molstar 3.8.2 → 3.9.0

package/lib/mol-plugin/behavior/dynamic/camera.js

@@ -18,13 +18,13 @@ var M = ModifiersKeys;
 var Trigger = Binding.Trigger;
 var DefaultFocusLociBindings = {
     clickCenterFocus: Binding([
-        Trigger(1 /* Primary */, M.create()),
-        Trigger(2 /* Secondary */, M.create()),
-        Trigger(1 /* Primary */, M.create({ control: true }))
+        Trigger(1 /* B.Flag.Primary */, M.create()),
+        Trigger(2 /* B.Flag.Secondary */, M.create()),
+        Trigger(1 /* B.Flag.Primary */, M.create({ control: true }))
     ], 'Camera center and focus', 'Click element using ${triggers}'),
     clickCenterFocusSelectMode: Binding([
-        Trigger(2 /* Secondary */, M.create()),
-        Trigger(1 /* Primary */, M.create({ control: true }))
+        Trigger(2 /* B.Flag.Secondary */, M.create()),
+        Trigger(1 /* B.Flag.Primary */, M.create({ control: true }))
     ], 'Camera center and focus', 'Click element using ${triggers}'),
 };
 var FocusLociParams = {
@@ -75,22 +75,22 @@ export var CameraAxisHelper = PluginBehavior.create({
         }
         class_2.prototype.register = function () {
             var _this = this;
-            var lastPlane = 0 /* None */;
+            var lastPlane = 0 /* CameraHelperAxis.None */;
             var state = 0;
             this.subscribeObservable(this.ctx.behaviors.interaction.click, function (_a) {
                 var current = _a.current;
                 if (!_this.ctx.canvas3d || !isCameraAxesLoci(current.loci))
                     return;
                 var axis = current.loci.elements[0].groupId;
-                if (axis === 0 /* None */) {
-                    lastPlane = 0 /* None */;
+                if (axis === 0 /* CameraHelperAxis.None */) {
+                    lastPlane = 0 /* CameraHelperAxis.None */;
                     state = 0;
                     return;
                 }
                 var camera = _this.ctx.canvas3d.camera;
                 var dir, up;
-                if (axis >= 1 /* X */ && axis <= 3 /* Z */) {
-                    lastPlane = 0 /* None */;
+                if (axis >= 1 /* CameraHelperAxis.X */ && axis <= 3 /* CameraHelperAxis.Z */) {
+                    lastPlane = 0 /* CameraHelperAxis.None */;
                     state = 0;
                     var d = Vec3.sub(Vec3(), camera.target, camera.position);
                     var c = Vec3.cross(Vec3(), d, camera.up);
@@ -108,11 +108,11 @@ export var CameraAxisHelper = PluginBehavior.create({
                         lastPlane = axis;
                         state = 0;
                     }
-                    if (axis === 4 /* XY */) {
+                    if (axis === 4 /* CameraHelperAxis.XY */) {
                         up = state ? Vec3.unitX : Vec3.unitY;
                         dir = Vec3.negUnitZ;
                     }
-                    else if (axis === 5 /* XZ */) {
+                    else if (axis === 5 /* CameraHelperAxis.XZ */) {
                         up = state ? Vec3.unitX : Vec3.unitZ;
                         dir = Vec3.negUnitY;
                     }

