molstar 3.8.2 → 3.10.0

package/lib/mol-plugin-ui/skin/colors/blue.scss

@@ -1,24 +1,24 @@
-$default-background:         #2D3E50;
-$font-color:                 #EDF1F2; 
-$hover-font-color:           #3B9AD9;
-$entity-current-font-color:  #FFFFFF;
-$msp-btn-remove-background:      #BF3A31;
-$msp-btn-remove-hover-font-color:#ffffff;
-$msp-btn-commit-on-font-color:   #ffffff; 
-$entity-badge-font-color:    #ccd4e0;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: rgba(0,0,0,0.75);
-
-@function color-lower-contrast($color, $amount) {
-    @return darken($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return lighten($color, $amount);
+$default-background:         #2D3E50;
+$font-color:                 #EDF1F2; 
+$hover-font-color:           #3B9AD9;
+$entity-current-font-color:  #FFFFFF;
+$msp-btn-remove-background:      #BF3A31;
+$msp-btn-remove-hover-font-color:#ffffff;
+$msp-btn-commit-on-font-color:   #ffffff; 
+$entity-badge-font-color:    #ccd4e0;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: rgba(0,0,0,0.75);
+
+@function color-lower-contrast($color, $amount) {
+    @return darken($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return lighten($color, $amount);
 }

package/lib/mol-plugin-ui/skin/colors/dark.scss

@@ -1,24 +1,24 @@
-$default-background:         #111318;
-$font-color:                 #ccd4e0;
-$hover-font-color:           #51A2FB;
-$entity-current-font-color:  #68BEFD;
-$msp-btn-remove-background:      #DE0A28;
-$msp-btn-remove-hover-font-color:#F2F4F7;
-$msp-btn-commit-on-font-color:   #68BEFD;
-$entity-badge-font-color:    #ccd4e0;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: rgba(0,0,0,0.75);
-
-@function color-lower-contrast($color, $amount) {
-    @return darken($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return lighten($color, $amount);
+$default-background:         #111318;
+$font-color:                 #ccd4e0;
+$hover-font-color:           #51A2FB;
+$entity-current-font-color:  #68BEFD;
+$msp-btn-remove-background:      #DE0A28;
+$msp-btn-remove-hover-font-color:#F2F4F7;
+$msp-btn-commit-on-font-color:   #68BEFD;
+$entity-badge-font-color:    #ccd4e0;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: rgba(0,0,0,0.75);
+
+@function color-lower-contrast($color, $amount) {
+    @return darken($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return lighten($color, $amount);
 }

package/lib/mol-plugin-ui/skin/colors/light.scss

@@ -1,30 +1,30 @@
-// this is complement of the dark theme
-
-@function compl($color) {
-    @return rgb(255 - red($color), 255 - green($color), 255 - blue($color));
-}
-
-$default-background:         compl(#111318);
-$font-color:                 compl(#ccd4e0);
-$hover-font-color:           compl(#51A2FB);
-$entity-current-font-color:  compl(#68BEFD);
-$msp-btn-commit-on-font-color:   compl(#68BEFD);
-$entity-badge-font-color:    lighten(#ccd4e0,10%);
-$msp-btn-remove-background:      #DE0A28;
-$msp-btn-remove-hover-font-color:#F2F4F7;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: compl(#111318);
-
-@function color-lower-contrast($color, $amount) {
-    @return lighten($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return darken($color, $amount);
+// this is complement of the dark theme
+
+@function compl($color) {
+    @return rgb(255 - red($color), 255 - green($color), 255 - blue($color));
+}
+
+$default-background:         compl(#111318);
+$font-color:                 compl(#ccd4e0);
+$hover-font-color:           compl(#51A2FB);
+$entity-current-font-color:  compl(#68BEFD);
+$msp-btn-commit-on-font-color:   compl(#68BEFD);
+$entity-badge-font-color:    lighten(#ccd4e0,10%);
+$msp-btn-remove-background:      #DE0A28;
+$msp-btn-remove-hover-font-color:#F2F4F7;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: compl(#111318);
+
+@function color-lower-contrast($color, $amount) {
+    @return lighten($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return darken($color, $amount);
 }

