molstar 3.0.0-dev.4 → 3.0.0-dev.8

package/lib/mol-model-props/computed/representations/interactions.d.ts

@@ -38,6 +38,16 @@ export declare const InteractionsParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type InteractionsParams = typeof InteractionsParams;
 export declare function getInteractionParams(ctx: ThemeRegistryContext, structure: Structure): {
@@ -70,6 +80,16 @@ export declare function getInteractionParams(ctx: ThemeRegistryContext, structur
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type InteractionRepresentation = StructureRepresentation<InteractionsParams>;
 export declare function InteractionRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, InteractionsParams>): InteractionRepresentation;
@@ -103,4 +123,14 @@ export declare const InteractionsRepresentationProvider: StructureRepresentation
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }, "interactions">;

package/lib/mol-model-props/integrative/cross-link-restraint/representation.d.ts

@@ -39,6 +39,16 @@ export declare const CrossLinkRestraintCylinderParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type CrossLinkRestraintCylinderParams = typeof CrossLinkRestraintCylinderParams;
 export declare function CrossLinkRestraintVisual(materialId: number): ComplexVisual<CrossLinkRestraintCylinderParams>;
@@ -71,6 +81,16 @@ export declare const CrossLinkRestraintParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type CrossLinkRestraintParams = typeof CrossLinkRestraintParams;
 export declare function getCrossLinkRestraintParams(ctx: ThemeRegistryContext, structure: Structure): {
@@ -102,6 +122,16 @@ export declare function getCrossLinkRestraintParams(ctx: ThemeRegistryContext, s
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type CrossLinkRestraintRepresentation = StructureRepresentation<CrossLinkRestraintParams>;
 export declare function CrossLinkRestraintRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, CrossLinkRestraintParams>): CrossLinkRestraintRepresentation;
@@ -134,4 +164,14 @@ export declare const CrossLinkRestraintRepresentationProvider: StructureRepresen
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }, CrossLinkRestraint.Tag>;

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

@@ -53,12 +53,11 @@ export var HighlightLoci = PluginBehavior.create({
         class_1.prototype.register = function () {
             var _this = this;
             this.subscribeObservable(this.ctx.behaviors.interaction.hover, function (_a) {
-                var _b;
                 var current = _a.current, buttons = _a.buttons, modifiers = _a.modifiers;
                 if (!_this.ctx.canvas3d || _this.ctx.isBusy)
                     return;
                 var loci = _this.getLoci(current.loci);
-                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(loci.kind)) >= 0) {
+                if (_this.params.ignore.includes(loci.kind)) {
                     _this.ctx.managers.interactivity.lociHighlights.highlightOnly({ repr: current.repr, loci: EmptyLoci });
                     return;
                 }
@@ -156,16 +155,15 @@ export var SelectLoci = PluginBehavior.create({
                 return l - k;
             });
             this.subscribeObservable(this.ctx.behaviors.interaction.click, function (_a) {
-                var _b;
                 var current = _a.current, button = _a.button, modifiers = _a.modifiers;
                 if (!_this.ctx.canvas3d || _this.ctx.isBusy || !_this.ctx.selectionMode)
                     return;
                 var loci = _this.getLoci(current.loci);
-                if (((_b = _this.params.ignore) === null || _b === void 0 ? void 0 : _b.indexOf(loci.kind)) >= 0)
+                if (_this.params.ignore.includes(loci.kind))
                     return;
                 // only trigger the 1st action that matches
                 for (var _i = 0, actions_1 = actions; _i < actions_1.length; _i++) {
-                    var _c = actions_1[_i], binding = _c[0], action = _c[1], condition = _c[2];
+                    var _b = actions_1[_i], binding = _b[0], action = _b[1], condition = _b[2];
                     if (Binding.match(_this.params.bindings[binding], button, modifiers) && (!condition || condition(loci))) {
                         action({ repr: current.repr, loci: loci });
                         break;
@@ -189,7 +187,7 @@ export var SelectLoci = PluginBehavior.create({
                         Structure.areEquivalent(structure, oldStructure) &&
                         Structure.areHierarchiesEqual(structure, oldStructure))
                         return;
-                    var reprs = _this.ctx.state.data.select(StateSelection.Generators.ofType(SO.Molecule.Structure.Representation3D, ref));
+                    var reprs = _this.ctx.state.data.select(StateSelection.children(ref).ofType(SO.Molecule.Structure.Representation3D));
                     for (var _i = 0, reprs_1 = reprs; _i < reprs_1.length; _i++) {
                         var repr = reprs_1[_i];
                         _this.applySelectMark(repr.transform.ref, true);

