npm - molstar - Versions diffs - 2.3.3 → 2.3.5 - Mend

molstar 2.3.3 → 2.3.5

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 (355) hide show

package/lib/commonjs/mol-plugin/commands.d.ts CHANGED Viewed

@@ -259,13 +259,13 @@ export declare const PluginCommands: {
                     selectStrength: number;
                     markerPriority: number;
                     xrayEdgeFalloff: number;
-                    style: import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
+                    style: import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "flat"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "metallic"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<{
                         lightIntensity: any;
                         ambientIntensity: any;
                         metalness: any;
                         roughness: any;
                         reflectivity: any;
-                    }>, "custom"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "matte"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "flat"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "glossy"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "metallic"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "plastic">;
+                    }>, "custom"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "matte"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "glossy"> | import("../mol-util/param-definition").ParamDefinition.NamedParams<import("../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "plastic">;
                     clip: import("../mol-util/param-definition").ParamDefinition.Normalize<{
                         variant: any;
                         objects: any;
@@ -302,6 +302,10 @@ export declare const PluginCommands: {
                         maxDistanceMin: any;
                     }>, "on">;
                 }>>;
+                interaction: import("../mol-util/param-definition").ParamDefinition.Group<import("../mol-util/param-definition").ParamDefinition.Normalize<{
+                    maxFps: number;
+                    preferAtomPixelPadding: number;
+                }>>;
                 debug: import("../mol-util/param-definition").ParamDefinition.Group<import("../mol-util/param-definition").ParamDefinition.Normalize<{
                     sceneBoundingSpheres: boolean;
                     visibleSceneBoundingSpheres: boolean;

package/lib/commonjs/mol-plugin/config.d.ts CHANGED Viewed

@@ -24,6 +24,7 @@ export declare const PluginConfig: {
         DisablePreserveDrawingBuffer: PluginConfigItem<boolean>;
         PixelScale: PluginConfigItem<number>;
         PickScale: PluginConfigItem<number>;
+        PickPadding: PluginConfigItem<number>;
         EnableWboit: PluginConfigItem<boolean>;
         PreferWebGl1: PluginConfigItem<boolean>;
     };

package/lib/commonjs/mol-plugin/config.js CHANGED Viewed

@@ -36,6 +36,7 @@ exports.PluginConfig = {
         DisablePreserveDrawingBuffer: item('plugin-config.disable-preserve-drawing-buffer', false),
         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),
         // 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