package/lib/mol-plugin-ui/skin/dark.scss

@@ -1,2 +1,2 @@
-@import 'colors/dark';
+@import 'colors/dark';
 @import 'base/base';

package/lib/mol-plugin-ui/skin/light.scss

@@ -1,2 +1,2 @@
-@import 'colors/light';
+@import 'colors/light';
 @import 'base/base';

package/lib/mol-plugin-ui/state/snapshots.js

@@ -293,6 +293,7 @@ var RemoteStateSnapshots = /** @class */ (function (_super) {
         // this.subscribe(UploadedEvent, this.refresh);
     };
     RemoteStateSnapshots.prototype.componentWillUnmount = function () {
+        _super.prototype.componentWillUnmount.call(this);
         this._mounted = false;
     };
     RemoteStateSnapshots.prototype.serverUrl = function (q) {

package/lib/mol-plugin-ui/structure/focus.js

@@ -51,7 +51,7 @@ function getFocusEntries(structure) {
             continue;
         l.unit = ug.units[0];
         l.element = ug.elements[0];
-        var isMultiChain = Unit.Traits.is(l.unit.traits, 1 /* MultiChain */);
+        var isMultiChain = Unit.Traits.is(l.unit.traits, 1 /* Unit.Trait.MultiChain */);
         var entityType = StructureProperties.entity.type(l);
         var isNonPolymer = entityType === 'non-polymer';
         var isBranched = entityType === 'branched';

package/lib/mol-plugin-ui/viewport/screenshot.js

@@ -71,6 +71,7 @@ var DownloadScreenshotControls = /** @class */ (function (_super) {
         });
     };
     DownloadScreenshotControls.prototype.componentWillUnmount = function () {
+        _super.prototype.componentWillUnmount.call(this);
         this.setState({ imageData: void 0 });
     };
     DownloadScreenshotControls.prototype.render = function () {

package/lib/mol-plugin-ui/viewport.d.ts

@@ -18,8 +18,8 @@ export declare class ViewportControls extends PluginUIComponent<ViewportControls
     state: ViewportControlsState;
     resetCamera: () => void;
     private toggle;
-    toggleSettingsExpanded: (e?: React.MouseEvent<HTMLButtonElement, MouseEvent> | undefined) => void;
-    toggleScreenshotExpanded: (e?: React.MouseEvent<HTMLButtonElement, MouseEvent> | undefined) => void;
+    toggleSettingsExpanded: (e?: React.MouseEvent<HTMLButtonElement>) => void;
+    toggleScreenshotExpanded: (e?: React.MouseEvent<HTMLButtonElement>) => void;
     toggleControls: () => void;
     toggleExpanded: () => void;
     setSettings: (p: {

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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/shape/representation.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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>
  */
@@ -131,6 +131,7 @@ export function ShapeRepresentation(getShape, geometryUtils, builder) {
                                 // console.log('update geometry')
                                 ValueCell.updateIfChanged(_renderObject.values.drawCount, Geometry.getDrawCount(_shape.geometry));
                                 ValueCell.updateIfChanged(_renderObject.values.uVertexCount, Geometry.getVertexCount(_shape.geometry));
+                                ValueCell.updateIfChanged(_renderObject.values.uGroupCount, Geometry.getGroupCount(_shape.geometry));
                             }
                             if (updateState.updateTransform || updateState.createGeometry) {
                                 // console.log('updateBoundingSphere')

package/lib/mol-repr/structure/complex-visual.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/structure/complex-visual.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>
  */
@@ -115,6 +115,7 @@ export function ComplexVisual(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-repr/structure/units-visual.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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/structure/units-visual.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 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>
  */
@@ -156,6 +156,7 @@ export function UnitsVisual(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-repr/structure/visual/bond-inter-unit-cylinder.js

