molstar 2.3.9 → 2.4.0

package/lib/mol-plugin/behavior/dynamic/selection/structure-focus-representation.d.ts

@@ -18,7 +18,7 @@ declare const StructureFocusRepresentationParams: (plugin: PluginContext) => {
     nciParams: PD.Group<PD.Normalize<{
         [x: string]: any;
     }>>;
-    components: PD.MultiSelect<"target" | "surroundings" | "interactions">;
+    components: PD.MultiSelect<"target" | "interactions" | "surroundings">;
     excludeTargetFromSurroundings: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
 };

package/lib/mol-plugin/behavior/dynamic/volume-streaming/behavior.d.ts

@@ -49,16 +49,16 @@ export declare namespace VolumeStreaming {
         channelParams?: DefaultChannelParams;
     }): {
         entry: PD.Mapped<PD.NamedParams<PD.Values<{
-            view: PD.Mapped<PD.NamedParams<PD.Normalize<{
-                bottomLeft: Vec3;
-                topRight: Vec3;
-            }>, "box"> | PD.NamedParams<PD.Normalize<{
+            view: PD.Mapped<PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
                 radius: number;
                 selectionDetailLevel: number;
                 isSelection: boolean;
                 bottomLeft: Vec3;
                 topRight: Vec3;
-            }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
+            }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{
+                bottomLeft: Vec3;
+                topRight: Vec3;
+            }>, "box"> | PD.NamedParams<PD.Normalize<{
                 radius: number;
                 bottomLeft: Vec3;
                 topRight: Vec3;
@@ -81,16 +81,16 @@ export declare namespace VolumeStreaming {
         structure?: Structure;
         channelParams?: DefaultChannelParams;
     }): {
-        view: PD.Mapped<PD.NamedParams<PD.Normalize<{
-            bottomLeft: Vec3;
-            topRight: Vec3;
-        }>, "box"> | PD.NamedParams<PD.Normalize<{
+        view: PD.Mapped<PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
             radius: number;
             selectionDetailLevel: number;
             isSelection: boolean;
             bottomLeft: Vec3;
             topRight: Vec3;
-        }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
+        }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{
+            bottomLeft: Vec3;
+            topRight: Vec3;
+        }>, "box"> | PD.NamedParams<PD.Normalize<{
             radius: number;
             bottomLeft: Vec3;
             topRight: Vec3;

package/lib/mol-plugin/behavior/dynamic/volume-streaming/transformers.d.ts

@@ -38,16 +38,16 @@ export { CreateVolumeStreamingBehavior };
 declare type CreateVolumeStreamingBehavior = typeof CreateVolumeStreamingBehavior;
 declare const CreateVolumeStreamingBehavior: StateTransformer<VolumeServerInfo, VolumeStreaming, PD.Normalize<{
     entry: PD.NamedParams<PD.Values<{
-        view: PD.Mapped<PD.NamedParams<PD.Normalize<{
-            bottomLeft: any;
-            topRight: any;
-        }>, "box"> | PD.NamedParams<PD.Normalize<{
+        view: PD.Mapped<PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
             radius: any;
             selectionDetailLevel: any;
             isSelection: any;
             bottomLeft: any;
             topRight: any;
-        }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{}>, "cell"> | PD.NamedParams<PD.Normalize<{
+        }>, "auto"> | PD.NamedParams<PD.Normalize<{}>, "off"> | PD.NamedParams<PD.Normalize<{
+            bottomLeft: any;
+            topRight: any;
+        }>, "box"> | PD.NamedParams<PD.Normalize<{
             radius: any;
             bottomLeft: any;
             topRight: any;

package/lib/mol-plugin/commands.d.ts

@@ -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>, "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>, "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>, "plastic">;
                     clip: import("../mol-util/param-definition").ParamDefinition.Normalize<{
                         variant: any;
                         objects: any;

package/lib/mol-plugin/layout.d.ts

@@ -12,10 +12,10 @@ export declare const PluginLayoutStateParams: {
     isExpanded: PD.BooleanParam;
     showControls: PD.BooleanParam;
     regionState: PD.Group<PD.Normalize<{
-        left: "hidden" | "full" | "collapsed";
-        top: "hidden" | "full";
-        right: "hidden" | "full";
-        bottom: "hidden" | "full";
+        left: "full" | "collapsed" | "hidden";
+        top: "full" | "hidden";
+        right: "full" | "hidden";
+        bottom: "full" | "hidden";
     }>>;
     controlsDisplay: PD.Value<PluginLayoutControlsDisplay>;
 };

