molstar 3.8.2 → 3.9.0

package/lib/commonjs/mol-model-props/computed/secondary-structure/dssp.js

@@ -133,71 +133,71 @@ function mapToKind(assignment) {
 }
 /** Original priority: H,B,E,G,I,T,S */
 function getOriginalResidueFlag(f) {
-    if (common_1.DSSPType.is(f, 1 /* H */))
+    if (common_1.DSSPType.is(f, 1 /* DSSPType.Flag.H */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.H;
-    if (common_1.DSSPType.is(f, 4 /* E */))
+    if (common_1.DSSPType.is(f, 4 /* DSSPType.Flag.E */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.E;
-    if (common_1.DSSPType.is(f, 2 /* B */))
+    if (common_1.DSSPType.is(f, 2 /* DSSPType.Flag.B */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.B;
-    if (common_1.DSSPType.is(f, 8 /* G */))
+    if (common_1.DSSPType.is(f, 8 /* DSSPType.Flag.G */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.G;
-    if (common_1.DSSPType.is(f, 16 /* I */))
+    if (common_1.DSSPType.is(f, 16 /* DSSPType.Flag.I */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.I;
-    if (common_1.DSSPType.is(f, 64 /* T */))
+    if (common_1.DSSPType.is(f, 64 /* DSSPType.Flag.T */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.T;
-    if (common_1.DSSPType.is(f, 32 /* S */))
+    if (common_1.DSSPType.is(f, 32 /* DSSPType.Flag.S */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.S;
-    return 0 /* None */;
+    return 0 /* SecondaryStructureType.Flag.None */;
 }
 function getOriginalFlagName(f) {
-    if (common_1.DSSPType.is(f, 1 /* H */))
+    if (common_1.DSSPType.is(f, 1 /* DSSPType.Flag.H */))
         return 'H';
-    if (common_1.DSSPType.is(f, 4 /* E */))
+    if (common_1.DSSPType.is(f, 4 /* DSSPType.Flag.E */))
         return 'E';
-    if (common_1.DSSPType.is(f, 2 /* B */))
+    if (common_1.DSSPType.is(f, 2 /* DSSPType.Flag.B */))
         return 'B';
-    if (common_1.DSSPType.is(f, 8 /* G */))
+    if (common_1.DSSPType.is(f, 8 /* DSSPType.Flag.G */))
         return 'G';
-    if (common_1.DSSPType.is(f, 16 /* I */))
+    if (common_1.DSSPType.is(f, 16 /* DSSPType.Flag.I */))
         return 'I';
-    if (common_1.DSSPType.is(f, 64 /* T */))
+    if (common_1.DSSPType.is(f, 64 /* DSSPType.Flag.T */))
         return 'T';
-    if (common_1.DSSPType.is(f, 32 /* S */))
+    if (common_1.DSSPType.is(f, 32 /* DSSPType.Flag.S */))
         return 'S';
     return '-';
 }
 /** Version 2.1.0 priority: I,H,B,E,G,T,S */
 function getUpdatedResidueFlag(f) {
-    if (common_1.DSSPType.is(f, 16 /* I */))
+    if (common_1.DSSPType.is(f, 16 /* DSSPType.Flag.I */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.I;
-    if (common_1.DSSPType.is(f, 1 /* H */))
+    if (common_1.DSSPType.is(f, 1 /* DSSPType.Flag.H */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.H;
-    if (common_1.DSSPType.is(f, 4 /* E */))
+    if (common_1.DSSPType.is(f, 4 /* DSSPType.Flag.E */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.E;
-    if (common_1.DSSPType.is(f, 2 /* B */))
+    if (common_1.DSSPType.is(f, 2 /* DSSPType.Flag.B */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.B;
-    if (common_1.DSSPType.is(f, 8 /* G */))
+    if (common_1.DSSPType.is(f, 8 /* DSSPType.Flag.G */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.G;
-    if (common_1.DSSPType.is(f, 64 /* T */))
+    if (common_1.DSSPType.is(f, 64 /* DSSPType.Flag.T */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.T;
-    if (common_1.DSSPType.is(f, 32 /* S */))
+    if (common_1.DSSPType.is(f, 32 /* DSSPType.Flag.S */))
         return types_1.SecondaryStructureType.SecondaryStructureDssp.S;
-    return 0 /* None */;
+    return 0 /* SecondaryStructureType.Flag.None */;
 }
 function getUpdatedFlagName(f) {
-    if (common_1.DSSPType.is(f, 16 /* I */))
+    if (common_1.DSSPType.is(f, 16 /* DSSPType.Flag.I */))
         return 'I';
-    if (common_1.DSSPType.is(f, 1 /* H */))
+    if (common_1.DSSPType.is(f, 1 /* DSSPType.Flag.H */))
         return 'H';
-    if (common_1.DSSPType.is(f, 4 /* E */))
+    if (common_1.DSSPType.is(f, 4 /* DSSPType.Flag.E */))
         return 'E';
-    if (common_1.DSSPType.is(f, 2 /* B */))
+    if (common_1.DSSPType.is(f, 2 /* DSSPType.Flag.B */))
         return 'B';
-    if (common_1.DSSPType.is(f, 8 /* G */))
+    if (common_1.DSSPType.is(f, 8 /* DSSPType.Flag.G */))
         return 'G';
-    if (common_1.DSSPType.is(f, 64 /* T */))
+    if (common_1.DSSPType.is(f, 64 /* DSSPType.Flag.T */))
         return 'T';
-    if (common_1.DSSPType.is(f, 32 /* S */))
+    if (common_1.DSSPType.is(f, 32 /* DSSPType.Flag.S */))
         return 'S';
     return '-';
 }