@@ -115,21 +115,21 @@ function getInterUnitBondCylinderBuilderProps(structure, theme, props) {
         style: function (edgeIndex) {
             var o = edges[edgeIndex].props.order;
             var f = BitFlags.create(edges[edgeIndex].props.flag);
-            if (BondType.is(f, 2 /* MetallicCoordination */) || BondType.is(f, 4 /* HydrogenBond */)) {
+            if (BondType.is(f, 2 /* BondType.Flag.MetallicCoordination */) || BondType.is(f, 4 /* BondType.Flag.HydrogenBond */)) {
                 // show metallic coordinations and hydrogen bonds with dashed cylinders
-                return 1 /* Dashed */;
+                return 1 /* LinkStyle.Dashed */;
             }
             else if (o === 3) {
-                return mbOff ? 0 /* Solid */ :
-                    mbSymmetric ? 4 /* Triple */ :
-                        5 /* OffsetTriple */;
+                return mbOff ? 0 /* LinkStyle.Solid */ :
+                    mbSymmetric ? 4 /* LinkStyle.Triple */ :
+                        5 /* LinkStyle.OffsetTriple */;
             }
-            else if (aromaticBonds && BondType.is(f, 16 /* Aromatic */)) {
-                return 7 /* Aromatic */;
+            else if (aromaticBonds && BondType.is(f, 16 /* BondType.Flag.Aromatic */)) {
+                return 7 /* LinkStyle.Aromatic */;
             }
-            return (o !== 2 || mbOff) ? 0 /* Solid */ :
-                mbSymmetric ? 2 /* Double */ :
-                    3 /* OffsetDouble */;
+            return (o !== 2 || mbOff) ? 0 /* LinkStyle.Solid */ :
+                mbSymmetric ? 2 /* LinkStyle.Double */ :
+                    3 /* LinkStyle.OffsetDouble */;
         },
         radius: function (edgeIndex) {
             return radius(edgeIndex) * sizeAspectRatio;

package/lib/mol-repr/structure/visual/bond-inter-unit-line.js

@@ -67,21 +67,21 @@ function createInterUnitBondLines(ctx, structure, theme, props, lines) {
         style: function (edgeIndex) {
             var o = edges[edgeIndex].props.order;
             var f = BitFlags.create(edges[edgeIndex].props.flag);
-            if (BondType.is(f, 2 /* MetallicCoordination */) || BondType.is(f, 4 /* HydrogenBond */)) {
+            if (BondType.is(f, 2 /* BondType.Flag.MetallicCoordination */) || BondType.is(f, 4 /* BondType.Flag.HydrogenBond */)) {
                 // show metallic coordinations and hydrogen bonds with dashed cylinders
-                return 1 /* Dashed */;
+                return 1 /* LinkStyle.Dashed */;
             }
             else if (o === 3) {
-                return mbOff ? 0 /* Solid */ :
-                    mbSymmetric ? 4 /* Triple */ :
-                        5 /* OffsetTriple */;
+                return mbOff ? 0 /* LinkStyle.Solid */ :
+                    mbSymmetric ? 4 /* LinkStyle.Triple */ :
+                        5 /* LinkStyle.OffsetTriple */;
             }
-            else if (aromaticBonds && BondType.is(f, 16 /* Aromatic */)) {
-                return 7 /* Aromatic */;
+            else if (aromaticBonds && BondType.is(f, 16 /* BondType.Flag.Aromatic */)) {
+                return 7 /* LinkStyle.Aromatic */;
             }
-            return (o !== 2 || mbOff) ? 0 /* Solid */ :
-                mbSymmetric ? 2 /* Double */ :
-                    3 /* OffsetDouble */;
+            return (o !== 2 || mbOff) ? 0 /* LinkStyle.Solid */ :
+                mbSymmetric ? 2 /* LinkStyle.Double */ :
+                    3 /* LinkStyle.OffsetDouble */;
         },
         radius: function (edgeIndex) {
             var b = edges[edgeIndex];