package/lib/commonjs/mol-plugin/config.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"config.js","sourceRoot":"","sources":["../../../src/mol-plugin/config.ts"],"names":[],"mappings":";AAAA;;;;;GAKG;;;AAEH,oDAA0D;AAM1D;IAGI,0BAAmB,GAAW,EAAS,YAAgB;QAApC,QAAG,GAAH,GAAG,CAAQ;QAAS,iBAAY,GAAZ,YAAY,CAAI;IAAI,CAAC;IAF5D,mCAAQ,GAAR,cAAa,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;IAC/B,kCAAO,GAAP,cAAY,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;IAElC,uBAAC;AAAD,CAAC,AAJD,IAIC;AAJY,4CAAgB;AAM7B,SAAS,IAAI,CAAI,GAAW,EAAE,YAAgB,IAAI,OAAO,IAAI,gBAAgB,CAAC,GAAG,EAAE,YAAY,CAAC,CAAC,CAAC,CAAC;AAGnG,mFAAmF;AACnF,SAAS,MAAM;IACX,IAAI,OAAO,SAAS,KAAK,WAAW,IAAI,OAAO,MAAM,KAAK,WAAW;QAAE,OAAO,KAAK,CAAC;IACpF,IAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,CAAC;IAC3D,IAAM,aAAa,GAAG,SAAS,CAAC,SAAS,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC;IAChE,IAAM,aAAa,GAAG,SAAS,CAAC,cAAc,IAAI,CAAC,CAAC,CAAC,yCAAyC;IAC9F,OAAO,CAAE,MAAc,CAAC,QAAQ,IAAI,CAAC,KAAK,IAAI,CAAC,aAAa,IAAI,aAAa,CAAC,CAAC,CAAC;AACpF,CAAC;AAEY,QAAA,YAAY,GAAG;IACxB,IAAI,MAAA;IACJ,OAAO,EAAE;QACL,eAAe,EAAE,IAAI,CAAC,+BAA+B,EAAE,GAAG,CAAC;QAC3D,mBAAmB,EAAE,IAAI,CAAC,oCAAoC,EAAE,KAAK,CAAC;QACtE,4BAA4B,EAAE,IAAI,CAAC,+CAA+C,EAAE,KAAK,CAAC;QAC1F,UAAU,EAAE,IAAI,CAAC,2BAA2B,EAAE,CAAC,CAAC;QAChD,SAAS,EAAE,IAAI,CAAC,0BAA0B,EAAE,IAAI,CAAC;QACjD,WAAW,EAAE,IAAI,CAAC,4BAA4B,EAAE,CAAC,CAAC;QAClD,WAAW,EAAE,IAAI,CAAC,4BAA4B,EAAE,IAAI,CAAC;QACrD,oDAAoD;QACpD,yDAAyD;QACzD,YAAY,EAAE,IAAI,CAAC,6BAA6B,EAAE,MAAM,EAAE,CAAC;KAC9D;IACD,KAAK,EAAE;QACH,aAAa,EAAE,IAAI,CAAC,qBAAqB,EAAE,4CAA4C,CAAC;QACxF,aAAa,EAAE,IAAI,CAAC,qBAAqB,EAAE,4CAA4C,CAAC;QACxF,eAAe,EAAE,IAAI,CAAC,yBAAyB,EAAE,CAAC,CAAC;KACtD;IACD,eAAe,EAAE;QACb,OAAO,EAAE,IAAI,CAAC,0BAA0B,EAAE,IAAI,CAAC;QAC/C,aAAa,EAAE,IAAI,CAAC,yBAAyB,EAAE,wBAAwB,CAAC;QACxE,SAAS,EAAE,IAAI,CAAC,6BAA6B,EAAE,UAAC,CAAY,EAAE,MAAqB;YAC/E,OAAO,CAAC,CAAC,MAAM,CAAC,MAAM,KAAK,CAAC,IAAI,iBAAK,CAAC,qBAAqB,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC;QAC7E,CAAC,CAAC;QACF,gBAAgB,EAAE,IAAI,CAAC,qCAAqC,EAAE,2CAA2C,CAAC;KAC7G;IACD,QAAQ,EAAE;QACN,UAAU,EAAE,IAAI,CAAC,2BAA2B,EAAE,IAAI,CAAC;QACnD,YAAY,EAAE,IAAI,CAAC,6BAA6B,EAAE,IAAI,CAAC;QACvD,YAAY,EAAE,IAAI,CAAC,6BAA6B,EAAE,IAAI,CAAC;QACvD,iBAAiB,EAAE,IAAI,CAAC,oCAAoC,EAAE,IAAI,CAAC;QACnE,aAAa,EAAE,IAAI,CAAC,8BAA8B,EAAE,IAAI,CAAC;KAC5D;IACD,QAAQ,EAAE;QACN,kBAAkB,EAAE,IAAI,CAAsB,+BAA+B,EAAE,MAAM,CAAC;QACtF,mBAAmB,EAAE,IAAI,CAAuB,gCAAgC,EAAE,MAAM,CAAC;KAC5F;IACD,SAAS,EAAE;QACP,cAAc,EAAE,IAAI,CAAC,2BAA2B,EAAE,qBAAS,CAAC,qBAAqB,CAAC;QAClF,iCAAiC,EAAE,IAAI,CAAqD,gDAAgD,EAAE,EAAG,CAAC;KACrJ;CACJ,CAAC;AAEF;IAgBI,6BAAY,OAAuC;QAAnD,iBAGC;QAlBO,YAAO,GAAG,IAAI,GAAG,EAAkC,CAAC;QAgBxD,IAAI,CAAC,OAAO;YAAE,OAAO;QACrB,OAAO,CAAC,OAAO,CAAC,UAAC,EAAM;gBAAL,CAAC,QAAA,EAAE,CAAC,QAAA;YAAM,OAAA,KAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC;QAAtB,CAAsB,CAAC,CAAC;IACxD,CAAC;IAhBD,iCAAG,GAAH,UAAO,GAAwB;QAC3B,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC;YAAE,OAAO,GAAG,CAAC,YAAY,CAAC;QACpD,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAM,CAAC;IACtC,CAAC;IAED,iCAAG,GAAH,UAAO,GAAwB,EAAE,KAAQ;QACrC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,EAAE,KAAK,CAAC,CAAC;IACjC,CAAC;IAED,oCAAM,GAAN,UAAU,GAAwB;QAC9B,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;IAC7B,CAAC;IAML,0BAAC;AAAD,CAAC,AApBD,IAoBC;AApBY,kDAAmB"}