package/lib/commonjs/mol-model-props/computed/themes/accessible-surface-area.js

@@ -69,7 +69,7 @@ exports.AccessibleSurfaceAreaColorTheme = AccessibleSurfaceAreaColorTheme;
 exports.AccessibleSurfaceAreaColorThemeProvider = {
     name: 'accessible-surface-area',
     label: 'Accessible Surface Area',
-    category: "Residue Property" /* Residue */,
+    category: "Residue Property" /* ColorTheme.Category.Residue */,
     factory: AccessibleSurfaceAreaColorTheme,
     getParams: getAccessibleSurfaceAreaColorThemeParams,
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.AccessibleSurfaceAreaColorThemeParams),

package/lib/commonjs/mol-model-props/computed/themes/interaction-type.js

@@ -36,23 +36,23 @@ var InteractionTypeColorTable = [
 ];
 function typeColor(type) {
     switch (type) {
-        case 4 /* HydrogenBond */:
+        case 4 /* InteractionType.HydrogenBond */:
             return InteractionTypeColors.HydrogenBond;
-        case 6 /* Hydrophobic */:
+        case 6 /* InteractionType.Hydrophobic */:
             return InteractionTypeColors.Hydrophobic;
-        case 5 /* HalogenBond */:
+        case 5 /* InteractionType.HalogenBond */:
             return InteractionTypeColors.HalogenBond;
-        case 1 /* Ionic */:
+        case 1 /* InteractionType.Ionic */:
             return InteractionTypeColors.Ionic;
-        case 7 /* MetalCoordination */:
+        case 7 /* InteractionType.MetalCoordination */:
             return InteractionTypeColors.MetalCoordination;
-        case 2 /* CationPi */:
+        case 2 /* InteractionType.CationPi */:
             return InteractionTypeColors.CationPi;
-        case 3 /* PiStacking */:
+        case 3 /* InteractionType.PiStacking */:
             return InteractionTypeColors.PiStacking;
-        case 8 /* WeakHydrogenBond */:
+        case 8 /* InteractionType.WeakHydrogenBond */:
             return InteractionTypeColors.WeakHydrogenBond;
-        case 0 /* Unknown */:
+        case 0 /* InteractionType.Unknown */:
             return DefaultColor;
     }
 }
@@ -100,7 +100,7 @@ exports.InteractionTypeColorTheme = InteractionTypeColorTheme;
 exports.InteractionTypeColorThemeProvider = {
     name: 'interaction-type',
     label: 'Interaction Type',
-    category: "Miscellaneous" /* Misc */,
+    category: "Miscellaneous" /* ColorTheme.Category.Misc */,
     factory: InteractionTypeColorTheme,
     getParams: getInteractionTypeColorThemeParams,
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.InteractionTypeColorThemeParams),

package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/color.js

@@ -55,7 +55,7 @@ exports.CrossLinkColorTheme = CrossLinkColorTheme;
 exports.CrossLinkColorThemeProvider = {
     name: 'cross-link',
     label: 'Cross Link',
-    category: "Miscellaneous" /* Misc */,
+    category: "Miscellaneous" /* ColorTheme.Category.Misc */,
     factory: CrossLinkColorTheme,
     getParams: getCrossLinkColorThemeParams,
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.CrossLinkColorThemeParams),

