+                return 0 /* Result.BelowMin */;
             if (d < maxDist)
                 withinRange = true;
         }
-        return withinRange ? 1 /* WithinMax */ : 2 /* Miss */;
+        return withinRange ? 1 /* Result.WithinMax */ : 2 /* Result.Miss */;
     }
     function toPoint(ctx, s, point, radius, minDist, maxDist, elementRadius) {
         var units = s.units;
         var withinRange = false;
         for (var i = 0, _i = units.length; i < _i; i++) {
             var iu = inUnit(ctx, units[i], point, radius, minDist, maxDist, elementRadius);
-            if (iu === 0 /* BelowMin */)
-                return 0 /* BelowMin */;
-            if (iu === 1 /* WithinMax */)
+            if (iu === 0 /* Result.BelowMin */)
+                return 0 /* Result.BelowMin */;
+            if (iu === 1 /* Result.WithinMax */)
                 withinRange = true;
         }
-        return withinRange ? 1 /* WithinMax */ : 2 /* Miss */;
+        return withinRange ? 1 /* Result.WithinMax */ : 2 /* Result.Miss */;
     }
     MinMaxDist.toPoint = toPoint;
     var distPivot = linear_algebra_1.Vec3.zero();
@@ -69,9 +69,9 @@ var MinMaxDist;
                 var e = elements[i_1];
                 ctx.element.element = e;
                 var tp = toPoint(ctx, b, position(e, distPivot), elementRadius(ctx), minDist, maxDist, elementRadius);
-                if (tp === 0 /* BelowMin */)
-                    return 0 /* BelowMin */;
-                if (tp === 1 /* WithinMax */)
+                if (tp === 0 /* Result.BelowMin */)
+                    return 0 /* Result.BelowMin */;
+                if (tp === 1 /* Result.WithinMax */)
                     withinRange = true;
             }
         }

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

@@ -23,49 +23,49 @@ exports.SaccharideColors = (0, color_1.ColorMap)({
     Secondary: 0xf1ece1
 });
 var SaccharideTypeNameMap = (_a = {},
-    _a[0 /* Hexose */] = 'Hexose',
-    _a[1 /* HexNAc */] = 'HexNAc',
-    _a[2 /* Hexosamine */] = 'Hexosamine',
-    _a[3 /* Hexuronate */] = 'Hexuronate',
-    _a[4 /* Deoxyhexose */] = 'Deoxyhexose',
-    _a[5 /* DeoxyhexNAc */] = 'DeoxyhexNAc',
-    _a[6 /* DiDeoxyhexose */] = 'Di-deoxyhexose',
-    _a[7 /* Pentose */] = 'Pentose',
-    _a[8 /* Deoxynonulosonate */] = 'Deoxynonulosonate',
-    _a[9 /* DiDeoxynonulosonate */] = 'Di-deoxynonulosonate',
-    _a[10 /* Unknown */] = 'Unknown',
-    _a[11 /* Assigned */] = 'Assigned',
+    _a[0 /* SaccharideType.Hexose */] = 'Hexose',
+    _a[1 /* SaccharideType.HexNAc */] = 'HexNAc',
+    _a[2 /* SaccharideType.Hexosamine */] = 'Hexosamine',
+    _a[3 /* SaccharideType.Hexuronate */] = 'Hexuronate',
+    _a[4 /* SaccharideType.Deoxyhexose */] = 'Deoxyhexose',
+    _a[5 /* SaccharideType.DeoxyhexNAc */] = 'DeoxyhexNAc',
+    _a[6 /* SaccharideType.DiDeoxyhexose */] = 'Di-deoxyhexose',
+    _a[7 /* SaccharideType.Pentose */] = 'Pentose',
+    _a[8 /* SaccharideType.Deoxynonulosonate */] = 'Deoxynonulosonate',
+    _a[9 /* SaccharideType.DiDeoxynonulosonate */] = 'Di-deoxynonulosonate',
+    _a[10 /* SaccharideType.Unknown */] = 'Unknown',
+    _a[11 /* SaccharideType.Assigned */] = 'Assigned',
     _a);
 function getSaccharideName(type) {
     return SaccharideTypeNameMap[type];
 }
 exports.getSaccharideName = getSaccharideName;
 var SaccharideTypeShapeMap = (_b = {},
-    _b[0 /* Hexose */] = 0 /* FilledSphere */,
-    _b[1 /* HexNAc */] = 1 /* FilledCube */,
-    _b[2 /* Hexosamine */] = 2 /* CrossedCube */,
-    _b[3 /* Hexuronate */] = 3 /* DividedDiamond */,
-    _b[4 /* Deoxyhexose */] = 4 /* FilledCone */,
-    _b[5 /* DeoxyhexNAc */] = 5 /* DevidedCone */,
-    _b[6 /* DiDeoxyhexose */] = 6 /* FlatBox */,
-    _b[7 /* Pentose */] = 7 /* FilledStar */,
