npm - molstar - Versions diffs - 2.3.7 → 2.4.1 - Mend

molstar 2.3.7 → 2.4.1

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 (1699) hide show

package/lib/mol-plugin-state/builder/structure/representation-preset.d.ts CHANGED Viewed

@@ -29,11 +29,11 @@ export declare namespace StructureRepresentationPresetProvider {
     };
     const CommonParams: {
         ignoreHydrogens: PD.Base<boolean | undefined>;
-        quality: PD.Base<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined>;
+        quality: PD.Base<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined>;
         theme: PD.Base<PD.Normalize<{
-            globalName: "occupancy" | "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | undefined;
-            carbonColor: "chain-id" | "operator-name" | "element-symbol" | undefined;
-            symmetryColor: "occupancy" | "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | undefined;
+            globalName: "uniform" | "occupancy" | "element-index" | "element-symbol" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "unit-index" | "uncertainty" | "entity-source" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-id" | undefined;
+            carbonColor: "element-symbol" | "chain-id" | "operator-name" | undefined;
+            symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "unit-index" | "uncertainty" | "entity-source" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-id" | undefined;
             focus: PD.Normalize<{
                 name: any;
                 params: any;
@@ -44,14 +44,14 @@ export declare namespace StructureRepresentationPresetProvider {
     function reprBuilder(plugin: PluginContext, params: CommonParams, structure?: Structure): {
         update: import("../../../mol-state/state/builder").StateBuilder.Root;
         builder: import("./representation").StructureRepresentationBuilder;
-        color: "occupancy" | "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | undefined;
-        symmetryColor: "occupancy" | "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | undefined;
+        color: "uniform" | "occupancy" | "element-index" | "element-symbol" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "unit-index" | "uncertainty" | "entity-source" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-id" | undefined;
+        symmetryColor: "uniform" | "occupancy" | "element-index" | "element-symbol" | "carbohydrate-symbol" | "chain-id" | "operator-name" | "molecule-type" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "unit-index" | "uncertainty" | "entity-source" | "illustrative" | "hydrophobicity" | "model-index" | "operator-hkl" | "partial-charge" | "atom-id" | "entity-id" | undefined;
         typeParams: {
-            quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+            quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
             ignoreHydrogens: boolean;
         };
         ballAndStickColor: Partial<PD.Values<{
-            carbonColor: PD.Mapped<PD.NamedParams<PD.Normalize<{
+            carbonColor: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "element-symbol"> | PD.NamedParams<PD.Normalize<{
                 palette: PD.NamedParams<PD.Normalize<{
                     maxCount: any;
                     hue: any;
@@ -74,7 +74,7 @@ export declare namespace StructureRepresentationPresetProvider {
                 }>, "generate"> | PD.NamedParams<PD.Normalize<{
                     list: any;
                 }>, "colors">;
-            }>, "operator-name"> | PD.NamedParams<PD.Normalize<unknown>, "element-symbol">>;
+            }>, "operator-name">>;
             saturation: PD.Numeric;
             lightness: PD.Numeric;
         }>>;
@@ -94,7 +94,7 @@ export declare const PresetStructureRepresentations: {
     empty: StructureRepresentationPresetProvider<unknown, {}>;
     auto: StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;
@@ -123,7 +123,7 @@ export declare const PresetStructureRepresentations: {
     'atomic-detail': StructureRepresentationPresetProvider<{
         showCarbohydrateSymbol: boolean;
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;
@@ -144,7 +144,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'polymer-cartoon': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;
@@ -164,7 +164,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'polymer-and-ligand': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;
@@ -199,7 +199,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'protein-and-nucleic': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;
@@ -221,7 +221,7 @@ export declare const PresetStructureRepresentations: {
     }>;
     'coarse-surface': StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;

package/lib/mol-plugin-state/builder/structure/representation-preset.js CHANGED Viewed