package/lib/commonjs/mol-plugin/context.js CHANGED Viewed

@@ -188,7 +188,7 @@ var PluginContext = /** @class */ (function () {
     };
     PluginContext.prototype.initViewer = function (canvas, container, canvas3dContext) {
         var _this = this;
-        var _a, _b, _c, _d, _e;
+        var _a, _b, _c, _d, _e, _f;
         try {
             this.layout.setRoot(container);
             if (this.spec.layout && this.spec.layout.initial)
@@ -201,19 +201,21 @@ var PluginContext = /** @class */ (function () {
                 var preserveDrawingBuffer = !((_b = this.config.get(config_1.PluginConfig.General.DisablePreserveDrawingBuffer)) !== null && _b !== void 0 ? _b : false);
                 var pixelScale = this.config.get(config_1.PluginConfig.General.PixelScale) || 1;
                 var pickScale = this.config.get(config_1.PluginConfig.General.PickScale) || 0.25;
+                var pickPadding = (_c = this.config.get(config_1.PluginConfig.General.PickPadding)) !== null && _c !== void 0 ? _c : 1;
                 var enableWboit = this.config.get(config_1.PluginConfig.General.EnableWboit) || false;
                 var preferWebGl1 = this.config.get(config_1.PluginConfig.General.PreferWebGl1) || false;
                 this.canvas3dContext = canvas3d_1.Canvas3DContext.fromCanvas(canvas, { antialias: antialias, preserveDrawingBuffer: preserveDrawingBuffer, pixelScale: pixelScale, pickScale: pickScale, enableWboit: enableWboit, preferWebGl1: preferWebGl1 });
+                this.canvas3dContext = canvas3d_1.Canvas3DContext.fromCanvas(canvas, { antialias: antialias, preserveDrawingBuffer: preserveDrawingBuffer, pixelScale: pixelScale, pickScale: pickScale, pickPadding: pickPadding, enableWboit: enableWboit });
             }
             this.canvas3d = canvas3d_1.Canvas3D.create(this.canvas3dContext);
             this.canvas3dInit.next(true);
             var props = this.spec.canvas3d;
             var backgroundColor_1 = (0, color_2.Color)(0xFCFBF9);
             if (!props) {
-                (_c = this.canvas3d) === null || _c === void 0 ? void 0 : _c.setProps({ renderer: { backgroundColor: backgroundColor_1 } });
+                (_d = this.canvas3d) === null || _d === void 0 ? void 0 : _d.setProps({ renderer: { backgroundColor: backgroundColor_1 } });
             }
             else {
-                if (((_d = props.renderer) === null || _d === void 0 ? void 0 : _d.backgroundColor) === void 0) {
+                if (((_e = props.renderer) === null || _e === void 0 ? void 0 : _e.backgroundColor) === void 0) {
                     props = (0, immer_1.default)(props, function (p) {
                         if (p.renderer)
                             p.renderer.backgroundColor = backgroundColor_1;
@@ -221,7 +223,7 @@ var PluginContext = /** @class */ (function () {
                             p.renderer = { backgroundColor: backgroundColor_1 };
                     });
                 }
-                (_e = this.canvas3d) === null || _e === void 0 ? void 0 : _e.setProps(props);
+                (_f = this.canvas3d) === null || _f === void 0 ? void 0 : _f.setProps(props);
             }
             this.animationLoop.start();
             this.helpers.viewportScreenshot = new viewport_screenshot_1.ViewportScreenshotHelper(this);

package/lib/commonjs/mol-plugin/context.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/commonjs/mol-plugin/util/viewport-screenshot.d.ts CHANGED Viewed