package/lib/mol-plugin/behavior/dynamic/representation.js

@@ -22,8 +22,8 @@ var M = ModifiersKeys;
 var Trigger = Binding.Trigger;
 //
 var DefaultHighlightLociBindings = {
-    hoverHighlightOnly: Binding([Trigger(0 /* None */)], 'Highlight', 'Hover element using ${triggers}'),
-    hoverHighlightOnlyExtend: Binding([Trigger(0 /* None */, M.create({ shift: true }))], 'Extend highlight', 'From selected to hovered element along polymer using ${triggers}'),
+    hoverHighlightOnly: Binding([Trigger(0 /* B.Flag.None */)], 'Highlight', 'Hover element using ${triggers}'),
+    hoverHighlightOnlyExtend: Binding([Trigger(0 /* B.Flag.None */, M.create({ shift: true }))], 'Extend highlight', 'From selected to hovered element along polymer using ${triggers}'),
 };
 var HighlightLociParams = {
     bindings: PD.Value(DefaultHighlightLociBindings, { isHidden: true }),
@@ -89,11 +89,11 @@ export var HighlightLoci = PluginBehavior.create({
 //
 var DefaultSelectLociBindings = {
     clickSelect: Binding.Empty,
-    clickToggleExtend: Binding([Trigger(1 /* Primary */, M.create({ shift: true }))], 'Toggle extended selection', '${triggers} to extend selection along polymer'),
+    clickToggleExtend: Binding([Trigger(1 /* B.Flag.Primary */, M.create({ shift: true }))], 'Toggle extended selection', '${triggers} to extend selection along polymer'),
     clickSelectOnly: Binding.Empty,
-    clickToggle: Binding([Trigger(1 /* Primary */, M.create())], 'Toggle selection', '${triggers} on element'),
+    clickToggle: Binding([Trigger(1 /* B.Flag.Primary */, M.create())], 'Toggle selection', '${triggers} on element'),
     clickDeselect: Binding.Empty,
-    clickDeselectAllOnEmpty: Binding([Trigger(1 /* Primary */, M.create())], 'Deselect all', 'Click on nothing using ${triggers}'),
+    clickDeselectAllOnEmpty: Binding([Trigger(1 /* B.Flag.Primary */, M.create())], 'Deselect all', 'Click on nothing using ${triggers}'),
 };
 var SelectLociParams = {
     bindings: PD.Value(DefaultSelectLociBindings, { isHidden: true }),
@@ -240,10 +240,10 @@ export var DefaultLociLabelProvider = PluginBehavior.create({
 //
 var DefaultFocusLociBindings = {
     clickFocus: Binding([
-        Trigger(1 /* Primary */, M.create()),
+        Trigger(1 /* B.Flag.Primary */, M.create()),
     ], 'Representation Focus', 'Click element using ${triggers}'),
     clickFocusAdd: Binding([
-        Trigger(1 /* Primary */, M.create({ shift: true })),
+        Trigger(1 /* B.Flag.Primary */, M.create({ shift: true })),
     ], 'Representation Focus Add', 'Click element using ${triggers}'),
     clickFocusSelectMode: Binding([
     // default is empty

package/lib/mol-plugin/context.d.ts

@@ -45,8 +45,8 @@ import { ViewportScreenshotHelper } from './util/viewport-screenshot';
 export declare class PluginContext {
     spec: PluginSpec;
     runTask: <T>(task: Task<T>, params?: {
-        useOverlay?: boolean | undefined;
-    } | undefined) => Promise<T>;
+        useOverlay?: boolean;
+    }) => Promise<T>;
     resolveTask: <T>(object: T | Task<T> | undefined) => T | Promise<T> | undefined;
     protected subs: Subscription[];
     private disposed;

package/lib/mol-plugin/state.d.ts

@@ -61,20 +61,7 @@ declare class PluginState extends PluginComponent {
             durationInMs: number;
         }>, "animate"> | PD.NamedParams<PD.Normalize<unknown>, "instant">>;
     }>>>;
-    setSnapshotParams: (params?: Partial<PD.Values<{
-        durationInMs: PD.Numeric;
-        data: PD.BooleanParam;
-        behavior: PD.BooleanParam;
-        componentManager: PD.BooleanParam;
-        animation: PD.BooleanParam;
-        startAnimation: PD.BooleanParam;
-        canvas3d: PD.BooleanParam;
-        interactivity: PD.BooleanParam;
-        camera: PD.BooleanParam;
-        cameraTransition: PD.Mapped<PD.NamedParams<PD.Normalize<{
-            durationInMs: number;
-        }>, "animate"> | PD.NamedParams<PD.Normalize<unknown>, "instant">>;
-    }>> | undefined) => void;
+    setSnapshotParams: (params?: PluginState.SnapshotParams) => void;
     getSnapshot(params?: PluginState.SnapshotParams): PluginState.Snapshot;
     setSnapshot(snapshot: PluginState.Snapshot): Promise<void>;
     updateTransform(state: State, a: StateTransform.Ref, params: any, canUndo?: string | boolean): Promise<void>;

