molstar 3.0.0-dev.4 → 3.0.0-dev.8

package/lib/mol-plugin-ui/skin/colors/blue.scss

@@ -1,24 +1,24 @@
-$default-background:         #2D3E50;
-$font-color:                 #EDF1F2; 
-$hover-font-color:           #3B9AD9;
-$entity-current-font-color:  #FFFFFF;
-$msp-btn-remove-background:      #BF3A31;
-$msp-btn-remove-hover-font-color:#ffffff;
-$msp-btn-commit-on-font-color:   #ffffff; 
-$entity-badge-font-color:    #ccd4e0;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: rgba(0,0,0,0.75);
-
-@function color-lower-contrast($color, $amount) {
-    @return darken($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return lighten($color, $amount);
+$default-background:         #2D3E50;
+$font-color:                 #EDF1F2; 
+$hover-font-color:           #3B9AD9;
+$entity-current-font-color:  #FFFFFF;
+$msp-btn-remove-background:      #BF3A31;
+$msp-btn-remove-hover-font-color:#ffffff;
+$msp-btn-commit-on-font-color:   #ffffff; 
+$entity-badge-font-color:    #ccd4e0;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: rgba(0,0,0,0.75);
+
+@function color-lower-contrast($color, $amount) {
+    @return darken($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return lighten($color, $amount);
 }

package/lib/mol-plugin-ui/skin/colors/dark.scss

@@ -1,24 +1,24 @@
-$default-background:         #111318;
-$font-color:                 #ccd4e0;
-$hover-font-color:           #51A2FB;
-$entity-current-font-color:  #68BEFD;
-$msp-btn-remove-background:      #DE0A28;
-$msp-btn-remove-hover-font-color:#F2F4F7;
-$msp-btn-commit-on-font-color:   #68BEFD;
-$entity-badge-font-color:    #ccd4e0;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: rgba(0,0,0,0.75);
-
-@function color-lower-contrast($color, $amount) {
-    @return darken($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return lighten($color, $amount);
+$default-background:         #111318;
+$font-color:                 #ccd4e0;
+$hover-font-color:           #51A2FB;
+$entity-current-font-color:  #68BEFD;
+$msp-btn-remove-background:      #DE0A28;
+$msp-btn-remove-hover-font-color:#F2F4F7;
+$msp-btn-commit-on-font-color:   #68BEFD;
+$entity-badge-font-color:    #ccd4e0;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: rgba(0,0,0,0.75);
+
+@function color-lower-contrast($color, $amount) {
+    @return darken($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return lighten($color, $amount);
 }

package/lib/mol-plugin-ui/skin/colors/light.scss

@@ -1,30 +1,30 @@
-// this is complement of the dark theme
-
-@function compl($color) {
-    @return rgb(255 - red($color), 255 - green($color), 255 - blue($color));
-}
-
-$default-background:         compl(#111318);
-$font-color:                 compl(#ccd4e0);
-$hover-font-color:           compl(#51A2FB);
-$entity-current-font-color:  compl(#68BEFD);
-$msp-btn-commit-on-font-color:   compl(#68BEFD);
-$entity-badge-font-color:    lighten(#ccd4e0,10%);
-$msp-btn-remove-background:      #DE0A28;
-$msp-btn-remove-hover-font-color:#F2F4F7;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: compl(#111318);
-
-@function color-lower-contrast($color, $amount) {
-    @return lighten($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return darken($color, $amount);
+// this is complement of the dark theme
+
+@function compl($color) {
+    @return rgb(255 - red($color), 255 - green($color), 255 - blue($color));
+}
+
+$default-background:         compl(#111318);
+$font-color:                 compl(#ccd4e0);
+$hover-font-color:           compl(#51A2FB);
+$entity-current-font-color:  compl(#68BEFD);
+$msp-btn-commit-on-font-color:   compl(#68BEFD);
+$entity-badge-font-color:    lighten(#ccd4e0,10%);
+$msp-btn-remove-background:      #DE0A28;
+$msp-btn-remove-hover-font-color:#F2F4F7;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: compl(#111318);
+
+@function color-lower-contrast($color, $amount) {
+    @return lighten($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return darken($color, $amount);
 }