@@ -26,7 +26,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
             height: number;
         }>, "custom"> | PD.NamedParams<PD.Normalize<unknown>, "viewport"> | PD.NamedParams<PD.Normalize<unknown>, "hd"> | PD.NamedParams<PD.Normalize<unknown>, "full-hd"> | PD.NamedParams<PD.Normalize<unknown>, "ultra-hd">>;
         transparent: PD.BooleanParam;
-        axes: PD.Mapped<PD.NamedParams<PD.Normalize<{
+        axes: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
             alpha: number;
             ignoreLight: boolean;
             colorX: Color;
@@ -38,7 +38,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
             flatShaded: boolean;
             xrayShaded: boolean;
             quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
-        }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
+        }>, "on">>;
     };
     readonly behaviors: {
         values: import("rxjs").BehaviorSubject<PD.Values<{
@@ -47,7 +47,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
                 height: number;
             }>, "custom">>;
             transparent: PD.BooleanParam;
-            axes: PD.Mapped<PD.NamedParams<PD.Normalize<{
+            axes: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
                 alpha: number;
                 ignoreLight: boolean;
                 colorX: Color;
@@ -59,7 +59,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
                 flatShaded: boolean;
                 xrayShaded: boolean;
                 quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
-            }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
+            }>, "on">>;
         }>>;
         cropParams: import("rxjs").BehaviorSubject<{
             auto: boolean;
@@ -76,7 +76,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
             height: number;
         }>, "custom">>;
         transparent: PD.BooleanParam;
-        axes: PD.Mapped<PD.NamedParams<PD.Normalize<{
+        axes: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
             alpha: number;
             ignoreLight: boolean;
             colorX: Color;
@@ -88,7 +88,7 @@ declare class ViewportScreenshotHelper extends PluginComponent {
             flatShaded: boolean;
             xrayShaded: boolean;
             quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
-        }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
+        }>, "on">>;
     }>;
     get cropParams(): {
         auto: boolean;

package/lib/commonjs/mol-plugin-state/animation/built-in/model-index.d.ts CHANGED Viewed

@@ -12,12 +12,12 @@ export declare const AnimateModelIndex: PluginStateAnimation<{
         direction: any;
     }>, "once">;
     duration: PD.NamedParams<PD.Normalize<{
+        targetFps: any;
+    }>, "computed"> | PD.NamedParams<PD.Normalize<{
         maxFps: any;
     }>, "sequential"> | PD.NamedParams<PD.Normalize<{
         durationInS: any;
-    }>, "fixed"> | PD.NamedParams<PD.Normalize<{
-        targetFps: any;
-    }>, "computed">;
+    }>, "fixed">;
 }, {
     palindromeDirections?: {
         [id: string]: 1 | -1 | undefined;

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

@@ -48,19 +48,19 @@ export declare const PresetTrajectoryHierarchy: {
         showUnitcell: boolean | undefined;
         structure: PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
-        }>, "auto"> | PD.NamedParams<PD.Normalize<{
-            dynamicBonds: any;
-        }>, "model"> | PD.NamedParams<PD.Normalize<{
+            ijkMin: any;
+            ijkMax: any;
+        }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
             id: any;
         }>, "assembly"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
+        }>, "auto"> | PD.NamedParams<PD.Normalize<{
+            dynamicBonds: any;
+        }>, "model"> | PD.NamedParams<PD.Normalize<{
+            dynamicBonds: any;
             radius: any;
         }>, "symmetry-mates"> | PD.NamedParams<PD.Normalize<{
-            dynamicBonds: any;
-            ijkMin: any;
-            ijkMax: any;
-        }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
             generators: any;
         }>, "symmetry-assembly"> | undefined;

package/lib/commonjs/mol-plugin-state/builder/structure/hierarchy.d.ts CHANGED Viewed

@@ -30,19 +30,19 @@ export declare class TrajectoryHierarchyBuilder {
         showUnitcell: boolean | undefined;
         structure: PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
-        }>, "auto"> | PD.NamedParams<PD.Normalize<{
-            dynamicBonds: any;
-        }>, "model"> | PD.NamedParams<PD.Normalize<{
+            ijkMin: any;
+            ijkMax: any;
+        }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
             id: any;
         }>, "assembly"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
+        }>, "auto"> | PD.NamedParams<PD.Normalize<{
+            dynamicBonds: any;
+        }>, "model"> | PD.NamedParams<PD.Normalize<{
+            dynamicBonds: any;
             radius: any;
         }>, "symmetry-mates"> | PD.NamedParams<PD.Normalize<{
-            dynamicBonds: any;
-            ijkMin: any;
-            ijkMax: any;
-        }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
             generators: any;
         }>, "symmetry-assembly"> | undefined;