package/lib/commonjs/mol-model-props/integrative/cross-link-restraint/format.js

@@ -62,9 +62,9 @@ var ModelCrossLinkRestraint;
         }
         function getMapByKind(kind) {
             switch (kind) {
-                case 0 /* Atomic */: return atomicElementMap;
-                case 1 /* Spheres */: return sphereElementMap;
-                case 2 /* Gaussians */: return gaussianElementMap;
+                case 0 /* Unit.Kind.Atomic */: return atomicElementMap;
+                case 1 /* Unit.Kind.Spheres */: return sphereElementMap;
+                case 2 /* Unit.Kind.Gaussians */: return gaussianElementMap;
             }
         }
         /** map from atomic element to cross link indices */

package/lib/commonjs/mol-model-props/sequence/sifts-mapping.js

@@ -72,7 +72,7 @@ var SIFTSMapping;
         var residue = new Array(count);
         for (var i = 0; i < count; i++) {
             var row = atomSourceIndex.value(residueOffsets[i]);
-            if (db_name.valueKind(row) !== 0 /* Present */) {
+            if (db_name.valueKind(row) !== 0 /* Column.ValueKind.Present */) {
                 dbName[i] = '';
                 accession[i] = '';
                 num[i] = '';

package/lib/commonjs/mol-model-props/sequence/themes/sifts-mapping.js

@@ -77,7 +77,7 @@ exports.SIFTSMappingColorTheme = SIFTSMappingColorTheme;
 exports.SIFTSMappingColorThemeProvider = {
     name: 'sifts-mapping',
     label: 'SIFTS Mapping',
-    category: "Residue Property" /* Residue */,
+    category: "Residue Property" /* ColorTheme.Category.Residue */,
     factory: SIFTSMappingColorTheme,
     getParams: getSIFTSMappingColorThemeParams,
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.SIFTSMappingColorThemeParams),

package/lib/commonjs/mol-plugin/animation-loop.d.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 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>
  */
 import { PluginContext } from './context';
 import { PluginAnimationManager } from '../mol-plugin-state/manager/animation';

package/lib/commonjs/mol-plugin/animation-loop.js

@@ -1,13 +1,16 @@
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.PluginAnimationLoop = void 0;
 var tslib_1 = require("tslib");
 var now_1 = require("../mol-util/now");
+var debug_1 = require("../mol-util/debug");
+var timer_1 = require("../mol-gl/webgl/timer");
 var PluginAnimationLoop = /** @class */ (function () {
     function PluginAnimationLoop(plugin) {
         var _this = this;
@@ -29,14 +32,24 @@ var PluginAnimationLoop = /** @class */ (function () {
         configurable: true
     });
     PluginAnimationLoop.prototype.tick = function (t, options) {
-        var _a;
+        var _a, _b;
         return tslib_1.__awaiter(this, void 0, void 0, function () {
-            return tslib_1.__generator(this, function (_b) {
-                switch (_b.label) {
+            var timerResults, _i, timerResults_1, result;
+            return tslib_1.__generator(this, function (_c) {
+                switch (_c.label) {
                     case 0: return [4 /*yield*/, this.plugin.managers.animation.tick(t, options === null || options === void 0 ? void 0 : options.isSynchronous, options === null || options === void 0 ? void 0 : options.animation)];
                     case 1:
-                        _b.sent();
+                        _c.sent();
                         (_a = this.plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.tick(t, options);
+                        if (debug_1.isTimingMode) {
+                            timerResults = (_b = this.plugin.canvas3d) === null || _b === void 0 ? void 0 : _b.webgl.timer.resolve();
+                            if (timerResults) {
+                                for (_i = 0, timerResults_1 = timerResults; _i < timerResults_1.length; _i++) {
+                                    result = timerResults_1[_i];
+                                    (0, timer_1.printTimerResults)([result]);
+                                }
+                            }
+                        }
                         return [2 /*return*/];
                 }
             });