package/lib/mol-plugin/util/viewport-screenshot.d.ts

@@ -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/mol-plugin/version.js

@@ -1,2 +1,2 @@
-export var PLUGIN_VERSION = '2.3.9';
-export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1637456207413);
+export var PLUGIN_VERSION = '2.4.0';
+export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1637880277798);

package/lib/mol-plugin-state/actions/file.js

@@ -71,7 +71,8 @@ export var OpenFiles = StateAction.build({
                                     case 6: return [3 /*break*/, 8];
                                     case 7:
                                         e_1 = _d.sent();
-                                        plugin.log.error(e_1);
+                                        console.error(e_1);
+                                        plugin.log.error("Error opening file '".concat(file.name, "'"));
                                         return [3 /*break*/, 8];
                                     case 8:
                                         _i++;
@@ -132,7 +133,8 @@ export var DownloadFile = StateAction.build({
                                     case 4: return [3 /*break*/, 6];
                                     case 5:
                                         e_2 = _b.sent();
-                                        plugin.log.error(e_2);
+                                        console.error(e_2);
+                                        plugin.log.error("Error downloading '".concat(typeof params.url === 'string' ? params.url : params.url.url, "'"));
                                         return [3 /*break*/, 6];
                                     case 6: return [2 /*return*/];
                                 }