@@ -437,7 +437,7 @@ export function presetStaticComponent(plugin, structure, type, params) {
     return plugin.builders.structure.tryCreateComponentStatic(structure, type, params);
 }
 export function presetSelectionComponent(plugin, structure, query, params) {
-    return plugin.builders.structure.tryCreateComponentFromSelection(structure, Q[query], "selection-" + query, params);
+    return plugin.builders.structure.tryCreateComponentFromSelection(structure, Q[query], "selection-".concat(query), params);
 }
 export var PresetStructureRepresentations = {
     empty: empty,

package/lib/mol-plugin-state/builder/structure/representation-preset.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-plugin-state/builder/structure/representation.d.ts CHANGED Viewed

@@ -17,7 +17,7 @@ export declare class StructureRepresentationBuilder {
     private get dataState();
     readonly defaultProvider: StructureRepresentationPresetProvider<{
         ignoreHydrogens: boolean | undefined;
-        quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined;
+        quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest" | undefined;
         theme: PD.Normalize<{
             globalName: any;
             carbonColor: any;

package/lib/mol-plugin-state/builder/structure/representation.js CHANGED Viewed

@@ -86,7 +86,7 @@ var StructureRepresentationBuilder = /** @class */ (function () {
     };
     StructureRepresentationBuilder.prototype.registerPreset = function (provider) {
         if (this.providerMap.has(provider.id)) {
-            throw new Error("Representation provider with id '" + provider.id + "' already registered.");
+            throw new Error("Representation provider with id '".concat(provider.id, "' already registered."));
         }
         this._providers.push(provider);
         this.providerMap.set(provider.id, provider);
@@ -114,7 +114,7 @@ var StructureRepresentationBuilder = /** @class */ (function () {
             : {});
         var defaults = this.plugin.config.get(PluginConfig.Structure.DefaultRepresentationPresetParams);
         prms = PD.merge(pd, defaults, prms);
-        var task = Task.create("" + provider.display.name, function () { return provider.apply(cell, prms, _this.plugin); });
+        var task = Task.create("".concat(provider.display.name), function () { return provider.apply(cell, prms, _this.plugin); });
         return this.plugin.runTask(task);
     };
     StructureRepresentationBuilder.prototype.addRepresentation = function (structure, props, options) {

package/lib/mol-plugin-state/builder/structure/representation.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/mol-plugin-state/builder/structure.js CHANGED Viewed

@@ -34,7 +34,7 @@ var StructureBuilder = /** @class */ (function () {
                     case 0:
                         provider = typeof format === 'string' ? this.plugin.dataFormats.get(format) : format;
                         if (!provider)
-                            throw new Error("'" + format + "' is not a supported data format.");
+                            throw new Error("'".concat(format, "' is not a supported data format."));
                         return [4 /*yield*/, provider.parse(this.plugin, data)];
                     case 1:
                         trajectory = (_a.sent()).trajectory;
@@ -120,7 +120,7 @@ var StructureBuilder = /** @class */ (function () {
                     case 0:
                         state = this.dataState;
                         root = state.build().to(structure);
-                        keyTag = "structure-component-" + key;
+                        keyTag = "structure-component-".concat(key);
                         component = root.applyOrUpdateTagged(keyTag, StateTransforms.Model.StructureComponent, params, {
                             tags: tags ? __spreadArray(__spreadArray([], tags, true), [keyTag], false) : [keyTag]
                         });
@@ -150,7 +150,7 @@ var StructureBuilder = /** @class */ (function () {
             type: { name: 'static', params: type },
             nullIfEmpty: true,
             label: ((params === null || params === void 0 ? void 0 : params.label) || '').trim()
-        }, "static-" + type, params === null || params === void 0 ? void 0 : params.tags);
+        }, "static-".concat(type), params === null || params === void 0 ? void 0 : params.tags);
     };
     StructureBuilder.prototype.tryCreateComponentFromSelection = function (structure, selection, key, params) {
         var _this = this;