-    _b[8 /* Deoxynonulosonate */] = 8 /* FilledDiamond */,
-    _b[9 /* DiDeoxynonulosonate */] = 9 /* FlatDiamond */,
-    _b[10 /* Unknown */] = 10 /* FlatHexagon */,
-    _b[11 /* Assigned */] = 11 /* Pentagon */,
+    _b[0 /* SaccharideType.Hexose */] = 0 /* SaccharideShape.FilledSphere */,
+    _b[1 /* SaccharideType.HexNAc */] = 1 /* SaccharideShape.FilledCube */,
+    _b[2 /* SaccharideType.Hexosamine */] = 2 /* SaccharideShape.CrossedCube */,
+    _b[3 /* SaccharideType.Hexuronate */] = 3 /* SaccharideShape.DividedDiamond */,
+    _b[4 /* SaccharideType.Deoxyhexose */] = 4 /* SaccharideShape.FilledCone */,
+    _b[5 /* SaccharideType.DeoxyhexNAc */] = 5 /* SaccharideShape.DevidedCone */,
+    _b[6 /* SaccharideType.DiDeoxyhexose */] = 6 /* SaccharideShape.FlatBox */,
+    _b[7 /* SaccharideType.Pentose */] = 7 /* SaccharideShape.FilledStar */,
+    _b[8 /* SaccharideType.Deoxynonulosonate */] = 8 /* SaccharideShape.FilledDiamond */,
+    _b[9 /* SaccharideType.DiDeoxynonulosonate */] = 9 /* SaccharideShape.FlatDiamond */,
+    _b[10 /* SaccharideType.Unknown */] = 10 /* SaccharideShape.FlatHexagon */,
+    _b[11 /* SaccharideType.Assigned */] = 11 /* SaccharideShape.Pentagon */,
     _b);
 function getSaccharideShape(type, ringMemberCount) {
-    if (type === 10 /* Unknown */) {
+    if (type === 10 /* SaccharideType.Unknown */) {
         if (ringMemberCount === 4)
-            return 12 /* DiamondPrism */;
+            return 12 /* SaccharideShape.DiamondPrism */;
         else if (ringMemberCount === 5)
-            return 13 /* PentagonalPrism */;
+            return 13 /* SaccharideShape.PentagonalPrism */;
         else if (ringMemberCount === 6)
-            return 14 /* HexagonalPrism */;
+            return 14 /* SaccharideShape.HexagonalPrism */;
         else if (ringMemberCount === 7)
-            return 15 /* HeptagonalPrism */;
+            return 15 /* SaccharideShape.HeptagonalPrism */;
         else
-            return 10 /* FlatHexagon */;
+            return 10 /* SaccharideShape.FlatHexagon */;
     }
     else {
         return SaccharideTypeShapeMap[type];
@@ -76,84 +76,84 @@ exports.UnknownSaccharideComponent = {
     abbr: 'Unk',
     name: 'Unknown',
     color: exports.SaccharideColors.Secondary,
-    type: 10 /* Unknown */
+    type: 10 /* SaccharideType.Unknown */
 };
 var Monosaccharides = [
-    { abbr: 'Glc', name: 'Glucose', color: exports.SaccharideColors.Blue, type: 0 /* Hexose */ },
-    { abbr: 'Man', name: 'Mannose', color: exports.SaccharideColors.Green, type: 0 /* Hexose */ },
-    { abbr: 'Gal', name: 'Galactose', color: exports.SaccharideColors.Yellow, type: 0 /* Hexose */ },
-    { abbr: 'Gul', name: 'Gulose', color: exports.SaccharideColors.Orange, type: 0 /* Hexose */ },
-    { abbr: 'Alt', name: 'Altrose', color: exports.SaccharideColors.Pink, type: 0 /* Hexose */ },
-    { abbr: 'All', name: 'Allose', color: exports.SaccharideColors.Purple, type: 0 /* Hexose */ },
-    { abbr: 'Tal', name: 'Talose', color: exports.SaccharideColors.LightBlue, type: 0 /* Hexose */ },
-    { abbr: 'Ido', name: 'Idose', color: exports.SaccharideColors.Brown, type: 0 /* Hexose */ },
-    { abbr: 'GlcNAc', name: 'N-Acetyl Glucosamine', color: exports.SaccharideColors.Blue, type: 1 /* HexNAc */ },
-    { abbr: 'ManNAc', name: 'N-Acetyl Mannosamine', color: exports.SaccharideColors.Green, type: 1 /* HexNAc */ },
-    { abbr: 'GalNAc', name: 'N-Acetyl Galactosamine', color: exports.SaccharideColors.Yellow, type: 1 /* HexNAc */ },
-    { abbr: 'GulNAc', name: 'N-Acetyl Gulosamine', color: exports.SaccharideColors.Orange, type: 1 /* HexNAc */ },
-    { abbr: 'AltNAc', name: 'N-Acetyl Altrosamine', color: exports.SaccharideColors.Pink, type: 1 /* HexNAc */ },
