molstar 3.8.2 → 3.9.0

package/lib/commonjs/mol-repr/structure/visual/util/link.js

@@ -107,31 +107,31 @@ function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
         v3sub(tmpV12, vb, va);
         var dirFlag = v3dot(tmpV12, up) > 0;
         var linkRadius = radius(edgeIndex);
-        var linkStyle = style ? style(edgeIndex) : 0 /* Solid */;
+        var linkStyle = style ? style(edgeIndex) : 0 /* LinkStyle.Solid */;
         var linkStub = stubCap && (stub ? stub(edgeIndex) : false);
         var _a = dirFlag ? [linkStub, linkCap] : [linkCap, linkStub], topCap = _a[0], bottomCap = _a[1];
         builderState.currentGroup = edgeIndex;
         var aromaticSegmentCount = aromaticDashCount + 1;
-        if (linkStyle === 0 /* Solid */) {
+        if (linkStyle === 0 /* LinkStyle.Solid */) {
             cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
             cylinderProps.topCap = topCap;
             cylinderProps.bottomCap = bottomCap;
             (0, cylinder_1.addCylinder)(builderState, va, vb, 0.5, cylinderProps);
         }
-        else if (linkStyle === 1 /* Dashed */) {
+        else if (linkStyle === 1 /* LinkStyle.Dashed */) {
             cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius * dashScale;
             cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
             (0, cylinder_1.addFixedCountDashedCylinder)(builderState, va, vb, 0.5, segmentCount, cylinderProps);
         }
-        else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ || linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ || linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
-            var order = (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */) ? 2 :
-                (linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */) ? 3 : 1.5;
+        else if (linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */ || linkStyle === 4 /* LinkStyle.Triple */ || linkStyle === 5 /* LinkStyle.OffsetTriple */ || linkStyle === 7 /* LinkStyle.Aromatic */ || linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
+            var order = (linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */) ? 2 :
+                (linkStyle === 4 /* LinkStyle.Triple */ || linkStyle === 5 /* LinkStyle.OffsetTriple */) ? 3 : 1.5;
             var multiRadius = linkRadius * (linkScale / (0.5 * order));
             var absOffset = (linkRadius - multiRadius) * linkSpacing;
             calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
             cylinderProps.topCap = topCap;
             cylinderProps.bottomCap = bottomCap;
-            if (linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
+            if (linkStyle === 7 /* LinkStyle.Aromatic */ || linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
                 cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
                 (0, cylinder_1.addCylinder)(builderState, va, vb, 0.5, cylinderProps);
                 var aromaticOffset = linkRadius + aromaticScale * linkRadius + aromaticScale * linkRadius * aromaticSpacing;
@@ -144,14 +144,14 @@ function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
                 v3sub(va, va, vShift);
                 v3sub(vb, vb, vShift);
                 (0, cylinder_1.addFixedCountDashedCylinder)(builderState, va, vb, 0.5, aromaticSegmentCount, cylinderProps);
-                if (linkStyle === 8 /* MirroredAromatic */) {
+                if (linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
                     v3setMagnitude(vShift, vShift, aromaticOffset * 2);
                     v3add(va, va, vShift);
                     v3add(vb, vb, vShift);
                     (0, cylinder_1.addFixedCountDashedCylinder)(builderState, va, vb, 0.5, aromaticSegmentCount, cylinderProps);
                 }
             }
-            else if (linkStyle === 3 /* OffsetDouble */ || linkStyle === 5 /* OffsetTriple */) {
+            else if (linkStyle === 3 /* LinkStyle.OffsetDouble */ || linkStyle === 5 /* LinkStyle.OffsetTriple */) {
                 var multipleOffset = linkRadius + multiRadius + linkScale * linkRadius * linkSpacing;
                 v3setMagnitude(vShift, vShift, multipleOffset);
                 cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
@@ -181,7 +181,7 @@ function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
                 (0, cylinder_1.addDoubleCylinder)(builderState, va, vb, 0.5, vShift, cylinderProps);
             }
         }
-        else if (linkStyle === 6 /* Disk */) {
+        else if (linkStyle === 6 /* LinkStyle.Disk */) {
             v3scale(tmpV12, tmpV12, 0.475);
             v3add(va, va, tmpV12);
             v3sub(vb, vb, tmpV12);
@@ -235,25 +235,25 @@ function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders) {
         v3add(center, center, vb);
         count += 2;
         var linkRadius = radius(edgeIndex);
-        var linkStyle = style ? style(edgeIndex) : 0 /* Solid */;
+        var linkStyle = style ? style(edgeIndex) : 0 /* LinkStyle.Solid */;
         var linkStub = stubCap && (stub ? stub(edgeIndex) : false);
-        if (linkStyle === 0 /* Solid */) {
+        if (linkStyle === 0 /* LinkStyle.Solid */) {
             v3scale(vm, v3add(vm, va, vb), 0.5);
             builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
         }
-        else if (linkStyle === 1 /* Dashed */) {
+        else if (linkStyle === 1 /* LinkStyle.Dashed */) {
             v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
             v3sub(vb, vb, tmpV12);
             builder.addFixedCountDashes(va, vb, segmentCount, dashScale, dashCap, dashCap, edgeIndex);
         }
-        else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ || linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ || linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
-            var order = (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */) ? 2 :
-                (linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */) ? 3 : 1.5;
+        else if (linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */ || linkStyle === 4 /* LinkStyle.Triple */ || linkStyle === 5 /* LinkStyle.OffsetTriple */ || linkStyle === 7 /* LinkStyle.Aromatic */ || linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
+            var order = (linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */) ? 2 :