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

@@ -21,13 +21,13 @@ var M = input_observer_1.ModifiersKeys;
 var Trigger = binding_1.Binding.Trigger;
 var DefaultFocusLociBindings = {
     clickCenterFocus: (0, binding_1.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: (0, binding_1.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 = {
@@ -78,22 +78,22 @@ exports.CameraAxisHelper = behavior_1.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 || !(0, camera_helper_1.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 = linear_algebra_1.Vec3.sub((0, linear_algebra_1.Vec3)(), camera.target, camera.position);
                     var c = linear_algebra_1.Vec3.cross((0, linear_algebra_1.Vec3)(), d, camera.up);
@@ -111,11 +111,11 @@ exports.CameraAxisHelper = behavior_1.PluginBehavior.create({
                         lastPlane = axis;
                         state = 0;
                     }
-                    if (axis === 4 /* XY */) {
+                    if (axis === 4 /* CameraHelperAxis.XY */) {
                         up = state ? linear_algebra_1.Vec3.unitX : linear_algebra_1.Vec3.unitY;
                         dir = linear_algebra_1.Vec3.negUnitZ;
                     }
-                    else if (axis === 5 /* XZ */) {
+                    else if (axis === 5 /* CameraHelperAxis.XZ */) {
                         up = state ? linear_algebra_1.Vec3.unitX : linear_algebra_1.Vec3.unitZ;
                         dir = linear_algebra_1.Vec3.negUnitY;
                     }

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

@@ -25,8 +25,8 @@ var M = input_observer_1.ModifiersKeys;
 var Trigger = binding_1.Binding.Trigger;
 //
 var DefaultHighlightLociBindings = {
-    hoverHighlightOnly: (0, binding_1.Binding)([Trigger(0 /* None */)], 'Highlight', 'Hover element using ${triggers}'),
-    hoverHighlightOnlyExtend: (0, binding_1.Binding)([Trigger(0 /* None */, M.create({ shift: true }))], 'Extend highlight', 'From selected to hovered element along polymer using ${triggers}'),
+    hoverHighlightOnly: (0, binding_1.Binding)([Trigger(0 /* B.Flag.None */)], 'Highlight', 'Hover element using ${triggers}'),
+    hoverHighlightOnlyExtend: (0, binding_1.Binding)([Trigger(0 /* B.Flag.None */, M.create({ shift: true }))], 'Extend highlight', 'From selected to hovered element along polymer using ${triggers}'),
 };
 var HighlightLociParams = {
     bindings: param_definition_1.ParamDefinition.Value(DefaultHighlightLociBindings, { isHidden: true }),
@@ -92,11 +92,11 @@ exports.HighlightLoci = behavior_1.PluginBehavior.create({
 //
 var DefaultSelectLociBindings = {
     clickSelect: binding_1.Binding.Empty,
-    clickToggleExtend: (0, binding_1.Binding)([Trigger(1 /* Primary */, M.create({ shift: true }))], 'Toggle extended selection', '${triggers} to extend selection along polymer'),
+    clickToggleExtend: (0, binding_1.Binding)([Trigger(1 /* B.Flag.Primary */, M.create({ shift: true }))], 'Toggle extended selection', '${triggers} to extend selection along polymer'),
     clickSelectOnly: binding_1.Binding.Empty,
-    clickToggle: (0, binding_1.Binding)([Trigger(1 /* Primary */, M.create())], 'Toggle selection', '${triggers} on element'),
+    clickToggle: (0, binding_1.Binding)([Trigger(1 /* B.Flag.Primary */, M.create())], 'Toggle selection', '${triggers} on element'),
     clickDeselect: binding_1.Binding.Empty,
-    clickDeselectAllOnEmpty: (0, binding_1.Binding)([Trigger(1 /* Primary */, M.create())], 'Deselect all', 'Click on nothing using ${triggers}'),
+    clickDeselectAllOnEmpty: (0, binding_1.Binding)([Trigger(1 /* B.Flag.Primary */, M.create())], 'Deselect all', 'Click on nothing using ${triggers}'),
 };
 var SelectLociParams = {
     bindings: param_definition_1.ParamDefinition.Value(DefaultSelectLociBindings, { isHidden: true }),
@@ -243,10 +243,10 @@ exports.DefaultLociLabelProvider = behavior_1.PluginBehavior.create({
 //
 var DefaultFocusLociBindings = {
     clickFocus: (0, binding_1.Binding)([
-        Trigger(1 /* Primary */, M.create()),
+        Trigger(1 /* B.Flag.Primary */, M.create()),
     ], 'Representation Focus', 'Click element using ${triggers}'),
     clickFocusAdd: (0, binding_1.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: (0, binding_1.Binding)([
     // default is empty

package/lib/commonjs/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/commonjs/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/commonjs/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/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 */
             ])
         ])
     })