npm - molstar - Versions diffs - 2.3.3 → 2.3.8 - Mend

molstar 2.3.3 → 2.3.8

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (1829) hide show

package/lib/extensions/cellpack/model.js.map CHANGED Viewed

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

@@ -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/extensions/cellpack/preset.js CHANGED Viewed

@@ -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 { __assign, __awaiter, __generator } from "tslib";
 import { StateObjectRef } from '../../mol-state';
@@ -9,8 +10,6 @@ import { StructureRepresentationPresetProvider, presetStaticComponent } from '..
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ColorNames } from '../../mol-util/color/names';
 import { CellPackGenerateColorThemeProvider } from './color/generate';
-import { CellPackInfoProvider } from './property';
-import { CellPackProvidedColorThemeProvider } from './color/provided';
 export var CellpackPackingPresetParams = {
     traceOnly: PD.Boolean(true),
     representation: PD.Select('gaussian-surface', PD.arrayToOptions(['gaussian-surface', 'spacefill', 'point', 'orientation'])),
@@ -20,12 +19,11 @@ export var CellpackPackingPreset = StructureRepresentationPresetProvider({
     display: { name: 'CellPack Packing' },
     params: function () { return CellpackPackingPresetParams; },
     apply: function (ref, params, plugin) {
-        var _a, _b;
         return __awaiter(this, void 0, void 0, function () {
-            var structureCell, reprProps, components, info, color, _c, update, builder, typeParams, representations;
-            var _d;
-            return __generator(this, function (_e) {
-                switch (_e.label) {
+            var structureCell, reprProps, components, color, _a, update, builder, typeParams, representations;
+            var _b;
+            return __generator(this, function (_c) {
+                switch (_c.label) {
                     case 0:
                         structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
                         if (!structureCell)
@@ -34,11 +32,11 @@ export var CellpackPackingPreset = StructureRepresentationPresetProvider({
                             ignoreHydrogens: true,
                             traceOnly: params.traceOnly
                         };
-                        _d = {};
+                        _b = {};
                         return [4 /*yield*/, 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
@@ -47,15 +45,14 @@ export var CellpackPackingPreset = StructureRepresentationPresetProvider({
                         else if (params.representation === 'spacefill' && params.traceOnly) {
                             Object.assign(reprProps, { sizeFactor: 2 });
                         }
-                        info = ((_a = structureCell.obj) === null || _a === void 0 ? void 0 : _a.data) && CellPackInfoProvider.get((_b = structureCell.obj) === null || _b === void 0 ? void 0 : _b.data).value;
-                        color = (info === null || info === void 0 ? void 0 : info.colors) ? CellPackProvidedColorThemeProvider.name : CellPackGenerateColorThemeProvider.name;
-                        _c = StructureRepresentationPresetProvider.reprBuilder(plugin, {}), update = _c.update, builder = _c.builder, typeParams = _c.typeParams;
+                        color = CellPackGenerateColorThemeProvider.name;
+                        _a = StructureRepresentationPresetProvider.reprBuilder(plugin, {}), update = _a.update, builder = _a.builder, typeParams = _a.typeParams;
                         representations = {
                             polymer: builder.buildRepresentation(update, components.polymer, { type: params.representation, typeParams: __assign(__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/extensions/cellpack/preset.js.map CHANGED Viewed

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

@@ -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/extensions/cellpack/property.js CHANGED Viewed

@@ -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/extensions/cellpack/representation.d.ts ADDED Viewed

@@ -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/extensions/cellpack/representation.js ADDED Viewed

@@ -0,0 +1,43 @@
+/**
+ * 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 { __assign } from "tslib";
+import { ShapeRepresentation } from '../../mol-repr/shape/representation';
+import { Shape } from '../../mol-model/shape';
+import { ColorNames } from '../../mol-util/color/names';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
+// import { Polyhedron, DefaultPolyhedronProps } from '../../mol-geo/primitive/polyhedron';
+// import { Icosahedron } from '../../mol-geo/primitive/icosahedron';
+import { Sphere } from '../../mol-geo/primitive/sphere';
+import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
+import { Representation } from '../../mol-repr/representation';
+var MembraneSphereParams = __assign(__assign({}, Mesh.Params), { cellColor: PD.Color(ColorNames.orange), cellScale: PD.Numeric(2, { min: 0.1, max: 5, step: 0.1 }), radius: PD.Numeric(2, { min: 0.1, max: 5, step: 0.1 }), center: PD.Vec3(Vec3.create(0, 0, 0)), quality: __assign(__assign({}, Mesh.Params.quality), { isEssential: false }) });
+var MembraneSphereVisuals = {
+    'mesh': function (ctx, getParams) { return ShapeRepresentation(getMBShape, Mesh.Utils); },
+};
+export var MBParams = __assign({}, MembraneSphereParams);
+function getMBMesh(data, props, mesh) {
+    var state = MeshBuilder.createState(256, 128, mesh);
+    var radius = props.radius;
+    var asphere = Sphere(3);
+    var trans = Mat4.identity();
+    Mat4.fromScaling(trans, Vec3.create(radius, radius, radius));
+    state.currentGroup = 1;
+    MeshBuilder.addPrimitive(state, trans, asphere);
+    var m = MeshBuilder.getMesh(state);
+    return m;
+}
+function getMBShape(ctx, data, props, shape) {
+    var geo = getMBMesh(data, props, shape && shape.geometry);
+    var label = 'mb';
+    return Shape.create(label, data, geo, function () { return props.cellColor; }, function () { return 1; }, function () { return label; });
+}
+export function MBRepresentation(ctx, getParams) {
+    return Representation.createMulti('MB', ctx, getParams, Representation.StateBuilder, MembraneSphereVisuals);
+}
+//# sourceMappingURL=representation.js.map