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

@@ -31,9 +31,9 @@ export declare namespace StructureRepresentationPresetProvider {
         ignoreHydrogens: PD.Base<boolean | undefined>;
         quality: PD.Base<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest" | undefined>;
         theme: PD.Base<PD.Normalize<{
-            globalName: "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "occupancy" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | undefined;
+            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: "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "occupancy" | "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;
             focus: PD.Normalize<{
                 name: any;
                 params: any;
@@ -44,8 +44,8 @@ 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: "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "occupancy" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | undefined;
-        symmetryColor: "uniform" | "atom-id" | "carbohydrate-symbol" | "chain-id" | "element-index" | "operator-name" | "element-symbol" | "entity-id" | "entity-source" | "hydrophobicity" | "illustrative" | "model-index" | "molecule-type" | "occupancy" | "operator-hkl" | "partial-charge" | "polymer-id" | "polymer-index" | "residue-name" | "secondary-structure" | "sequence-id" | "shape-group" | "uncertainty" | "unit-index" | undefined;
+        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;
         typeParams: {
             quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
             ignoreHydrogens: boolean;
@@ -53,27 +53,27 @@ export declare namespace StructureRepresentationPresetProvider {
         ballAndStickColor: Partial<PD.Values<{
             carbonColor: PD.Mapped<PD.NamedParams<PD.Normalize<{
                 palette: PD.NamedParams<PD.Normalize<{
-                    list: any;
-                }>, "colors"> | PD.NamedParams<PD.Normalize<{
                     maxCount: any;
                     hue: any;
                     chroma: any;
                     luminance: any;
                     clusteringStepCount: any;
                     minSampleCount: any;
-                }>, "generate">;
+                }>, "generate"> | PD.NamedParams<PD.Normalize<{
+                    list: any;
+                }>, "colors">;
                 asymId: "label" | "auth";
             }>, "chain-id"> | PD.NamedParams<PD.Normalize<{
                 palette: PD.NamedParams<PD.Normalize<{
-                    list: any;
-                }>, "colors"> | PD.NamedParams<PD.Normalize<{
                     maxCount: any;
                     hue: any;
                     chroma: any;
                     luminance: any;
                     clusteringStepCount: any;
                     minSampleCount: any;
-                }>, "generate">;
+                }>, "generate"> | PD.NamedParams<PD.Normalize<{
+                    list: any;
+                }>, "colors">;
             }>, "operator-name"> | PD.NamedParams<PD.Normalize<unknown>, "element-symbol">>;
             saturation: PD.Numeric;
             lightness: PD.Numeric;

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

@@ -69,19 +69,19 @@ 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;
-            }>, "auto"> | 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<{
+                ijkMin: any;
+                ijkMax: any;
+            }>, "symmetry"> | 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<{
+                dynamicBonds: any;
+            }>, "model"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+                dynamicBonds: any;
                 radius: any;
             }>, "symmetry-mates"> | 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<{
                 dynamicBonds: any;
                 generators: any;
             }>, "symmetry-assembly">;
@@ -90,7 +90,7 @@ export declare const CubeProvider: {
     visuals: (plugin: PluginContext, data: {
         volume: StateObjectSelector<PluginStateObject.Volume.Data>;
         structure: StateObjectSelector<PluginStateObject.Molecule.Structure>;
-    }) => Promise<(StateObjectSelector<PluginStateObject.Volume.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>)[]>;
+    }) => Promise<(StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | StateObjectSelector<PluginStateObject.Volume.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>)[]>;
 };
 declare type DsCifParams = {
     entryId?: string | string[];
@@ -150,19 +150,19 @@ 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;
-            }>, "auto"> | 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<{
+                ijkMin: any;
+                ijkMax: any;
+            }>, "symmetry"> | 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<{
+                dynamicBonds: any;
+            }>, "model"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+                dynamicBonds: any;
                 radius: any;
             }>, "symmetry-mates"> | 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<{
                 dynamicBonds: any;
                 generators: any;
             }>, "symmetry-assembly">;
@@ -171,7 +171,7 @@ export declare const BuiltInVolumeFormats: readonly [readonly ["ccp4", {
     visuals: (plugin: PluginContext, data: {
         volume: StateObjectSelector<PluginStateObject.Volume.Data>;
         structure: StateObjectSelector<PluginStateObject.Molecule.Structure>;
-    }) => Promise<(StateObjectSelector<PluginStateObject.Volume.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>)[]>;
+    }) => Promise<(StateObjectSelector<PluginStateObject.Molecule.Structure.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>> | StateObjectSelector<PluginStateObject.Volume.Representation3D, import("../../mol-state/transformer").StateTransformer<import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>>, any>>)[]>;
 }], readonly ["dx", {
     label: string;
     description: string;