package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts

@@ -7,6 +7,7 @@
 import { PluginBehavior } from '../../../behavior';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { PluginContext } from '../../../context';
+import { Clip } from '../../../../mol-util/clip';
 declare const StructureFocusRepresentationParams: (plugin: PluginContext) => {
     expandRadius: PD.Numeric;
     targetParams: PD.Group<PD.Normalize<{
@@ -26,6 +27,16 @@ declare const StructureFocusRepresentationParams: (plugin: PluginContext) => {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 declare type StructureFocusRepresentationProps = PD.ValuesFor<ReturnType<typeof StructureFocusRepresentationParams>>;
 export declare enum StructureFocusRepresentationTags {

package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.js

@@ -17,6 +17,7 @@ import { SizeTheme } from '../../../../mol-theme/size';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { PluginCommands } from '../../../commands';
 import { Material } from '../../../../mol-util/material';
+import { Clip } from '../../../../mol-util/clip';
 var StructureFocusRepresentationParams = function (plugin) {
     var reprParams = StateTransforms.Representation.StructureRepresentation3D.definition.params(void 0, plugin);
     return {
@@ -41,6 +42,7 @@ var StructureFocusRepresentationParams = function (plugin) {
         excludeTargetFromSurroundings: PD.Boolean(false, { label: 'Exclude Target', description: 'Exclude the focus "target" from the surroudings component.' }),
         ignoreHydrogens: PD.Boolean(false),
         material: Material.getParam(),
+        clip: PD.Group(Clip.Params),
     };
 };
 var FocusComponents = ['target', 'surroundings', 'interactions'];
@@ -68,7 +70,7 @@ var StructureFocusRepresentationBehavior = /** @class */ (function (_super) {
     StructureFocusRepresentationBehavior.prototype.getReprParams = function (reprParams) {
         return __assign(__assign({}, this.params.targetParams), { type: {
                 name: reprParams.type.name,
-                params: __assign(__assign({}, reprParams.type.params), { ignoreHydrogens: this.params.ignoreHydrogens, material: this.params.material })
+                params: __assign(__assign({}, reprParams.type.params), { ignoreHydrogens: this.params.ignoreHydrogens, material: this.params.material, clip: this.params.clip })
             } });
     };
     StructureFocusRepresentationBehavior.prototype.ensureShape = function (cell) {

package/lib/mol-plugin/behavior/dynamic/volume-streaming/model.d.ts

@@ -9,12 +9,12 @@ import { Volume } from '../../../../mol-model/volume';
 import { Structure } from '../../../../mol-model/structure';
 declare const VolumeServerInfo_base: {
     new (data: VolumeServerInfo.Data, props?: {
-        /** Precision data the server can show. */
-        label: string;
+        label: string; /** Precision data the server can show. */
         description?: string | undefined;
     } | undefined): {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
+        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;
@@ -23,6 +23,7 @@ declare const VolumeServerInfo_base: {
     is(obj?: import("../../../../mol-state/object").StateObject<any, import("../../../../mol-state/object").StateObject.Type<any>> | undefined): obj is {
         id: import("../../../../mol-util/uuid").UUID;
         type: PluginStateObject.TypeInfo;
+        /** The value are stored in blockSize^3 cubes */
         label: string;
         description?: string | undefined;
         data: VolumeServerInfo.Data;

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

@@ -272,10 +272,6 @@ export declare const PluginCommands: {
                     }>[];
                     ambientColor: import("../mol-util/color").Color;
                     ambientIntensity: number;
-                    clip: import("../mol-util/param-definition").ParamDefinition.Normalize<{
-                        variant: any;
-                        objects: any;
-                    }>;
                 }>>;
                 trackball: import("../mol-util/param-definition").ParamDefinition.Group<import("../mol-util/param-definition").ParamDefinition.Normalize<{
                     noScroll: boolean;
@@ -334,6 +330,7 @@ export declare const PluginCommands: {
                         bumpAmplitude: any;
                         quality: any;
                         material: any;
+                        clip: any;
                     }>, "on">;
                 }>>;
             }>> | ((old: Canvas3DProps) => Partial<Canvas3DProps> | void);