package/lib/mol-plugin-state/actions/file.js.map

@@ -1 +1 @@
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+{"version":3,"file":"file.js","sourceRoot":"","sources":["../../../src/mol-plugin-state/actions/file.ts"],"names":[],"mappings":"AAAA;;;;GAIG;;AAGH,OAAO,EAAE,WAAW,EAAE,MAAM,iBAAiB,CAAC;AAC9C,OAAO,EAAE,IAAI,EAAE,MAAM,gBAAgB,CAAC;AACtC,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAC;AACvD,OAAO,EAAE,eAAe,IAAI,EAAE,EAAE,MAAM,iCAAiC,CAAC;AACxE,OAAO,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAE/C,MAAM,CAAC,IAAM,SAAS,GAAG,WAAW,CAAC,KAAK,CAAC;IACvC,OAAO,EAAE,EAAE,IAAI,EAAE,YAAY,EAAE,WAAW,EAAE,8DAA8D,EAAE;IAC5G,IAAI,EAAE,iBAAiB,CAAC,IAAI;IAC5B,MAAM,EAAE,UAAC,CAAC,EAAE,GAAkB;QACpB,IAAA,KAA0B,GAAG,CAAC,WAAW,EAAvC,UAAU,gBAAA,EAAE,OAAO,aAAoB,CAAC;QAChD,OAAO;YACH,KAAK,EAAE,EAAE,CAAC,QAAQ,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,MAAM,EAAE,CAAC,CAAC,GAAG,CAAC,UAAA,CAAC,IAAI,OAAA,WAAI,CAAC,CAAE,EAAP,CAAO,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,WAAW,EAAE,QAAQ,EAAE,IAAI,EAAE,CAAC;YACzH,MAAM,EAAE,EAAE,CAAC,YAAY,CAAC,MAAM,EAAE;gBAC5B,IAAI,EAAE,EAAE,CAAC,UAAU,EAAE;gBACrB,QAAQ,EAAE,EAAE,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC;aAC9C,CAAC;YACF,OAAO,EAAE,EAAE,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,WAAW,EAAE,qBAAqB,EAAE,CAAC;SACpE,CAAC;IACN,CAAC;CACJ,CAAC,CAAC,UAAC,EAAiB,EAAE,MAAqB;QAAtC,MAAM,YAAA,EAAE,KAAK,WAAA;IAA8B,OAAA,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,UAAM,OAAO;;;;oBACpF,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;oBAEtD,qBAAM,KAAK,CAAC,WAAW,CAAC;;;;;;wCACpB,IAAI,MAAM,CAAC,KAAK,KAAK,IAAI,EAAE;4CACvB,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAC;4CACxC,sBAAO;yCACV;8CAC8B,EAAZ,KAAA,MAAM,CAAC,KAAK;;;6CAAZ,CAAA,cAAY,CAAA;wCAApB,IAAI;;;;wCAED,IAAI,GAAG,WAAW,CAAC,IAAI,CAAC,IAAK,CAAC,CAAC;wCAC/B,QAAQ,GAAG,MAAM,CAAC,WAAW,CAAC,gBAAgB,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;wCAClD,qBAAM,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,IAAI,MAAA,EAAE,QAAQ,UAAA,EAAE,CAAC,EAAA;;wCAAhE,IAAI,GAAK,CAAA,SAAuD,CAAA,KAA5D;wCACN,QAAQ,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,KAAK,MAAM;4CAC1C,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,EAAE,MAAA,IAAI,CAAC,IAAI,0CAAE,GAAI,CAAC;4CAChD,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;wCAEnD,IAAI,CAAC,QAAQ,EAAE;4CACX,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,uDAAgD,IAAI,CAAC,IAAI,cAAI,IAAI,CAAC,GAAG,MAAG,CAAC,CAAC;4CAC1F,wBAAS;yCACZ;wCAGc,qBAAM,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,EAAA;;wCAA3C,MAAM,GAAG,SAAkC;6CAC7C,MAAM,CAAC,OAAO,EAAd,wBAAc;wCACd,qBAAM,CAAA,MAAA,QAAQ,CAAC,OAAO,+CAAhB,QAAQ,EAAW,MAAM,EAAE,MAAM,CAAC,CAAA,EAAA;;wCAAxC,SAAwC,CAAC;;;;;wCAG7C,OAAO,CAAC,KAAK,CAAC,GAAC,CAAC,CAAC;wCACjB,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,8BAAuB,IAAI,CAAC,IAAI,MAAG,CAAC,CAAC;;;wCArB3C,IAAY,CAAA;;;;;6BAwBlC,CAAC,CAAC,YAAY,CAAC,OAAO,CAAC,EAAA;;oBA7BxB,SA6BwB,CAAC;;;;SAC5B,CAAC;AAjC+C,CAiC/C,CAAC,CAAC;AAEJ,MAAM,CAAC,IAAM,YAAY,GAAG,WAAW,CAAC,KAAK,CAAC;IAC1C,OAAO,EAAE,EAAE,IAAI,EAAE,eAAe,EAAE,WAAW,EAAE,mCAAmC,EAAE;IACpF,IAAI,EAAE,iBAAiB,CAAC,IAAI;IAC5B,MAAM,EAAE,UAAC,CAAC,EAAE,GAAkB;QAClB,IAAA,OAAO,GAAK,GAAG,CAAC,WAAW,QAApB,CAAqB;QACpC,OAAO;YACH,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;YACf,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC;YACzC,QAAQ,EAAE,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC;YAC3B,OAAO,EAAE,EAAE,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,WAAW,EAAE,qBAAqB,EAAE,CAAC;SACpE,CAAC;IACN,CAAC;CACJ,CAAC,CAAC,UAAC,EAAiB,EAAE,MAAqB;QAAtC,MAAM,YAAA,EAAE,KAAK,WAAA;IAA8B,OAAA,IAAI,CAAC,MAAM,CAAC,YAAY,EAAE,UAAM,OAAO;;;;oBACpF,MAAM,CAAC,SAAS,CAAC,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;oBAEtD,qBAAM,KAAK,CAAC,WAAW,CAAC;;;;;;;wCAEV,QAAQ,GAAG,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;wCACvD,IAAI,CAAC,QAAQ,EAAE;4CACX,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,0DAAmD,MAAM,CAAC,MAAM,MAAG,CAAC,CAAC;4CACrF,sBAAO;yCACV;wCAEY,qBAAM,MAAM,CAAC,QAAQ,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAE,CAAC,EAAA;;wCAA1F,IAAI,GAAG,SAAmF;wCACjF,qBAAM,QAAQ,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,EAAA;;wCAA3C,MAAM,GAAG,SAAkC;6CAC7C,MAAM,CAAC,OAAO,EAAd,wBAAc;wCACd,qBAAM,CAAA,MAAA,QAAQ,CAAC,OAAO,+CAAhB,QAAQ,EAAW,MAAM,EAAE,MAAM,CAAC,CAAA,EAAA;;wCAAxC,SAAwC,CAAC;;;;;wCAG7C,OAAO,CAAC,KAAK,CAAC,GAAC,CAAC,CAAC;wCACjB,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,6BAAsB,OAAO,MAAM,CAAC,GAAG,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,GAAG,MAAG,CAAC,CAAC;;;;;6BAE/G,CAAC,CAAC,YAAY,CAAC,OAAO,CAAC,EAAA;;oBAjBxB,SAiBwB,CAAC;;;;SAC5B,CAAC;AArB+C,CAqB/C,CAAC,CAAC"}

