molstar 2.3.5 → 2.3.9

package/lib/examples/task.js

@@ -30,14 +30,14 @@ function messageTree(root, prefix) {
     var p = root.progress;
     if (!root.children.length) {
         if (p.isIndeterminate)
-            return "" + prefix + p.taskName + ": " + p.message;
-        return "" + prefix + p.taskName + ": [" + p.current + "/" + p.max + "] " + p.message;
+            return "".concat(prefix).concat(p.taskName, ": ").concat(p.message);
+        return "".concat(prefix).concat(p.taskName, ": [").concat(p.current, "/").concat(p.max, "] ").concat(p.message);
     }
     var newPrefix = prefix + '  |_ ';
     var subTree = root.children.map(function (c) { return messageTree(c, newPrefix); });
     if (p.isIndeterminate)
-        return "" + prefix + p.taskName + ": " + p.message + "\n" + subTree.join('\n');
-    return "" + prefix + p.taskName + ": [" + p.current + "/" + p.max + "] " + p.message + "\n" + subTree.join('\n');
+        return "".concat(prefix).concat(p.taskName, ": ").concat(p.message, "\n").concat(subTree.join('\n'));
+    return "".concat(prefix).concat(p.taskName, ": [").concat(p.current, "/").concat(p.max, "] ").concat(p.message, "\n").concat(subTree.join('\n'));
 }
 function createTask(delayMs, r) {
     var _this = this;
@@ -45,12 +45,12 @@ function createTask(delayMs, r) {
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
-                    ctx.update("Processing delayed " + r + " after " + delayMs + "ms", true);
+                    ctx.update("Processing delayed ".concat(r, " after ").concat(delayMs, "ms"), true);
                     return [4 /*yield*/, Scheduler.delay(delayMs)];
                 case 1:
                     _a.sent();
                     if (!ctx.shouldUpdate) return [3 /*break*/, 3];
-                    return [4 /*yield*/, ctx.update({ message: "hello from delayed " + r + " " + delayMs })];
+                    return [4 /*yield*/, ctx.update({ message: "hello from delayed ".concat(r, " ").concat(delayMs) })];
                 case 2:
                     _a.sent();
                     _a.label = 3;

package/lib/examples/task.js.map

@@ -1 +1 @@
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package/lib/extensions/alpha-orbitals/transforms.js

@@ -44,7 +44,7 @@ export var StaticBasisAndOrbitals = PluginStateTransform.BuiltIn({
 var CreateOrbitalVolumeParamBase = {
     cutoffThreshold: PD.Numeric(0.0015, { min: 0, max: 0.1, step: 0.0001 }),
     boxExpand: PD.Numeric(4.5, { min: 0, max: 7, step: 0.1 }),
-    gridSpacing: PD.ObjectList({ atomCount: PD.Numeric(0), spacing: PD.Numeric(0.35, { min: 0.1, max: 2, step: 0.01 }) }, function (e) { return "Atoms " + e.atomCount + ": " + e.spacing; }, {
+    gridSpacing: PD.ObjectList({ atomCount: PD.Numeric(0), spacing: PD.Numeric(0.35, { min: 0.1, max: 2, step: 0.01 }) }, function (e) { return "Atoms ".concat(e.atomCount, ": ").concat(e.spacing); }, {
         defaultValue: [
             { atomCount: 55, spacing: 0.5 },
             { atomCount: 40, spacing: 0.45 },
@@ -96,7 +96,7 @@ export var CreateOrbitalVolume = PluginStateTransform.BuiltIn({
         if (!a) {
             return __assign({ index: PD.Numeric(0) }, CreateOrbitalVolumeParamBase);
         }
-        return __assign({ index: PD.Select(0, a.data.orbitals.map(function (o, i) { return [i, "[" + (i + 1) + "] " + o.energy.toFixed(4)]; })) }, CreateOrbitalVolumeParamBase);
+        return __assign({ index: PD.Select(0, a.data.orbitals.map(function (o, i) { return [i, "[".concat(i + 1, "] ").concat(o.energy.toFixed(4))]; })) }, CreateOrbitalVolumeParamBase);
     }
 })({
     apply: function (_a, plugin) {

package/lib/extensions/alpha-orbitals/transforms.js.map

@@ -1 +1 @@
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package/lib/extensions/anvil/representation.js