package/lib/commonjs/mol-plugin-state/helpers/root-structure.d.ts CHANGED Viewed

@@ -14,19 +14,19 @@ 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;
-        }>, "auto"> | PD.NamedParams<PD.Normalize<{
-            dynamicBonds: boolean | undefined;
-        }>, "model"> | PD.NamedParams<PD.Normalize<{
+            ijkMin: Vec3;
+            ijkMax: Vec3;
+        }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;
             id: string | undefined;
         }>, "assembly"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;
+        }>, "auto"> | PD.NamedParams<PD.Normalize<{
+            dynamicBonds: boolean | undefined;
+        }>, "model"> | PD.NamedParams<PD.Normalize<{
+            dynamicBonds: boolean | undefined;
             radius: number;
         }>, "symmetry-mates"> | PD.NamedParams<PD.Normalize<{
-            dynamicBonds: boolean | undefined;
-            ijkMin: Vec3;
-            ijkMax: Vec3;
-        }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;
             generators: PD.Normalize<{
                 operators: {

package/lib/commonjs/mol-plugin-state/helpers/structure-component.d.ts CHANGED Viewed

@@ -13,7 +13,7 @@ import { Script } from '../../mol-script/script';
 export declare const StaticStructureComponentTypes: readonly ["all", "polymer", "protein", "nucleic", "water", "ion", "lipid", "branched", "ligand", "non-standard", "coarse"];
 export declare type StaticStructureComponentType = (typeof StaticStructureComponentTypes)[number];
 export declare const StructureComponentParams: () => {
-    type: PD.Mapped<PD.NamedParams<Script, "script"> | PD.NamedParams<"all" | "polymer" | "protein" | "nucleic" | "water" | "branched" | "ligand" | "non-standard" | "coarse" | "ion" | "lipid", "static"> | PD.NamedParams<Expression, "expression"> | PD.NamedParams<StructureElement.Bundle, "bundle">>;
+    type: PD.Mapped<PD.NamedParams<Script, "script"> | PD.NamedParams<"polymer" | "water" | "branched" | "ligand" | "ion" | "all" | "protein" | "nucleic" | "lipid" | "non-standard" | "coarse", "static"> | PD.NamedParams<Expression, "expression"> | PD.NamedParams<StructureElement.Bundle, "bundle">>;
     nullIfEmpty: PD.Base<boolean | undefined>;
     label: PD.Text<string>;
 };

package/lib/commonjs/mol-plugin-state/manager/interactivity.d.ts CHANGED Viewed

@@ -37,7 +37,7 @@ declare class InteractivityManager extends StatefulPluginComponent<Interactivity
 }
 declare namespace InteractivityManager {
     const Params: {
-        granularity: PD.Select<"model" | "structure" | "residue" | "chain" | "element" | "entity" | "operator" | "elementInstances" | "residueInstances" | "chainInstances">;
+        granularity: PD.Select<"residue" | "entity" | "model" | "chain" | "element" | "structure" | "operator" | "elementInstances" | "residueInstances" | "chainInstances">;
     };
     type Params = typeof Params;
     type Props = PD.Values<Params>;
@@ -80,7 +80,7 @@ declare namespace InteractivityManager {
         setProps(props: Partial<Props>): void;
         addProvider(provider: LociMarkProvider): void;
         removeProvider(provider: LociMarkProvider): void;
-        protected normalizedLoci(reprLoci: Representation.Loci, applyGranularity?: boolean): {
+        protected normalizedLoci(reprLoci: Representation.Loci, applyGranularity: boolean, alwaysConvertBonds?: boolean): {
             loci: Loci;
             repr: Representation.Any | undefined;
         };