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

@@ -14,10 +14,10 @@ export declare const AnimateModelIndex: PluginStateAnimation<{
     duration: PD.NamedParams<PD.Normalize<{
         durationInS: any;
     }>, "fixed"> | PD.NamedParams<PD.Normalize<{
-        maxFps: any;
-    }>, "sequential"> | PD.NamedParams<PD.Normalize<{
         targetFps: any;
-    }>, "computed">;
+    }>, "computed"> | PD.NamedParams<PD.Normalize<{
+        maxFps: any;
+    }>, "sequential">;
 }, {
     palindromeDirections?: {
         [id: string]: 1 | -1 | undefined;

package/lib/mol-plugin-state/animation/helpers.d.ts

@@ -13,13 +13,13 @@ export declare function unwindStructureAssembly(structure: Structure, unitTransf
 export declare function explodeStructure(structure: Structure, unitTransforms: StructureUnitTransforms, t: number, sphere: Sphere3D): void;
 export declare const SpinStructureParams: {
     axis: PD.Mapped<PD.NamedParams<PD.Normalize<{
-        vector: Vec3;
-    }>, "custom"> | PD.NamedParams<PD.Normalize<{
         principalAxis: "dirA" | "dirB" | "dirC";
-    }>, "structure">>;
-    origin: PD.Mapped<PD.NamedParams<PD.Normalize<{
+    }>, "structure"> | PD.NamedParams<PD.Normalize<{
+        vector: Vec3;
+    }>, "custom">>;
+    origin: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "structure"> | PD.NamedParams<PD.Normalize<{
         vector: Vec3;
-    }>, "custom"> | PD.NamedParams<PD.Normalize<unknown>, "structure">>;
+    }>, "custom">>;
 };
 export declare type SpinStructureProps = PD.Values<typeof SpinStructureParams>;
 export declare function getSpinStructureAxisAndOrigin(structure: Structure, props: SpinStructureProps): {

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

@@ -48,8 +48,6 @@ export declare const PresetTrajectoryHierarchy: {
         showUnitcell: boolean | undefined;
         structure: PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
-        }>, "auto"> | PD.NamedParams<PD.Normalize<{
-            dynamicBonds: any;
             ijkMin: any;
             ijkMax: any;
         }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
@@ -59,6 +57,8 @@ export declare const PresetTrajectoryHierarchy: {
             id: any;
         }>, "assembly"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
+        }>, "auto"> | PD.NamedParams<PD.Normalize<{
+            dynamicBonds: any;
             radius: any;
         }>, "symmetry-mates"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;

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

@@ -30,8 +30,6 @@ export declare class TrajectoryHierarchyBuilder {
         showUnitcell: boolean | undefined;
         structure: PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
-        }>, "auto"> | PD.NamedParams<PD.Normalize<{
-            dynamicBonds: any;
             ijkMin: any;
             ijkMax: any;
         }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
@@ -41,6 +39,8 @@ export declare class TrajectoryHierarchyBuilder {
             id: any;
         }>, "assembly"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;
+        }>, "auto"> | PD.NamedParams<PD.Normalize<{
+            dynamicBonds: any;
             radius: any;
         }>, "symmetry-mates"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: any;