+                (linkStyle === 4 /* LinkStyle.Triple */ || linkStyle === 5 /* LinkStyle.OffsetTriple */) ? 3 : 1.5;
             var multiScale = linkScale / (0.5 * order);
             var absOffset = (linkRadius - multiScale * linkRadius) * linkSpacing;
             v3scale(vm, v3add(vm, va, vb), 0.5);
             calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
-            if (linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
+            if (linkStyle === 7 /* LinkStyle.Aromatic */ || linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
                 builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
                 var aromaticOffset = linkRadius + aromaticScale * linkRadius + aromaticScale * linkRadius * aromaticSpacing;
                 v3scale(tmpV12, v3sub(tmpV12, vb, va), aromaticLengthScale);
@@ -264,14 +264,14 @@ function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders) {
                 v3sub(va, va, vShift);
                 v3sub(vb, vb, vShift);
                 builder.addFixedCountDashes(va, vb, aromaticSegmentCount, aromaticScale, dashCap, dashCap, edgeIndex);
-                if (linkStyle === 8 /* MirroredAromatic */) {
+                if (linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
                     v3setMagnitude(vShift, vShift, aromaticOffset * 2);
                     v3add(va, va, vShift);
                     v3add(vb, vb, vShift);
                     builder.addFixedCountDashes(va, vb, aromaticSegmentCount, aromaticScale, dashCap, dashCap, edgeIndex);
                 }
             }
-            else if (linkStyle === 3 /* OffsetDouble */ || linkStyle === 5 /* OffsetTriple */) {
+            else if (linkStyle === 3 /* LinkStyle.OffsetDouble */ || linkStyle === 5 /* LinkStyle.OffsetTriple */) {
                 var multipleOffset = linkRadius + multiScale * linkRadius + linkScale * linkRadius * linkSpacing;
                 v3setMagnitude(vShift, vShift, multipleOffset);
                 builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
@@ -289,7 +289,7 @@ function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders) {
                 builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], multiScale, linkCap, linkStub, edgeIndex);
             }
         }
-        else if (linkStyle === 6 /* Disk */) {
+        else if (linkStyle === 6 /* LinkStyle.Disk */) {
             v3scale(tmpV12, v3sub(tmpV12, vb, va), 0.475);
             v3add(va, va, tmpV12);
             v3sub(vb, vb, tmpV12);
@@ -341,24 +341,24 @@ function createLinkLines(ctx, linkBuilder, props, lines) {
         v3add(center, center, va);
         v3add(center, center, vb);
         count += 2;
-        var linkStyle = style ? style(edgeIndex) : 0 /* Solid */;
-        if (linkStyle === 0 /* Solid */) {
+        var linkStyle = style ? style(edgeIndex) : 0 /* LinkStyle.Solid */;
+        if (linkStyle === 0 /* LinkStyle.Solid */) {
             v3scale(vm, v3add(vm, va, vb), 0.5);
             builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
         }
-        else if (linkStyle === 1 /* Dashed */) {
+        else if (linkStyle === 1 /* LinkStyle.Dashed */) {
             v3scale(tmpV12, v3sub(tmpV12, vb, va), lengthScale);
             v3sub(vb, vb, tmpV12);
             builder.addFixedCountDashes(va, vb, segmentCount, edgeIndex);
         }
-        else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ || linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ || linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
-            var order = linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ ? 2 :
-                linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ ? 3 : 1.5;
+        else if (linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */ || linkStyle === 4 /* LinkStyle.Triple */ || linkStyle === 5 /* LinkStyle.OffsetTriple */ || linkStyle === 7 /* LinkStyle.Aromatic */ || linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
+            var order = linkStyle === 2 /* LinkStyle.Double */ || linkStyle === 3 /* LinkStyle.OffsetDouble */ ? 2 :
+                linkStyle === 4 /* LinkStyle.Triple */ || linkStyle === 5 /* LinkStyle.OffsetTriple */ ? 3 : 1.5;
             var multiRadius = 1 * (linkScale / (0.5 * order));
             var absOffset = (1 - multiRadius) * linkSpacing;
             v3scale(vm, v3add(vm, va, vb), 0.5);
             calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
-            if (linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
+            if (linkStyle === 7 /* LinkStyle.Aromatic */ || linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
                 builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
                 v3scale(tmpV12, v3sub(tmpV12, vb, va), aromaticLengthScale);
                 v3sub(vb, vb, tmpV12);
@@ -366,14 +366,14 @@ function createLinkLines(ctx, linkBuilder, props, lines) {
                 v3sub(va, va, vShift);
                 v3sub(vb, vb, vShift);
                 builder.addFixedCountDashes(va, vb, aromaticSegmentCount, edgeIndex);
-                if (linkStyle === 8 /* MirroredAromatic */) {
+                if (linkStyle === 8 /* LinkStyle.MirroredAromatic */) {
                     v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
                     v3add(va, va, vShift);
                     v3add(vb, vb, vShift);
                     builder.addFixedCountDashes(va, vb, aromaticSegmentCount, edgeIndex);
                 }
             }
-            else if (linkStyle === 3 /* OffsetDouble */ || linkStyle === 5 /* OffsetTriple */) {
+            else if (linkStyle === 3 /* LinkStyle.OffsetDouble */ || linkStyle === 5 /* LinkStyle.OffsetTriple */) {
                 v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor);
                 builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
                 v3scale(tmpV12, v3sub(tmpV12, va, vb), linkSpacing * linkScale);
@@ -390,7 +390,7 @@ function createLinkLines(ctx, linkBuilder, props, lines) {
                 builder.add(va[0] - vShift[0], va[1] - vShift[1], va[2] - vShift[2], vm[0] - vShift[0], vm[1] - vShift[1], vm[2] - vShift[2], edgeIndex);
             }
         }
-        else if (linkStyle === 6 /* Disk */) {
+        else if (linkStyle === 6 /* LinkStyle.Disk */) {
             v3scale(tmpV12, v3sub(tmpV12, vb, va), 0.475);
             v3add(va, va, tmpV12);
             v3sub(vb, vb, tmpV12);