-    { abbr: 'AllNAc', name: 'N-Acetyl Allosamine', color: exports.SaccharideColors.Purple, type: 1 /* HexNAc */ },
-    { abbr: 'TalNAc', name: 'N-Acetyl Talosamine', color: exports.SaccharideColors.LightBlue, type: 1 /* HexNAc */ },
-    { abbr: 'IdoNAc', name: 'N-Acetyl Idosamine', color: exports.SaccharideColors.Brown, type: 1 /* HexNAc */ },
-    { abbr: 'GlcN', name: 'Glucosamine', color: exports.SaccharideColors.Blue, type: 2 /* Hexosamine */ },
-    { abbr: 'ManN', name: 'Mannosamine', color: exports.SaccharideColors.Green, type: 2 /* Hexosamine */ },
-    { abbr: 'GalN', name: 'Galactosamine', color: exports.SaccharideColors.Yellow, type: 2 /* Hexosamine */ },
-    { abbr: 'GulN', name: 'Gulosamine', color: exports.SaccharideColors.Orange, type: 2 /* Hexosamine */ },
-    { abbr: 'AltN', name: 'Altrosamine', color: exports.SaccharideColors.Pink, type: 2 /* Hexosamine */ },
-    { abbr: 'AllN', name: 'Allosamine', color: exports.SaccharideColors.Purple, type: 2 /* Hexosamine */ },
-    { abbr: 'TalN', name: 'Talosamine', color: exports.SaccharideColors.LightBlue, type: 2 /* Hexosamine */ },
-    { abbr: 'IdoN', name: 'Idosamine', color: exports.SaccharideColors.Brown, type: 2 /* Hexosamine */ },
-    { abbr: 'GlcA', name: 'Glucuronic Acid', color: exports.SaccharideColors.Blue, type: 3 /* Hexuronate */ },
-    { abbr: 'ManA', name: 'Mannuronic Acid', color: exports.SaccharideColors.Green, type: 3 /* Hexuronate */ },
-    { abbr: 'GalA', name: 'Galacturonic Acid', color: exports.SaccharideColors.Yellow, type: 3 /* Hexuronate */ },
-    { abbr: 'GulA', name: 'Guluronic Acid', color: exports.SaccharideColors.Orange, type: 3 /* Hexuronate */ },
-    { abbr: 'AltA', name: 'Altruronic Acid', color: exports.SaccharideColors.Pink, type: 3 /* Hexuronate */ },
-    { abbr: 'AllA', name: 'Alluronic Acid', color: exports.SaccharideColors.Purple, type: 3 /* Hexuronate */ },
-    { abbr: 'TalA', name: 'Taluronic Acid', color: exports.SaccharideColors.LightBlue, type: 3 /* Hexuronate */ },
-    { abbr: 'IdoA', name: 'Iduronic Acid', color: exports.SaccharideColors.Brown, type: 3 /* Hexuronate */ },
-    { abbr: 'Qui', name: 'Quinovose', color: exports.SaccharideColors.Blue, type: 4 /* Deoxyhexose */ },
-    { abbr: 'Rha', name: 'Rhamnose', color: exports.SaccharideColors.Green, type: 4 /* Deoxyhexose */ },
-    { abbr: '6dGul', name: '6-Deoxy Gulose', color: exports.SaccharideColors.Orange, type: 4 /* Deoxyhexose */ },
-    { abbr: '6dAlt', name: '6-Deoxy Altrose', color: exports.SaccharideColors.Pink, type: 4 /* Deoxyhexose */ },
-    { abbr: '6dTal', name: '6-Deoxy Talose', color: exports.SaccharideColors.LightBlue, type: 4 /* Deoxyhexose */ },
-    { abbr: 'Fuc', name: 'Fucose', color: exports.SaccharideColors.Red, type: 4 /* Deoxyhexose */ },
-    { abbr: 'QuiNAc', name: 'N-Acetyl Quinovosamine', color: exports.SaccharideColors.Blue, type: 5 /* DeoxyhexNAc */ },
-    { abbr: 'RhaNAc', name: 'N-Acetyl Rhamnosamine', color: exports.SaccharideColors.Green, type: 5 /* DeoxyhexNAc */ },
-    { abbr: '6dAltNAc', name: 'N-Acetyl 6-Deoxy Altrosamine', color: exports.SaccharideColors.Pink, type: 5 /* DeoxyhexNAc */ },
-    { abbr: '6dTalNAc', name: 'N-Acetyl 6-Deoxy Talosamine', color: exports.SaccharideColors.LightBlue, type: 5 /* DeoxyhexNAc */ },
-    { abbr: 'FucNAc', name: 'N-Acetyl Fucosamine', color: exports.SaccharideColors.Red, type: 5 /* DeoxyhexNAc */ },
-    { abbr: 'Oli', name: 'Olivose', color: exports.SaccharideColors.Blue, type: 6 /* DiDeoxyhexose */ },
-    { abbr: 'Tyv', name: 'Tyvelose', color: exports.SaccharideColors.Green, type: 6 /* DiDeoxyhexose */ },
-    { abbr: 'Abe', name: 'Abequose', color: exports.SaccharideColors.Orange, type: 6 /* DiDeoxyhexose */ },
-    { abbr: 'Par', name: 'Paratose', color: exports.SaccharideColors.Pink, type: 6 /* DiDeoxyhexose */ },