package/lib/mol-plugin-state/builder/structure.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"structure.js","sourceRoot":"","sources":["../../../src/mol-plugin-state/builder/structure.ts"],"names":[],"mappings":"AAAA;;;;GAIG;;AAGH,OAAO,EAAE,cAAc,EAA0E,MAAM,iBAAiB,CAAC;AACzH,OAAO,EAAE,iBAAiB,IAAI,EAAE,EAAE,MAAM,YAAY,CAAC;AACrD,OAAO,EAAE,eAAe,EAAE,MAAM,eAAe,CAAC;AAIhD,OAAO,EAAE,8BAA8B,EAAE,MAAM,4BAA4B,CAAC;AAE5E,OAAO,EAAE,IAAI,EAAE,MAAM,gBAAgB,CAAC;AACtC,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAC;AAC7D,OAAO,EAAE,aAAa,EAAE,MAAM,qDAAqD,CAAC;AACpF,OAAO,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAC;AAEzD,OAAO,EAAE,0BAA0B,EAAE,MAAM,uBAAuB,CAAC;AAEnE;IAgKI,0BAAmB,MAAqB;QAArB,WAAM,GAAN,MAAM,CAAe;QA5I/B,cAAS,GAAG,IAAI,0BAA0B,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QACxD,mBAAc,GAAG,IAAI,8BAA8B,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IA4I1E,CAAC;IAhKD,sBAAY,uCAAS;aAArB;YACI,OAAO,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC;QAClC,CAAC;;;OAAA;IAEa,8CAAmB,GAAjC,UAAkC,IAAqD,EAAE,MAA0D;;;;;;wBACzI,QAAQ,GAAG,OAAO,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,MAAM,CAA6B,CAAC,CAAC,CAAC,MAAM,CAAC;wBACvH,IAAI,CAAC,QAAQ;4BAAE,MAAM,IAAI,KAAK,CAAC,WAAI,MAAM,sCAAmC,CAAC,CAAC;wBACvD,qBAAM,QAAQ,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,EAAA;;wBAAtD,UAAU,GAAK,CAAA,SAAuC,CAAA,WAA5C;wBAClB,sBAAO,UAAU,EAAC;;;;KACrB;IAEO,8CAAmB,GAA3B,UAA4B,IAAkC,EAAE,MAAqE;QACjI,IAAM,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC;QAC7B,IAAM,UAAU,GAAG,KAAK,CAAC,KAAK,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC;aACpC,KAAK,CAAC,eAAe,CAAC,IAAI,CAAC,SAAS,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,IAAI,EAAE,EAAE,CAAC;aAC3E,KAAK,CAAC,eAAe,CAAC,KAAK,CAAC,kBAAkB,EAAE,KAAK,CAAC,CAAC,CAAC;QAC7D,OAAO,UAAU,CAAC,MAAM,CAAC,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;IACtD,CAAC;IAOD,0CAAe,GAAf,UAAgB,IAAoB,EAAE,MAAW;QAC7C,IAAM,IAAI,GAAG,cAAc,CAAC,eAAe,CAAC,IAAI,CAAC,SAAS,EAAE,IAAsB,CAAC,CAAC;QACpF,IAAI,CAAC,IAAI;YAAE,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAC;QAEjD,IAAI,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE;YAC3B,OAAO,IAAI,CAAC,mBAAmB,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;SACjD;aAAM;YACH,OAAO,IAAI,CAAC,mBAAmB,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;SACjD;IACL,CAAC;IAED,sCAAW,GAAX,UAAY,UAAkD,EAAE,MAAiF,EAAE,YAA4C;QAC3L,IAAM,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC;QAC7B,IAAM,KAAK,GAAG,KAAK,CAAC,KAAK,EAAE,CAAC,EAAE,CAAC,UAAU,CAAC;aACrC,KAAK,CAAC,eAAe,CAAC,KAAK,CAAC,mBAAmB,EAAE,MAAM,IAAI,EAAE,UAAU,EAAE,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,YAAY,EAAE,CAAC,CAAC;QAE5G,OAAO,KAAK,CAAC,MAAM,CAAC,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;IACjD,CAAC;IAED,gDAAqB,GAArB,UAAsB,KAAwC,EAAE,MAAmF,EAAE,YAA4C;QAC7L,IAAM,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC;QAC7B,IAAM,KAAK,GAAG,KAAK,CAAC,KAAK,EAAE,CAAC,EAAE,CAAC,KAAK,CAAC;aAChC,KAAK,CAAC,eAAe,CAAC,KAAK,CAAC,qBAAqB,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,YAAY,EAAE,CAAC,CAAC;QACzF,OAAO,KAAK,CAAC,MAAM,CAAC,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;IACjD,CAAC;IAED,4CAAiB,GAAjB,UAAkB,KAAwC,EAAE,MAAsF,EAAE,YAA4C;;QAC5L,IAAM,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC;QAC7B,IAAM,CAAC,GAAG,MAAA,MAAA,cAAc,CAAC,eAAe,CAAC,KAAK,EAAE,KAAK,CAAC,0CAAE,GAAG,0CAAE,IAAI,CAAC;QAClE,IAAI,CAAC,CAAC;YAAE,OAAO;QACf,IAAM,IAAI,GAAG,MAAA,aAAa,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,0CAAE,UAAU,CAAC,IAAI,CAAC;QAC5D,IAAI,cAAc,CAAC,MAAM,CAAC,IAAI,CAAC;YAAE,OAAO;QAExC,IAAM,QAAQ,GAAG,KAAK,CAAC,KAAK,EAAE,CAAC,EAAE,CAAC,KAAK,CAAC;aACnC,KAAK,CAAC,eAAe,CAAC,cAAc,CAAC,eAAe,EAAE,MAAM,EAAE,EAAE,KAAK,EAAE,YAAY,EAAE,CAAC,CAAC;QAC5F,OAAO,QAAQ,CAAC,MAAM,CAAC,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;IACpD,CAAC;IAED,0CAAe,GAAf,UAAgB,QAA2C,EAAE,MAAuC,EAAE,YAA4C;;QAC9I,IAAM,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC;QAE7B,IAAI,CAAC,MAAM,EAAE;YACT,IAAM,KAAK,GAAG,cAAc,CAAC,eAAe,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC;YAC9D,IAAI,KAAK,EAAE;gBACP,IAAM,IAAI,GAAG,aAAa,CAAC,QAAQ,CAAC,GAAG,CAAC,MAAA,KAAK,CAAC,GAAG,0CAAE,IAAK,CAAC,CAAC;gBAC1D,IAAI,CAAC,IAAI,IAAI,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,UAAU,CAAC,MAAM,MAAK,CAAC;oBAAE,MAAM,GAAG,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,EAAG,EAAE,CAAC;aACvF;SACJ;QAED,IAAM,SAAS,GAAG,KAAK,CAAC,KAAK,EAAE,CAAC,EAAE,CAAC,QAAQ,CAAC;aACvC,KAAK,CAAC,eAAe,CAAC,KAAK,CAAC,kBAAkB,EAAE,EAAE,IAAI,EAAE,MAAM,IAAI,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,EAAE,EAAG,EAAE,EAAE,EAAE,EAAE,KAAK,EAAE,YAAY,EAAE,CAAC,CAAC;QAErI,OAAO,SAAS,CAAC,MAAM,CAAC,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;IACrD,CAAC;IAED,oDAAyB,GAAzB,UAA0B,SAAgD,EAAE,MAAuF;QAC/J,IAAM,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC;QAC7B,IAAM,KAAK,GAAG,KAAK,CAAC,KAAK,EAAE,CAAC,EAAE,CAAC,SAAS,CAAC;aACpC,KAAK,CAAC,eAAe,CAAC,KAAK,CAAC,yBAAyB,EAAE,MAAM,CAAC,CAAC;QACpE,OAAO,KAAK,CAAC,MAAM,CAAC,EAAE,aAAa,EAAE,IAAI,EAAE,CAAC,CAAC;IACjD,CAAC;IAED,+CAAoB,GAApB,UAAqB,IAAqB;QACtC,OAAO,IAAI,CAAC,SAAS,CAAC,WAAW,KAAK,eAAe,CAAC,KAAK,CAAC,kBAAkB,CAAC;IACnF,CAAC;IAED,uDAAuD;IACjD,6CAAkB,GAAxB,UAAyB,SAAgD,EAAE,MAAgC,EAAE,GAAW,EAAE,IAAe;;;;;;;wBAC/H,KAAK,GAAG,IAAI,CAAC,SAAS,CAAC;wBAEvB,IAAI,GAAG,KAAK,CAAC,KAAK,EAAE,CAAC,EAAE,CAAC,SAAS,CAAC,CAAC;wBAEnC,MAAM,GAAG,8BAAuB,GAAG,CAAE,CAAC;wBACtC,SAAS,GAAG,IAAI,CAAC,mBAAmB,CAAC,MAAM,EAAE,eAAe,CAAC,KAAK,CAAC,kBAAkB,EAAE,MAAM,EAAE;4BACjG,IAAI,EAAE,IAAI,CAAC,CAAC,iCAAK,IAAI,UAAE,MAAM,UAAE,CAAC,CAAC,CAAC,MAAM,CAAC;yBAC5C,CAAC,CAAC;wBAEH,qBAAM,SAAS,CAAC,MAAM,EAAE,EAAA;;wBAAxB,SAAwB,CAAC;wBAEnB,QAAQ,GAAG,SAAS,CAAC,QAAQ,CAAC;6BAEhC,CAAA,CAAC,QAAQ,CAAC,IAA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package/lib/mol-plugin-state/formats/registry.js CHANGED Viewed

