molstar 3.8.2 → 3.10.0

package/lib/commonjs/mol-plugin-state/formats/volume.js

@@ -1,9 +1,10 @@
 "use strict";
 /**
- * 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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Aliaksei Chareshneu <chareshneu.tech@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BuiltInVolumeFormats = exports.DscifProvider = exports.CubeProvider = exports.DxProvider = exports.Dsn6Provider = exports.Ccp4Provider = exports.VolumeFormatCategory = void 0;
@@ -246,35 +247,41 @@ exports.DscifProvider = (0, provider_1.DataFormatProvider)({
     },
     parse: function (plugin, data, params) { return tslib_1.__awaiter(void 0, void 0, void 0, function () {
         var cifCell, b, blocks, volumes, i, _i, blocks_1, block, entryId, _a, volumes_1, v;
-        return tslib_1.__generator(this, function (_b) {
-            switch (_b.label) {
+        var _b;
+        return tslib_1.__generator(this, function (_c) {
+            switch (_c.label) {
                 case 0: return [4 /*yield*/, plugin.build().to(data).apply(transforms_1.StateTransforms.Data.ParseCif).commit()];
                 case 1:
-                    cifCell = _b.sent();
+                    cifCell = _c.sent();
                     b = plugin.build().to(cifCell);
-                    blocks = cifCell.obj.data.blocks.slice(1);
-                    if (blocks.length !== 1 && blocks.length !== 2)
-                        throw new Error('unknown number of blocks');
+                    blocks = cifCell.obj.data.blocks;
+                    if (blocks.length === 0)
+                        throw new Error('no data blocks');
                     volumes = [];
                     i = 0;
                     for (_i = 0, blocks_1 = blocks; _i < blocks_1.length; _i++) {
                         block = blocks_1[_i];
+                        // Skip "server" data block.
+                        if (block.header.toUpperCase() === 'SERVER')
+                            continue;
                         entryId = Array.isArray(params === null || params === void 0 ? void 0 : params.entryId) ? params === null || params === void 0 ? void 0 : params.entryId[i] : params === null || params === void 0 ? void 0 : params.entryId;
-                        volumes.push(b.apply(transforms_1.StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: block.header, entryId: entryId }).selector);
-                        i++;
+                        if (((_b = block.categories['volume_data_3d_info']) === null || _b === void 0 ? void 0 : _b.rowCount) > 0) {
+                            volumes.push(b.apply(transforms_1.StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: block.header, entryId: entryId }).selector);
+                            i++;
+                        }
                     }
                     return [4 /*yield*/, b.commit()];
                 case 2:
-                    _b.sent();
+                    _c.sent();
                     _a = 0, volumes_1 = volumes;
-                    _b.label = 3;
+                    _c.label = 3;
                 case 3:
                     if (!(_a < volumes_1.length)) return [3 /*break*/, 6];
                     v = volumes_1[_a];
                     return [4 /*yield*/, tryObtainRecommendedIsoValue(plugin, v.data)];
                 case 4:
-                    _b.sent();
-                    _b.label = 5;
+                    _c.sent();
+                    _c.label = 5;
                 case 5:
                     _a++;
                     return [3 /*break*/, 3];