package/lib/commonjs/mol-plugin-state/manager/interactivity.js CHANGED Viewed

@@ -76,11 +76,11 @@ exports.InteractivityManager = InteractivityManager;
             this.providers = this.providers.filter(function (p) { return p !== provider; });
             // TODO clear, then re-apply remaining providers
         };
-        LociMarkManager.prototype.normalizedLoci = function (reprLoci, applyGranularity) {
-            if (applyGranularity === void 0) { applyGranularity = true; }
+        LociMarkManager.prototype.normalizedLoci = function (reprLoci, applyGranularity, alwaysConvertBonds) {
+            if (alwaysConvertBonds === void 0) { alwaysConvertBonds = false; }
             var loci = reprLoci.loci, repr = reprLoci.repr;
             var granularity = applyGranularity ? this.props.granularity : undefined;
-            return { loci: loci_1.Loci.normalize(loci, granularity), repr: repr };
+            return { loci: loci_1.Loci.normalize(loci, granularity, alwaysConvertBonds), repr: repr };
         };
         LociMarkManager.prototype.mark = function (current, action, noRender) {
             if (noRender === void 0) { noRender = false; }
@@ -174,7 +174,7 @@ exports.InteractivityManager = InteractivityManager;
             if (applyGranularity === void 0) { applyGranularity = true; }
             if (loci_1.Loci.isEmpty(current.loci))
                 return;
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (structure_1.StructureElement.Loci.is(normalized.loci)) {
                 this.toggleSel(normalized);
             }
@@ -186,7 +186,7 @@ exports.InteractivityManager = InteractivityManager;
             if (applyGranularity === void 0) { applyGranularity = true; }
             if (loci_1.Loci.isEmpty(current.loci))
                 return;
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (structure_1.StructureElement.Loci.is(normalized.loci)) {
                 var loci = this.sel.tryGetRange(normalized.loci) || normalized.loci;
                 this.toggleSel({ loci: loci, repr: normalized.repr });
@@ -194,7 +194,7 @@ exports.InteractivityManager = InteractivityManager;
         };
         LociSelectManager.prototype.select = function (current, applyGranularity) {
             if (applyGranularity === void 0) { applyGranularity = true; }
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (structure_1.StructureElement.Loci.is(normalized.loci)) {
                 this.sel.modify('add', normalized.loci);
             }
@@ -202,7 +202,7 @@ exports.InteractivityManager = InteractivityManager;
         };
         LociSelectManager.prototype.selectJoin = function (current, applyGranularity) {
             if (applyGranularity === void 0) { applyGranularity = true; }
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (structure_1.StructureElement.Loci.is(normalized.loci)) {
                 this.sel.modify('intersect', normalized.loci);
             }
@@ -210,7 +210,7 @@ exports.InteractivityManager = InteractivityManager;
         };
         LociSelectManager.prototype.selectOnly = function (current, applyGranularity) {
             if (applyGranularity === void 0) { applyGranularity = true; }
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (structure_1.StructureElement.Loci.is(normalized.loci)) {
                 // only deselect for the structure of the given loci
                 this.deselect({ loci: structure_1.Structure.toStructureElementLoci(normalized.loci.structure), repr: normalized.repr }, false);
@@ -220,7 +220,7 @@ exports.InteractivityManager = InteractivityManager;
         };
         LociSelectManager.prototype.deselect = function (current, applyGranularity) {
             if (applyGranularity === void 0) { applyGranularity = true; }
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (structure_1.StructureElement.Loci.is(normalized.loci)) {
                 this.sel.modify('remove', normalized.loci);
             }
@@ -241,8 +241,9 @@ exports.InteractivityManager = InteractivityManager;
                     // do a full deselect/select for the current structure so visuals that are
                     // marked with granularity unequal to 'element' and join/intersect operations
                     // are handled properly
-                    _super.prototype.mark.call(this, { loci: structure_1.Structure.Loci(loci.structure) }, marker_action_1.MarkerAction.Deselect, true);
-                    _super.prototype.mark.call(this, { loci: this.sel.getLoci(loci.structure) }, marker_action_1.MarkerAction.Select);
+                    var selLoci = this.sel.getLoci(loci.structure);
+                    _super.prototype.mark.call(this, { loci: structure_1.Structure.Loci(loci.structure) }, marker_action_1.MarkerAction.Deselect, !loci_1.Loci.isEmpty(selLoci));
+                    _super.prototype.mark.call(this, { loci: selLoci }, marker_action_1.MarkerAction.Select);
                 }
                 else {
                     _super.prototype.mark.call(this, current, action);