package/lib/mol-plugin-ui/skin/dark.scss

@@ -1,2 +1,2 @@
-@import 'colors/dark';
+@import 'colors/dark';
 @import 'base/base';

package/lib/mol-plugin-ui/skin/light.scss

@@ -1,2 +1,2 @@
-@import 'colors/light';
+@import 'colors/light';
 @import 'base/base';

package/lib/mol-plugin-ui/viewport/simple-settings.js

@@ -58,7 +58,7 @@ var SimpleSettingsParams = {
         outline: Canvas3DParams.postprocessing.params.outline,
         fog: Canvas3DParams.cameraFog,
     }, { isFlat: true }),
-    clipping: PD.Group(__assign(__assign({}, Canvas3DParams.cameraClipping.params), Canvas3DParams.renderer.params.clip.params), { pivot: 'radius' }),
+    clipping: PD.Group(__assign({}, Canvas3DParams.cameraClipping.params), { pivot: 'radius' }),
     layout: PD.MultiSelect([], PD.objectToOptions(LayoutOptions)),
 };
 var SimpleSettingsMapping = ParamMapping({
@@ -108,7 +108,7 @@ var SimpleSettingsMapping = ParamMapping({
                 outline: canvas.postprocessing.outline,
                 fog: canvas.cameraFog,
             },
-            clipping: __assign(__assign({}, canvas.cameraClipping), canvas.renderer.clip)
+            clipping: __assign({}, canvas.cameraClipping)
         };
     },
     update: function (s, props) {
@@ -125,10 +125,6 @@ var SimpleSettingsMapping = ParamMapping({
             radius: s.clipping.radius,
             far: s.clipping.far,
         };
-        canvas.renderer.clip = {
-            variant: s.clipping.variant,
-            objects: s.clipping.objects,
-        };
         props.layout = s.layout;
     },
     apply: function (props, ctx) {

package/lib/mol-repr/shape/loci/angle.d.ts

@@ -40,6 +40,16 @@ export declare const AngleParams: {
         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;
+        }>[];
+    }>>;
     ignoreLight: PD.BooleanParam;
     sectorOpacity: PD.Numeric;
     color: PD.Color;

package/lib/mol-repr/shape/loci/common.d.ts

@@ -40,5 +40,15 @@ export declare const LociLabelTextParams: {
         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 LociLabelTextParams = typeof LociLabelTextParams;

package/lib/mol-repr/shape/loci/dihedral.d.ts

@@ -40,6 +40,16 @@ export declare const DihedralParams: {
         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;
+        }>[];
+    }>>;
     ignoreLight: PD.BooleanParam;
     sectorOpacity: PD.Numeric;
     color: PD.Color;

package/lib/mol-repr/shape/loci/distance.d.ts

@@ -41,6 +41,16 @@ export declare const DistanceParams: {
         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;
+        }>[];
+    }>>;
     lineSizeAttenuation: PD.BooleanParam;
     linesColor: PD.Color;
     linesSize: PD.Numeric;

package/lib/mol-repr/shape/loci/label.d.ts

@@ -44,6 +44,16 @@ 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 type LabelProps = PD.Values<LabelParams>;

package/lib/mol-repr/shape/loci/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 type OrientationProps = PD.Values<OrientationParams>;

package/lib/mol-repr/shape/loci/plane.d.ts

@@ -27,6 +27,16 @@ export declare const PlaneParams: {
         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 PlaneParams = typeof PlaneParams;
 export declare type PlaneProps = PD.Values<PlaneParams>;

package/lib/mol-repr/shape/model/unitcell.d.ts

@@ -30,6 +30,16 @@ export declare const UnitcellParams: {
         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 UnitcellParams = typeof UnitcellParams;
 export declare type UnitcellProps = PD.Values<UnitcellParams>;