-    { abbr: 'Dig', name: 'Digitoxose', color: exports.SaccharideColors.Purple, type: 6 /* DiDeoxyhexose */ },
-    { abbr: 'Col', name: 'Colitose', color: exports.SaccharideColors.LightBlue, type: 6 /* DiDeoxyhexose */ },
-    { abbr: 'Ara', name: 'Arabinose', color: exports.SaccharideColors.Green, type: 7 /* Pentose */ },
-    { abbr: 'Lyx', name: 'Lyxose', color: exports.SaccharideColors.Yellow, type: 7 /* Pentose */ },
-    { abbr: 'Xyl', name: 'Xylose', color: exports.SaccharideColors.Orange, type: 7 /* Pentose */ },
-    { abbr: 'Rib', name: 'Ribose', color: exports.SaccharideColors.Pink, type: 7 /* Pentose */ },
-    { abbr: 'Kdn', name: 'Keto-Deoxy Nonulonic Acid', color: exports.SaccharideColors.Green, type: 8 /* Deoxynonulosonate */ },
-    { abbr: 'Neu5Ac', name: 'N-Acetyl Neuraminic Acid', color: exports.SaccharideColors.Purple, type: 8 /* Deoxynonulosonate */ },
-    { abbr: 'Neu5Gc', name: 'N-Glycolyl Neuraminic Acid', color: exports.SaccharideColors.LightBlue, type: 8 /* Deoxynonulosonate */ },
-    { abbr: 'Neu', name: 'Neuraminic Acid', color: exports.SaccharideColors.Brown, type: 8 /* Deoxynonulosonate */ },
-    { abbr: 'Sia', name: 'Sialic acid', color: exports.SaccharideColors.Red, type: 8 /* Deoxynonulosonate */ },
-    { abbr: 'Pse', name: 'Pseudaminic Acid', color: exports.SaccharideColors.Green, type: 9 /* DiDeoxynonulosonate */ },
-    { abbr: 'Leg', name: 'Legionaminic Acid', color: exports.SaccharideColors.Yellow, type: 9 /* DiDeoxynonulosonate */ },
-    { abbr: 'Aci', name: 'Acinetaminic Acid', color: exports.SaccharideColors.Pink, type: 9 /* DiDeoxynonulosonate */ },
-    { abbr: '4eLeg', name: '4-Epilegionaminic Acid', color: exports.SaccharideColors.LightBlue, type: 9 /* DiDeoxynonulosonate */ },
-    { abbr: 'Bac', name: 'Bacillosamine', color: exports.SaccharideColors.Blue, type: 10 /* Unknown */ },
-    { abbr: 'LDmanHep', name: 'L-Glycero-D-Manno Heptose', color: exports.SaccharideColors.Green, type: 10 /* Unknown */ },
-    { abbr: 'Kdo', name: 'Keto-Deoxy Octulonic Acid', color: exports.SaccharideColors.Yellow, type: 10 /* Unknown */ },
-    { abbr: 'Dha', name: '3-Deoxy Lyxo-Heptulosaric Acid', color: exports.SaccharideColors.Orange, type: 10 /* Unknown */ },
-    { abbr: 'DDmanHep', name: 'D-Glycero-D-Manno-Heptose', color: exports.SaccharideColors.Pink, type: 10 /* Unknown */ },
-    { abbr: 'MurNAc', name: 'N-Acetyl Muramic Acid', color: exports.SaccharideColors.Purple, type: 10 /* Unknown */ },
-    { abbr: 'MurNGc', name: 'N-Glycolyl Muramic Acid', color: exports.SaccharideColors.LightBlue, type: 10 /* Unknown */ },
-    { abbr: 'Mur', name: 'Muramic Acid', color: exports.SaccharideColors.Brown, type: 10 /* Unknown */ },
-    { abbr: 'Api', name: 'Apicose', color: exports.SaccharideColors.Green, type: 11 /* Assigned */ },
-    { abbr: 'Fru', name: 'Fructose', color: exports.SaccharideColors.Green, type: 11 /* Assigned */ },
-    { abbr: 'Tag', name: 'Tagatose', color: exports.SaccharideColors.Yellow, type: 11 /* Assigned */ },
-    { abbr: 'Sor', name: 'Sorbose', color: exports.SaccharideColors.Orange, type: 11 /* Assigned */ },
-    { abbr: 'Psi', name: 'Psicose', color: exports.SaccharideColors.Pink, type: 11 /* Assigned */ },
+    { abbr: 'Glc', name: 'Glucose', color: exports.SaccharideColors.Blue, type: 0 /* SaccharideType.Hexose */ },
+    { abbr: 'Man', name: 'Mannose', color: exports.SaccharideColors.Green, type: 0 /* SaccharideType.Hexose */ },
+    { abbr: 'Gal', name: 'Galactose', color: exports.SaccharideColors.Yellow, type: 0 /* SaccharideType.Hexose */ },
+    { abbr: 'Gul', name: 'Gulose', color: exports.SaccharideColors.Orange, type: 0 /* SaccharideType.Hexose */ },
+    { abbr: 'Alt', name: 'Altrose', color: exports.SaccharideColors.Pink, type: 0 /* SaccharideType.Hexose */ },