@@ -55,7 +55,7 @@ export var MembraneOrientationRepresentationProvider = StructureRepresentationPr
     }
 });
 function membraneLabel(data) {
-    return lociLabel(Structure.Loci(data)) + " | Membrane Orientation";
+    return "".concat(lociLabel(Structure.Loci(data)), " | Membrane Orientation");
 }
 function getBilayerRims(ctx, data, props, shape) {
     var _a = MembraneOrientationProvider.get(data).value, p1 = _a.planePoint1, p2 = _a.planePoint2, centroid = _a.centroid, radius = _a.radius;

package/lib/extensions/anvil/representation.js.map

@@ -1 +1 @@
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+{"version":3,"file":"representation.js","sourceRoot":"","sources":["../../../src/extensions/anvil/representation.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;;AAEH,OAAO,EAAE,eAAe,IAAI,EAAE,EAAE,MAAM,iCAAiC,CAAC;AACxE,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,MAAM,+BAA+B,CAAC;AAC3D,OAAO,EAAE,cAAc,EAAqD,MAAM,+BAA+B,CAAC;AAClH,OAAO,EAAE,SAAS,EAAE,MAAM,2BAA2B,CAAC;AACtD,OAAO,EAAE,+BAA+B,EAA2B,mCAAmC,EAAE,MAAM,yCAAyC,CAAC;AAGxJ,OAAO,EAAE,mBAAmB,EAAE,MAAM,qCAAqC,CAAC;AAC1E,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAC;AAE9C,OAAO,EAAE,KAAK,EAAE,MAAM,oCAAoC,CAAC;AAC3D,OAAO,EAAE,IAAI,EAAE,MAAM,kCAAkC,CAAC;AACxD,OAAO,EAAE,YAAY,EAAE,MAAM,4CAA4C,CAAC;AAC1E,OAAO,EAAE,MAAM,EAAE,MAAM,gCAAgC,CAAC;AACxD,OAAO,EAAE,kBAAkB,EAAE,MAAM,mCAAmC,CAAC;AACvE,OAAO,EAAE,WAAW,EAAE,MAAM,0CAA0C,CAAC;AACvE,OAAO,EAAE,2BAA2B,EAAE,MAAM,QAAQ,CAAC;AACrD,OAAO,EAAE,aAAa,EAAE,MAAM,8BAA8B,CAAC;AAC7D,OAAO,EAAE,SAAS,EAAE,MAAM,uBAAuB,CAAC;AAClD,OAAO,EAAE,UAAU,EAAE,MAAM,4BAA4B,CAAC;AAGxD,IAAM,YAAY,GAAG;IACjB,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,UAAU,CAAC,SAAS,CAAC;IACrC,YAAY,EAAE,EAAE,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE,EAAE,WAAW,EAAE,wCAAwC,EAAE,CAAC;CAC/H,CAAC;AAEF,IAAM,mBAAmB,kCAClB,IAAI,CAAC,MAAM,GACX,YAAY,KACf,aAAa,EAAE,EAAE,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,GACjE,CAAC;AAIF,IAAM,iBAAiB,kCAChB,KAAK,CAAC,MAAM,GACZ,YAAY,KACf,mBAAmB,EAAE,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,EACrC,SAAS,EAAE,EAAE,CAAC,OAAO,CAAC,GAAG,EAAE,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,EAC9D,WAAW,EAAE,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,GAChC,CAAC;AAIF,IAAM,0BAA0B,GAAG;IAC/B,gBAAgB,EAAE,UAAC,GAA0B,EAAE,SAA+E,IAAK,OAAA,mBAAmB,CAAC,gBAAgB,EAAE,IAAI,CAAC,KAAK,EAAE,EAAE,WAAW,EAAE,UAAA,CAAC,IAAI,OAAA,uBAAM,CAAC,KAAE,aAAa,EAAE,aAAa,CAAC,YAAY,IAAG,EAArD,CAAqD,EAAE,WAAW,EAAE,UAAA,CAAC,IAAI,OAAA,uBAAM,CAAC,KAAE,KAAK,EAAE,CAAC,CAAC,aAAa,EAAE,WAAW,EAAE,IAAI,EAAE,WAAW,EAAE,KAAK,IAAG,EAAzE,CAAyE,EAAE,CAAC,EAA3N,CAA2N;IAC9V,cAAc,EAAE,UAAC,GAA0B,EAAE,SAA6E,IAAK,OAAA,mBAAmB,CAAC,cAAc,EAAE,KAAK,CAAC,KAAK,EAAE,EAAE,WAAW,EAAE,UAAA,CAAC,IAAI,OAAA,uBAAM,CAAC,KAAE,aAAa,EAAE,aAAa,CAAC,YAAY,IAAG,EAArD,CAAqD,EAAE,CAAC,EAA7H,CAA6H;CAC/P,CAAC;AAEF,MAAM,CAAC,IAAM,yBAAyB,kCAC/B,mBAAmB,GACnB,iBAAiB,KACpB,OAAO,EAAE,EAAE,CAAC,WAAW,CAAC,CAAC,gBAAgB,EAAE,cAAc,CAAC,EAAE,EAAE,CAAC,eAAe,CAAC,0BAA0B,CAAC,CAAC,GAC9G,CAAC;AAIF,MAAM,UAAU,4BAA4B,CAAC,GAAyB,EAAE,SAAoB;IACxF,OAAO,EAAE,CAAC,KAAK,CAAC,yBAAyB,CAAC,CAAC;AAC/C,CAAC;AAGD,MAAM,