molstar 3.8.2 → 3.10.0

package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.js

@@ -31,9 +31,9 @@ export function OrientationEllipsoidMeshVisual(materialId) {
     }, materialId);
 }
 function isUnitApplicable(unit) {
-    if (Unit.Traits.is(unit.traits, 1 /* MultiChain */))
+    if (Unit.Traits.is(unit.traits, 1 /* Unit.Trait.MultiChain */))
         return false;
-    if (Unit.Traits.is(unit.traits, 2 /* Partitioned */))
+    if (Unit.Traits.is(unit.traits, 2 /* Unit.Trait.Partitioned */))
         return false;
     if (Unit.isCoarse(unit))
         return true;
@@ -42,9 +42,9 @@ function isUnitApplicable(unit) {
     unit.model.atomicHierarchy.derived.residue.moleculeType;
     var rI = unit.residueIndex[unit.elements[0]];
     var mt = unit.model.atomicHierarchy.derived.residue.moleculeType[rI];
-    if (mt === 3 /* Ion */)
+    if (mt === 3 /* MoleculeType.Ion */)
         return false;
-    if (mt === 2 /* Water */)
+    if (mt === 2 /* MoleculeType.Water */)
         return false;
     return true;
 }

package/lib/mol-repr/structure/visual/polymer-direction-wedge.js

@@ -42,7 +42,7 @@ function createPolymerDirectionWedgeMesh(ctx, unit, structure, theme, props, mes
         var v = polymerTraceIt.move();
         builderState.currentGroup = i;
         var isNucleicType = isNucleic(v.moleculeType);
-        var isSheet = SecondaryStructureType.is(v.secStrucType, 4 /* Beta */);
+        var isSheet = SecondaryStructureType.is(v.secStrucType, 4 /* SecondaryStructureType.Flag.Beta */);
         var tension = (isNucleicType || isSheet) ? 0.5 : 0.9;
         var shift = isNucleicType ? 0.3 : 0.5;
         interpolateCurveSegment(state, v, tension, shift);

package/lib/mol-repr/structure/visual/polymer-trace-mesh.js

@@ -47,8 +47,8 @@ function createPolymerTraceMesh(ctx, unit, structure, theme, props, mesh) {
         var v = polymerTraceIt.move();
         builderState.currentGroup = i;
         var isNucleicType = isNucleic(v.moleculeType);
-        var isSheet = SecondaryStructureType.is(v.secStrucType, 4 /* Beta */);
-        var isHelix = SecondaryStructureType.is(v.secStrucType, 2 /* Helix */);
+        var isSheet = SecondaryStructureType.is(v.secStrucType, 4 /* SecondaryStructureType.Flag.Beta */);
+        var isHelix = SecondaryStructureType.is(v.secStrucType, 2 /* SecondaryStructureType.Flag.Helix */);
         var tension = isHelix && !tubularHelices ? HelixTension : StandardTension;
         var shift = isNucleicType ? NucleicShift : StandardShift;
         interpolateCurveSegment(state, v, tension, shift);

package/lib/mol-repr/structure/visual/util/bond.js

@@ -37,7 +37,7 @@ export function makeIntraBondIgnoreTest(structure, unit, props) {
     var ignoreHydrogens = props.ignoreHydrogens, includeTypes = props.includeTypes, excludeTypes = props.excludeTypes;
     var include = BondType.fromNames(includeTypes);
     var exclude = BondType.fromNames(excludeTypes);
-    var allBondTypes = BondType.isAll(include) && 0 /* None */ === exclude;
+    var allBondTypes = BondType.isAll(include) && 0 /* BondType.Flag.None */ === exclude;
     var child = structure.child;
     var childUnit = child === null || child === void 0 ? void 0 : child.unitMap.get(unit.id);
     if (child && !childUnit)
@@ -56,7 +56,7 @@ export function makeInterBondIgnoreTest(structure, props) {
     var ignoreHydrogens = props.ignoreHydrogens, includeTypes = props.includeTypes, excludeTypes = props.excludeTypes;
     var include = BondType.fromNames(includeTypes);
     var exclude = BondType.fromNames(excludeTypes);
-    var allBondTypes = BondType.isAll(include) && 0 /* None */ === exclude;
+    var allBondTypes = BondType.isAll(include) && 0 /* BondType.Flag.None */ === exclude;
     var child = structure.child;
     if (allBondTypes && !ignoreHydrogens && !child)
         return;

package/lib/mol-repr/structure/visual/util/common.js

@@ -118,9 +118,9 @@ export function ensureReasonableResolution(box, props, maxCells) {
 }
 export function getConformation(unit) {
     switch (unit.kind) {
-        case 0 /* Atomic */: return unit.model.atomicConformation;
-        case 1 /* Spheres */: return unit.model.coarseConformation.spheres;
-        case 2 /* Gaussians */: return unit.model.coarseConformation.gaussians;
+        case 0 /* Unit.Kind.Atomic */: return unit.model.atomicConformation;
+        case 1 /* Unit.Kind.Spheres */: return unit.model.coarseConformation.spheres;
+        case 2 /* Unit.Kind.Gaussians */: return unit.model.coarseConformation.gaussians;
     }
 }
 export var CommonSurfaceParams = {

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

@@ -103,31 +103,31 @@ export 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;
             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;
             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;
                 addCylinder(builderState, va, vb, 0.5, cylinderProps);
                 var aromaticOffset = linkRadius + aromaticScale * linkRadius + aromaticScale * linkRadius * aromaticSpacing;
@@ -140,14 +140,14 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
                 v3sub(va, va, vShift);
                 v3sub(vb, vb, vShift);
                 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);
                     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;
@@ -177,7 +177,7 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
                 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);
@@ -230,25 +230,25 @@ export 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);
@@ -259,14 +259,14 @@ export 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);
@@ -284,7 +284,7 @@ export 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);
@@ -335,24 +335,24 @@ export 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);
@@ -360,14 +360,14 @@ export 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);
@@ -384,7 +384,7 @@ export 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/mol-repr/structure/visual/util/polymer/backbone.js