package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.js

@@ -31,7 +31,7 @@ function getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props) {
     var mbSymmetric = multipleBonds === 'symmetric';
     var include = BondType.fromNames(includeTypes);
     var exclude = BondType.fromNames(excludeTypes);
-    var ignoreComputedAromatic = ignoreBondType(include, exclude, 32 /* Computed */);
+    var ignoreComputedAromatic = ignoreBondType(include, exclude, 32 /* BondType.Flag.Computed */);
     var vRef = Vec3(), delta = Vec3();
     var pos = unit.conformation.invariantPosition;
     var stub;
@@ -115,35 +115,32 @@ function getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props) {
         style: function (edgeIndex) {
             var o = _order[edgeIndex];
             var f = _flags[edgeIndex];
-            if (isBondType(f, 2 /* MetallicCoordination */) || isBondType(f, 4 /* HydrogenBond */)) {
+            if (isBondType(f, 2 /* BondType.Flag.MetallicCoordination */) || isBondType(f, 4 /* BondType.Flag.HydrogenBond */)) {
                 // show metallic coordinations and hydrogen bonds with dashed cylinders
-                return 1 /* Dashed */;
+                return 1 /* LinkStyle.Dashed */;
             }
             else if (o === 3) {
-                return mbOff ? 0 /* Solid */ :
-                    mbSymmetric ? 4 /* Triple */ :
-                        5 /* OffsetTriple */;
+                return mbOff ? 0 /* LinkStyle.Solid */ :
+                    mbSymmetric ? 4 /* LinkStyle.Triple */ :
+                        5 /* LinkStyle.OffsetTriple */;
             }
             else if (aromaticBonds) {
                 var aI = a[edgeIndex], bI = b[edgeIndex];
                 var aR = elementAromaticRingIndices.get(aI);
                 var bR = elementAromaticRingIndices.get(bI);
                 var arCount = (aR && bR) ? arrayIntersectionSize(aR, bR) : 0;
-                if (isBondType(f, 16 /* Aromatic */) || (arCount && !ignoreComputedAromatic)) {
+                if (isBondType(f, 16 /* BondType.Flag.Aromatic */) || (arCount && !ignoreComputedAromatic)) {
                     if (arCount === 2) {
-                        return 8 /* MirroredAromatic */;
-                    }
-                    else if (arCount === 1 || (deloTriplets === null || deloTriplets === void 0 ? void 0 : deloTriplets.getThirdElement(aI, bI))) {
-                        return 7 /* Aromatic */;
+                        return 8 /* LinkStyle.MirroredAromatic */;
                     }
                     else {
-                        // case for bonds between two aromatic rings
+                        return 7 /* LinkStyle.Aromatic */;
                     }
                 }
             }
-            return (o !== 2 || mbOff) ? 0 /* Solid */ :
-                mbSymmetric ? 2 /* Double */ :
-                    3 /* OffsetDouble */;
+            return (o !== 2 || mbOff) ? 0 /* LinkStyle.Solid */ :
+                mbSymmetric ? 2 /* LinkStyle.Double */ :
+                    3 /* LinkStyle.OffsetDouble */;
         },
         radius: function (edgeIndex) {
             return radius(edgeIndex) * sizeAspectRatio;