package/lib/commonjs/mol-plugin-state/helpers/structure-selection-query.js

@@ -224,7 +224,7 @@ var helix = StructureSelectionQuery('Helix', builder_1.MolScriptBuilder.struct.m
         'entity-test': _proteinEntityTest,
         'residue-test': builder_1.MolScriptBuilder.core.flags.hasAny([
             builder_1.MolScriptBuilder.ammp('secondaryStructureFlags'),
-            builder_1.MolScriptBuilder.core.type.bitflags([2 /* Helix */])
+            builder_1.MolScriptBuilder.core.type.bitflags([2 /* SecondaryStructureType.Flag.Helix */])
         ])
     })
 ]), {
@@ -238,7 +238,7 @@ var beta = StructureSelectionQuery('Beta Strand/Sheet', builder_1.MolScriptBuild
         'entity-test': _proteinEntityTest,
         'residue-test': builder_1.MolScriptBuilder.core.flags.hasAny([
             builder_1.MolScriptBuilder.ammp('secondaryStructureFlags'),
-            builder_1.MolScriptBuilder.core.type.bitflags([4 /* Beta */])
+            builder_1.MolScriptBuilder.core.type.bitflags([4 /* SecondaryStructureType.Flag.Beta */])
         ])
     })
 ]), {
@@ -341,7 +341,7 @@ var ligandPlusConnected = StructureSelectionQuery('Ligand with Connected', build
                 'bond-test': builder_1.MolScriptBuilder.core.flags.hasAny([
                     builder_1.MolScriptBuilder.struct.bondProperty.flags(),
                     builder_1.MolScriptBuilder.core.type.bitflags([
-                        1 /* Covalent */ | 2 /* MetallicCoordination */
+                        1 /* BondType.Flag.Covalent */ | 2 /* BondType.Flag.MetallicCoordination */
                     ])
                 ])
             })
@@ -385,7 +385,7 @@ var disulfideBridges = StructureSelectionQuery('Disulfide Bridges', builder_1.Mo
                     builder_1.MolScriptBuilder.struct.generator.bondedAtomicPairs({
                         0: builder_1.MolScriptBuilder.core.flags.hasAny([
                             builder_1.MolScriptBuilder.struct.bondProperty.flags(),
-                            builder_1.MolScriptBuilder.core.type.bitflags([8 /* Disulfide */])
+                            builder_1.MolScriptBuilder.core.type.bitflags([8 /* BondType.Flag.Disulfide */])
                         ])
                     })
                 ])
@@ -503,7 +503,7 @@ var covalentlyOrMetallicBonded = StructureSelectionQuery('Residues with Cov. or
         'bond-test': builder_1.MolScriptBuilder.core.flags.hasAny([
             builder_1.MolScriptBuilder.struct.bondProperty.flags(),
             builder_1.MolScriptBuilder.core.type.bitflags([
-                1 /* Covalent */ | 2 /* MetallicCoordination */
+                1 /* BondType.Flag.Covalent */ | 2 /* BondType.Flag.MetallicCoordination */
             ])
         ])
     })

package/lib/commonjs/mol-plugin-state/transforms/representation.js

@@ -657,7 +657,7 @@ var ClippingStructureRepresentation3DFromScript = objects_1.PluginStateTransform
         }, function (e) { return "".concat(clipping_1.Clipping.Groups.toNames(e.groups).length, " group(s)"); }, {
             defaultValue: [{
                     script: (0, script_1.Script)('(sel.atom.all)', 'mol-script'),
-                    groups: 0 /* None */,
+                    groups: 0 /* Clipping.Groups.Flag.None */,
                 }]
         }),
     }); }
@@ -706,7 +706,7 @@ var ClippingStructureRepresentation3DFromBundle = objects_1.PluginStateTransform
         }, function (e) { return "".concat(clipping_1.Clipping.Groups.toNames(e.groups).length, " group(s)"); }, {
             defaultValue: [{
                     bundle: structure_1.StructureElement.Bundle.Empty,
-                    groups: 0 /* None */,
+                    groups: 0 /* Clipping.Groups.Flag.None */,
                 }],
             isHidden: true
         }),

package/lib/commonjs/mol-plugin-ui/controls/parameters.d.ts

@@ -94,7 +94,7 @@ export declare class LineGraphControl extends React.PureComponent<ParamProps<PD.
         isOverPoint: boolean;
         message: string;
     };
-    onHover: (point?: Vec2 | undefined) => void;
+    onHover: (point?: Vec2) => void;
     onDrag: (point: Vec2) => void;
     onChange: (value: PD.LineGraph['defaultValue']) => void;
     toggleExpanded: (e: React.MouseEvent<HTMLButtonElement>) => void;