package/lib/mol-plugin/version.js

@@ -1,2 +1,2 @@
-export var PLUGIN_VERSION = '3.8.2';
-export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1653233699685);
+export var PLUGIN_VERSION = '3.9.0';
+export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1653936303170);

package/lib/mol-plugin-state/formats/volume.d.ts

@@ -1,8 +1,9 @@
 /**
- * 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>
  */
 import { PluginContext } from '../../mol-plugin/context';
 import { StateObjectSelector } from '../../mol-state';
@@ -20,7 +21,7 @@ export declare const Ccp4Provider: {
     description: string;
     category: string;
     binaryExtensions: string[];
-    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params | undefined) => Promise<{
+    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params) => Promise<{
         format: StateObjectSelector<PluginStateObject.Format.Ccp4, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Data.Binary, PluginStateObject.Format.Ccp4, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
         volume: StateObjectSelector<PluginStateObject.Volume.Data, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Format.Ccp4, PluginStateObject.Volume.Data, import("../../mol-util/param-definition").ParamDefinition.Normalize<{
             voxelSize: import("../../mol-math/linear-algebra/3d/vec3").Vec3;
@@ -35,7 +36,7 @@ export declare const Dsn6Provider: {
     description: string;
     category: string;
     binaryExtensions: string[];
-    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params | undefined) => Promise<{
+    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params) => Promise<{
         format: StateObjectSelector<PluginStateObject.Format.Dsn6, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Data.Binary, PluginStateObject.Format.Dsn6, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
         volume: StateObjectSelector<PluginStateObject.Volume.Data, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Format.Dsn6, PluginStateObject.Volume.Data, import("../../mol-util/param-definition").ParamDefinition.Normalize<{
             voxelSize: import("../../mol-math/linear-algebra/3d/vec3").Vec3;
@@ -50,7 +51,7 @@ export declare const DxProvider: {
     category: string;
     stringExtensions: string[];
     binaryExtensions: string[];
-    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params | undefined) => Promise<{
+    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params) => Promise<{
         volume: StateObjectSelector<PluginStateObject.Volume.Data, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Format.Dx, PluginStateObject.Volume.Data, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
     }>;
     visuals: typeof defaultVisuals;
@@ -60,7 +61,7 @@ export declare const CubeProvider: {
     description: string;
     category: string;
     stringExtensions: string[];
-    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params | undefined) => Promise<{
+    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params) => Promise<{
         format: StateObjectSelector<PluginStateObject.Format.Cube, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Data.String, PluginStateObject.Format.Cube, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
         volume: StateObjectSelector<PluginStateObject.Volume.Data, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Format.Cube, PluginStateObject.Volume.Data, import("../../mol-util/param-definition").ParamDefinition.Normalize<{
             dataIndex: number;
@@ -102,7 +103,7 @@ export declare const DscifProvider: {
     stringExtensions: string[];
     binaryExtensions: string[];
     isApplicable: (info: import("../../mol-util/file-info").FileInfo, data: string | Uint8Array) => boolean;
-    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: DsCifParams | undefined) => Promise<{
+    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: DsCifParams) => Promise<{
         volumes: StateObjectSelector<PluginStateObject.Volume.Data, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>[];