@@ -8,9 +8,9 @@ import { SortedRanges } from '../../../../../mol-data/int/sorted-ranges';
 import { getPolymerRanges } from '../polymer';
 export 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);
     }
 }
@@ -74,9 +74,9 @@ function eachCoarsePolymerBackboneLink(unit, callback) {
 }
 export 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/mol-repr/structure/visual/util/polymer/gap-iterator.js

@@ -9,9 +9,9 @@ import { getGapRanges } from '../polymer';
 /** Iterates over gaps, i.e. the stem residues/coarse elements adjacent to gaps */
 export 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/mol-repr/structure/visual/util/polymer/trace-iterator.js

@@ -12,10 +12,10 @@ import { getPolymerRanges } from '../polymer';
 import { SecondaryStructureProvider } from '../../../../../mol-model-props/computed/secondary-structure';
 import { HelixOrientationProvider } from '../../../../../mol-model-props/computed/helix-orientation';
 function isHelixSS(ss) {
-    return SecondaryStructureType.is(ss, 2 /* Helix */);
+    return SecondaryStructureType.is(ss, 2 /* SecondaryStructureType.Flag.Helix */);
 }
 function isSheetSS(ss) {
-    return SecondaryStructureType.is(ss, 4 /* Beta */);
+    return SecondaryStructureType.is(ss, 4 /* SecondaryStructureType.Flag.Beta */);
 }
 /**
  * Iterates over individual residues/coarse elements in polymers of a unit while
@@ -24,13 +24,13 @@ function isSheetSS(ss) {
 export 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);
     }
 }
-var SecStrucTypeNA = SecondaryStructureType.create(536870912 /* NA */);
+var SecStrucTypeNA = SecondaryStructureType.create(536870912 /* SecondaryStructureType.Flag.NA */);
 function createPolymerTraceElement(structure, unit) {
     return {
         center: StructureElement.Location.create(structure, unit),
@@ -40,7 +40,7 @@ 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: Vec3(), p1: Vec3(), p2: Vec3(), p3: Vec3(), p4: Vec3(),
@@ -55,7 +55,7 @@ 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 = Vec3();
         this.p1 = Vec3();
         this.p2 = Vec3();
@@ -137,7 +137,7 @@ 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;
@@ -168,13 +168,13 @@ 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);
@@ -185,7 +185,7 @@ 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);
@@ -348,7 +348,7 @@ 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;
@@ -360,17 +360,17 @@ export { 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 = SortedRanges.transientSegments(getPolymerRanges(unit), unit.elements);
         this.value = createPolymerTraceElement(structure, unit);
         Vec3.set(this.value.d12, 1, 0, 0);
         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;
         }
@@ -386,17 +386,17 @@ 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);
@@ -432,7 +432,7 @@ 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/mol-repr/structure/visual/util/polymer.js

@@ -20,16 +20,16 @@ export var NucleicShift = 0.3;
 export var OverhangFactor = 2;
 export 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;
     }
 }
 export 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;
     }
 }
 export var PolymerLocationIterator;

package/lib/mol-repr/volume/representation.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-repr/volume/representation.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -90,6 +90,7 @@ export function VolumeVisual(builder, materialId) {
                 if (newGeometry) {
                     ValueCell.updateIfChanged(renderObject.values.drawCount, Geometry.getDrawCount(newGeometry));
                     ValueCell.updateIfChanged(renderObject.values.uVertexCount, Geometry.getVertexCount(newGeometry));
+                    ValueCell.updateIfChanged(renderObject.values.uGroupCount, Geometry.getGroupCount(newGeometry));
                 }
                 else {
                     throw new Error('expected geometry to be given');

package/lib/mol-script/language/builder.d.ts

@@ -10,6 +10,7 @@ export declare namespace MolScriptBuilder {
         '@header': string;
         type: {
             '@header': string;
+            /** atom macromolecular property set */
             bool: MSymbol<import("./symbol").Arguments<import("./symbol").Arguments.PropTypes<{
                 0: import("./symbol").Argument<import("./type").Type.AnyValue>;
             }>>, import("./type").Type.OneOf<boolean>>;

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

@@ -209,7 +209,7 @@ var symbols = [
     C(MolScript.structureQuery.type.elementSymbol, function (ctx, v) { return ElementSymbol(v[0](ctx)); }),
     C(MolScript.structureQuery.type.atomName, function (ctx, v) { return upperCaseAny(v[0](ctx)); }),
     C(MolScript.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));
@@ -224,7 +224,7 @@ var symbols = [
     }),
     C(MolScript.structureQuery.type.ringFingerprint, function (ctx, xs) { return UnitRing.elementFingerprint(getArray(ctx, xs)); }),
     C(MolScript.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));
@@ -386,20 +386,20 @@ function atomProp(p) {
     return function (ctx, xs) { return p((xs && xs[0] && xs[0](ctx)) || ctx.element); };
 }
 function bondFlag(current, f) {
-    return current | (BondType.isName(f) ? BondType.fromName(f) : 0 /* None */);
+    return current | (BondType.isName(f) ? 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/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/mol-task/util/user-timing.js

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { isProductionMode } from '../../mol-util/debug';
-var hasPerformance = (typeof performance !== 'undefined') && performance.mark && performance.measure;
+var hasPerformance = (typeof performance !== 'undefined') && !!performance.mark && performance.measure;
 var timingEnabled = hasPerformance && !isProductionMode;
 export var UserTiming;
 (function (UserTiming) {