package/lib/commonjs/mol-plugin-ui/controls.js

@@ -77,7 +77,7 @@ var TrajectoryViewportControls = /** @class */ (function (_super) {
     };
     TrajectoryViewportControls.prototype.render = function () {
         var isAnimating = this.plugin.behaviors.state.isAnimating.value;
-        if (!this.state.show || (isAnimating && !this.state.label))
+        if (!this.state.show || (isAnimating && !this.state.label) || !this.plugin.config.get(config_1.PluginConfig.Viewport.ShowTrajectoryControls))
             return null;
         return (0, jsx_runtime_1.jsxs)("div", tslib_1.__assign({ className: 'msp-traj-controls' }, { children: [!isAnimating && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.SkipPreviousSvg, title: 'First Model', onClick: this.reset, disabled: isAnimating }), !isAnimating && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.NavigateBeforeSvg, title: 'Previous Model', onClick: this.prev, disabled: isAnimating }), !isAnimating && (0, jsx_runtime_1.jsx)(common_1.IconButton, { svg: icons_1.NavigateNextSvg, title: 'Next Model', onClick: this.next, disabled: isAnimating }), !!this.state.label && (0, jsx_runtime_1.jsx)("span", { children: this.state.label })] }));
     };

package/lib/commonjs/mol-plugin-ui/sequence/polymer.js

@@ -97,7 +97,7 @@ function createResidueQuery(chainGroupId, operatorName, label_seq_id) {
                 structure_1.StructureProperties.unit.operator_name(ctx.element) === operatorName);
         },
         residueTest: function (ctx) {
-            if (ctx.element.unit.kind === 0 /* Atomic */) {
+            if (ctx.element.unit.kind === 0 /* Unit.Kind.Atomic */) {
                 return structure_1.StructureProperties.residue.label_seq_id(ctx.element) === label_seq_id;
             }
             else {

package/lib/commonjs/mol-plugin-ui/sequence/sequence.js

@@ -96,7 +96,7 @@ var Sequence = /** @class */ (function (_super) {
                 _this.lastMouseOverSeqIdx = seqIdx;
                 if (_this.mouseDownLoci !== undefined) {
                     var loci = _this.getLoci(seqIdx);
-                    _this.hover(loci, 0 /* None */, 0 /* None */, tslib_1.__assign(tslib_1.__assign({}, modifiers), { shift: true }));
+                    _this.hover(loci, 0 /* ButtonsType.Flag.None */, 0 /* ButtonsType.Flag.None */, tslib_1.__assign(tslib_1.__assign({}, modifiers), { shift: true }));
                 }
                 else {
                     _this.highlightQueue.next({ seqIdx: seqIdx, buttons: buttons, button: button, modifiers: modifiers });

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

@@ -296,6 +296,7 @@ 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/commonjs/mol-plugin-ui/structure/focus.js

@@ -54,7 +54,7 @@ function getFocusEntries(structure) {
             continue;
         l.unit = ug.units[0];
         l.element = ug.elements[0];
-        var isMultiChain = structure_1.Unit.Traits.is(l.unit.traits, 1 /* MultiChain */);
+        var isMultiChain = structure_1.Unit.Traits.is(l.unit.traits, 1 /* Unit.Trait.MultiChain */);
         var entityType = structure_1.StructureProperties.entity.type(l);
         var isNonPolymer = entityType === 'non-polymer';
         var isBranched = entityType === 'branched';

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

@@ -74,6 +74,7 @@ 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/commonjs/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/commonjs/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/commonjs/mol-repr/shape/representation.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -134,6 +134,7 @@ function ShapeRepresentation(getShape, geometryUtils, builder) {
                                 // console.log('update geometry')
                                 mol_util_1.ValueCell.updateIfChanged(_renderObject.values.drawCount, geometry_1.Geometry.getDrawCount(_shape.geometry));
                                 mol_util_1.ValueCell.updateIfChanged(_renderObject.values.uVertexCount, geometry_1.Geometry.getVertexCount(_shape.geometry));
+                                mol_util_1.ValueCell.updateIfChanged(_renderObject.values.uGroupCount, geometry_1.Geometry.getGroupCount(_shape.geometry));
                             }
                             if (updateState.updateTransform || updateState.createGeometry) {
                                 // console.log('updateBoundingSphere')