     }>;
     visuals: (plugin: PluginContext, data: {
@@ -114,7 +115,7 @@ export declare const BuiltInVolumeFormats: readonly [readonly ["ccp4", {
     description: string;
     category: string;
     binaryExtensions: string[];
-    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params | undefined) => Promise<{
+    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params) => Promise<{
         format: StateObjectSelector<PluginStateObject.Format.Ccp4, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Data.Binary, PluginStateObject.Format.Ccp4, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
         volume: StateObjectSelector<PluginStateObject.Volume.Data, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Format.Ccp4, PluginStateObject.Volume.Data, import("../../mol-util/param-definition").ParamDefinition.Normalize<{
             voxelSize: import("../../mol-math/linear-algebra/3d/vec3").Vec3;
@@ -128,7 +129,7 @@ export declare const BuiltInVolumeFormats: readonly [readonly ["ccp4", {
     description: string;
     category: string;
     binaryExtensions: string[];
-    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params | undefined) => Promise<{
+    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params) => Promise<{
         format: StateObjectSelector<PluginStateObject.Format.Dsn6, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Data.Binary, PluginStateObject.Format.Dsn6, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
         volume: StateObjectSelector<PluginStateObject.Volume.Data, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Format.Dsn6, PluginStateObject.Volume.Data, import("../../mol-util/param-definition").ParamDefinition.Normalize<{
             voxelSize: import("../../mol-math/linear-algebra/3d/vec3").Vec3;
@@ -141,7 +142,7 @@ export declare const BuiltInVolumeFormats: readonly [readonly ["ccp4", {
     description: string;
     category: string;
     stringExtensions: string[];
-    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params | undefined) => Promise<{
+    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params) => Promise<{
         format: StateObjectSelector<PluginStateObject.Format.Cube, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Data.String, PluginStateObject.Format.Cube, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
         volume: StateObjectSelector<PluginStateObject.Volume.Data, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Format.Cube, PluginStateObject.Volume.Data, import("../../mol-util/param-definition").ParamDefinition.Normalize<{
             dataIndex: number;
@@ -178,7 +179,7 @@ export declare const BuiltInVolumeFormats: readonly [readonly ["ccp4", {
     category: string;
     stringExtensions: string[];
     binaryExtensions: string[];
-    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params | undefined) => Promise<{
+    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: Params) => Promise<{
         volume: StateObjectSelector<PluginStateObject.Volume.Data, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Format.Dx, PluginStateObject.Volume.Data, import("../../mol-util/param-definition").ParamDefinition.Normalize<{}>>>;
     }>;
     visuals: typeof defaultVisuals;
@@ -189,7 +190,7 @@ export declare const BuiltInVolumeFormats: readonly [readonly ["ccp4", {
     stringExtensions: string[];
     binaryExtensions: string[];
     isApplicable: (info: import("../../mol-util/file-info").FileInfo, data: string | Uint8Array) => boolean;
-    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: DsCifParams | undefined) => Promise<{
+    parse: (plugin: PluginContext, data: import("../../mol-state").StateObjectRef<PluginStateObject.Data.String | PluginStateObject.Data.Binary>, params?: DsCifParams) => Promise<{
         volumes: StateObjectSelector<PluginStateObject.Volume.Data, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>[];
     }>;
     visuals: (plugin: PluginContext, data: {