package/lib/mol-repr/structure/visual/bond-intra-unit-line.js

@@ -37,7 +37,7 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
     var mbSymmetric = multipleBonds === 'symmetric';
     var include = BondType.fromNames(includeTypes);
     var exclude = BondType.fromNames(excludeTypes);
-    var ignoreComputedAromatic = ignoreBondType(include, exclude, 32 /* Computed */);
+    var ignoreComputedAromatic = ignoreBondType(include, exclude, 32 /* BondType.Flag.Computed */);
     var vRef = Vec3();
     var pos = unit.conformation.invariantPosition;
     var _a = unit.rings, elementRingIndices = _a.elementRingIndices, elementAromaticRingIndices = _a.elementAromaticRingIndices;
@@ -83,35 +83,32 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
         style: function (edgeIndex) {
             var o = _order[edgeIndex];
             var f = _flags[edgeIndex];
-            if (isBondType(f, 2 /* MetallicCoordination */) || isBondType(f, 4 /* HydrogenBond */)) {
+            if (isBondType(f, 2 /* BondType.Flag.MetallicCoordination */) || isBondType(f, 4 /* BondType.Flag.HydrogenBond */)) {
                 // show metallic coordinations and hydrogen bonds with dashed cylinders
-                return 1 /* Dashed */;
+                return 1 /* LinkStyle.Dashed */;
             }
             else if (o === 3) {
-                return mbOff ? 0 /* Solid */ :
-                    mbSymmetric ? 4 /* Triple */ :
-                        5 /* OffsetTriple */;
+                return mbOff ? 0 /* LinkStyle.Solid */ :
+                    mbSymmetric ? 4 /* LinkStyle.Triple */ :
+                        5 /* LinkStyle.OffsetTriple */;
             }
             else if (aromaticBonds) {
                 var aI = a[edgeIndex], bI = b[edgeIndex];
                 var aR = elementAromaticRingIndices.get(aI);
                 var bR = elementAromaticRingIndices.get(bI);
                 var arCount = (aR && bR) ? arrayIntersectionSize(aR, bR) : 0;
-                if (isBondType(f, 16 /* Aromatic */) || (arCount && !ignoreComputedAromatic)) {
+                if (isBondType(f, 16 /* BondType.Flag.Aromatic */) || (arCount && !ignoreComputedAromatic)) {
                     if (arCount === 2) {
-                        return 8 /* MirroredAromatic */;
-                    }
-                    else if (arCount === 1 || (deloTriplets === null || deloTriplets === void 0 ? void 0 : deloTriplets.getThirdElement(aI, bI))) {
-                        return 7 /* Aromatic */;
+                        return 8 /* LinkStyle.MirroredAromatic */;
                     }
                     else {
-                        // case for bonds between two aromatic rings
+                        return 7 /* LinkStyle.Aromatic */;
                     }
                 }
             }
-            return (o !== 2 || mbOff) ? 0 /* Solid */ :
-                mbSymmetric ? 2 /* Double */ :
-                    3 /* OffsetDouble */;
+            return (o !== 2 || mbOff) ? 0 /* LinkStyle.Solid */ :
+                mbSymmetric ? 2 /* LinkStyle.Double */ :
+                    3 /* LinkStyle.OffsetDouble */;
         },
         radius: function (edgeIndex) {
             location.element = elements[a[edgeIndex]];