+    { abbr: 'All', name: 'Allose', color: exports.SaccharideColors.Purple, type: 0 /* SaccharideType.Hexose */ },
+    { abbr: 'Tal', name: 'Talose', color: exports.SaccharideColors.LightBlue, type: 0 /* SaccharideType.Hexose */ },
+    { abbr: 'Ido', name: 'Idose', color: exports.SaccharideColors.Brown, type: 0 /* SaccharideType.Hexose */ },
+    { abbr: 'GlcNAc', name: 'N-Acetyl Glucosamine', color: exports.SaccharideColors.Blue, type: 1 /* SaccharideType.HexNAc */ },
+    { abbr: 'ManNAc', name: 'N-Acetyl Mannosamine', color: exports.SaccharideColors.Green, type: 1 /* SaccharideType.HexNAc */ },
+    { abbr: 'GalNAc', name: 'N-Acetyl Galactosamine', color: exports.SaccharideColors.Yellow, type: 1 /* SaccharideType.HexNAc */ },
+    { abbr: 'GulNAc', name: 'N-Acetyl Gulosamine', color: exports.SaccharideColors.Orange, type: 1 /* SaccharideType.HexNAc */ },
+    { abbr: 'AltNAc', name: 'N-Acetyl Altrosamine', color: exports.SaccharideColors.Pink, type: 1 /* SaccharideType.HexNAc */ },
+    { abbr: 'AllNAc', name: 'N-Acetyl Allosamine', color: exports.SaccharideColors.Purple, type: 1 /* SaccharideType.HexNAc */ },
+    { abbr: 'TalNAc', name: 'N-Acetyl Talosamine', color: exports.SaccharideColors.LightBlue, type: 1 /* SaccharideType.HexNAc */ },
+    { abbr: 'IdoNAc', name: 'N-Acetyl Idosamine', color: exports.SaccharideColors.Brown, type: 1 /* SaccharideType.HexNAc */ },
+    { abbr: 'GlcN', name: 'Glucosamine', color: exports.SaccharideColors.Blue, type: 2 /* SaccharideType.Hexosamine */ },
+    { abbr: 'ManN', name: 'Mannosamine', color: exports.SaccharideColors.Green, type: 2 /* SaccharideType.Hexosamine */ },
+    { abbr: 'GalN', name: 'Galactosamine', color: exports.SaccharideColors.Yellow, type: 2 /* SaccharideType.Hexosamine */ },
+    { abbr: 'GulN', name: 'Gulosamine', color: exports.SaccharideColors.Orange, type: 2 /* SaccharideType.Hexosamine */ },
+    { abbr: 'AltN', name: 'Altrosamine', color: exports.SaccharideColors.Pink, type: 2 /* SaccharideType.Hexosamine */ },
+    { abbr: 'AllN', name: 'Allosamine', color: exports.SaccharideColors.Purple, type: 2 /* SaccharideType.Hexosamine */ },
+    { abbr: 'TalN', name: 'Talosamine', color: exports.SaccharideColors.LightBlue, type: 2 /* SaccharideType.Hexosamine */ },
+    { abbr: 'IdoN', name: 'Idosamine', color: exports.SaccharideColors.Brown, type: 2 /* SaccharideType.Hexosamine */ },
+    { abbr: 'GlcA', name: 'Glucuronic Acid', color: exports.SaccharideColors.Blue, type: 3 /* SaccharideType.Hexuronate */ },
+    { abbr: 'ManA', name: 'Mannuronic Acid', color: exports.SaccharideColors.Green, type: 3 /* SaccharideType.Hexuronate */ },
+    { abbr: 'GalA', name: 'Galacturonic Acid', color: exports.SaccharideColors.Yellow, type: 3 /* SaccharideType.Hexuronate */ },
+    { abbr: 'GulA', name: 'Guluronic Acid', color: exports.SaccharideColors.Orange, type: 3 /* SaccharideType.Hexuronate */ },
+    { abbr: 'AltA', name: 'Altruronic Acid', color: exports.SaccharideColors.Pink, type: 3 /* SaccharideType.Hexuronate */ },
+    { abbr: 'AllA', name: 'Alluronic Acid', color: exports.SaccharideColors.Purple, type: 3 /* SaccharideType.Hexuronate */ },
+    { abbr: 'TalA', name: 'Taluronic Acid', color: exports.SaccharideColors.LightBlue, type: 3 /* SaccharideType.Hexuronate */ },
+    { abbr: 'IdoA', name: 'Iduronic Acid', color: exports.SaccharideColors.Brown, type: 3 /* SaccharideType.Hexuronate */ },
+    { abbr: 'Qui', name: 'Quinovose', color: exports.SaccharideColors.Blue, type: 4 /* SaccharideType.Deoxyhexose */ },
+    { abbr: 'Rha', name: 'Rhamnose', color: exports.SaccharideColors.Green, type: 4 /* SaccharideType.Deoxyhexose */ },
+    { abbr: '6dGul', name: '6-Deoxy Gulose', color: exports.SaccharideColors.Orange, type: 4 /* SaccharideType.Deoxyhexose */ },