UAAU,iCAAiC,CAAC,GAA0B,EAAE,SAA2E;IACrJ,OAAO,cAAc,CAAC,WAAW,CAAC,sBAAsB,EAAE,GAAG,EAAE,SAAS,EAAE,mCAAmC,EAAE,0BAAiG,CAAC,CAAC;AACtN,CAAC;AAED,MAAM,CAAC,IAAM,yCAAyC,GAAG,+BAA+B,CAAC;IACrF,IAAI,EAAE,sBAAsB;IAC5B,KAAK,EAAE,sBAAsB;IAC7B,WAAW,EAAE,yDAAyD;IACtE,OAAO,EAAE,iCAAiC;IAC1C,SAAS,EAAE,4BAA4B;IACvC,aAAa,EAAE,EAAE,CAAC,gBAAgB,CAAC,yBAAyB,CAAC;IAC7D,iBAAiB,EAAE,EAAE,IAAI,EAAE,aAAa,EAAE;IAC1C,gBAAgB,EAAE,EAAE,IAAI,EAAE,aAAa,EAAE;IACzC,YAAY,EAAE,UAAC,SAAoB,IAAK,OAAA,SAAS,CAAC,YAAY,GAAG,CAAC,EAA1B,CAA0B;IAClE,sBAAsB,EAAE;QACpB,MAAM,EAAE,UAAC,GAA2B,EAAE,SAAoB,IAAK,OAAA,2BAA2B,CAAC,MAAM,CAAC,GAAG,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,IAAI,CAAC,EAAhE,CAAgE;QAC/H,MAAM,EAAE,UAAC,IAAI,IAAK,OAAA,2BAA2B,CAAC,GAAG,CAAC,IAAI,EAAE,KAAK,CAAC,EAA5C,CAA4C;KACjE;CACJ,CAAC,CAAC;AAEH,SAAS,aAAa,CAAC,IAAe;IAClC,OAAO,UAAG,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,4BAAyB,CAAC;AACvE,CAAC;AAED,SAAS,cAAc,CAAC,GAAmB,EAAE,IAAe,EAAE,KAAuB,EAAE,KAAoB;IACjG,IAAA,KAAyD,2BAA2B,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,KAAM,EAAtF,EAAE,iBAAA,EAAe,EAAE,iBAAA,EAAE,QAAQ,cAAA,EAAE,MAAM,YAAiD,CAAC;IAC5G,IAAM,YAAY,GAAG,KAAK,CAAC,YAAY,GAAG,MAAM,CAAC;IACjD,IAAM,OAAO,GAAG,YAAY,CAAC,MAAM,CAAC,GAAG,EAAE,EAAE,EAAE,KAAK,aAAL,KAAK,uBAAL,KAAK,CAAE,QAAQ,CAAC,CAAC;IAC9D,cAAc,CAAC,OAAO,EAAE,EAAE,EAAE,QAAQ,EAAE,YAAY,EAAE,KAAK,CAAC,CAAC;IAC3D,cAAc,CAAC,OAAO,EAAE,EAAE,EAAE,QAAQ,EAAE,YAAY,EAAE,KAAK,CAAC,CAAC;IAC3D,OAAO,KAAK,CAAC,MAAM,CAAC,cAAc,EAAE,IAAI,EAAE,OAAO,CAAC,QAAQ,EAAE,EAAE,cAAM,OAAA,KAAK,CAAC,KAAK,EAAX,CAAW,EAAE,cAAM,OAAA,KAAK,CAAC,SAAS,EAAf,CAAe,EAAE,cAAM,OAAA,aAAa,CAAC,IAAI,CAAC,EAAnB,CAAmB,CAAC,CAAC;AACvI,CAAC;AAED,SAAS,cAAc,CAAC,OAAqB,EAAE,CAAO,EAAE,QAAc,EAAE,MAAc,EAAE,KAAuB,EAAE,KAAoB;IACjI,IAAM,MAAM,GAAG,SAAS,CAAC,CAAC,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;IACtC,IAAA,OAAO,GAAe,MAAM,QAArB,EAAE,QAAQ,GAAK,MAAM,SAAX,CAAY;IACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,IAAI,CAAC,EAAE;QACjD,IAAI,KAAK,CAAC,WAAW,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC;YAAE,SAAS,CAAC,yCAAyC;QACzF,IAAM,KAAK,GAAG,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;QAC7B,IAAM,GAAG,GAAG,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC;QAC/B,IAAM,MAAM,GAAG,QAAQ,CAAC,KAAK,CAAC,CAAC;QAC/B,IAAM,MAAM,GAAG,QAAQ,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;QACnC,IAAM,MAAM,GAAG,QAAQ,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;QACnC,IAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC;QAC3B,IAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC;QAC/B,IAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC;QAC/B,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC;KAC5D;AACL,CAAC;AAED,IAAM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package/lib/extensions/cellpack/color/generate.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2021 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/color/generate.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2021 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/color/provided.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/extensions/cellpack/color/provided.js