package/lib/commonjs/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/commonjs/mol-repr/structure/complex-visual.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -118,6 +118,7 @@ function ComplexVisual(builder, materialId) {
                 if (newGeometry) {
                     mol_util_1.ValueCell.updateIfChanged(renderObject.values.drawCount, geometry_1.Geometry.getDrawCount(newGeometry));
                     mol_util_1.ValueCell.updateIfChanged(renderObject.values.uVertexCount, geometry_1.Geometry.getVertexCount(newGeometry));
+                    mol_util_1.ValueCell.updateIfChanged(renderObject.values.uGroupCount, geometry_1.Geometry.getGroupCount(newGeometry));
                 }
                 else {
                     throw new Error('expected geometry to be given');

package/lib/commonjs/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/commonjs/mol-repr/structure/units-visual.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * 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>
  */
@@ -159,6 +159,7 @@ function UnitsVisual(builder, materialId) {
                 if (newGeometry) {
                     mol_util_1.ValueCell.updateIfChanged(renderObject.values.drawCount, geometry_1.Geometry.getDrawCount(newGeometry));
                     mol_util_1.ValueCell.updateIfChanged(renderObject.values.uVertexCount, geometry_1.Geometry.getVertexCount(newGeometry));
+                    mol_util_1.ValueCell.updateIfChanged(renderObject.values.uGroupCount, geometry_1.Geometry.getGroupCount(newGeometry));
                 }
                 else {
                     throw new Error('expected geometry to be given');

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

@@ -118,21 +118,21 @@ function getInterUnitBondCylinderBuilderProps(structure, theme, props) {
         style: function (edgeIndex) {
             var o = edges[edgeIndex].props.order;
             var f = mol_util_1.BitFlags.create(edges[edgeIndex].props.flag);
-            if (types_1.BondType.is(f, 2 /* MetallicCoordination */) || types_1.BondType.is(f, 4 /* HydrogenBond */)) {
+            if (types_1.BondType.is(f, 2 /* BondType.Flag.MetallicCoordination */) || types_1.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 && types_1.BondType.is(f, 16 /* Aromatic */)) {
-                return 7 /* Aromatic */;
+            else if (aromaticBonds && types_1.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/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js

@@ -70,21 +70,21 @@ function createInterUnitBondLines(ctx, structure, theme, props, lines) {
         style: function (edgeIndex) {
             var o = edges[edgeIndex].props.order;
             var f = mol_util_1.BitFlags.create(edges[edgeIndex].props.flag);
-            if (types_1.BondType.is(f, 2 /* MetallicCoordination */) || types_1.BondType.is(f, 4 /* HydrogenBond */)) {
+            if (types_1.BondType.is(f, 2 /* BondType.Flag.MetallicCoordination */) || types_1.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 && types_1.BondType.is(f, 16 /* Aromatic */)) {
-                return 7 /* Aromatic */;
+            else if (aromaticBonds && types_1.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/commonjs/mol-repr/structure/visual/bond-intra-unit-cylinder.js

@@ -34,7 +34,7 @@ function getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props) {
     var mbSymmetric = multipleBonds === 'symmetric';
     var include = types_1.BondType.fromNames(includeTypes);
     var exclude = types_1.BondType.fromNames(excludeTypes);
-    var ignoreComputedAromatic = (0, bond_1.ignoreBondType)(include, exclude, 32 /* Computed */);
+    var ignoreComputedAromatic = (0, bond_1.ignoreBondType)(include, exclude, 32 /* BondType.Flag.Computed */);
     var vRef = (0, linear_algebra_1.Vec3)(), delta = (0, linear_algebra_1.Vec3)();
     var pos = unit.conformation.invariantPosition;
     var stub;
@@ -118,35 +118,32 @@ 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) ? (0, array_1.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/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js