@@ -121,7 +121,7 @@ var DataFormatRegistry = /** @class */ (function () {
             return this._map.get(name);
         }
         else {
-            throw new Error("unknown data format name '" + name + "'");
+            throw new Error("unknown data format name '".concat(name, "'"));
         }
     };
     Object.defineProperty(DataFormatRegistry.prototype, "list", {

package/lib/mol-plugin-state/formats/registry.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"registry.js","sourceRoot":"","sources":["../../../src/mol-plugin-state/formats/registry.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,EAAE,wBAAwB,EAAE,MAAM,cAAc,CAAC;AACxD,OAAO,EAAE,oBAAoB,EAAE,MAAM,UAAU,CAAC;AAChD,OAAO,EAAE,mBAAmB,EAAE,MAAM,SAAS,CAAC;AAC9C,OAAO,EAAE,uBAAuB,EAAE,MAAM,aAAa,CAAC;AAEtD;IAsCI;QArCQ,UAAK,GAAqD,EAAE,CAAA;QAC5D,SAAI,GAAG,IAAI,GAAG,EAA8B,CAAA;QAC5C,gBAAW,GAA4B,SAAS,CAAA;QAChD,sBAAiB,GAA4B,SAAS,CAAA;QACtD,aAAQ,GAA2C,SAAS,CAAA;QAkChE,KAAsB,UAAoB,EAApB,6CAAoB,EAApB,kCAAoB,EAApB,IAAoB;YAA/B,IAAA,+BAAO,EAAN,EAAE,QAAA,EAAE,CAAC,QAAA;YAA2B,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;SAAA;QAC5D,KAAsB,UAAuB,EAAvB,mDAAuB,EAAvB,qCAAuB,EAAvB,IAAuB;YAAlC,IAAA,kCAAO,EAAN,EAAE,QAAA,EAAE,CAAC,QAAA;YAA8B,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;SAAA;QAC/D,KAAsB,UAAmB,EAAnB,2CAAmB,EAAnB,iCAAmB,EAAnB,IAAmB;YAA9B,IAAA,8BAAO,EAAN,EAAE,QAAA,EAAE,CAAC,QAAA;YAA0B,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;SAAA;QAC3D,KAAsB,UAAwB,EAAxB,qDAAwB,EAAxB,sCAAwB,EAAxB,IAAwB;YAAnC,IAAA,mCAAO,EAAN,EAAE,QAAA,EAAE,CAAC,QAAA;YAA+B,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC;SAAA;IACpE,CAAC;IApCD,sBAAI,qCAAK;aAAT;YACI,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAqB,EAA9C,CAA8C,CAAC,CAAC;QAC/E,CAAC;;;OAAA;IAED,sBAAI,0CAAU;aAAd;YACI,IAAI,IAAI,CAAC,WAAW;gBAAE,OAAO,IAAI,CAAC,WAAW,CAAC;YAC9C,IAAM,UAAU,GAAG,IAAI,GAAG,EAAU,CAAC;YACrC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,UAAC,EAAY;;oBAAV,QAAQ,cAAA;gBAC1B,MAAA,QAAQ,CAAC,gBAAgB,0CAAE,OAAO,CAAC,UAAA,GAAG,IAAI,OAAA,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAnB,CAAmB,CAAC,CAAC;gBAC/D,MAAA,QAAQ,CAAC,gBAAgB,0CAAE,OAAO,CAAC,UAAA,GAAG,IAAI,OAAA,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAnB,CAAmB,CAAC,CAAC;YACnE,CAAC,CAAC,CAAC;YACH,IAAI,CAAC,WAAW,GAAG,UAAU,CAAC;YAC9B,OAAO,UAAU,CAAC;QACtB,CAAC;;;OAAA;IAED,sBAAI,gDAAgB;aAApB;YACI,IAAI,IAAI,CAAC,iBAAiB;gBAAE,OAAO,IAAI,CAAC,iBAAiB,CAAC;YAC1D,IAAM,gBAAgB,GAAG,IAAI,GAAG,EAAU,CAAC;YAC3C,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,UAAC,EAAY;;oBAAV,QAAQ,cAAA;gBAAO,OAAA,MAAA,QAAQ,CAAC,gBAAgB,0CAAE,OAAO,CAAC,UAAA,GAAG,IAAI,OAAA,gBAAgB,CAAC,GAAG,CAAC,GAAG,CAAC,EAAzB,CAAyB,CAAC,CAAA;aAAA,CAAC,CAAC;YAC3G,IAAI,CAAC,iBAAiB,GAAG,gBAAgB,CAAC;YAC1C,OAAO,gBAAgB,CAAC;QAC5B,CAAC;;;OAAA;IAED,sBAAI,uCAAO;aAAX;YACI,IAAI,IAAI,CAAC,QAAQ;gBAAE,OAAO,IAAI,CAAC,QAAQ,CAAC;YACxC,IAAM,OAAO,GAA+B,EAAE,CAAC;YAC/C,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,UAAC,EAAkB;oBAAhB,IAAI,UAAA,EAAE,QAAQ,cAAA;gBAAO,OAAA,OAAO,CAAC,IAAI,CAAC,CAAC,IAAI,EAAE,QAAQ,CAAC,KAAK,EAAE,QAAQ,CAAC,QAAQ,IAAI,EAAE,CAAC,CAAC;YAA7D,CAA6D,CAAC,CAAC;YAC1G,IAAI,CAAC,QAAQ,GAAG,OAAO,CAAC;YACxB,OAAO,OAAO,CAAC;QACnB,CAAC;;;OAAA;IAOA,CAAC;IAEM,mCAAM,GAAd;QACI,IAAI,CAAC,WAAW,GAAG,SAAS,CAAC;QAC7B,IAAI,CAAC,iBAAiB,GAAG,SAAS,CAAC;QACnC,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAC;IAC9B,CAAC;IAED,gCAAG,GAAH,UAAI,IAAY,EAAE,QAA4B;QAC1C,IAAI,CAAC,MAAM,EAAE,CAAC;QACd,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,MAAA,EAAE,QAAQ,UAAA,EAAE,CAAC,CAAC;QACpC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAC;IAClC,CAAC;IAED,mCAAM,GAAN,UAAO,IAAY;QACf,IAAI,CAAC,MAAM,EAAE,CAAC;QACd,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,IAAI,KAAK,IAAI,EAAf,CAAe,CAAC,EAAE,CAAC,CAAC,CAAC;QACjE,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;IAC3B,CAAC;IAED,iCAAI,GAAJ,UAAK,IAAc,EAAE,eAA8E;QAC/F,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,EAAE;YACxC,IAAA,QAAQ,GAAK,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,SAAlB,CAAmB;YAEnC,IAAI,MAAM,GAAG,KAAK,CAAC;YACnB,IAAI,QAAQ,CAAC,gBAAgB,IAAI,QAAQ,CAAC,gBAAgB,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC;gBAAE,MAAM,GAAG,IAAI,CAAC;iBAC5F,IAAI,QAAQ,CAAC,gBAAgB,IAAI,QAAQ,CAAC,gBAAgB,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC;gBAAE,MAAM,GAAG,IAAI,CAAC;YACtG,IAAI,MAAM,IAAI,CAAC,CAAC,QAAQ,CAAC,YAAY,IAAI,QAAQ,CAAC,YAAY,CAAC,IAAI,EAAE,eAAe,CAAC,IAAI,CAAC,CAAC;gBAAE,OAAO,QAAQ,CAAC;SAChH;QACD,OAAO;IACX,CAAC;IAED,gCAAG,GAAH,UAAI,IAAY;QACZ,IAAI,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;YACrB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,CAAE,CAAC;SAC/B;aAAM;YACH,MAAM,IAAI,KAAK,CAAC,oCAA6B,IAAI,MAAG,CAAC,CAAC;SACzD;IACL,CAAC;IAED,sBAAI,oCAAI;aAAR;YACI,OAAO,IAAI,CAAC,KAAK,CAAC;QACtB,CAAC;;;OAAA;IACL,yBAAC;AAAD,CAAC,AAtFD,IAsFC"}

