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-state/manager/interactivity.js.map CHANGED Viewed

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1	+ 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package/lib/commonjs/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/commonjs/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 | number[] | ArrayBuffer | Uint8Array;
+    data: string | number[] | Uint8Array | ArrayBuffer;
     label: string | undefined;
 }>>;
 declare type ReadFile = typeof ReadFile;

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

@@ -84,19 +84,19 @@ declare type StructureFromModel = typeof StructureFromModel;
 declare const StructureFromModel: StateTransformer<SO.Molecule.Model, SO.Molecule.Structure, PD.Normalize<{
     type: 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">;
@@ -154,11 +154,11 @@ export declare const StructureComplexElementTypes: {
 export declare type StructureComplexElementTypes = keyof typeof StructureComplexElementTypes;
 declare type StructureComplexElement = typeof StructureComplexElement;
 declare const StructureComplexElement: StateTransformer<SO.Molecule.Structure, SO.Molecule.Structure, PD.Normalize<{
-    type: "spheres" | "polymer" | "protein" | "nucleic" | "water" | "branched" | "ligand" | "non-standard" | "coarse" | "atomic-sequence" | "atomic-het";
+    type: "polymer" | "water" | "branched" | "ligand" | "spheres" | "protein" | "nucleic" | "non-standard" | "coarse" | "atomic-sequence" | "atomic-het";
 }>>;
 declare type StructureComponent = typeof StructureComponent;
 declare const StructureComponent: StateTransformer<SO.Molecule.Structure, SO.Molecule.Structure, PD.Normalize<{
-    type: 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.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: boolean | undefined;
     label: string;
 }>>;

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

@@ -287,7 +287,7 @@ declare const StructureSelectionsLabel3D: StateTransformer<SO.Molecule.Structure
 export { StructureSelectionsOrientation3D };
 declare type StructureSelectionsOrientation3D = typeof StructureSelectionsOrientation3D;
 declare const StructureSelectionsOrientation3D: StateTransformer<SO.Molecule.Structure.Selections, SO.Shape.Representation3D, PD.Normalize<{
-    visuals: ("box" | "axes" | "ellipsoid")[];
+    visuals: ("axes" | "ellipsoid" | "box")[];
     color: Color;
     scale: number;
     doubleSided: boolean;

package/lib/commonjs/mol-plugin-ui/controls/parameters.d.ts CHANGED Viewed

@@ -186,7 +186,7 @@ export declare class ColorListControl extends React.PureComponent<ParamProps<PD.
 }> {
     state: {
         showHelp: boolean;
-        show: "edit" | "presets" | undefined;
+        show: "presets" | "edit" | undefined;
     };
     protected update(value: PD.ColorList['defaultValue']): void;
     toggleEdit: () => void;
@@ -205,7 +205,7 @@ export declare class OffsetColorListControl extends React.PureComponent<ParamPro
 }> {
     state: {
         showHelp: boolean;
-        show: "edit" | "presets" | undefined;
+        show: "presets" | "edit" | undefined;
     };
     protected update(value: PD.ColorList['defaultValue']): void;
     toggleEdit: () => void;

package/lib/commonjs/mol-repr/shape/loci/orientation.d.ts CHANGED Viewed

@@ -10,7 +10,7 @@ export interface OrientationData {
     locis: Loci[];
 }
 export declare const OrientationParams: {
-    visuals: PD.MultiSelect<"box" | "axes" | "ellipsoid">;
+    visuals: PD.MultiSelect<"axes" | "ellipsoid" | "box">;
     color: PD.Color;
     scale: PD.Numeric;
     doubleSided: PD.BooleanParam;

package/lib/commonjs/mol-repr/structure/complex-visual.d.ts CHANGED Viewed

@@ -121,7 +121,7 @@ export declare const ComplexDirectVolumeParams: {
     renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
         controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
         list: {
-            kind: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{

package/lib/commonjs/mol-repr/structure/params.d.ts CHANGED Viewed

@@ -89,7 +89,7 @@ export declare const StructureDirectVolumeParams: {
     renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
         controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
         list: {
-            kind: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{