+    { abbr: '6dAlt', name: '6-Deoxy Altrose', color: exports.SaccharideColors.Pink, type: 4 /* SaccharideType.Deoxyhexose */ },
+    { abbr: '6dTal', name: '6-Deoxy Talose', color: exports.SaccharideColors.LightBlue, type: 4 /* SaccharideType.Deoxyhexose */ },
+    { abbr: 'Fuc', name: 'Fucose', color: exports.SaccharideColors.Red, type: 4 /* SaccharideType.Deoxyhexose */ },
+    { abbr: 'QuiNAc', name: 'N-Acetyl Quinovosamine', color: exports.SaccharideColors.Blue, type: 5 /* SaccharideType.DeoxyhexNAc */ },
+    { abbr: 'RhaNAc', name: 'N-Acetyl Rhamnosamine', color: exports.SaccharideColors.Green, type: 5 /* SaccharideType.DeoxyhexNAc */ },
+    { abbr: '6dAltNAc', name: 'N-Acetyl 6-Deoxy Altrosamine', color: exports.SaccharideColors.Pink, type: 5 /* SaccharideType.DeoxyhexNAc */ },
+    { abbr: '6dTalNAc', name: 'N-Acetyl 6-Deoxy Talosamine', color: exports.SaccharideColors.LightBlue, type: 5 /* SaccharideType.DeoxyhexNAc */ },
+    { abbr: 'FucNAc', name: 'N-Acetyl Fucosamine', color: exports.SaccharideColors.Red, type: 5 /* SaccharideType.DeoxyhexNAc */ },
+    { abbr: 'Oli', name: 'Olivose', color: exports.SaccharideColors.Blue, type: 6 /* SaccharideType.DiDeoxyhexose */ },
+    { abbr: 'Tyv', name: 'Tyvelose', color: exports.SaccharideColors.Green, type: 6 /* SaccharideType.DiDeoxyhexose */ },
+    { abbr: 'Abe', name: 'Abequose', color: exports.SaccharideColors.Orange, type: 6 /* SaccharideType.DiDeoxyhexose */ },
+    { abbr: 'Par', name: 'Paratose', color: exports.SaccharideColors.Pink, type: 6 /* SaccharideType.DiDeoxyhexose */ },
+    { abbr: 'Dig', name: 'Digitoxose', color: exports.SaccharideColors.Purple, type: 6 /* SaccharideType.DiDeoxyhexose */ },
+    { abbr: 'Col', name: 'Colitose', color: exports.SaccharideColors.LightBlue, type: 6 /* SaccharideType.DiDeoxyhexose */ },
+    { abbr: 'Ara', name: 'Arabinose', color: exports.SaccharideColors.Green, type: 7 /* SaccharideType.Pentose */ },
+    { abbr: 'Lyx', name: 'Lyxose', color: exports.SaccharideColors.Yellow, type: 7 /* SaccharideType.Pentose */ },
+    { abbr: 'Xyl', name: 'Xylose', color: exports.SaccharideColors.Orange, type: 7 /* SaccharideType.Pentose */ },
+    { abbr: 'Rib', name: 'Ribose', color: exports.SaccharideColors.Pink, type: 7 /* SaccharideType.Pentose */ },
+    { abbr: 'Kdn', name: 'Keto-Deoxy Nonulonic Acid', color: exports.SaccharideColors.Green, type: 8 /* SaccharideType.Deoxynonulosonate */ },
+    { abbr: 'Neu5Ac', name: 'N-Acetyl Neuraminic Acid', color: exports.SaccharideColors.Purple, type: 8 /* SaccharideType.Deoxynonulosonate */ },
+    { abbr: 'Neu5Gc', name: 'N-Glycolyl Neuraminic Acid', color: exports.SaccharideColors.LightBlue, type: 8 /* SaccharideType.Deoxynonulosonate */ },
+    { abbr: 'Neu', name: 'Neuraminic Acid', color: exports.SaccharideColors.Brown, type: 8 /* SaccharideType.Deoxynonulosonate */ },
+    { abbr: 'Sia', name: 'Sialic acid', color: exports.SaccharideColors.Red, type: 8 /* SaccharideType.Deoxynonulosonate */ },
+    { abbr: 'Pse', name: 'Pseudaminic Acid', color: exports.SaccharideColors.Green, type: 9 /* SaccharideType.DiDeoxynonulosonate */ },
+    { abbr: 'Leg', name: 'Legionaminic Acid', color: exports.SaccharideColors.Yellow, type: 9 /* SaccharideType.DiDeoxynonulosonate */ },
+    { abbr: 'Aci', name: 'Acinetaminic Acid', color: exports.SaccharideColors.Pink, type: 9 /* SaccharideType.DiDeoxynonulosonate */ },
+    { abbr: '4eLeg', name: '4-Epilegionaminic Acid', color: exports.SaccharideColors.LightBlue, type: 9 /* SaccharideType.DiDeoxynonulosonate */ },
+    { abbr: 'Bac', name: 'Bacillosamine', color: exports.SaccharideColors.Blue, type: 10 /* SaccharideType.Unknown */ },
