molstar 3.0.0-dev.6 → 3.0.0

package/lib/mol-plugin-ui/structure/superposition.js

@@ -159,8 +159,8 @@ var SuperpositionControls = /** @class */ (function (_super) {
                         _i++;
                         return [3 /*break*/, 1];
                     case 4:
-                        rmsd /= transforms.length - 1;
-                        this.plugin.log.info("Superposed ".concat(input.length, " structures with avg. RMSD ").concat(rmsd.toFixed(2), "."));
+                        rmsd /= Math.max(transforms.length - 1, 1);
+                        this.plugin.log.info("Superposed ".concat(input.length, " structures with avg. RMSD ").concat(rmsd.toFixed(2), " \u00C5."));
                         return [4 /*yield*/, new Promise(function (res) { return requestAnimationFrame(res); })];
                     case 5:
                         _a.sent();

package/lib/mol-plugin-ui/viewport/simple-settings.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>

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

@@ -1,7 +1,7 @@
 import { __assign, __awaiter, __extends, __generator } from "tslib";
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -44,10 +44,7 @@ var LayoutOptions = {
     'left': 'Left Panel'
 };
 var SimpleSettingsParams = {
-    spin: PD.Group({
-        spin: Canvas3DParams.trackball.params.spin,
-        speed: Canvas3DParams.trackball.params.spinSpeed
-    }, { pivot: 'spin' }),
+    animate: Canvas3DParams.trackball.params.animate,
     camera: Canvas3DParams.camera,
     background: PD.Group({
         color: PD.Color(Color(0xFCFBF9), { label: 'Background', description: 'Custom background color' }),
@@ -58,7 +55,7 @@ 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({
@@ -97,7 +94,7 @@ var SimpleSettingsMapping = ParamMapping({
         var renderer = canvas.renderer;
         return {
             layout: props.layout,
-            spin: { spin: !!canvas.trackball.spin, speed: canvas.trackball.spinSpeed },
+            animate: canvas.trackball.animate,
             camera: canvas.camera,
             background: {
                 color: renderer.backgroundColor,
@@ -108,13 +105,12 @@ 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) {
         var canvas = props.canvas;
-        canvas.trackball.spin = s.spin.spin;
-        canvas.trackball.spinSpeed = s.spin.speed;
+        canvas.trackball.animate = s.animate;
         canvas.camera = s.camera;
         canvas.transparentBackground = s.background.transparent;
         canvas.renderer.backgroundColor = s.background.color;
@@ -125,10 +121,6 @@ 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;