package/lib/commonjs/mol-repr/structure/visual/util/polymer/backbone.js

@@ -11,9 +11,9 @@ var sorted_ranges_1 = require("../../../../../mol-data/int/sorted-ranges");
 var polymer_1 = require("../polymer");
 function eachPolymerBackboneLink(unit, callback) {
     switch (unit.kind) {
-        case 0 /* Atomic */: return eachAtomicPolymerBackboneLink(unit, callback);
-        case 1 /* Spheres */:
-        case 2 /* Gaussians */:
+        case 0 /* Unit.Kind.Atomic */: return eachAtomicPolymerBackboneLink(unit, callback);
+        case 1 /* Unit.Kind.Spheres */:
+        case 2 /* Unit.Kind.Gaussians */:
             return eachCoarsePolymerBackboneLink(unit, callback);
     }
 }
@@ -78,9 +78,9 @@ function eachCoarsePolymerBackboneLink(unit, callback) {
 }
 function eachPolymerBackboneElement(unit, callback) {
     switch (unit.kind) {
-        case 0 /* Atomic */: return eachAtomicPolymerBackboneElement(unit, callback);
-        case 1 /* Spheres */:
-        case 2 /* Gaussians */:
+        case 0 /* Unit.Kind.Atomic */: return eachAtomicPolymerBackboneElement(unit, callback);
+        case 1 /* Unit.Kind.Spheres */:
+        case 2 /* Unit.Kind.Gaussians */:
             return eachCoarsePolymerBackboneElement(unit, callback);
     }
 }

package/lib/commonjs/mol-repr/structure/visual/util/polymer/gap-iterator.js

@@ -12,9 +12,9 @@ var polymer_1 = require("../polymer");
 /** Iterates over gaps, i.e. the stem residues/coarse elements adjacent to gaps */
 function PolymerGapIterator(structure, unit) {
     switch (unit.kind) {
-        case 0 /* Atomic */: return new AtomicPolymerGapIterator(structure, unit);
-        case 1 /* Spheres */:
-        case 2 /* Gaussians */:
+        case 0 /* Unit.Kind.Atomic */: return new AtomicPolymerGapIterator(structure, unit);
+        case 1 /* Unit.Kind.Spheres */:
+        case 2 /* Unit.Kind.Gaussians */:
             return new CoarsePolymerGapIterator(structure, unit);
     }
 }