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

@@ -16,7 +16,6 @@ export declare class PluginConfigItem<T = any> {
     constructor(key: string, defaultValue?: T | undefined);
 }
 declare function item<T>(key: string, defaultValue?: T): PluginConfigItem<T>;
-export declare function preferWebGl1(): boolean;
 export declare const PluginConfig: {
     item: typeof item;
     General: {
@@ -59,6 +58,7 @@ export declare const PluginConfig: {
             highSymmetryUnitCount: number;
             fiberResidueCount: number;
         }>;
+        DefaultRepresentationPreset: PluginConfigItem<string>;
         DefaultRepresentationPresetParams: PluginConfigItem<StructureRepresentationPresetProvider.CommonParams>;
     };
 };

package/lib/mol-plugin/config.js

@@ -5,6 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Structure, Model } from '../mol-model/structure';
+import { PluginFeatureDetection } from './features';
 var PluginConfigItem = /** @class */ (function () {
     function PluginConfigItem(key, defaultValue) {
         this.key = key;
@@ -16,27 +17,6 @@ var PluginConfigItem = /** @class */ (function () {
 }());
 export { PluginConfigItem };
 function item(key, defaultValue) { return new PluginConfigItem(key, defaultValue); }
-export function preferWebGl1() {
-    if (typeof navigator === 'undefined' || typeof window === 'undefined')
-        return false;
-    // WebGL2 isn't working in MacOS 12.0.1 Safari 15.1, 15.2. It is working in Safari 15.4 tech preview, so disabling all versions before that.
-    // prefer webgl 1 based on the userAgent substring
-    var unpportedSafariVersions = [
-        'Version/15.1 Safari',
-        'Version/15.2 Safari',
-        'Version/15.3 Safari'
-    ];
-    if (unpportedSafariVersions.some(function (v) { return navigator.userAgent.indexOf(v) > 0; })) {
-        return true;
-    }
-    // Check for iOS device which enabled WebGL2 recently but it doesn't seem
-    // to be full up to speed yet.
-    // adapted from https://stackoverflow.com/questions/9038625/detect-if-device-is-ios
-    var isIOS = /iPad|iPhone|iPod/.test(navigator.userAgent);
-    var isAppleDevice = navigator.userAgent.includes('Macintosh');
-    var isTouchScreen = navigator.maxTouchPoints >= 4; // true for iOS 13 (and hopefully beyond)
-    return !window.MSStream && (isIOS || (isAppleDevice && isTouchScreen));
-}
 export var PluginConfig = {
     item: item,
     General: {
@@ -46,10 +26,10 @@ export var PluginConfig = {
         PixelScale: item('plugin-config.pixel-scale', 1),
         PickScale: item('plugin-config.pick-scale', 0.25),
         PickPadding: item('plugin-config.pick-padding', 3),
-        EnableWboit: item('plugin-config.enable-wboit', true),
+        EnableWboit: item('plugin-config.enable-wboit', PluginFeatureDetection.wboit),
         // as of Oct 1 2021, WebGL 2 doesn't work on iOS 15.
         // TODO: check back in a few weeks to see if it was fixed
-        PreferWebGl1: item('plugin-config.prefer-webgl1', preferWebGl1()),
+        PreferWebGl1: item('plugin-config.prefer-webgl1', PluginFeatureDetection.preferWebGl1),
     },
     State: {
         DefaultServer: item('plugin-state.server', 'https://webchem.ncbr.muni.cz/molstar-state'),
@@ -77,6 +57,7 @@ export var PluginConfig = {
     },
     Structure: {
         SizeThresholds: item('structure.size-thresholds', Structure.DefaultSizeThresholds),
+        DefaultRepresentationPreset: item('structure.default-representation-preset', 'auto'),
         DefaultRepresentationPresetParams: item('structure.default-representation-preset-params', {})
     }
 };

