molstar 2.3.5 → 2.3.9

package/lib/commonjs/extensions/cellpack/model.js.map

@@ -1 +1 @@
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package/lib/commonjs/extensions/cellpack/preset.d.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
  */
 import { StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';

package/lib/commonjs/extensions/cellpack/preset.js

@@ -1,8 +1,9 @@
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.CellpackMembranePreset = exports.CellpackMembranePresetParams = exports.CellpackPackingPreset = exports.CellpackPackingPresetParams = void 0;
@@ -12,8 +13,6 @@ var representation_preset_1 = require("../../mol-plugin-state/builder/structure/
 var param_definition_1 = require("../../mol-util/param-definition");
 var names_1 = require("../../mol-util/color/names");
 var generate_1 = require("./color/generate");
-var property_1 = require("./property");
-var provided_1 = require("./color/provided");
 exports.CellpackPackingPresetParams = {
     traceOnly: param_definition_1.ParamDefinition.Boolean(true),
     representation: param_definition_1.ParamDefinition.Select('gaussian-surface', param_definition_1.ParamDefinition.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'])),
@@ -23,12 +22,11 @@ exports.CellpackPackingPreset = (0, representation_preset_1.StructureRepresentat
     display: { name: 'CellPack Packing' },
     params: function () { return exports.CellpackPackingPresetParams; },
     apply: function (ref, params, plugin) {
-        var _a, _b;
         return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-            var structureCell, reprProps, components, info, color, _c, update, builder, typeParams, representations;
-            var _d;
-            return (0, tslib_1.__generator)(this, function (_e) {
-                switch (_e.label) {
+            var structureCell, reprProps, components, color, _a, update, builder, typeParams, representations;
+            var _b;
+            return (0, tslib_1.__generator)(this, function (_c) {
+                switch (_c.label) {
                     case 0:
                         structureCell = mol_state_1.StateObjectRef.resolveAndCheck(plugin.state.data, ref);
                         if (!structureCell)
@@ -37,11 +35,11 @@ exports.CellpackPackingPreset = (0, representation_preset_1.StructureRepresentat
                             ignoreHydrogens: true,
                             traceOnly: params.traceOnly
                         };
-                        _d = {};
+                        _b = {};
                         return [4 /*yield*/, (0, representation_preset_1.presetStaticComponent)(plugin, structureCell, 'polymer')];
                     case 1:
-                        components = (_d.polymer = _e.sent(),
-                            _d);
+                        components = (_b.polymer = _c.sent(),
+                            _b);
                         if (params.representation === 'gaussian-surface') {
                             Object.assign(reprProps, {
                                 quality: 'custom', resolution: 10, radiusOffset: 2, doubleSided: false
@@ -50,15 +48,14 @@ exports.CellpackPackingPreset = (0, representation_preset_1.StructureRepresentat
                         else if (params.representation === 'spacefill' && params.traceOnly) {
                             Object.assign(reprProps, { sizeFactor: 2 });
                         }
-                        info = ((_a = structureCell.obj) === null || _a === void 0 ? void 0 : _a.data) && property_1.CellPackInfoProvider.get((_b = structureCell.obj) === null || _b === void 0 ? void 0 : _b.data).value;
-                        color = (info === null || info === void 0 ? void 0 : info.colors) ? provided_1.CellPackProvidedColorThemeProvider.name : generate_1.CellPackGenerateColorThemeProvider.name;
-                        _c = representation_preset_1.StructureRepresentationPresetProvider.reprBuilder(plugin, {}), update = _c.update, builder = _c.builder, typeParams = _c.typeParams;
+                        color = generate_1.CellPackGenerateColorThemeProvider.name;
+                        _a = representation_preset_1.StructureRepresentationPresetProvider.reprBuilder(plugin, {}), update = _a.update, builder = _a.builder, typeParams = _a.typeParams;
                         representations = {
                             polymer: builder.buildRepresentation(update, components.polymer, { type: params.representation, typeParams: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, typeParams), reprProps), color: color }, { tag: 'polymer' })
                         };
                         return [4 /*yield*/, update.commit({ revertOnError: true })];
                     case 2:
-                        _e.sent();
+                        _c.sent();
                         return [2 /*return*/, { components: components, representations: representations }];
                 }
             });

package/lib/commonjs/extensions/cellpack/preset.js.map

@@ -1 +1 @@
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package/lib/commonjs/extensions/cellpack/property.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/extensions/cellpack/property.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/commonjs/extensions/cellpack/representation.d.ts

