molstar 3.0.0-dev.4 → 3.0.0-dev.8

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -17,27 +17,9 @@ export declare const GaussianVolumeParams: {
     radiusOffset: PD.Numeric;
     smoothness: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
-    doubleSided: PD.BooleanParam;
-    flipSided: PD.BooleanParam;
-    flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
-        controlPoints: import("../../../mol-math/linear-algebra/3d/vec2").Vec2[];
-        list: {
-            kind: "set" | "interpolate";
-            colors: import("../../../mol-util/color/color").ColorListEntry[];
-        };
-    }>, "volume"> | PD.NamedParams<PD.Normalize<{
-        isoValue: Readonly<{
-            kind: "absolute";
-            absoluteValue: number;
-        }> | Readonly<{
-            kind: "relative";
-            relativeValue: number;
-        }>;
-        singleLayer: boolean;
-    }>, "isosurface">>;
+    controlPoints: PD.LineGraph;
     stepsPerCell: PD.Numeric;
     jumpLength: PD.Numeric;
     alpha: PD.Numeric;
@@ -47,6 +29,16 @@ export declare const GaussianVolumeParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type GaussianVolumeParams = typeof GaussianVolumeParams;
 export declare function getGaussianVolumeParams(ctx: ThemeRegistryContext, structure: Structure): {
@@ -58,27 +50,9 @@ export declare function getGaussianVolumeParams(ctx: ThemeRegistryContext, struc
     radiusOffset: PD.Numeric;
     smoothness: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
-    doubleSided: PD.BooleanParam;
-    flipSided: PD.BooleanParam;
-    flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
-        controlPoints: import("../../../mol-math/linear-algebra/3d/vec2").Vec2[];
-        list: {
-            kind: "set" | "interpolate";
-            colors: import("../../../mol-util/color/color").ColorListEntry[];
-        };
-    }>, "volume"> | PD.NamedParams<PD.Normalize<{
-        isoValue: Readonly<{
-            kind: "absolute";
-            absoluteValue: number;
-        }> | Readonly<{
-            kind: "relative";
-            relativeValue: number;
-        }>;
-        singleLayer: boolean;
-    }>, "isosurface">>;
+    controlPoints: PD.LineGraph;
     stepsPerCell: PD.Numeric;
     jumpLength: PD.Numeric;
     alpha: PD.Numeric;
@@ -88,6 +62,16 @@ export declare function getGaussianVolumeParams(ctx: ThemeRegistryContext, struc
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type GaussianVolumeRepresentation = StructureRepresentation<GaussianVolumeParams>;
 export declare function GaussianVolumeRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, GaussianVolumeParams>): GaussianVolumeRepresentation;
@@ -100,27 +84,9 @@ export declare const GaussianVolumeRepresentationProvider: StructureRepresentati
     radiusOffset: PD.Numeric;
     smoothness: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
-    doubleSided: PD.BooleanParam;
-    flipSided: PD.BooleanParam;
-    flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
-        controlPoints: import("../../../mol-math/linear-algebra/3d/vec2").Vec2[];
-        list: {
-            kind: "set" | "interpolate";
-            colors: import("../../../mol-util/color/color").ColorListEntry[];
-        };
-    }>, "volume"> | PD.NamedParams<PD.Normalize<{
-        isoValue: Readonly<{
-            kind: "absolute";
-            absoluteValue: number;
-        }> | Readonly<{
-            kind: "relative";
-            relativeValue: number;
-        }>;
-        singleLayer: boolean;
-    }>, "isosurface">>;
+    controlPoints: PD.LineGraph;
     stepsPerCell: PD.Numeric;
     jumpLength: PD.Numeric;
     alpha: PD.Numeric;
@@ -130,4 +96,14 @@ export declare const GaussianVolumeRepresentationProvider: StructureRepresentati
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }, "gaussian-volume">;