package/lib/commonjs/mol-repr/structure/visual/util/polymer/trace-iterator.js

@@ -15,10 +15,10 @@ var polymer_1 = require("../polymer");
 var secondary_structure_1 = require("../../../../../mol-model-props/computed/secondary-structure");
 var helix_orientation_1 = require("../../../../../mol-model-props/computed/helix-orientation");
 function isHelixSS(ss) {
-    return types_1.SecondaryStructureType.is(ss, 2 /* Helix */);
+    return types_1.SecondaryStructureType.is(ss, 2 /* SecondaryStructureType.Flag.Helix */);
 }
 function isSheetSS(ss) {
-    return types_1.SecondaryStructureType.is(ss, 4 /* Beta */);
+    return types_1.SecondaryStructureType.is(ss, 4 /* SecondaryStructureType.Flag.Beta */);
 }
 /**
  * Iterates over individual residues/coarse elements in polymers of a unit while
@@ -27,14 +27,14 @@ function isSheetSS(ss) {
 function PolymerTraceIterator(unit, structure, options) {
     if (options === void 0) { options = {}; }
     switch (unit.kind) {
-        case 0 /* Atomic */: return new AtomicPolymerTraceIterator(unit, structure, options);
-        case 1 /* Spheres */:
-        case 2 /* Gaussians */:
+        case 0 /* Unit.Kind.Atomic */: return new AtomicPolymerTraceIterator(unit, structure, options);
+        case 1 /* Unit.Kind.Spheres */:
+        case 2 /* Unit.Kind.Gaussians */:
             return new CoarsePolymerTraceIterator(unit, structure);
     }
 }
 exports.PolymerTraceIterator = PolymerTraceIterator;
-var SecStrucTypeNA = types_1.SecondaryStructureType.create(536870912 /* NA */);
+var SecStrucTypeNA = types_1.SecondaryStructureType.create(536870912 /* SecondaryStructureType.Flag.NA */);
 function createPolymerTraceElement(structure, unit) {
     return {
         center: structure_1.StructureElement.Location.create(structure, unit),
@@ -44,7 +44,7 @@ function createPolymerTraceElement(structure, unit) {
         initial: false, final: false,
         secStrucFirst: false, secStrucLast: false,
         secStrucType: SecStrucTypeNA,
-        moleculeType: 0 /* Unknown */,
+        moleculeType: 0 /* MoleculeType.Unknown */,
         coarseBackboneFirst: false, coarseBackboneLast: false,
         isCoarseBackbone: false,
         p0: (0, linear_algebra_1.Vec3)(), p1: (0, linear_algebra_1.Vec3)(), p2: (0, linear_algebra_1.Vec3)(), p3: (0, linear_algebra_1.Vec3)(), p4: (0, linear_algebra_1.Vec3)(),
@@ -59,7 +59,7 @@ var AtomicPolymerTraceIterator = /** @class */ (function () {
         if (options === void 0) { options = {}; }
         var _a;
         this.unit = unit;
-        this.state = 0 /* nextPolymer */;
+        this.state = 0 /* AtomicPolymerTraceIteratorState.nextPolymer */;
         this.p0 = (0, linear_algebra_1.Vec3)();
         this.p1 = (0, linear_algebra_1.Vec3)();
         this.p2 = (0, linear_algebra_1.Vec3)();
@@ -141,7 +141,7 @@ var AtomicPolymerTraceIterator = /** @class */ (function () {
             var _a = this.secondaryStructure, type = _a.type, getIndex = _a.getIndex;
             var ss = type[getIndex(residueIndex)];
             // normalize helix-type
-            return isHelixSS(ss) ? 2 /* Helix */ : ss;
+            return isHelixSS(ss) ? 2 /* SecondaryStructureType.Flag.Helix */ : ss;
         }
         else {
             return SecStrucTypeNA;
@@ -172,13 +172,13 @@ var AtomicPolymerTraceIterator = /** @class */ (function () {
     };
     AtomicPolymerTraceIterator.prototype.move = function () {
         var _a = this, residueIt = _a.residueIt, polymerIt = _a.polymerIt, value = _a.value;
-        if (this.state === 0 /* nextPolymer */) {
+        if (this.state === 0 /* AtomicPolymerTraceIteratorState.nextPolymer */) {
             while (polymerIt.hasNext) {
                 this.polymerSegment = polymerIt.move();
                 residueIt.setSegment(this.polymerSegment);
                 this.updateResidueSegmentRange(this.polymerSegment);
                 if (residueIt.hasNext) {
-                    this.state = 1 /* nextResidue */;
+                    this.state = 1 /* AtomicPolymerTraceIteratorState.nextResidue */;