@@ -0,0 +1,53 @@
+/**
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
+ */
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { RepresentationParamsGetter, Representation, RepresentationContext } from '../../mol-repr/representation';
+interface MembraneSphereData {
+    radius: number;
+    center: Vec3;
+}
+export declare const MBParams: {
+    cellColor: PD.Color;
+    cellScale: PD.Numeric;
+    radius: PD.Numeric;
+    center: PD.Vec3;
+    quality: {
+        isEssential: boolean;
+        type: "select";
+        options: readonly (readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string] | readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string, string | undefined])[];
+        cycle?: boolean | undefined;
+        isOptional?: boolean | undefined;
+        defaultValue: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+        label?: string | undefined;
+        description?: string | undefined;
+        legend?: import("../../mol-util/legend").Legend | undefined;
+        fieldLabels?: {
+            [name: string]: string;
+        } | undefined;
+        isHidden?: boolean | undefined;
+        shortLabel?: boolean | undefined;
+        twoColumns?: boolean | undefined;
+        category?: string | undefined;
+        hideIf?: ((currentGroup: any) => boolean) | undefined;
+        help?: ((value: any) => {
+            description?: string | undefined;
+            legend?: import("../../mol-util/legend").Legend | undefined;
+        }) | undefined;
+    };
+    doubleSided: PD.BooleanParam;
+    flipSided: PD.BooleanParam;
+    flatShaded: PD.BooleanParam;
+    ignoreLight: PD.BooleanParam;
+    xrayShaded: PD.BooleanParam;
+    alpha: PD.Numeric;
+};
+export declare type MBParams = typeof MBParams;
+export declare type UnitcellProps = PD.Values<MBParams>;
+export declare type MBRepresentation = Representation<MembraneSphereData, MBParams>;
+export declare function MBRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<MembraneSphereData, MBParams>): MBRepresentation;
+export {};

package/lib/commonjs/extensions/cellpack/representation.js

@@ -0,0 +1,47 @@
+"use strict";
+/**
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.MBRepresentation = exports.MBParams = void 0;
+var tslib_1 = require("tslib");
+var representation_1 = require("../../mol-repr/shape/representation");
+var shape_1 = require("../../mol-model/shape");
+var names_1 = require("../../mol-util/color/names");
+var param_definition_1 = require("../../mol-util/param-definition");
+var mesh_1 = require("../../mol-geo/geometry/mesh/mesh");
+var mesh_builder_1 = require("../../mol-geo/geometry/mesh/mesh-builder");
+// import { Polyhedron, DefaultPolyhedronProps } from '../../mol-geo/primitive/polyhedron';
+// import { Icosahedron } from '../../mol-geo/primitive/icosahedron';
+var sphere_1 = require("../../mol-geo/primitive/sphere");
+var linear_algebra_1 = require("../../mol-math/linear-algebra");
+var representation_2 = require("../../mol-repr/representation");
+var MembraneSphereParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, mesh_1.Mesh.Params), { cellColor: param_definition_1.ParamDefinition.Color(names_1.ColorNames.orange), cellScale: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 5, step: 0.1 }), radius: param_definition_1.ParamDefinition.Numeric(2, { min: 0.1, max: 5, step: 0.1 }), center: param_definition_1.ParamDefinition.Vec3(linear_algebra_1.Vec3.create(0, 0, 0)), quality: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, mesh_1.Mesh.Params.quality), { isEssential: false }) });
+var MembraneSphereVisuals = {
+    'mesh': function (ctx, getParams) { return (0, representation_1.ShapeRepresentation)(getMBShape, mesh_1.Mesh.Utils); },
+};
+exports.MBParams = (0, tslib_1.__assign)({}, MembraneSphereParams);
+function getMBMesh(data, props, mesh) {
+    var state = mesh_builder_1.MeshBuilder.createState(256, 128, mesh);
+    var radius = props.radius;
+    var asphere = (0, sphere_1.Sphere)(3);
+    var trans = linear_algebra_1.Mat4.identity();
+    linear_algebra_1.Mat4.fromScaling(trans, linear_algebra_1.Vec3.create(radius, radius, radius));
+    state.currentGroup = 1;
+    mesh_builder_1.MeshBuilder.addPrimitive(state, trans, asphere);
+    var m = mesh_builder_1.MeshBuilder.getMesh(state);
+    return m;
+}
+function getMBShape(ctx, data, props, shape) {
+    var geo = getMBMesh(data, props, shape && shape.geometry);
+    var label = 'mb';
+    return shape_1.Shape.create(label, data, geo, function () { return props.cellColor; }, function () { return 1; }, function () { return label; });
+}
+function MBRepresentation(ctx, getParams) {
+    return representation_2.Representation.createMulti('MB', ctx, getParams, representation_2.Representation.StateBuilder, MembraneSphereVisuals);
+}
+exports.MBRepresentation = MBRepresentation;
+//# sourceMappingURL=representation.js.map