package/lib/mol-repr/structure/representation/gaussian-volume.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -8,7 +8,6 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { GaussianDensityVolumeParams, GaussianDensityVolumeVisual, UnitsGaussianDensityVolumeVisual } from '../visual/gaussian-density-volume';
 import { StructureRepresentationProvider, ComplexRepresentation, StructureRepresentationStateBuilder, UnitsRepresentation } from '../representation';
 import { Representation } from '../../../mol-repr/representation';
-import { DirectVolume } from '../../../mol-geo/geometry/direct-volume/direct-volume';
 var GaussianVolumeVisuals = {
     'gaussian-volume': function (ctx, getParams) { return ComplexRepresentation('Gaussian volume', ctx, getParams, GaussianDensityVolumeVisual); },
     'units-gaussian-volume': function (ctx, getParams) { return UnitsRepresentation('Units-Gaussian volume', ctx, getParams, UnitsGaussianDensityVolumeVisual); }
@@ -16,10 +15,6 @@ var GaussianVolumeVisuals = {
 export var GaussianVolumeParams = __assign(__assign({}, GaussianDensityVolumeParams), { visuals: PD.MultiSelect(['gaussian-volume'], PD.objectToOptions(GaussianVolumeVisuals)) });
 export function getGaussianVolumeParams(ctx, structure) {
     var p = PD.clone(GaussianVolumeParams);
-    p.renderMode = DirectVolume.createRenderModeParam({
-        // TODO find a better way to set
-        min: 0, max: 1, mean: 0.04, sigma: 0.01
-    });
     p.jumpLength = PD.Numeric(4, { min: 0, max: 20, step: 0.1 });
     return p;
 }
@@ -34,7 +29,7 @@ export var GaussianVolumeRepresentationProvider = StructureRepresentationProvide
     getParams: getGaussianVolumeParams,
     defaultValues: PD.getDefaultValues(GaussianVolumeParams),
     defaultColorTheme: { name: 'chain-id' },
-    defaultSizeTheme: { name: 'uniform' },
+    defaultSizeTheme: { name: 'physical' },
     isApplicable: function (structure) { return structure.elementCount > 0; }
 });
 //# sourceMappingURL=gaussian-volume.js.map

package/lib/mol-repr/structure/representation/label.d.ts

@@ -42,6 +42,16 @@ export declare const LabelParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type LabelParams = typeof LabelParams;
 export declare function getLabelParams(ctx: ThemeRegistryContext, structure: Structure): {
@@ -78,6 +88,16 @@ export declare function getLabelParams(ctx: ThemeRegistryContext, structure: Str
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type LabelRepresentation = StructureRepresentation<LabelParams>;
 export declare function LabelRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, LabelParams>): LabelRepresentation;
@@ -115,4 +135,14 @@ export declare const LabelRepresentationProvider: StructureRepresentationProvide
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }, "label">;

package/lib/mol-repr/structure/representation/label.js

@@ -29,7 +29,7 @@ export var LabelRepresentationProvider = StructureRepresentationProvider({
     getParams: getLabelParams,
     defaultValues: PD.getDefaultValues(LabelParams),
     defaultColorTheme: { name: 'uniform' },
-    defaultSizeTheme: { name: 'uniform' },
+    defaultSizeTheme: { name: 'physical' },
     isApplicable: function (structure) { return structure.elementCount > 0; }
 });
 //# sourceMappingURL=label.js.map

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

@@ -26,6 +26,16 @@ export declare const LineParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     pointSizeAttenuation: PD.BooleanParam;
     pointStyle: PD.Select<"circle" | "square" | "fuzzy">;
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
@@ -55,6 +65,16 @@ export declare function getLineParams(ctx: ThemeRegistryContext, structure: Stru
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     pointSizeAttenuation: PD.BooleanParam;
     pointStyle: PD.Select<"circle" | "square" | "fuzzy">;
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
@@ -85,6 +105,16 @@ export declare const LineRepresentationProvider: StructureRepresentationProvider
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     pointSizeAttenuation: PD.BooleanParam;
     pointStyle: PD.Select<"circle" | "square" | "fuzzy">;
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;