package/lib/extensions/cellpack/representation.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"representation.js","sourceRoot":"","sources":["../../../src/extensions/cellpack/representation.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;;AAEH,OAAO,EAAE,mBAAmB,EAAE,MAAM,qCAAqC,CAAC;AAC1E,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAC;AAC9C,OAAO,EAAE,UAAU,EAAE,MAAM,4BAA4B,CAAC;AAExD,OAAO,EAAE,eAAe,IAAI,EAAE,EAAE,MAAM,iCAAiC,CAAC;AACxE,OAAO,EAAE,IAAI,EAAE,MAAM,kCAAkC,CAAC;AACxD,OAAO,EAAE,WAAW,EAAE,MAAM,0CAA0C,CAAC;AACvE,2FAA2F;AAC3F,qEAAqE;AACrE,OAAO,EAAE,MAAM,EAAE,MAAM,gCAAgC,CAAC;AACxD,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,MAAM,+BAA+B,CAAC;AAC3D,OAAO,EAA8B,cAAc,EAAyB,MAAM,+BAA+B,CAAC;AASlH,IAAM,oBAAoB,yBACnB,IAAI,CAAC,MAAM,KACd,SAAS,EAAE,EAAE,CAAC,KAAK,CAAC,UAAU,CAAC,MAAM,CAAC,EACtC,SAAS,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC,EACzD,MAAM,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC,EACtD,MAAM,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,EACrC,OAAO,wBAAO,IAAI,CAAC,MAAM,CAAC,OAAO,KAAE,WAAW,EAAE,KAAK,MACxD,CAAC;AAIF,IAAM,qBAAqB,GAAG;IAC1B,MAAM,EAAE,UAAC,GAA0B,EAAE,SAAqE,IAAK,OAAA,mBAAmB,CAAC,UAAU,EAAE,IAAI,CAAC,KAAK,CAAC,EAA3C,CAA2C;CAC7J,CAAC;AAEF,MAAM,CAAC,IAAM,QAAQ,gBACd,oBAAoB,CAC1B,CAAC;AAIF,SAAS,SAAS,CAAC,IAAwB,EAAE,KAAoB,EAAE,IAAW;IAC1E,IAAM,KAAK,GAAG,WAAW,CAAC,WAAW,CAAC,GAAG,EAAE,GAAG,EAAE,IAAI,CAAC,CAAC;IACtD,IAAM,MAAM,GAAG,KAAK,CAAC,MAAM,CAAC;IAC5B,IAAM,OAAO,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;IAC1B,IAAM,KAAK,GAAS,IAAI,CAAC,QAAQ,EAAE,CAAC;IACpC,IAAI,CAAC,WAAW,CAAC,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC;IAC7D,KAAK,CAAC,YAAY,GAAG,CAAC,CAAC;IACvB,WAAW,CAAC,YAAY,CAAC,KAAK,EAAE,KAAK,EAAE,OAAO,CAAC,CAAC;IAChD,IAAM,CAAC,GAAG,WAAW,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;IACrC,OAAO,CAAC,CAAC;AACb,CAAC;AAED,SAAS,UAAU,CAAC,GAAmB,EAAE,IAAwB,EAAE,KAAoB,EAAE,KAAmB;IACxG,IAAM,GAAG,GAAG,SAAS,CAAC,IAAI,EAAE,KAAK,EAAE,KAAK,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC;IAC5D,IAAM,KAAK,GAAG,IAAI,CAAC;IACnB,OAAO,KAAK,CAAC,MAAM,CAAC,KAAK,EAAE,IAAI,EAAE,GAAG,EAAE,cAAM,OAAA,KAAK,CAAC,SAAS,EAAf,CAAe,EAAE,cAAM,OAAA,CAAC,EAAD,CAAC,EAAE,cAAM,OAAA,KAAK,EAAL,CAAK,CAAC,CAAC;AACvF,CAAC;AAGD,MAAM,UAAU,gBAAgB,CAAC,GAA0B,EAAE,SAAmE;IAC5H,OAAO,cAAc,CAAC,WAAW,CAAC,IAAI,EAAE,GAAG,EAAE,SAAS,EAAE,cAAc,CAAC,YAAY,EAAE,qBAAoF,CAAC,CAAC;AAC/K,CAAC"}

package/lib/extensions/cellpack/state.d.ts CHANGED Viewed

@@ -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;
+}>>;