@@ -40,7 +40,7 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
     var mbSymmetric = multipleBonds === 'symmetric';
     var include = types_1.BondType.fromNames(includeTypes);
     var exclude = types_1.BondType.fromNames(excludeTypes);
-    var ignoreComputedAromatic = (0, bond_1.ignoreBondType)(include, exclude, 32 /* Computed */);
+    var ignoreComputedAromatic = (0, bond_1.ignoreBondType)(include, exclude, 32 /* BondType.Flag.Computed */);
     var vRef = (0, linear_algebra_1.Vec3)();
     var pos = unit.conformation.invariantPosition;
     var _a = unit.rings, elementRingIndices = _a.elementRingIndices, elementAromaticRingIndices = _a.elementAromaticRingIndices;
@@ -86,35 +86,32 @@ 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) ? (0, array_1.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/commonjs/mol-repr/structure/visual/carbohydrate-symbol-mesh.js

@@ -61,47 +61,47 @@ function createCarbohydrateSymbolMesh(ctx, structure, theme, props, mesh) {
         linear_algebra_1.Mat4.setTranslation(t, center);
         builderState.currentGroup = i * 2;
         switch (shapeType) {
-            case 0 /* FilledSphere */:
+            case 0 /* SaccharideShape.FilledSphere */:
                 (0, sphere_1.addSphere)(builderState, center, radius, detail);
                 break;
-            case 1 /* FilledCube */:
+            case 1 /* SaccharideShape.FilledCube */:
                 linear_algebra_1.Mat4.scaleUniformly(t, t, side);
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, box);
                 break;
-            case 2 /* CrossedCube */:
+            case 2 /* SaccharideShape.CrossedCube */:
                 linear_algebra_1.Mat4.scaleUniformly(t, t, side);
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, perforatedBox);
                 linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZ90X180);
                 builderState.currentGroup += 1;
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, perforatedBox);
                 break;
-            case 4 /* FilledCone */:
+            case 4 /* SaccharideShape.FilledCone */:
                 linear_algebra_1.Mat4.scaleUniformly(t, t, side * 1.2);
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, octagonalPyramid);
                 break;
-            case 5 /* DevidedCone */:
+            case 5 /* SaccharideShape.DevidedCone */:
                 linear_algebra_1.Mat4.scaleUniformly(t, t, side * 1.2);
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, perforatedOctagonalPyramid);
                 linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZ90);
                 builderState.currentGroup += 1;
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, perforatedOctagonalPyramid);
                 break;
-            case 6 /* FlatBox */:
+            case 6 /* SaccharideShape.FlatBox */:
                 linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90);
                 linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side, side, side / 2));
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, box);
                 break;
-            case 7 /* FilledStar */:
+            case 7 /* SaccharideShape.FilledStar */:
                 linear_algebra_1.Mat4.scaleUniformly(t, t, side);
                 linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90);
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, star);
                 break;
-            case 8 /* FilledDiamond */:
+            case 8 /* SaccharideShape.FilledDiamond */:
                 linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90);
                 linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4));
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, octahedron);
                 break;
-            case 3 /* DividedDiamond */:
+            case 3 /* SaccharideShape.DividedDiamond */:
                 linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90);
                 linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side * 1.4, side * 1.4, side * 1.4));
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, perforatedOctahedron);
@@ -109,33 +109,33 @@ function createCarbohydrateSymbolMesh(ctx, structure, theme, props, mesh) {
                 builderState.currentGroup += 1;
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, perforatedOctahedron);
                 break;
-            case 9 /* FlatDiamond */:
+            case 9 /* SaccharideShape.FlatDiamond */:
                 linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90);
                 linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side, side / 2, side / 2));
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, diamondPrism);
                 break;
-            case 12 /* DiamondPrism */:
+            case 12 /* SaccharideShape.DiamondPrism */:
                 linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90);
                 linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side, side, side / 2));
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, diamondPrism);
                 break;
-            case 13 /* PentagonalPrism */:
-            case 11 /* Pentagon */:
+            case 13 /* SaccharideShape.PentagonalPrism */:
+            case 11 /* SaccharideShape.Pentagon */:
                 linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90);
                 linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side, side, side / 2));
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, pentagonalPrism);
                 break;
-            case 14 /* HexagonalPrism */:
+            case 14 /* SaccharideShape.HexagonalPrism */:
                 linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90);
                 linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side, side, side / 2));
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, hexagonalPrism);
                 break;
-            case 15 /* HeptagonalPrism */:
+            case 15 /* SaccharideShape.HeptagonalPrism */:
                 linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZY90);
                 linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side, side, side / 2));
                 mesh_builder_1.MeshBuilder.addPrimitive(builderState, t, heptagonalPrism);
                 break;
-            case 10 /* FlatHexagon */:
+            case 10 /* SaccharideShape.FlatHexagon */:
             default:
                 linear_algebra_1.Mat4.mul(t, t, linear_algebra_1.Mat4.rotZYZ90);
                 linear_algebra_1.Mat4.scale(t, t, linear_algebra_1.Vec3.set(sVec, side / 1.5, side, side / 2));