package/lib/commonjs/mol-repr/structure/registry.d.ts CHANGED Viewed

@@ -55,10 +55,11 @@ export declare namespace StructureRepresentationRegistry {
             visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"element-sphere" | "intra-bond" | "inter-bond">;
             tryUseImpostor: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             adjustCylinderLength: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
-            includeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-            excludeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+            includeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+            excludeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
             ignoreHydrogens: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             aromaticBonds: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            multipleBonds: import("../../mol-util/param-definition").ParamDefinition.Select<"off" | "symmetric" | "offset">;
             linkScale: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             linkSpacing: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             linkCap: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
@@ -110,10 +111,11 @@ export declare namespace StructureRepresentationRegistry {
             linkCap: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"intra-bond" | "inter-bond" | "ellipsoid-mesh">;
             tryUseImpostor: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
-            includeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-            excludeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+            includeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+            excludeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
             ignoreHydrogens: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             aromaticBonds: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            multipleBonds: import("../../mol-util/param-definition").ParamDefinition.Select<"off" | "symmetric" | "offset">;
             linkScale: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             linkSpacing: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             dashCount: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -144,10 +146,10 @@ export declare namespace StructureRepresentationRegistry {
             alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             quality: import("../../mol-util/param-definition").ParamDefinition.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
             tryUseGpu: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
-            smoothColors: import("../../mol-util/param-definition").ParamDefinition.Mapped<import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "off"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "auto"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+            smoothColors: import("../../mol-util/param-definition").ParamDefinition.Mapped<import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "auto"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 resolutionFactor: number;
                 sampleStride: number;
-            }>, "on">>;
+            }>, "on"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "off">>;
             doubleSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             flipSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             flatShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
@@ -171,7 +173,7 @@ export declare namespace StructureRepresentationRegistry {
             renderMode: import("../../mol-util/param-definition").ParamDefinition.Mapped<import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
                 list: {
-                    kind: "interpolate" | "set";
+                    kind: "set" | "interpolate";
                     colors: import("../../mol-util/color/color").ColorListEntry[];
                 };
             }>, "volume"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
@@ -220,20 +222,26 @@ export declare namespace StructureRepresentationRegistry {
             quality: import("../../mol-util/param-definition").ParamDefinition.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
         }, "label">;
         line: import("./representation").StructureRepresentationProvider<{
+            multipleBonds: import("../../mol-util/param-definition").ParamDefinition.Select<"off" | "symmetric" | "offset">;
             includeParent: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             sizeFactor: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             unitKinds: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"spheres" | "atomic" | "gaussians">;
-            visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"intra-bond" | "inter-bond">;
-            includeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-            excludeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+            visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"intra-bond" | "inter-bond" | "element-point" | "element-cross">;
+            lineSizeAttenuation: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             ignoreHydrogens: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            traceOnly: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            crosses: import("../../mol-util/param-definition").ParamDefinition.Select<"all" | "lone">;
+            crossSize: import("../../mol-util/param-definition").ParamDefinition.Numeric;
+            alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
+            quality: import("../../mol-util/param-definition").ParamDefinition.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+            pointSizeAttenuation: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            pointStyle: import("../../mol-util/param-definition").ParamDefinition.Select<"square" | "circle" | "fuzzy">;
+            includeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+            excludeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
             aromaticBonds: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             linkScale: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             linkSpacing: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             dashCount: import("../../mol-util/param-definition").ParamDefinition.Numeric;
-            lineSizeAttenuation: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
-            alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
-            quality: import("../../mol-util/param-definition").ParamDefinition.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
         }, "line">;
         'molecular-surface': import("./representation").StructureRepresentationProvider<{
             visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"molecular-surface-mesh" | "molecular-surface-wireframe">;
@@ -248,10 +256,10 @@ export declare namespace StructureRepresentationRegistry {
             lineSizeAttenuation: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             quality: import("../../mol-util/param-definition").ParamDefinition.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
-            smoothColors: import("../../mol-util/param-definition").ParamDefinition.Mapped<import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "off"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "auto"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+            smoothColors: import("../../mol-util/param-definition").ParamDefinition.Mapped<import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "auto"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
                 resolutionFactor: number;
                 sampleStride: number;
-            }>, "on">>;
+            }>, "on"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<unknown>, "off">>;
             doubleSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             flipSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             flatShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;

package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.d.ts CHANGED Viewed

@@ -16,10 +16,11 @@ export declare const BallAndStickParams: {
     visuals: PD.MultiSelect<"element-sphere" | "intra-bond" | "inter-bond">;
     tryUseImpostor: PD.BooleanParam;
     adjustCylinderLength: PD.BooleanParam;
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
@@ -47,10 +48,11 @@ export declare function getBallAndStickParams(ctx: ThemeRegistryContext, structu
     visuals: PD.MultiSelect<"element-sphere" | "intra-bond" | "inter-bond">;
     tryUseImpostor: PD.BooleanParam;
     adjustCylinderLength: PD.BooleanParam;
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
@@ -79,10 +81,11 @@ export declare const BallAndStickRepresentationProvider: StructureRepresentation
     visuals: PD.MultiSelect<"element-sphere" | "intra-bond" | "inter-bond">;
     tryUseImpostor: PD.BooleanParam;
     adjustCylinderLength: PD.BooleanParam;
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;

package/lib/commonjs/mol-repr/structure/representation/ellipsoid.d.ts CHANGED Viewed