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

@@ -97,7 +97,7 @@ export function ComplexRepresentation(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;
             }

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

@@ -56,6 +56,16 @@ export declare const ComplexMeshParams: {
         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 ComplexMeshParams = typeof ComplexMeshParams;
 export interface ComplexMeshVisualBuilder<P extends ComplexMeshParams> extends ComplexVisualBuilder<P, Mesh> {
@@ -78,6 +88,16 @@ export declare const ComplexCylindersParams: {
         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 ComplexCylindersParams = typeof ComplexCylindersParams;
 export interface ComplexCylindersVisualBuilder<P extends ComplexCylindersParams> extends ComplexVisualBuilder<P, Cylinders> {
@@ -95,6 +115,16 @@ export declare const ComplexLinesParams: {
         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 ComplexLinesParams = typeof ComplexLinesParams;
 export interface ComplexLinesVisualBuilder<P extends ComplexLinesParams> extends ComplexVisualBuilder<P, Lines> {
@@ -129,6 +159,16 @@ export declare const ComplexTextParams: {
         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 ComplexTextParams = typeof ComplexTextParams;
 export interface ComplexTextVisualBuilder<P extends ComplexTextParams> extends ComplexVisualBuilder<P, Text> {
@@ -137,27 +177,9 @@ export declare function ComplexTextVisual<P extends ComplexTextParams>(builder:
 export declare const ComplexDirectVolumeParams: {
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
-    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;
@@ -167,6 +189,16 @@ export declare const ComplexDirectVolumeParams: {
         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 ComplexDirectVolumeParams = typeof ComplexDirectVolumeParams;
 export interface ComplexDirectVolumeVisualBuilder<P extends ComplexDirectVolumeParams> extends ComplexVisualBuilder<P, DirectVolume> {
@@ -189,6 +221,16 @@ export declare const ComplexTextureMeshParams: {
         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 ComplexTextureMeshParams = typeof ComplexTextureMeshParams;
 export interface ComplexTextureMeshVisualBuilder<P extends ComplexTextureMeshParams> extends ComplexVisualBuilder<P, TextureMesh> {

package/lib/mol-repr/structure/params.d.ts

@@ -27,6 +27,16 @@ export declare const StructureMeshParams: {
         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 StructureMeshParams = typeof StructureMeshParams;
 export declare const StructureSpheresParams: {
@@ -43,6 +53,16 @@ export declare const StructureSpheresParams: {
         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 StructureSpheresParams = typeof StructureSpheresParams;
 export declare const StructureCylindersParams: {
@@ -60,6 +80,16 @@ export declare const StructureCylindersParams: {
         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 StructureCylindersParams = typeof StructureCylindersParams;
 export declare const StructurePointsParams: {
@@ -73,6 +103,16 @@ export declare const StructurePointsParams: {
         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 StructurePointsParams = typeof StructurePointsParams;
 export declare const StructureLinesParams: {
@@ -85,6 +125,16 @@ export declare const StructureLinesParams: {
         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 StructureLinesParams = typeof StructureLinesParams;
 export declare const StructureTextParams: {
@@ -114,30 +164,22 @@ export declare const StructureTextParams: {
         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 StructureTextParams = typeof StructureTextParams;
 export declare const StructureDirectVolumeParams: {
-    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;
@@ -147,6 +189,16 @@ export declare const StructureDirectVolumeParams: {
         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 StructureDirectVolumeParams = typeof StructureDirectVolumeParams;
 export declare const StructureTextureMeshParams: {
@@ -164,5 +216,15 @@ export declare const StructureTextureMeshParams: {
         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 StructureTextureMeshParams = typeof StructureTextureMeshParams;