package/lib/mol-plugin-state/formats/volume.d.ts CHANGED Viewed

@@ -69,14 +69,14 @@ export declare const CubeProvider: {
         structure: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Molecule.Model, PluginStateObject.Molecule.Structure, import("../../mol-util/param-definition").ParamDefinition.Normalize<{
             type: import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
-                ijkMin: any;
-                ijkMax: any;
-            }>, "symmetry"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+            }>, "auto"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
                 id: any;
             }>, "assembly"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
-            }>, "auto"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+                ijkMin: any;
+                ijkMax: any;
+            }>, "symmetry"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
             }>, "model"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
@@ -150,14 +150,14 @@ export declare const BuiltInVolumeFormats: readonly [readonly ["ccp4", {
         structure: StateObjectSelector<PluginStateObject.Molecule.Structure, import("../../mol-state/transformer").StateTransformer<PluginStateObject.Molecule.Model, PluginStateObject.Molecule.Structure, import("../../mol-util/param-definition").ParamDefinition.Normalize<{
             type: import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
-                ijkMin: any;
-                ijkMax: any;
-            }>, "symmetry"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+            }>, "auto"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
                 id: any;
             }>, "assembly"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
-            }>, "auto"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+                ijkMin: any;
+                ijkMax: any;
+            }>, "symmetry"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
             }>, "model"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;

package/lib/mol-plugin-state/formats/volume.js CHANGED Viewed

@@ -40,6 +40,7 @@ function tryObtainRecommendedIsoValue(plugin, volume) {
                                 return [3 /*break*/, 3];
                             case 2:
                                 e_1 = _a.sent();
+                                console.warn(e_1);
                                 return [3 /*break*/, 3];
                             case 3: return [2 /*return*/];
                         }

package/lib/mol-plugin-state/formats/volume.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/mol-plugin-state/helpers/root-structure.d.ts CHANGED Viewed

@@ -14,14 +14,14 @@ export declare namespace RootStructureDefinition {
     function getParams(model?: Model, defaultValue?: 'auto' | 'model' | 'assembly' | 'symmetry' | 'symmetry-mates' | 'symmetry-assembly'): {
         type: PD.Mapped<PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;
-            ijkMin: Vec3;
-            ijkMax: Vec3;
-        }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
+        }>, "auto"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;
             id: string | undefined;
         }>, "assembly"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;
-        }>, "auto"> | PD.NamedParams<PD.Normalize<{
+            ijkMin: Vec3;
+            ijkMax: Vec3;
+        }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;
         }>, "model"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;