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

@@ -1,8 +1,9 @@
 /**
- * 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>
  */
 import { __awaiter, __generator, __spreadArray } from "tslib";
 import { StateTransforms } from '../transforms';
@@ -243,35 +244,41 @@ export var DscifProvider = DataFormatProvider({
     },
     parse: function (plugin, data, params) { return __awaiter(void 0, void 0, void 0, function () {
         var cifCell, b, blocks, volumes, i, _i, blocks_1, block, entryId, _a, volumes_1, v;
-        return __generator(this, function (_b) {
-            switch (_b.label) {
+        var _b;
+        return __generator(this, function (_c) {
+            switch (_c.label) {
                 case 0: return [4 /*yield*/, plugin.build().to(data).apply(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(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(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/mol-plugin-state/helpers/structure-selection-query.js

@@ -221,7 +221,7 @@ var helix = StructureSelectionQuery('Helix', MS.struct.modifier.union([
         'entity-test': _proteinEntityTest,
         'residue-test': MS.core.flags.hasAny([
             MS.ammp('secondaryStructureFlags'),
-            MS.core.type.bitflags([2 /* Helix */])
+            MS.core.type.bitflags([2 /* SecondaryStructureType.Flag.Helix */])
         ])
     })
 ]), {
@@ -235,7 +235,7 @@ var beta = StructureSelectionQuery('Beta Strand/Sheet', MS.struct.modifier.union
         'entity-test': _proteinEntityTest,
         'residue-test': MS.core.flags.hasAny([
             MS.ammp('secondaryStructureFlags'),
-            MS.core.type.bitflags([4 /* Beta */])
+            MS.core.type.bitflags([4 /* SecondaryStructureType.Flag.Beta */])
         ])
     })
 ]), {
@@ -338,7 +338,7 @@ var ligandPlusConnected = StructureSelectionQuery('Ligand with Connected', MS.st
                 'bond-test': MS.core.flags.hasAny([
                     MS.struct.bondProperty.flags(),
                     MS.core.type.bitflags([
-                        1 /* Covalent */ | 2 /* MetallicCoordination */
+                        1 /* BondType.Flag.Covalent */ | 2 /* BondType.Flag.MetallicCoordination */
                     ])
                 ])
             })
@@ -382,7 +382,7 @@ var disulfideBridges = StructureSelectionQuery('Disulfide Bridges', MS.struct.mo
                     MS.struct.generator.bondedAtomicPairs({
                         0: MS.core.flags.hasAny([
                             MS.struct.bondProperty.flags(),
-                            MS.core.type.bitflags([8 /* Disulfide */])
+                            MS.core.type.bitflags([8 /* BondType.Flag.Disulfide */])
                         ])
                     })
                 ])
@@ -500,7 +500,7 @@ var covalentlyOrMetallicBonded = StructureSelectionQuery('Residues with Cov. or
         'bond-test': MS.core.flags.hasAny([
             MS.struct.bondProperty.flags(),
             MS.core.type.bitflags([
-                1 /* Covalent */ | 2 /* MetallicCoordination */
+                1 /* BondType.Flag.Covalent */ | 2 /* BondType.Flag.MetallicCoordination */
             ])
         ])
     })

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

@@ -657,7 +657,7 @@ var ClippingStructureRepresentation3DFromScript = PluginStateTransform.BuiltIn({
         }, function (e) { return "".concat(Clipping.Groups.toNames(e.groups).length, " group(s)"); }, {
             defaultValue: [{
                     script: Script('(sel.atom.all)', 'mol-script'),
-                    groups: 0 /* None */,
+                    groups: 0 /* Clipping.Groups.Flag.None */,
                 }]
         }),
     }); }
@@ -705,7 +705,7 @@ var ClippingStructureRepresentation3DFromBundle = PluginStateTransform.BuiltIn({
         }, function (e) { return "".concat(Clipping.Groups.toNames(e.groups).length, " group(s)"); }, {
             defaultValue: [{
                     bundle: StructureElement.Bundle.Empty,
-                    groups: 0 /* None */,
+                    groups: 0 /* Clipping.Groups.Flag.None */,
                 }],
             isHidden: true
         }),

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

@@ -94,7 +94,7 @@ function createResidueQuery(chainGroupId, operatorName, label_seq_id) {
                 SP.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 SP.residue.label_seq_id(ctx.element) === label_seq_id;
             }
             else {

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

@@ -93,7 +93,7 @@ var Sequence = /** @class */ (function (_super) {
                 _this.lastMouseOverSeqIdx = seqIdx;
                 if (_this.mouseDownLoci !== undefined) {
                     var loci = _this.getLoci(seqIdx);
-                    _this.hover(loci, 0 /* None */, 0 /* None */, __assign(__assign({}, modifiers), { shift: true }));
+                    _this.hover(loci, 0 /* ButtonsType.Flag.None */, 0 /* ButtonsType.Flag.None */, __assign(__assign({}, modifiers), { shift: true }));
                 }
                 else {
                     _this.highlightQueue.next({ seqIdx: seqIdx, buttons: buttons, button: button, modifiers: modifiers });

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.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/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 +115,35 @@ 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 */;
+                        return 8 /* LinkStyle.MirroredAromatic */;
                     }
                     else if (arCount === 1 || (deloTriplets === null || deloTriplets === void 0 ? void 0 : deloTriplets.getThirdElement(aI, bI))) {
-                        return 7 /* Aromatic */;
+                        return 7 /* LinkStyle.Aromatic */;
                     }
                     else {
                         // case for bonds between two aromatic rings
                     }
                 }
             }
-            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 +83,35 @@ 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 */;
+                        return 8 /* LinkStyle.MirroredAromatic */;
                     }
                     else if (arCount === 1 || (deloTriplets === null || deloTriplets === void 0 ? void 0 : deloTriplets.getThirdElement(aI, bI))) {
-                        return 7 /* Aromatic */;
+                        return 7 /* LinkStyle.Aromatic */;
                     }
                     else {
                         // case for bonds between two aromatic rings
                     }
                 }
             }
-            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]];