+    { abbr: 'LDmanHep', name: 'L-Glycero-D-Manno Heptose', color: exports.SaccharideColors.Green, type: 10 /* SaccharideType.Unknown */ },
+    { abbr: 'Kdo', name: 'Keto-Deoxy Octulonic Acid', color: exports.SaccharideColors.Yellow, type: 10 /* SaccharideType.Unknown */ },
+    { abbr: 'Dha', name: '3-Deoxy Lyxo-Heptulosaric Acid', color: exports.SaccharideColors.Orange, type: 10 /* SaccharideType.Unknown */ },
+    { abbr: 'DDmanHep', name: 'D-Glycero-D-Manno-Heptose', color: exports.SaccharideColors.Pink, type: 10 /* SaccharideType.Unknown */ },
+    { abbr: 'MurNAc', name: 'N-Acetyl Muramic Acid', color: exports.SaccharideColors.Purple, type: 10 /* SaccharideType.Unknown */ },
+    { abbr: 'MurNGc', name: 'N-Glycolyl Muramic Acid', color: exports.SaccharideColors.LightBlue, type: 10 /* SaccharideType.Unknown */ },
+    { abbr: 'Mur', name: 'Muramic Acid', color: exports.SaccharideColors.Brown, type: 10 /* SaccharideType.Unknown */ },
+    { abbr: 'Api', name: 'Apicose', color: exports.SaccharideColors.Green, type: 11 /* SaccharideType.Assigned */ },
+    { abbr: 'Fru', name: 'Fructose', color: exports.SaccharideColors.Green, type: 11 /* SaccharideType.Assigned */ },
+    { abbr: 'Tag', name: 'Tagatose', color: exports.SaccharideColors.Yellow, type: 11 /* SaccharideType.Assigned */ },
+    { abbr: 'Sor', name: 'Sorbose', color: exports.SaccharideColors.Orange, type: 11 /* SaccharideType.Assigned */ },
+    { abbr: 'Psi', name: 'Psicose', color: exports.SaccharideColors.Pink, type: 11 /* SaccharideType.Assigned */ },
 ];
 exports.SaccharidesSnfgMap = (function () {
     var map = new Map();

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

@@ -282,7 +282,7 @@ exports.Loci = Loci;
                 elements[elements.length] = lociElement;
                 continue;
             }
-            if (lociElement.unit.kind === 0 /* Atomic */) {
+            if (lociElement.unit.kind === 0 /* Unit.Kind.Atomic */) {
                 var unitElements = lociElement.unit.elements;
                 var h = lociElement.unit.model.atomicHierarchy;
                 var label_alt_id = lociElement.unit.model.atomicHierarchy.atoms.label_alt_id;
@@ -326,9 +326,9 @@ exports.Loci = Loci;
     Loci.extendToWholeResidues = extendToWholeResidues;
     function getChainSegments(unit) {
         switch (unit.kind) {
-            case 0 /* Atomic */: return unit.model.atomicHierarchy.chainAtomSegments;
-            case 1 /* Spheres */: return unit.model.coarseHierarchy.spheres.chainElementSegments;
-            case 2 /* Gaussians */: return unit.model.coarseHierarchy.gaussians.chainElementSegments;
+            case 0 /* Unit.Kind.Atomic */: return unit.model.atomicHierarchy.chainAtomSegments;
+            case 1 /* Unit.Kind.Spheres */: return unit.model.coarseHierarchy.spheres.chainElementSegments;
+            case 2 /* Unit.Kind.Gaussians */: return unit.model.coarseHierarchy.gaussians.chainElementSegments;
         }
     }
     function isWholeUnit(element) {
@@ -393,7 +393,7 @@ exports.Loci = Loci;
         var elements = [];
         for (var i = 0, len = loci.elements.length; i < len; i++) {
             var e = loci.elements[i];
-            if (unit_1.Unit.Traits.is(e.unit.traits, 2 /* Partitioned */)) {
+            if (unit_1.Unit.Traits.is(e.unit.traits, 2 /* Unit.Trait.Partitioned */)) {
                 var start = i;
                 while (i < len && unit_1.Unit.areSameChainOperatorGroup(loci.elements[i].unit, e.unit)) {
                     i++;

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

@@ -51,7 +51,7 @@ var Stats;
             }
         }
         else if (size === 1) {
-            if (unit_1.Unit.Traits.is(unit.traits, 1 /* MultiChain */)) {
+            if (unit_1.Unit.Traits.is(unit.traits, 1 /* Unit.Trait.MultiChain */)) {
                 // handled in `handleUnitChainsSimple`