package/lib/mol-plugin-state/helpers/root-structure.js CHANGED Viewed

@@ -20,19 +20,19 @@ export var RootStructureDefinition;
 (function (RootStructureDefinition) {
     function getParams(model, defaultValue) {
         var symmetry = model && ModelSymmetry.Provider.get(model);
-        var assemblyIds = symmetry ? symmetry.assemblies.map(function (a) { return [a.id, a.id + ": " + stringToWords(a.details)]; }) : [];
+        var assemblyIds = symmetry ? symmetry.assemblies.map(function (a) { return [a.id, "".concat(a.id, ": ").concat(stringToWords(a.details))]; }) : [];
         var showSymm = !symmetry ? true : !SpacegroupCell.isZero(symmetry.spacegroup.cell);
         var operatorOptions = [];
         if (symmetry) {
             var operators = symmetry.spacegroup.operators;
             for (var i = 0, il = operators.length; i < il; i++) {
-                operatorOptions.push([i, i + 1 + ": " + Spacegroup.getOperatorXyz(operators[i])]);
+                operatorOptions.push([i, "".concat(i + 1, ": ").concat(Spacegroup.getOperatorXyz(operators[i]))]);
             }
         }
         var asymIdsOptions = [];
         if (model) {
             model.properties.structAsymMap.forEach(function (v) {
-                var label = v.id === v.auth_id ? v.id : v.id + " [auth " + v.auth_id + "]";
+                var label = v.id === v.auth_id ? v.id : "".concat(v.id, " [auth ").concat(v.auth_id, "]");
                 asymIdsOptions.push([v.id, label]);
             });
         }
@@ -48,11 +48,11 @@ export var RootStructureDefinition;
                     operators: PD.ObjectList({
                         index: PD.Select(0, operatorOptions),
                         shift: PD.Vec3(Vec3(), { step: 1 }, { label: 'IJK', fieldLabels: { x: 'I', y: 'J', z: 'K' } })
-                    }, function (e) { return e.index + 1 + "_" + e.shift.map(function (a) { return a + 5; }).join(''); }, {
+                    }, function (e) { return "".concat(e.index + 1, "_").concat(e.shift.map(function (a) { return a + 5; }).join('')); }, {
                         defaultValue: []
                     }),
                     asymIds: PD.MultiSelect([], asymIdsOptions)
-                }, function (e) { return e.asymIds.length + " asym ids, " + e.operators.length + " operators"; }, {
+                }, function (e) { return "".concat(e.asymIds.length, " asym ids, ").concat(e.operators.length, " operators"); }, {
                     defaultValue: []
                 }) }, CommonStructureParams), { isFlat: true })
         };
@@ -93,12 +93,12 @@ export var RootStructureDefinition;
                             id = symmetry.assemblies[0].id;
                         }
                         if (!symmetry || symmetry.assemblies.length === 0) {
-                            plugin.log.warn("Model '" + model.entryId + "' has no assembly, returning model structure.");
+                            plugin.log.warn("Model '".concat(model.entryId, "' has no assembly, returning model structure."));
                         }
                         else {
                             asm = Symmetry.findAssembly(model, id || '');
                             if (!asm) {
-                                plugin.log.warn("Model '" + model.entryId + "' has no assembly called '" + id + "', returning model structure.");
+                                plugin.log.warn("Model '".concat(model.entryId, "' has no assembly called '").concat(id, "', returning model structure."));
                             }
                         }
                         base = Structure.ofModel(model, props);
@@ -110,7 +110,7 @@ export var RootStructureDefinition;
                         return [4 /*yield*/, StructureSymmetry.buildAssembly(base, id).runInContext(ctx)];
                     case 1:
                         s = _a.sent();
-                        objProps = { label: "Assembly " + id, description: Structure.elementDescription(s) };
+                        objProps = { label: "Assembly ".concat(id), description: Structure.elementDescription(s) };
                         return [2 /*return*/, new SO.Molecule.Structure(s, objProps)];
                 }
             });
@@ -126,7 +126,7 @@ export var RootStructureDefinition;
                         return [4 /*yield*/, StructureSymmetry.buildSymmetryRange(base, ijkMin, ijkMax).runInContext(ctx)];
                     case 1:
                         s = _a.sent();
-                        objProps = { label: "Symmetry [" + ijkMin + "] to [" + ijkMax + "]", description: Structure.elementDescription(s) };
+                        objProps = { label: "Symmetry [".concat(ijkMin, "] to [").concat(ijkMax, "]"), description: Structure.elementDescription(s) };
                         return [2 /*return*/, new SO.Molecule.Structure(s, objProps)];
                 }
             });
@@ -195,7 +195,7 @@ export var RootStructureDefinition;
                 if (params.name === 'symmetry-assembly') {
                     return [2 /*return*/, buildSymmetryAssembly(ctx, model, params.params.generators, symmetry, props)];
                 }
-                throw new Error("Unknown represetation type: " + params.name);
+                throw new Error("Unknown represetation type: ".concat(params.name));
             });
         });
     }