package/lib/mol-repr/structure/visual/carbohydrate-symbol-mesh.js

@@ -58,47 +58,47 @@ function createCarbohydrateSymbolMesh(ctx, structure, theme, props, mesh) {
         Mat4.setTranslation(t, center);
         builderState.currentGroup = i * 2;
         switch (shapeType) {
-            case 0 /* FilledSphere */:
+            case 0 /* SaccharideShape.FilledSphere */:
                 addSphere(builderState, center, radius, detail);
                 break;
-            case 1 /* FilledCube */:
+            case 1 /* SaccharideShape.FilledCube */:
                 Mat4.scaleUniformly(t, t, side);
                 MeshBuilder.addPrimitive(builderState, t, box);
                 break;
-            case 2 /* CrossedCube */:
+            case 2 /* SaccharideShape.CrossedCube */:
                 Mat4.scaleUniformly(t, t, side);
                 MeshBuilder.addPrimitive(builderState, t, perforatedBox);
                 Mat4.mul(t, t, Mat4.rotZ90X180);
                 builderState.currentGroup += 1;
                 MeshBuilder.addPrimitive(builderState, t, perforatedBox);
                 break;
-            case 4 /* FilledCone */:
+            case 4 /* SaccharideShape.FilledCone */:
                 Mat4.scaleUniformly(t, t, side * 1.2);
                 MeshBuilder.addPrimitive(builderState, t, octagonalPyramid);
                 break;
-            case 5 /* DevidedCone */:
+            case 5 /* SaccharideShape.DevidedCone */:
                 Mat4.scaleUniformly(t, t, side * 1.2);
                 MeshBuilder.addPrimitive(builderState, t, perforatedOctagonalPyramid);
                 Mat4.mul(t, t, Mat4.rotZ90);
                 builderState.currentGroup += 1;
                 MeshBuilder.addPrimitive(builderState, t, perforatedOctagonalPyramid);
                 break;
-            case 6 /* FlatBox */:
+            case 6 /* SaccharideShape.FlatBox */:
                 Mat4.mul(t, t, Mat4.rotZY90);
                 Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2));
                 MeshBuilder.addPrimitive(builderState, t, box);
                 break;
-            case 7 /* FilledStar */:
+            case 7 /* SaccharideShape.FilledStar */:
                 Mat4.scaleUniformly(t, t, side);
                 Mat4.mul(t, t, Mat4.rotZY90);
                 MeshBuilder.addPrimitive(builderState, t, star);
                 break;
-            case 8 /* FilledDiamond */:
+            case 8 /* SaccharideShape.FilledDiamond */:
                 Mat4.mul(t, t, Mat4.rotZY90);
                 Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4));
                 MeshBuilder.addPrimitive(builderState, t, octahedron);
                 break;
-            case 3 /* DividedDiamond */:
+            case 3 /* SaccharideShape.DividedDiamond */:
                 Mat4.mul(t, t, Mat4.rotZY90);
                 Mat4.scale(t, t, Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4));
                 MeshBuilder.addPrimitive(builderState, t, perforatedOctahedron);
@@ -106,33 +106,33 @@ function createCarbohydrateSymbolMesh(ctx, structure, theme, props, mesh) {
                 builderState.currentGroup += 1;
                 MeshBuilder.addPrimitive(builderState, t, perforatedOctahedron);
                 break;
-            case 9 /* FlatDiamond */:
+            case 9 /* SaccharideShape.FlatDiamond */:
                 Mat4.mul(t, t, Mat4.rotZY90);
                 Mat4.scale(t, t, Vec3.set(sVec, side, side / 2, side / 2));
                 MeshBuilder.addPrimitive(builderState, t, diamondPrism);
                 break;
-            case 12 /* DiamondPrism */:
+            case 12 /* SaccharideShape.DiamondPrism */:
                 Mat4.mul(t, t, Mat4.rotZY90);
                 Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2));
                 MeshBuilder.addPrimitive(builderState, t, diamondPrism);
                 break;
-            case 13 /* PentagonalPrism */:
-            case 11 /* Pentagon */:
+            case 13 /* SaccharideShape.PentagonalPrism */:
+            case 11 /* SaccharideShape.Pentagon */:
                 Mat4.mul(t, t, Mat4.rotZY90);
                 Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2));
                 MeshBuilder.addPrimitive(builderState, t, pentagonalPrism);
                 break;
-            case 14 /* HexagonalPrism */:
+            case 14 /* SaccharideShape.HexagonalPrism */:
                 Mat4.mul(t, t, Mat4.rotZY90);
                 Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2));
                 MeshBuilder.addPrimitive(builderState, t, hexagonalPrism);
                 break;
-            case 15 /* HeptagonalPrism */:
+            case 15 /* SaccharideShape.HeptagonalPrism */:
                 Mat4.mul(t, t, Mat4.rotZY90);
                 Mat4.scale(t, t, Vec3.set(sVec, side, side, side / 2));
                 MeshBuilder.addPrimitive(builderState, t, heptagonalPrism);
                 break;
-            case 10 /* FlatHexagon */:
+            case 10 /* SaccharideShape.FlatHexagon */:
             default:
                 Mat4.mul(t, t, Mat4.rotZYZ90);
                 Mat4.scale(t, t, Vec3.set(sVec, side / 1.5, side, side / 2));

package/lib/mol-repr/structure/visual/carbohydrate-terminal-link-cylinder.js

@@ -51,7 +51,7 @@ function createCarbohydrateTerminalLinkCylinderMesh(ctx, structure, theme, props
             var l = terminalLinks[edgeIndex];
             var eI = l.elementUnit.elements[l.elementIndex];
             var beI = getElementIdx(l.elementUnit.model.atomicHierarchy.atoms.type_symbol.value(eI));
-            return MetalsSet.has(beI) ? 1 /* Dashed */ : 0 /* Solid */;
+            return MetalsSet.has(beI) ? 1 /* LinkStyle.Dashed */ : 0 /* LinkStyle.Solid */;
         }
     };
     var _b = createLinkCylinderMesh(ctx, builderProps, props, mesh), m = _b.mesh, boundingSphere = _b.boundingSphere;