package/lib/commonjs/extensions/cellpack/representation.js.map

@@ -0,0 +1 @@
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package/lib/commonjs/extensions/cellpack/state.d.ts

@@ -1,13 +1,16 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
  */
 import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { CellPack as _CellPack } from './data';
 import { Asset } from '../../mol-util/assets';
-export declare const DefaultCellPackBaseUrl = "https://mesoscope.scripps.edu/data/cellPACK_data/cellPACK_database_1.1.0/";
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { StateTransformer } from '../../mol-state';
+export declare const DefaultCellPackBaseUrl = "https://raw.githubusercontent.com/mesoscope/cellPACK_data/master/cellPACK_database_1.1.0";
 declare const CellPack_base: {
     new (data: _CellPack, props?: {
         label: string;
@@ -32,14 +35,22 @@ export declare class CellPack extends CellPack_base {
 }
 export { ParseCellPack };
 declare type ParseCellPack = typeof ParseCellPack;
-declare const ParseCellPack: import("../../mol-state/transformer").StateTransformer<PSO.Format.Json, CellPack, PD.Normalize<{}>>;
+declare const ParseCellPack: StateTransformer<PSO.Format.Json, CellPack, PD.Normalize<{
+    resultsFile: Asset.File | null;
+    baseUrl: string;
+}>>;
 export { StructureFromCellpack };
 declare type StructureFromCellpack = typeof ParseCellPack;
-declare const StructureFromCellpack: import("../../mol-state/transformer").StateTransformer<CellPack, PSO.Molecule.Structure, PD.Normalize<{
+declare const StructureFromCellpack: StateTransformer<CellPack, PSO.Molecule.Structure, PD.Normalize<{
     packing: number;
     baseUrl: string;
     ingredientFiles: Asset.File[] | null;
 }>>;
 export { StructureFromAssemblies };
 declare type StructureFromAssemblies = typeof StructureFromAssemblies;
-declare const StructureFromAssemblies: import("../../mol-state/transformer").StateTransformer<PSO.Molecule.Model, PSO.Molecule.Structure, PD.Normalize<{}>>;
+declare const StructureFromAssemblies: StateTransformer<PSO.Molecule.Model, PSO.Molecule.Structure, PD.Normalize<{}>>;
+export declare const CreateCompartmentSphere: StateTransformer<PSO.Root, PSO.Shape.Representation3D, PD.Normalize<{
+    center: Vec3;
+    radius: number;
+    label: string;
+}>>;