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/mol-plugin/context.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/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/mol-plugin/version.js CHANGED Viewed

@@ -1,2 +1,2 @@
-export var PLUGIN_VERSION = '2.3.3';
-export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1633103737320);
+export var PLUGIN_VERSION = '2.3.5';
+export var PLUGIN_VERSION_DATE = new Date(typeof __MOLSTAR_DEBUG_TIMESTAMP__ !== 'undefined' ? __MOLSTAR_DEBUG_TIMESTAMP__ : 1634660519467);

package/lib/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/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/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/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/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/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/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" | "ion" | "lipid" | "branched" | "ligand" | "non-standard" | "coarse", "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/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" | "element" | "chain" | "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/mol-plugin-state/manager/interactivity.js CHANGED Viewed

@@ -73,11 +73,11 @@ var InteractivityManager = /** @class */ (function (_super) {
             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.normalize(loci, granularity), repr: repr };
+            return { loci: Loci.normalize(loci, granularity, alwaysConvertBonds), repr: repr };
         };
         LociMarkManager.prototype.mark = function (current, action, noRender) {
             if (noRender === void 0) { noRender = false; }
@@ -171,7 +171,7 @@ var InteractivityManager = /** @class */ (function (_super) {
             if (applyGranularity === void 0) { applyGranularity = true; }
             if (Loci.isEmpty(current.loci))
                 return;
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (StructureElement.Loci.is(normalized.loci)) {
                 this.toggleSel(normalized);
             }
@@ -183,7 +183,7 @@ var InteractivityManager = /** @class */ (function (_super) {
             if (applyGranularity === void 0) { applyGranularity = true; }
             if (Loci.isEmpty(current.loci))
                 return;
-            var normalized = this.normalizedLoci(current, applyGranularity);
+            var normalized = this.normalizedLoci(current, applyGranularity, true);
             if (StructureElement.Loci.is(normalized.loci)) {
                 var loci = this.sel.tryGetRange(normalized.loci) || normalized.loci;
                 this.toggleSel({ loci: loci, repr: normalized.repr });
@@ -191,7 +191,7 @@ var InteractivityManager = /** @class */ (function (_super) {
         };
         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 (StructureElement.Loci.is(normalized.loci)) {
                 this.sel.modify('add', normalized.loci);
             }
@@ -199,7 +199,7 @@ var InteractivityManager = /** @class */ (function (_super) {
         };
         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 (StructureElement.Loci.is(normalized.loci)) {
                 this.sel.modify('intersect', normalized.loci);
             }
@@ -207,7 +207,7 @@ var InteractivityManager = /** @class */ (function (_super) {
         };
         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 (StructureElement.Loci.is(normalized.loci)) {
                 // only deselect for the structure of the given loci
                 this.deselect({ loci: Structure.toStructureElementLoci(normalized.loci.structure), repr: normalized.repr }, false);
@@ -217,7 +217,7 @@ var InteractivityManager = /** @class */ (function (_super) {
         };
         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 (StructureElement.Loci.is(normalized.loci)) {
                 this.sel.modify('remove', normalized.loci);
             }
@@ -238,8 +238,9 @@ var InteractivityManager = /** @class */ (function (_super) {
                     // 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.Loci(loci.structure) }, MarkerAction.Deselect, true);
-                    _super.prototype.mark.call(this, { loci: this.sel.getLoci(loci.structure) }, MarkerAction.Select);
+                    var selLoci = this.sel.getLoci(loci.structure);
+                    _super.prototype.mark.call(this, { loci: Structure.Loci(loci.structure) }, MarkerAction.Deselect, !Loci.isEmpty(selLoci));
+                    _super.prototype.mark.call(this, { loci: selLoci }, MarkerAction.Select);
                 }
                 else {
                     _super.prototype.mark.call(this, current, action);

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

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

@@ -50,9 +50,9 @@ export declare class StructureSelectionManager extends StatefulPluginComponent<S
     private onUpdate;
     /** Removes all selections and returns them */
     clear(): StructureElement.Loci[];
-    getLoci(structure: Structure): {
+    getLoci(structure: Structure): StructureElement.Loci | {
         kind: "empty-loci";
-    } | StructureElement.Loci;
+    };
     getStructure(structure: Structure): Structure | undefined;
     structureHasSelection(structure: StructureRef): boolean;
     has(loci: Loci): boolean;

package/lib/mol-plugin-state/transforms/data.d.ts CHANGED Viewed

@@ -42,7 +42,7 @@ declare const DownloadBlob: StateTransformer<SO.Root, SO.Data.Blob, PD.Normalize
 }>>;
 declare type RawData = typeof RawData;
 declare const RawData: StateTransformer<SO.Root, SO.Data.String | SO.Data.Binary, PD.Normalize<{
-    data: string | ArrayBuffer | Uint8Array | number[];
+    data: string | number[] | Uint8Array | ArrayBuffer;
     label: string | undefined;
 }>>;
 declare type ReadFile = typeof ReadFile;