                     var residueIndexBeg = this.residueAtomSegments.index[this.unit.elements[this.polymerSegment.start]];
                     var residueIndexBegPrev = this.getResidueIndex(residueIndexBeg - 1);
                     this.currSecStrucType = residueIndexBeg === residueIndexBegPrev ? SecStrucTypeNA : this.getSecStruc(residueIndexBegPrev);
@@ -189,7 +189,7 @@ var AtomicPolymerTraceIterator = /** @class */ (function () {
                 }
             }
         }
-        if (this.state === 1 /* nextResidue */) {
+        if (this.state === 1 /* AtomicPolymerTraceIteratorState.nextResidue */) {
             var residueIndex = residueIt.move().index;
             var residueIndexPrev3 = this.getResidueIndex(residueIndex - 3);
             var residueIndexPrev2 = this.getResidueIndex(residueIndex - 2);
@@ -352,7 +352,7 @@ var AtomicPolymerTraceIterator = /** @class */ (function () {
             this.setDirection(value.d12, this.d01, this.d12, this.d23);
             this.setDirection(value.d23, this.d12, this.d23, this.d34);
             if (!residueIt.hasNext) {
-                this.state = 0 /* nextPolymer */;
+                this.state = 0 /* AtomicPolymerTraceIteratorState.nextPolymer */;
             }
         }
         this.hasNext = residueIt.hasNext || polymerIt.hasNext;
@@ -364,17 +364,17 @@ exports.AtomicPolymerTraceIterator = AtomicPolymerTraceIterator;
 var CoarsePolymerTraceIterator = /** @class */ (function () {
     function CoarsePolymerTraceIterator(unit, structure) {
         this.unit = unit;
-        this.state = 0 /* nextPolymer */;
+        this.state = 0 /* CoarsePolymerTraceIteratorState.nextPolymer */;
         this.hasNext = false;
         this.polymerIt = sorted_ranges_1.SortedRanges.transientSegments((0, polymer_1.getPolymerRanges)(unit), unit.elements);
         this.value = createPolymerTraceElement(structure, unit);
         linear_algebra_1.Vec3.set(this.value.d12, 1, 0, 0);
         linear_algebra_1.Vec3.set(this.value.d23, 1, 0, 0);
         switch (unit.kind) {
-            case 1 /* Spheres */:
+            case 1 /* Unit.Kind.Spheres */:
                 this.conformation = unit.model.coarseConformation.spheres;
                 break;
-            case 2 /* Gaussians */:
+            case 2 /* Unit.Kind.Gaussians */:
                 this.conformation = unit.model.coarseConformation.gaussians;
                 break;
         }
@@ -390,17 +390,17 @@ var CoarsePolymerTraceIterator = /** @class */ (function () {
         target[2] = this.conformation.z[index];
     };
     CoarsePolymerTraceIterator.prototype.move = function () {
-        if (this.state === 0 /* nextPolymer */) {
+        if (this.state === 0 /* CoarsePolymerTraceIteratorState.nextPolymer */) {
             while (this.polymerIt.hasNext) {
                 this.polymerSegment = this.polymerIt.move();
                 this.elementIndex = this.polymerSegment.start;
                 if (this.elementIndex < this.polymerSegment.end) {
-                    this.state = 1 /* nextElement */;
+                    this.state = 1 /* CoarsePolymerTraceIteratorState.nextElement */;
                     break;
                 }
             }
         }
-        if (this.state === 1 /* nextElement */) {
+        if (this.state === 1 /* CoarsePolymerTraceIteratorState.nextElement */) {
             var elementIndexPrev2 = this.getElementIndex(this.elementIndex - 2);
             var elementIndexPrev1 = this.getElementIndex(this.elementIndex - 1);
             var elementIndexNext1 = this.getElementIndex(this.elementIndex + 1);
@@ -436,7 +436,7 @@ var CoarsePolymerTraceIterator = /** @class */ (function () {
             this.value.first = this.elementIndex === this.polymerSegment.start;
             this.value.last = this.elementIndex === this.polymerSegment.end - 1;
             if (this.elementIndex + 1 >= this.polymerSegment.end) {
-                this.state = 0 /* nextPolymer */;
+                this.state = 0 /* CoarsePolymerTraceIteratorState.nextPolymer */;
             }
         }
         this.hasNext = this.elementIndex + 1 < this.polymerSegment.end || this.polymerIt.hasNext;