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

@@ -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" | "occupancy" | "element-symbol" | "element-index" | "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-symbol" | "element-index" | "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;
+            globalName: "occupancy" | "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" | "uniform" | undefined;
+            carbonColor: "chain-id" | "operator-name" | "element-symbol" | undefined;
+            symmetryColor: "occupancy" | "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" | "uniform" | 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: "uniform" | "occupancy" | "element-symbol" | "element-index" | "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-symbol" | "element-index" | "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;
+        color: "occupancy" | "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" | "uniform" | undefined;
+        symmetryColor: "occupancy" | "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" | "uniform" | undefined;
         typeParams: {
             quality: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
             ignoreHydrogens: boolean;
         };
         ballAndStickColor: Partial<PD.Values<{
-            carbonColor: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "element-symbol"> | PD.NamedParams<PD.Normalize<{
+            carbonColor: PD.Mapped<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">>;
+            }>, "operator-name"> | PD.NamedParams<PD.Normalize<unknown>, "element-symbol">>;
             saturation: PD.Numeric;
             lightness: PD.Numeric;
         }>>;

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

@@ -69,8 +69,6 @@ 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;
                 ijkMin: any;
                 ijkMax: any;
             }>, "symmetry"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
@@ -80,6 +78,8 @@ export declare const CubeProvider: {
                 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;
                 radius: any;
             }>, "symmetry-mates"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;
@@ -150,8 +150,6 @@ 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;
                 ijkMin: any;
                 ijkMax: any;
             }>, "symmetry"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
@@ -161,6 +159,8 @@ export declare const BuiltInVolumeFormats: readonly [readonly ["ccp4", {
                 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;
                 radius: any;
             }>, "symmetry-mates"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 dynamicBonds: any;

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

@@ -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

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

@@ -14,8 +14,6 @@ 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;
             ijkMin: Vec3;
             ijkMax: Vec3;
         }>, "symmetry"> | PD.NamedParams<PD.Normalize<{
@@ -25,6 +23,8 @@ export declare namespace RootStructureDefinition {
             id: string | undefined;
         }>, "assembly"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;
+        }>, "auto"> | PD.NamedParams<PD.Normalize<{
+            dynamicBonds: boolean | undefined;
             radius: number;
         }>, "symmetry-mates"> | PD.NamedParams<PD.Normalize<{
             dynamicBonds: boolean | undefined;

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

@@ -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<"polymer" | "water" | "branched" | "ligand" | "ion" | "lipid" | "all" | "coarse" | "protein" | "nucleic" | "non-standard", "static"> | PD.NamedParams<StructureElement.Bundle, "bundle"> | PD.NamedParams<Expression, "expression">>;
+    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/mol-plugin-state/helpers/structure-selection-query.d.ts

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

package/lib/mol-plugin-state/helpers/structure-selection-query.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -12,6 +12,7 @@ import { compile } from '../../mol-script/runtime/query/compiler';
 import { SetUtils } from '../../mol-util/set';
 import { StateTransforms } from '../transforms';
 import { ElementNames } from '../../mol-model/structure/model/properties/atomic/types';
+import { SecondaryStructureProvider } from '../../mol-model-props/computed/secondary-structure';
 export var StructureSelectionCategory;
 (function (StructureSelectionCategory) {
     StructureSelectionCategory["Type"] = "Type";
@@ -223,7 +224,12 @@ var helix = StructureSelectionQuery('Helix', MS.struct.modifier.union([
             MS.core.type.bitflags([2 /* Helix */])
         ])
     })
-]), { category: StructureSelectionCategory.Structure });
+]), {
+    category: StructureSelectionCategory.Structure,
+    ensureCustomProperties: function (ctx, structure) {
+        return SecondaryStructureProvider.attach(ctx, structure);
+    }
+});
 var beta = StructureSelectionQuery('Beta Strand/Sheet', MS.struct.modifier.union([
     MS.struct.generator.atomGroups({
         'entity-test': _proteinEntityTest,
@@ -232,7 +238,12 @@ var beta = StructureSelectionQuery('Beta Strand/Sheet', MS.struct.modifier.union
             MS.core.type.bitflags([4 /* Beta */])
         ])
     })
-]), { category: StructureSelectionCategory.Structure });
+]), {
+    category: StructureSelectionCategory.Structure,
+    ensureCustomProperties: function (ctx, structure) {
+        return SecondaryStructureProvider.attach(ctx, structure);
+    }
+});
 var water = StructureSelectionQuery('Water', MS.struct.modifier.union([
     MS.struct.generator.atomGroups({
         'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'water'])