                 return;
             }
@@ -136,7 +136,7 @@ var Stats;
         if (size === 0)
             return;
         var elements = unit.elements;
-        if (!unit_1.Unit.Traits.is(unit.traits, 1 /* MultiChain */)) {
+        if (!unit_1.Unit.Traits.is(unit.traits, 1 /* Unit.Trait.MultiChain */)) {
             if (size === elements.length) {
                 stats.chainCount += 1;
                 if (stats.chainCount === 1) {
@@ -210,7 +210,7 @@ var Stats;
             if (size === 0)
                 continue;
             var elements = unit.elements;
-            if (!unit_1.Unit.Traits.is(unit.traits, 1 /* MultiChain */)) {
+            if (!unit_1.Unit.Traits.is(unit.traits, 1 /* Unit.Trait.MultiChain */)) {
                 var eI = elements[int_1.OrderedSet.start(indices)];
                 addCountHelper(chainCounts, index[eI], elements.length);
                 continue;
@@ -278,7 +278,7 @@ var Stats;
             for (var _i = 0, _b = loci.elements; _i < _b.length; _i++) {
                 var e = _b[_i];
                 handleElement(stats, loci.structure, e);
-                if (!unit_1.Unit.Traits.is(e.unit.traits, 2 /* Partitioned */)) {
+                if (!unit_1.Unit.Traits.is(e.unit.traits, 2 /* Unit.Trait.Partitioned */)) {
                     handleUnitChainsSimple(stats, loci.structure, e);
                 }
                 else {
@@ -289,7 +289,7 @@ var Stats;
         if (hasPartitions) {
             for (var i = 0, len = loci.elements.length; i < len; i++) {
                 var e = loci.elements[i];
-                if (!unit_1.Unit.Traits.is(e.unit.traits, 2 /* Partitioned */))
+                if (!unit_1.Unit.Traits.is(e.unit.traits, 2 /* Unit.Trait.Partitioned */))
                     continue;
                 var start = i;
                 while (i < len && unit_1.Unit.areSameChainOperatorGroup(loci.elements[i].unit, e.unit)) {

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

@@ -90,7 +90,7 @@ var residue = {
         if (!unit_1.Unit.isAtomic(l.unit))
             notAtomic();
         var secStruc = (_a = secondary_structure_1.SecondaryStructureProvider.get(l.structure).value) === null || _a === void 0 ? void 0 : _a.get(l.unit.invariantId);
-        return secStruc ? secStruc.type[secStruc.getIndex(l.unit.residueIndex[l.element])] : 536870912 /* NA */;
+        return secStruc ? secStruc.type[secStruc.getIndex(l.unit.residueIndex[l.element])] : 536870912 /* SecondaryStructureType.Flag.NA */;
     }),
     secondary_structure_key: p(function (l) {
         var _a;
@@ -124,11 +124,11 @@ var coarse = {
 };
 function eK(l) {
     switch (l.unit.kind) {
-        case 0 /* Atomic */:
+        case 0 /* Unit.Kind.Atomic */:
             return l.unit.model.atomicHierarchy.index.getEntityFromChain(l.unit.chainIndex[l.element]);
-        case 1 /* Spheres */:
+        case 1 /* Unit.Kind.Spheres */:
             return l.unit.model.coarseHierarchy.spheres.entityKey[l.element];
-        case 2 /* Gaussians */:
+        case 2 /* Unit.Kind.Gaussians */:
             return l.unit.model.coarseHierarchy.gaussians.entityKey[l.element];
     }
 }
@@ -151,7 +151,7 @@ var _emptyList = [];
 var unit = {
     id: p(function (l) { return l.unit.id; }),
     chainGroupId: p(function (l) { return l.unit.chainGroupId; }),
-    multiChain: p(function (l) { return unit_1.Unit.Traits.is(l.unit.traits, 1 /* MultiChain */); }),
+    multiChain: p(function (l) { return unit_1.Unit.Traits.is(l.unit.traits, 1 /* Unit.Trait.MultiChain */); }),
     object_primitive: p(function (l) { return l.unit.objectPrimitive; }),
     operator_name: p(function (l) { return l.unit.conformation.operator.name; }),
     model_index: p(function (l) { return l.unit.model.modelNum; }),