package/lib/commonjs/mol-repr/structure/visual/util/polymer.js

@@ -24,17 +24,17 @@ exports.NucleicShift = 0.3;
 exports.OverhangFactor = 2;
 function getPolymerRanges(unit) {
     switch (unit.kind) {
-        case 0 /* Atomic */: return unit.model.atomicRanges.polymerRanges;
-        case 1 /* Spheres */: return unit.model.coarseHierarchy.spheres.polymerRanges;
-        case 2 /* Gaussians */: return unit.model.coarseHierarchy.gaussians.polymerRanges;
+        case 0 /* Unit.Kind.Atomic */: return unit.model.atomicRanges.polymerRanges;
+        case 1 /* Unit.Kind.Spheres */: return unit.model.coarseHierarchy.spheres.polymerRanges;
+        case 2 /* Unit.Kind.Gaussians */: return unit.model.coarseHierarchy.gaussians.polymerRanges;
     }
 }
 exports.getPolymerRanges = getPolymerRanges;
 function getGapRanges(unit) {
     switch (unit.kind) {
-        case 0 /* Atomic */: return unit.model.atomicRanges.gapRanges;
-        case 1 /* Spheres */: return unit.model.coarseHierarchy.spheres.gapRanges;
-        case 2 /* Gaussians */: return unit.model.coarseHierarchy.gaussians.gapRanges;
+        case 0 /* Unit.Kind.Atomic */: return unit.model.atomicRanges.gapRanges;
+        case 1 /* Unit.Kind.Spheres */: return unit.model.coarseHierarchy.spheres.gapRanges;
+        case 2 /* Unit.Kind.Gaussians */: return unit.model.coarseHierarchy.gaussians.gapRanges;
     }
 }
 exports.getGapRanges = getGapRanges;

package/lib/commonjs/mol-script/language/symbol-table/core.d.ts

@@ -16,8 +16,8 @@ export declare namespace Types {
     const Regex: Type.Value<RegExp>;
     const Set: <T extends Type<any>>(t?: T | undefined) => Type.Container<Set<T["@type"]>>;
     const List: <T extends Type<any>>(t?: T | undefined) => Type.Container<List<T["@type"]>>;
-    const Fn: <T extends Type<any>>(t?: T | undefined, alias?: string | undefined) => Type.Container<(env: any) => T["@type"]>;
-    const Flags: <T extends Type<any>>(t: T, alias?: string | undefined) => Type.Container<number>;
+    const Fn: <T extends Type<any>>(t?: T | undefined, alias?: string) => Type.Container<(env: any) => T["@type"]>;
+    const Flags: <T extends Type<any>>(t: T, alias?: string) => Type.Container<number>;
     const BitFlags: Type.Container<number>;
 }
 export declare const TTargs: Arguments<Arguments.PropTypes<{