package/lib/mol-repr/structure/representation/molecular-surface.d.ts

@@ -27,6 +27,16 @@ export declare const MolecularSurfaceParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;
@@ -58,6 +68,16 @@ export declare function getMolecularSurfaceParams(ctx: ThemeRegistryContext, str
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;
@@ -90,6 +110,16 @@ export declare const MolecularSurfaceRepresentationProvider: StructureRepresenta
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;

package/lib/mol-repr/structure/representation/molecular-surface.js

@@ -30,7 +30,7 @@ export var MolecularSurfaceRepresentationProvider = StructureRepresentationProvi
     getParams: getMolecularSurfaceParams,
     defaultValues: PD.getDefaultValues(MolecularSurfaceParams),
     defaultColorTheme: { name: 'chain-id' },
-    defaultSizeTheme: { name: 'uniform' },
+    defaultSizeTheme: { name: 'physical' },
     isApplicable: function (structure) { return structure.elementCount > 0; }
 });
 //# sourceMappingURL=molecular-surface.js.map

package/lib/mol-repr/structure/representation/orientation.d.ts

@@ -28,6 +28,16 @@ export declare const OrientationParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type OrientationParams = typeof OrientationParams;
 export declare function getOrientationParams(ctx: ThemeRegistryContext, structure: Structure): {
@@ -50,6 +60,16 @@ export declare function getOrientationParams(ctx: ThemeRegistryContext, structur
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type OrientationRepresentation = StructureRepresentation<OrientationParams>;
 export declare function OrientationRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, OrientationParams>): OrientationRepresentation;
@@ -73,4 +93,14 @@ export declare const OrientationRepresentationProvider: StructureRepresentationP
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }, "orientation">;

package/lib/mol-repr/structure/representation/point.d.ts

@@ -23,6 +23,16 @@ export declare const PointParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type PointParams = typeof PointParams;
 export declare function getPointParams(ctx: ThemeRegistryContext, structure: Structure): {
@@ -40,6 +50,16 @@ export declare function getPointParams(ctx: ThemeRegistryContext, structure: Str
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type PointRepresentation = StructureRepresentation<PointParams>;
 export declare function PointRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, PointParams>): PointRepresentation;
@@ -58,4 +78,14 @@ export declare const PointRepresentationProvider: StructureRepresentationProvide
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }, "point">;

package/lib/mol-repr/structure/representation/putty.d.ts

@@ -28,6 +28,16 @@ export declare const PuttyParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     detail: PD.Numeric;
     linearSegments: PD.Numeric;
 };
@@ -52,6 +62,16 @@ export declare function getPuttyParams(ctx: ThemeRegistryContext, structure: Str
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     detail: PD.Numeric;
     linearSegments: PD.Numeric;
 };
@@ -77,6 +97,16 @@ export declare const PuttyRepresentationProvider: StructureRepresentationProvide
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     detail: PD.Numeric;
     linearSegments: PD.Numeric;
 }, "putty">;

package/lib/mol-repr/structure/representation/spacefill.d.ts

@@ -28,6 +28,16 @@ export declare const SpacefillParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 };
@@ -52,6 +62,16 @@ export declare function getSpacefillParams(ctx: ThemeRegistryContext, structure:
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 };
@@ -77,6 +97,16 @@ export declare const SpacefillRepresentationProvider: StructureRepresentationPro
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 }, "spacefill">;

package/lib/mol-repr/structure/units-representation.js

@@ -283,7 +283,7 @@ export function UnitsRepresentation(label, ctx, getParams, visualCtor) {
                 return false;
             // Remap `loci` from equivalent structure to the current `_structure`
             loci = Loci.remap(loci, _structure);
-            if (StructureElement.Loci.is(loci) && StructureElement.Loci.isWholeStructure(loci)) {
+            if (Structure.isLoci(loci) || (StructureElement.Loci.is(loci) && StructureElement.Loci.isWholeStructure(loci))) {
                 // Change to `EveryLoci` to allow for downstream optimizations
                 loci = EveryLoci;
             }