@@ -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/curve.d.ts

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2019 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 Ludovic Autin <autin@scripps.edu>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Mat4 } from '../../mol-math/linear-algebra';

package/lib/extensions/cellpack/curve.js

@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2019 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 Ludovic Autin <autin@scripps.edu>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 import { Vec3, Quat, Mat4 } from '../../mol-math/linear-algebra';

package/lib/extensions/cellpack/data.d.ts

@@ -12,13 +12,26 @@ export interface CellPacking {
     name: string;
     location: 'surface' | 'interior' | 'cytoplasme';
     ingredients: Packing['ingredients'];
+    compartment?: CellCompartment;
+}
+export interface CellCompartment {
+    filename?: string;
+    geom_type?: 'raw' | 'file' | 'sphere' | 'mb' | 'None';
+    compartment_primitives?: CompartmentPrimitives;
 }
 export interface Cell {
     recipe: Recipe;
+    options?: RecipeOptions;
     cytoplasme?: Packing;
     compartments?: {
         [key: string]: Compartment;
     };
+    mapping_ids?: {
+        [key: number]: [number, string];
+    };
+}
+export interface RecipeOptions {
+    resultfile?: string;
 }
 export interface Recipe {
     setupfile: string;
@@ -29,6 +42,23 @@ export interface Recipe {
 export interface Compartment {
     surface?: Packing;
     interior?: Packing;
+    geom?: unknown;
+    geom_type?: 'raw' | 'file' | 'sphere' | 'mb' | 'None';
+    mb?: CompartmentPrimitives;
+}
+export declare const enum CompartmentPrimitiveType {
+    MetaBall = 0,
+    Sphere = 1,
+    Cube = 2,
+    Cylinder = 3,
+    Cone = 4,
+    Plane = 5,
+    None = 6
+}
+export interface CompartmentPrimitives {
+    positions?: number[];
+    radii?: number[];
+    types?: CompartmentPrimitiveType[];
 }
 export interface Packing {
     ingredients: {
@@ -56,11 +86,13 @@ export interface Ingredient {
     [curveX: string]: unknown;
     /** the orientation in the membrane */
     principalAxis?: Vec3;
+    principalVector?: Vec3;
     /** offset along membrane */
     offset?: Vec3;
     ingtype?: string;
     color?: Vec3;
     confidence?: number;
+    Type?: string;
 }
 export interface IngredientSource {
     pdb: string;

package/lib/extensions/cellpack/index.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/extensions/cellpack/index.js

@@ -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/model.d.ts

@@ -2,6 +2,7 @@
  * 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 { StateAction } from '../../mol-state';
 import { PluginContext } from '../../mol-plugin/context';
@@ -16,12 +17,13 @@ import { Color } from '../../mol-util/color';
 export declare function createStructureFromCellPack(plugin: PluginContext, packing: CellPacking, baseUrl: string, ingredientFiles: IngredientFiles): Task<{
     structure: Structure;
     assets: Asset.Wrapper<import("../../mol-util/data-source").DataType>[];
-    colors: Color[] | undefined;
+    colors: Color[];
 }>;
 export declare const LoadCellPackModel: StateAction<PSO.Root, void, PD.Normalize<{
-    source: PD.NamedParams<"InfluenzaModel2.json" | "blood_hiv_immature_inside.json" | "HIV_immature_model.json" | "BloodHIV1.0_mixed_fixed_nc1.cpr" | "HIV-1_0.1.6-8_mixed_radii_pdb.cpr" | "influenza_model1.json" | "ExosomeModel.json" | "Mycoplasma1.5_mixed_pdb_fixed.cpr" | "MycoplasmaModel.json", "id"> | PD.NamedParams<Asset.File | null, "file">;
+    source: PD.NamedParams<"InfluenzaModel2.json" | "blood_hiv_immature_inside.json" | "HIV_immature_model.json" | "Blood_HIV.json" | "HIV-1_0.1.6-8_mixed_radii_pdb.json" | "influenza_model1.json" | "ExosomeModel.json" | "MycoplasmaGenitalium.json", "id"> | PD.NamedParams<Asset.File | null, "file">;
     baseUrl: string;
-    membrane: boolean;
+    results: Asset.File | null;
+    membrane: string;
     ingredients: Asset.File[] | null;
     preset: PD.Normalize<{
         traceOnly: any;