package/lib/commonjs/mol-script/runtime/query/table.js

@@ -211,7 +211,7 @@ var symbols = [
     C(symbol_table_1.MolScriptSymbolTable.structureQuery.type.elementSymbol, function (ctx, v) { return (0, types_1.ElementSymbol)(v[0](ctx)); }),
     C(symbol_table_1.MolScriptSymbolTable.structureQuery.type.atomName, function (ctx, v) { return (0, string_1.upperCaseAny)(v[0](ctx)); }),
     C(symbol_table_1.MolScriptSymbolTable.structureQuery.type.bondFlags, function (ctx, xs) {
-        var ret = 0 /* None */;
+        var ret = 0 /* BondType.Flag.None */;
         if (typeof xs.length === 'number') {
             for (var i = 0, _i = xs.length; i < _i; i++)
                 ret = bondFlag(ret, xs[i](ctx));
@@ -226,7 +226,7 @@ var symbols = [
     }),
     C(symbol_table_1.MolScriptSymbolTable.structureQuery.type.ringFingerprint, function (ctx, xs) { return structure_1.UnitRing.elementFingerprint(getArray(ctx, xs)); }),
     C(symbol_table_1.MolScriptSymbolTable.structureQuery.type.secondaryStructureFlags, function (ctx, xs) {
-        var ret = 0 /* None */;
+        var ret = 0 /* SecondaryStructureType.Flag.None */;
         if (typeof xs.length === 'number') {
             for (var i = 0, _i = xs.length; i < _i; i++)
                 ret = secondaryStructureFlag(ret, xs[i](ctx));
@@ -388,20 +388,20 @@ function atomProp(p) {
     return function (ctx, xs) { return p((xs && xs[0] && xs[0](ctx)) || ctx.element); };
 }
 function bondFlag(current, f) {
-    return current | (types_1.BondType.isName(f) ? types_1.BondType.fromName(f) : 0 /* None */);
+    return current | (types_1.BondType.isName(f) ? types_1.BondType.fromName(f) : 0 /* BondType.Flag.None */);
 }
 function secondaryStructureFlag(current, f) {
     switch (f.toLowerCase()) {
-        case 'helix': return current | 2 /* Helix */;
-        case 'alpha': return current | 2 /* Helix */ | 4096 /* HelixAlpha */;
-        case 'pi': return current | 2 /* Helix */ | 32768 /* HelixPi */;
-        case '310': return current | 2 /* Helix */ | 2048 /* Helix3Ten */;
-        case 'beta': return current | 4 /* Beta */;
-        case 'strand': return current | 4 /* Beta */ | 4194304 /* BetaStrand */;
-        case 'sheet': return current | 4 /* Beta */ | 8388608 /* BetaSheet */;
-        case 'turn': return current | 16 /* Turn */;
-        case 'bend': return current | 8 /* Bend */;
-        case 'coil': return current | 536870912 /* NA */;
+        case 'helix': return current | 2 /* SecondaryStructureType.Flag.Helix */;
+        case 'alpha': return current | 2 /* SecondaryStructureType.Flag.Helix */ | 4096 /* SecondaryStructureType.Flag.HelixAlpha */;
+        case 'pi': return current | 2 /* SecondaryStructureType.Flag.Helix */ | 32768 /* SecondaryStructureType.Flag.HelixPi */;
+        case '310': return current | 2 /* SecondaryStructureType.Flag.Helix */ | 2048 /* SecondaryStructureType.Flag.Helix3Ten */;
+        case 'beta': return current | 4 /* SecondaryStructureType.Flag.Beta */;
+        case 'strand': return current | 4 /* SecondaryStructureType.Flag.Beta */ | 4194304 /* SecondaryStructureType.Flag.BetaStrand */;
+        case 'sheet': return current | 4 /* SecondaryStructureType.Flag.Beta */ | 8388608 /* SecondaryStructureType.Flag.BetaSheet */;
+        case 'turn': return current | 16 /* SecondaryStructureType.Flag.Turn */;
+        case 'bend': return current | 8 /* SecondaryStructureType.Flag.Bend */;
+        case 'coil': return current | 536870912 /* SecondaryStructureType.Flag.NA */;
         default: return current;
     }
 }

package/lib/commonjs/mol-state/object.d.ts

@@ -52,8 +52,8 @@ declare namespace StateObject {
     function create<Data, T extends Type>(type: T): {
         new (data: Data, props?: {
             label: string;
-            description?: string | undefined;
-        } | undefined): {
+            description?: string;
+        }): {
             id: UUID;
             type: T;
             label: string;
@@ -61,7 +61,7 @@ declare namespace StateObject {
             data: Data;
         };
         type: T;
-        is(obj?: StateObject<any, Type<any>> | undefined): obj is {
+        is(obj?: StateObject): obj is {
             id: UUID;
             type: T;
             label: string;

package/lib/commonjs/mol-task/util/user-timing.js

@@ -7,7 +7,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.UserTiming = void 0;
 var debug_1 = require("../../mol-util/debug");
-var hasPerformance = (typeof performance !== 'undefined') && performance.mark && performance.measure;
+var hasPerformance = (typeof performance !== 'undefined') && !!performance.mark && performance.measure;
 var timingEnabled = hasPerformance && !debug_1.isProductionMode;
 var UserTiming;
 (function (UserTiming) {

package/lib/commonjs/mol-theme/clipping.js

@@ -24,12 +24,12 @@ exports.Clipping = Clipping;
         }
         Groups.create = create;
         Groups.Names = {
-            'one': 1 /* One */,
-            'two': 2 /* Two */,
-            'three': 4 /* Three */,
-            'four': 8 /* Four */,
-            'five': 16 /* Five */,
-            'six': 32 /* Six */,
+            'one': 1 /* Flag.One */,
+            'two': 2 /* Flag.Two */,
+            'three': 4 /* Flag.Three */,
+            'four': 8 /* Flag.Four */,
+            'five': 16 /* Flag.Five */,
+            'six': 32 /* Flag.Six */,
         };
         function isName(name) {
             return name in Groups.Names;
@@ -37,17 +37,17 @@ exports.Clipping = Clipping;
         Groups.isName = isName;
         function fromName(name) {
             switch (name) {
-                case 'one': return 1 /* One */;
-                case 'two': return 2 /* Two */;
-                case 'three': return 4 /* Three */;
-                case 'four': return 8 /* Four */;
-                case 'five': return 16 /* Five */;
-                case 'six': return 32 /* Six */;
+                case 'one': return 1 /* Flag.One */;
+                case 'two': return 2 /* Flag.Two */;
+                case 'three': return 4 /* Flag.Three */;
+                case 'four': return 8 /* Flag.Four */;
+                case 'five': return 16 /* Flag.Five */;
+                case 'six': return 32 /* Flag.Six */;
             }
         }
         Groups.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]);
             }
@@ -56,17 +56,17 @@ exports.Clipping = Clipping;
         Groups.fromNames = fromNames;
         function toNames(groups) {
             var names = [];
-            if (Groups.is(groups, 1 /* One */))
+            if (Groups.is(groups, 1 /* Flag.One */))
                 names.push('one');
-            if (Groups.is(groups, 2 /* Two */))
+            if (Groups.is(groups, 2 /* Flag.Two */))
                 names.push('two');
-            if (Groups.is(groups, 4 /* Three */))
+            if (Groups.is(groups, 4 /* Flag.Three */))
                 names.push('three');
-            if (Groups.is(groups, 8 /* Four */))
+            if (Groups.is(groups, 8 /* Flag.Four */))
                 names.push('four');
-            if (Groups.is(groups, 16 /* Five */))
+            if (Groups.is(groups, 16 /* Flag.Five */))
                 names.push('five');
-            if (Groups.is(groups, 32 /* Six */))
+            if (Groups.is(groups, 32 /* Flag.Six */))
                 names.push('six');
             return names;
         }