package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js

@@ -19,6 +19,7 @@ import { applyMeshColorSmoothing } from '../../../mol-geo/geometry/mesh/color-sm
 import { applyTextureMeshColorSmoothing } from '../../../mol-geo/geometry/texture-mesh/color-smoothing';
 import { ColorSmoothingParams, getColorSmoothingProps } from '../../../mol-geo/geometry/base';
 import { Vec3 } from '../../../mol-math/linear-algebra';
+import { isTimingMode } from '../../../mol-util/debug';
 var SharedParams = __assign(__assign(__assign({}, GaussianDensityParams), ColorSmoothingParams), { ignoreHydrogens: PD.Boolean(false), tryUseGpu: PD.Boolean(true), includeParent: PD.Boolean(false, { isHidden: true }) });
 export var GaussianSurfaceMeshParams = __assign(__assign(__assign({}, UnitsMeshParams), UnitsTextureMeshParams), SharedParams);
 export var StructureGaussianSurfaceMeshParams = __assign(__assign(__assign({}, ComplexMeshParams), ComplexTextureMeshParams), SharedParams);
@@ -210,6 +211,8 @@ function createGaussianSurfaceTextureMesh(ctx, unit, structure, theme, props, te
                 case 0:
                     if (!ctx.webgl)
                         throw new Error('webgl context required to create gaussian surface texture-mesh');
+                    if (isTimingMode)
+                        ctx.webgl.timer.mark('createGaussianSurfaceTextureMesh');
                     _a = ctx.webgl, namedTextures = _a.namedTextures, resources = _a.resources, _b = _a.extensions, colorBufferFloat = _b.colorBufferFloat, textureFloat = _b.textureFloat, colorBufferHalfFloat = _b.colorBufferHalfFloat, textureHalfFloat = _b.textureHalfFloat;
                     if (!namedTextures[GaussianSurfaceName]) {
                         namedTextures[GaussianSurfaceName] = colorBufferHalfFloat && textureHalfFloat
@@ -225,6 +228,8 @@ function createGaussianSurfaceTextureMesh(ctx, unit, structure, theme, props, te
                     axisOrder = Vec3.create(0, 1, 2);
                     buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
                     gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, axisOrder, buffer === null || buffer === void 0 ? void 0 : buffer.vertex, buffer === null || buffer === void 0 ? void 0 : buffer.group, buffer === null || buffer === void 0 ? void 0 : buffer.normal);
+                    if (isTimingMode)
+                        ctx.webgl.timer.markEnd('createGaussianSurfaceTextureMesh');
                     boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, densityTextureData.maxRadius);
                     surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
                     surface.meta.resolution = densityTextureData.resolution;
@@ -293,6 +298,8 @@ function createStructureGaussianSurfaceTextureMesh(ctx, structure, theme, props,
                 case 0:
                     if (!ctx.webgl)
                         throw new Error('webgl context required to create structure gaussian surface texture-mesh');
+                    if (isTimingMode)
+                        ctx.webgl.timer.mark('createStructureGaussianSurfaceTextureMesh');
                     _a = ctx.webgl, namedTextures = _a.namedTextures, resources = _a.resources, _b = _a.extensions, colorBufferFloat = _b.colorBufferFloat, textureFloat = _b.textureFloat, colorBufferHalfFloat = _b.colorBufferHalfFloat, textureHalfFloat = _b.textureHalfFloat;
                     if (!namedTextures[GaussianSurfaceName]) {
                         namedTextures[GaussianSurfaceName] = colorBufferHalfFloat && textureHalfFloat
@@ -308,6 +315,8 @@ function createStructureGaussianSurfaceTextureMesh(ctx, structure, theme, props,
                     axisOrder = Vec3.create(0, 1, 2);
                     buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
                     gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, axisOrder, buffer === null || buffer === void 0 ? void 0 : buffer.vertex, buffer === null || buffer === void 0 ? void 0 : buffer.group, buffer === null || buffer === void 0 ? void 0 : buffer.normal);
+                    if (isTimingMode)
+                        ctx.webgl.timer.markEnd('createStructureGaussianSurfaceTextureMesh');
                     boundingSphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, densityTextureData.maxRadius);
                     surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
                     surface.meta.resolution = densityTextureData.resolution;