@@ -17,10 +17,11 @@ export declare const EllipsoidParams: {
     linkCap: PD.BooleanParam;
     visuals: PD.MultiSelect<"intra-bond" | "inter-bond" | "ellipsoid-mesh">;
     tryUseImpostor: PD.BooleanParam;
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     dashCount: PD.Numeric;
@@ -47,10 +48,11 @@ export declare function getEllipsoidParams(ctx: ThemeRegistryContext, structure:
     linkCap: PD.BooleanParam;
     visuals: PD.MultiSelect<"intra-bond" | "inter-bond" | "ellipsoid-mesh">;
     tryUseImpostor: PD.BooleanParam;
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     dashCount: PD.Numeric;
@@ -78,10 +80,11 @@ export declare const EllipsoidRepresentationProvider: StructureRepresentationPro
     linkCap: PD.BooleanParam;
     visuals: PD.MultiSelect<"intra-bond" | "inter-bond" | "ellipsoid-mesh">;
     tryUseImpostor: PD.BooleanParam;
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     dashCount: PD.Numeric;

package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.d.ts CHANGED Viewed

@@ -22,10 +22,10 @@ export declare const GaussianSurfaceParams: {
     alpha: PD.Numeric;
     quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
     tryUseGpu: PD.BooleanParam;
-    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
+    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;
-    }>, "on">>;
+    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
@@ -47,10 +47,10 @@ export declare function getGaussianSurfaceParams(ctx: ThemeRegistryContext, stru
     alpha: PD.Numeric;
     quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
     tryUseGpu: PD.BooleanParam;
-    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
+    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;
-    }>, "on">>;
+    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
@@ -73,10 +73,10 @@ export declare const GaussianSurfaceRepresentationProvider: StructureRepresentat
     alpha: PD.Numeric;
     quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
     tryUseGpu: PD.BooleanParam;
-    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
+    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;
-    }>, "on">>;
+    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;

package/lib/commonjs/mol-repr/structure/representation/gaussian-volume.d.ts CHANGED Viewed

@@ -25,7 +25,7 @@ export declare const GaussianVolumeParams: {
     renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
         controlPoints: import("../../../mol-math/linear-algebra/3d/vec2").Vec2[];
         list: {
-            kind: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("../../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{
@@ -61,7 +61,7 @@ export declare function getGaussianVolumeParams(ctx: ThemeRegistryContext, struc
     renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
         controlPoints: import("../../../mol-math/linear-algebra/3d/vec2").Vec2[];
         list: {
-            kind: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("../../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{
@@ -98,7 +98,7 @@ export declare const GaussianVolumeRepresentationProvider: StructureRepresentati
     renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
         controlPoints: import("../../../mol-math/linear-algebra/3d/vec2").Vec2[];
         list: {
-            kind: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("../../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{