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

@@ -54,7 +54,7 @@ function createCarbohydrateTerminalLinkCylinderMesh(ctx, structure, theme, props
             var l = terminalLinks[edgeIndex];
             var eI = l.elementUnit.elements[l.elementIndex];
             var beI = (0, common_1.getElementIdx)(l.elementUnit.model.atomicHierarchy.atoms.type_symbol.value(eI));
-            return common_1.MetalsSet.has(beI) ? 1 /* Dashed */ : 0 /* Solid */;
+            return common_1.MetalsSet.has(beI) ? 1 /* LinkStyle.Dashed */ : 0 /* LinkStyle.Solid */;
         }
     };
     var _b = (0, link_1.createLinkCylinderMesh)(ctx, builderProps, props, mesh), m = _b.mesh, boundingSphere = _b.boundingSphere;

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

@@ -22,6 +22,7 @@ var color_smoothing_1 = require("../../../mol-geo/geometry/mesh/color-smoothing"
 var color_smoothing_2 = require("../../../mol-geo/geometry/texture-mesh/color-smoothing");
 var base_1 = require("../../../mol-geo/geometry/base");
 var linear_algebra_1 = require("../../../mol-math/linear-algebra");
+var debug_1 = require("../../../mol-util/debug");
 var SharedParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, gaussian_1.GaussianDensityParams), base_1.ColorSmoothingParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), tryUseGpu: param_definition_1.ParamDefinition.Boolean(true), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
 exports.GaussianSurfaceMeshParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsTextureMeshParams), SharedParams);
 exports.StructureGaussianSurfaceMeshParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexMeshParams), complex_visual_1.ComplexTextureMeshParams), SharedParams);
@@ -217,6 +218,8 @@ 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 (debug_1.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
@@ -232,6 +235,8 @@ function createGaussianSurfaceTextureMesh(ctx, unit, structure, theme, props, te
                     axisOrder = linear_algebra_1.Vec3.create(0, 1, 2);
                     buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
                     gv = (0, isosurface_1.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 (debug_1.isTimingMode)
+                        ctx.webgl.timer.markEnd('createGaussianSurfaceTextureMesh');
                     boundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), unit.boundary.sphere, densityTextureData.maxRadius);
                     surface = texture_mesh_1.TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
                     surface.meta.resolution = densityTextureData.resolution;
@@ -301,6 +306,8 @@ 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 (debug_1.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
@@ -316,6 +323,8 @@ function createStructureGaussianSurfaceTextureMesh(ctx, structure, theme, props,
                     axisOrder = linear_algebra_1.Vec3.create(0, 1, 2);
                     buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
                     gv = (0, isosurface_1.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 (debug_1.isTimingMode)
+                        ctx.webgl.timer.markEnd('createStructureGaussianSurfaceTextureMesh');
                     boundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), structure.boundary.sphere, densityTextureData.maxRadius);
                     surface = texture_mesh_1.TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
                     surface.meta.resolution = densityTextureData.resolution;