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

@@ -0,0 +1,9 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+export declare const PluginFeatureDetection: {
+    readonly preferWebGl1: boolean;
+    readonly wboit: boolean;
+};

package/lib/mol-plugin/features.js

@@ -0,0 +1,35 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+export var PluginFeatureDetection = {
+    get preferWebGl1() {
+        if (typeof navigator === 'undefined' || typeof window === 'undefined')
+            return false;
+        // WebGL2 isn't working in MacOS 12.0.1 Safari 15.1, 15.2. It is working in Safari 15.4 tech preview, so disabling all versions before that.
+        // prefer webgl 1 based on the userAgent substring
+        var unpportedSafariVersions = [
+            'Version/15.1 Safari',
+            'Version/15.2 Safari',
+            'Version/15.3 Safari'
+        ];
+        if (unpportedSafariVersions.some(function (v) { return navigator.userAgent.indexOf(v) > 0; })) {
+            return true;
+        }
+        // Check for iOS device which enabled WebGL2 recently but it doesn't seem
+        // to be full up to speed yet.
+        // adapted from https://stackoverflow.com/questions/9038625/detect-if-device-is-ios
+        var isIOS = /iPad|iPhone|iPod/.test(navigator.userAgent);
+        var isAppleDevice = navigator.userAgent.includes('Macintosh');
+        var isTouchScreen = navigator.maxTouchPoints >= 4; // true for iOS 13 (and hopefully beyond)
+        return !window.MSStream && (isIOS || (isAppleDevice && isTouchScreen));
+    },
+    get wboit() {
+        if (typeof navigator === 'undefined' || typeof window === 'undefined')
+            return true;
+        // disable Wboit in Safari 15
+        return !/Version\/15.\d Safari/.test(navigator.userAgent);
+    }
+};
+//# sourceMappingURL=features.js.map

package/lib/mol-plugin/spec.js

@@ -67,6 +67,7 @@ export var DefaultPluginSpec = function () { return ({
         PluginSpec.Action(StateTransforms.Representation.UnwindStructureAssemblyRepresentation3D),
         PluginSpec.Action(StateTransforms.Representation.OverpaintStructureRepresentation3DFromScript),
         PluginSpec.Action(StateTransforms.Representation.TransparencyStructureRepresentation3DFromScript),
+        PluginSpec.Action(StateTransforms.Representation.ClippingStructureRepresentation3DFromScript),
         PluginSpec.Action(StateTransforms.Representation.SubstanceStructureRepresentation3DFromScript),
         PluginSpec.Action(AssignColorVolume),
         PluginSpec.Action(StateTransforms.Volume.VolumeFromCcp4),

package/lib/mol-plugin/util/viewport-screenshot.d.ts

@@ -45,6 +45,10 @@ declare class ViewportScreenshotHelper extends PluginComponent {
                 roughness: number;
                 bumpiness: number;
             }>;
+            clip: PD.Normalize<{
+                variant: any;
+                objects: any;
+            }>;
         }>, "on">>;
     };
     readonly behaviors: {
@@ -73,6 +77,10 @@ declare class ViewportScreenshotHelper extends PluginComponent {
                     roughness: number;
                     bumpiness: number;
                 }>;
+                clip: PD.Normalize<{
+                    variant: any;
+                    objects: any;
+                }>;
             }>, "on">>;
         }>>;
         cropParams: import("rxjs").BehaviorSubject<{
@@ -109,6 +117,10 @@ declare class ViewportScreenshotHelper extends PluginComponent {
                 roughness: number;
                 bumpiness: number;
             }>;
+            clip: PD.Normalize<{
+                variant: any;
+                objects: any;
+            }>;
         }>, "on">>;
     }>;
     get cropParams(): {

package/lib/mol-plugin/version.js

@@ -1,2 +1,2 @@
-export var PLUGIN_VERSION = '3.0.0-dev.4';
-export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1639488302617);
+export var PLUGIN_VERSION = '3.0.0-dev.8';
+export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1640979636220);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 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>
@@ -36,6 +36,12 @@ declare const DownloadStructure: StateAction<PluginStateObject.Root, void, PD.No
     }>, "swissmodel"> | PD.NamedParams<PD.Normalize<{
         id: any;
         options: any;
+    }>, "alphafolddb"> | PD.NamedParams<PD.Normalize<{
+        id: any;
+        options: any;
+    }>, "modelarchive"> | PD.NamedParams<PD.Normalize<{
+        id: any;
+        options: any;
     }>, "pubchem">;
 }>>;
 export declare const UpdateTrajectory: StateAction<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, void, PD.Normalize<{