package/lib/commonjs/mol-repr/structure/representation/line.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -9,53 +9,71 @@ import { RepresentationParamsGetter, RepresentationContext } from '../../../mol-
 import { ThemeRegistryContext } from '../../../mol-theme/theme';
 import { Structure } from '../../../mol-model/structure';
 export declare const LineParams: {
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     includeParent: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
-    visuals: PD.MultiSelect<"intra-bond" | "inter-bond">;
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    visuals: PD.MultiSelect<"intra-bond" | "inter-bond" | "element-point" | "element-cross">;
+    lineSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    traceOnly: PD.BooleanParam;
+    crosses: PD.Select<"all" | "lone">;
+    crossSize: PD.Numeric;
+    alpha: PD.Numeric;
+    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    pointSizeAttenuation: PD.BooleanParam;
+    pointStyle: PD.Select<"square" | "circle" | "fuzzy">;
+    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     aromaticBonds: PD.BooleanParam;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     dashCount: PD.Numeric;
-    lineSizeAttenuation: PD.BooleanParam;
-    alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
 };
 export declare type LineParams = typeof LineParams;
 export declare function getLineParams(ctx: ThemeRegistryContext, structure: Structure): {
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     includeParent: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
-    visuals: PD.MultiSelect<"intra-bond" | "inter-bond">;
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    visuals: PD.MultiSelect<"intra-bond" | "inter-bond" | "element-point" | "element-cross">;
+    lineSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    traceOnly: PD.BooleanParam;
+    crosses: PD.Select<"all" | "lone">;
+    crossSize: PD.Numeric;
+    alpha: PD.Numeric;
+    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    pointSizeAttenuation: PD.BooleanParam;
+    pointStyle: PD.Select<"square" | "circle" | "fuzzy">;
+    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     aromaticBonds: PD.BooleanParam;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     dashCount: PD.Numeric;
-    lineSizeAttenuation: PD.BooleanParam;
-    alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
 };
 export declare type LineRepresentation = StructureRepresentation<LineParams>;
 export declare function LineRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, LineParams>): LineRepresentation;
 export declare const LineRepresentationProvider: StructureRepresentationProvider<{
+    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     includeParent: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
-    visuals: PD.MultiSelect<"intra-bond" | "inter-bond">;
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    visuals: PD.MultiSelect<"intra-bond" | "inter-bond" | "element-point" | "element-cross">;
+    lineSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    traceOnly: PD.BooleanParam;
+    crosses: PD.Select<"all" | "lone">;
+    crossSize: PD.Numeric;
+    alpha: PD.Numeric;
+    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    pointSizeAttenuation: PD.BooleanParam;
+    pointStyle: PD.Select<"square" | "circle" | "fuzzy">;
+    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
     aromaticBonds: PD.BooleanParam;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     dashCount: PD.Numeric;
-    lineSizeAttenuation: PD.BooleanParam;
-    alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
 }, "line">;

package/lib/commonjs/mol-repr/structure/representation/line.js CHANGED Viewed

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -15,13 +15,19 @@ var complex_representation_1 = require("../complex-representation");
 var representation_1 = require("../representation");
 var representation_2 = require("../../../mol-repr/representation");
 var params_1 = require("../params");
+var element_point_1 = require("../visual/element-point");
+var element_cross_1 = require("../visual/element-cross");
 var LineVisuals = {
     'intra-bond': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Intra-unit bond line', ctx, getParams, bond_intra_unit_line_1.IntraUnitBondLineVisual); },
     'inter-bond': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Inter-unit bond line', ctx, getParams, bond_inter_unit_line_1.InterUnitBondLineVisual); },
+    'element-point': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Points', ctx, getParams, element_point_1.ElementPointVisual); },
+    'element-cross': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Crosses', ctx, getParams, element_cross_1.ElementCrossVisual); },
 };
-exports.LineParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, bond_intra_unit_line_1.IntraUnitBondLineParams), bond_inter_unit_line_1.InterUnitBondLineParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false), sizeFactor: param_definition_1.ParamDefinition.Numeric(1.5, { min: 0.01, max: 10, step: 0.01 }), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), visuals: param_definition_1.ParamDefinition.MultiSelect(['intra-bond', 'inter-bond'], param_definition_1.ParamDefinition.objectToOptions(LineVisuals)) });
+exports.LineParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, bond_intra_unit_line_1.IntraUnitBondLineParams), bond_inter_unit_line_1.InterUnitBondLineParams), element_point_1.ElementPointParams), element_cross_1.ElementCrossParams), { multipleBonds: param_definition_1.ParamDefinition.Select('offset', param_definition_1.ParamDefinition.arrayToOptions(['off', 'symmetric', 'offset'])), includeParent: param_definition_1.ParamDefinition.Boolean(false), sizeFactor: param_definition_1.ParamDefinition.Numeric(3, { min: 0.01, max: 10, step: 0.01 }), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), visuals: param_definition_1.ParamDefinition.MultiSelect(['intra-bond', 'inter-bond', 'element-point', 'element-cross'], param_definition_1.ParamDefinition.objectToOptions(LineVisuals)) });
 function getLineParams(ctx, structure) {
-    return param_definition_1.ParamDefinition.clone(exports.LineParams);
+    var params = param_definition_1.ParamDefinition.clone(exports.LineParams);
+    params.pointStyle.defaultValue = 'circle';
+    return params;
 }
 exports.getLineParams = getLineParams;
 function LineRepresentation(ctx, getParams) {
@@ -31,7 +37,7 @@ exports.LineRepresentation = LineRepresentation;
 exports.LineRepresentationProvider = (0, representation_1.StructureRepresentationProvider)({
     name: 'line',
     label: 'Line',
-    description: 'Displays bonds as lines.',
+    description: 'Displays bonds as lines and atoms as points or croses.',
     factory: LineRepresentation,
     getParams: getLineParams,
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.LineParams),

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