package/lib/commonjs/mol-theme/color/atom-id.js

@@ -75,7 +75,7 @@ exports.AtomIdColorTheme = AtomIdColorTheme;
 exports.AtomIdColorThemeProvider = {
     name: 'atom-id',
     label: 'Atom Id',
-    category: "Atom Property" /* Atom */,
+    category: "Atom Property" /* ColorTheme.Category.Atom */,
     factory: AtomIdColorTheme,
     getParams: getAtomIdColorThemeParams,
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.AtomIdColorThemeParams),

package/lib/commonjs/mol-theme/color/carbohydrate-symbol.js

@@ -59,7 +59,7 @@ exports.CarbohydrateSymbolColorTheme = CarbohydrateSymbolColorTheme;
 exports.CarbohydrateSymbolColorThemeProvider = {
     name: 'carbohydrate-symbol',
     label: 'Carbohydrate Symbol',
-    category: "Residue Property" /* Residue */,
+    category: "Residue Property" /* ColorTheme.Category.Residue */,
     factory: CarbohydrateSymbolColorTheme,
     getParams: getCarbohydrateSymbolColorThemeParams,
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.CarbohydrateSymbolColorThemeParams),

package/lib/commonjs/mol-theme/color/chain-id.js

@@ -26,12 +26,12 @@ function getChainIdColorThemeParams(ctx) {
 exports.getChainIdColorThemeParams = getChainIdColorThemeParams;
 function getAsymId(unit, type) {
     switch (unit.kind) {
-        case 0 /* Atomic */:
+        case 0 /* Unit.Kind.Atomic */:
             return type === 'auth'
                 ? structure_1.StructureProperties.chain.auth_asym_id
                 : structure_1.StructureProperties.chain.label_asym_id;
-        case 1 /* Spheres */:
-        case 2 /* Gaussians */:
+        case 1 /* Unit.Kind.Spheres */:
+        case 2 /* Unit.Kind.Gaussians */:
             return structure_1.StructureProperties.coarse.asym_id;
     }
 }
@@ -109,7 +109,7 @@ exports.ChainIdColorTheme = ChainIdColorTheme;
 exports.ChainIdColorThemeProvider = {
     name: 'chain-id',
     label: 'Chain Id',
-    category: "Chain Property" /* Chain */,
+    category: "Chain Property" /* ColorTheme.Category.Chain */,
     factory: ChainIdColorTheme,
     getParams: getChainIdColorThemeParams,
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.ChainIdColorThemeParams),

package/lib/commonjs/mol-theme/color/element-index.js

@@ -66,7 +66,7 @@ exports.ElementIndexColorTheme = ElementIndexColorTheme;
 exports.ElementIndexColorThemeProvider = {
     name: 'element-index',
     label: 'Element Index',
-    category: "Atom Property" /* Atom */,
+    category: "Atom Property" /* ColorTheme.Category.Atom */,
     factory: ElementIndexColorTheme,
     getParams: getElementIndexColorThemeParams,
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.ElementIndexColorThemeParams),

package/lib/commonjs/mol-theme/color/element-symbol.js

@@ -94,7 +94,7 @@ exports.ElementSymbolColorTheme = ElementSymbolColorTheme;
 exports.ElementSymbolColorThemeProvider = {
     name: 'element-symbol',
     label: 'Element Symbol',
-    category: "Atom Property" /* Atom */,
+    category: "Atom Property" /* ColorTheme.Category.Atom */,
     factory: ElementSymbolColorTheme,
     getParams: getElementSymbolColorThemeParams,
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.ElementSymbolColorThemeParams),