molstar 3.0.0-dev.5 → 3.0.0-dev.9

package/lib/commonjs/mol-repr/structure/visual/util/common.d.ts

@@ -10,6 +10,7 @@ import { Loci } from '../../../../mol-model/loci';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { AssignableArrayLike } from '../../../../mol-util/type-helpers';
 import { Box3D } from '../../../../mol-math/geometry';
+import { SizeTheme } from '../../../../mol-theme/size';
 /** Return a Loci for the elements of a whole residue the elementIndex belongs to. */
 export declare function getResidueLoci(structure: Structure, unit: Unit.Atomic, elementIndex: ElementIndex): Loci;
 /**
@@ -60,7 +61,7 @@ export declare const DefaultCommonSurfaceProps: PD.Values<{
     includeParent: PD.BooleanParam;
 }>;
 export declare type CommonSurfaceProps = typeof DefaultCommonSurfaceProps;
-export declare function getUnitConformationAndRadius(structure: Structure, unit: Unit, props: CommonSurfaceProps): {
+export declare function getUnitConformationAndRadius(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, props: CommonSurfaceProps): {
     position: {
         indices: SortedArray<ElementIndex>;
         x: ArrayLike<number>;
@@ -71,7 +72,7 @@ export declare function getUnitConformationAndRadius(structure: Structure, unit:
     boundary: import("../../../../mol-math/geometry/boundary").Boundary;
     radius: (index: number) => number;
 };
-export declare function getStructureConformationAndRadius(structure: Structure, ignoreHydrogens: boolean, traceOnly: boolean): {
+export declare function getStructureConformationAndRadius(structure: Structure, sizeTheme: SizeTheme<any>, ignoreHydrogens: boolean, traceOnly: boolean): {
     position: {
         indices: OrderedSet<number>;
         x: ArrayLike<number>;

package/lib/commonjs/mol-repr/structure/visual/util/common.js

@@ -12,7 +12,6 @@ var linear_algebra_1 = require("../../../../mol-math/linear-algebra");
 var transform_data_1 = require("../../../../mol-geo/geometry/transform-data");
 var int_1 = require("../../../../mol-data/int");
 var loci_1 = require("../../../../mol-model/loci");
-var physical_1 = require("../../../../mol-theme/size/physical");
 var atomic_1 = require("../../../../mol-model/structure/model/properties/atomic");
 var array_1 = require("../../../../mol-util/array");
 var param_definition_1 = require("../../../../mol-util/param-definition");
@@ -160,7 +159,7 @@ function filterId(id, elements, indices) {
         }
     }
 }
-function getUnitConformationAndRadius(structure, unit, props) {
+function getUnitConformationAndRadius(structure, unit, sizeTheme, props) {
     var ignoreHydrogens = props.ignoreHydrogens, traceOnly = props.traceOnly, includeParent = props.includeParent;
     var rootUnit = includeParent ? structure.root.unitMap.get(unit.id) : unit;
     var _a = getConformation(rootUnit), x = _a.x, y = _a.y, z = _a.z;
@@ -197,7 +196,6 @@ function getUnitConformationAndRadius(structure, unit, props) {
     var position = { indices: indices, x: x, y: y, z: z, id: id };
     var boundary = unit === rootUnit ? unit.boundary : (0, boundary_1.getBoundary)(position);
     var l = structure_1.StructureElement.Location.create(structure, rootUnit);
-    var sizeTheme = (0, physical_1.PhysicalSizeTheme)({}, { scale: 1 });
     var radius = function (index) {
         l.element = index;
         return sizeTheme.size(l);
@@ -205,9 +203,8 @@ function getUnitConformationAndRadius(structure, unit, props) {
     return { position: position, boundary: boundary, radius: radius };
 }
 exports.getUnitConformationAndRadius = getUnitConformationAndRadius;
-function getStructureConformationAndRadius(structure, ignoreHydrogens, traceOnly) {
+function getStructureConformationAndRadius(structure, sizeTheme, ignoreHydrogens, traceOnly) {
     var l = structure_1.StructureElement.Location.create(structure);
-    var sizeTheme = (0, physical_1.PhysicalSizeTheme)({}, { scale: 1 });
     var xs;
     var ys;
     var zs;

package/lib/commonjs/mol-repr/structure/visual/util/gaussian.d.ts

@@ -8,6 +8,7 @@ import { Task } from '../../../../mol-task';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 import { Texture } from '../../../../mol-gl/webgl/texture';
 import { WebGLContext } from '../../../../mol-gl/webgl/context';
+import { SizeTheme } from '../../../../mol-theme/size';
 export declare const GaussianDensityParams: {
     ignoreHydrogens: PD.BooleanParam;
     traceOnly: PD.BooleanParam;
@@ -26,9 +27,9 @@ export declare const DefaultGaussianDensityProps: PD.Values<{
 }>;
 export declare type GaussianDensityProps = typeof DefaultGaussianDensityProps;
 export declare function getTextureMaxCells(webgl: WebGLContext, structure?: Structure): number;
-export declare function computeUnitGaussianDensity(structure: Structure, unit: Unit, props: GaussianDensityProps): Task<import("../../../../mol-math/geometry/gaussian-density").GaussianDensityData>;
-export declare function computeUnitGaussianDensityTexture(structure: Structure, unit: Unit, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture): Task<import("../../../../mol-math/geometry/gaussian-density").GaussianDensityTextureData>;
-export declare function computeUnitGaussianDensityTexture2d(structure: Structure, unit: Unit, powerOfTwo: boolean, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture): Task<import("../../../../mol-math/geometry/gaussian-density").GaussianDensityTextureData>;
-export declare function computeStructureGaussianDensity(structure: Structure, props: GaussianDensityProps): Task<import("../../../../mol-math/geometry/gaussian-density").GaussianDensityData>;
-export declare function computeStructureGaussianDensityTexture(structure: Structure, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture): Task<import("../../../../mol-math/geometry/gaussian-density").GaussianDensityTextureData>;
-export declare function computeStructureGaussianDensityTexture2d(structure: Structure, powerOfTwo: boolean, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture): Task<import("../../../../mol-math/geometry/gaussian-density").GaussianDensityTextureData>;
+export declare function computeUnitGaussianDensity(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, props: GaussianDensityProps): Task<import("../../../../mol-math/geometry/gaussian-density").GaussianDensityData>;
+export declare function computeUnitGaussianDensityTexture(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture): Task<import("../../../../mol-math/geometry/gaussian-density").GaussianDensityTextureData>;
+export declare function computeUnitGaussianDensityTexture2d(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, powerOfTwo: boolean, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture): Task<import("../../../../mol-math/geometry/gaussian-density").GaussianDensityTextureData>;
+export declare function computeStructureGaussianDensity(structure: Structure, sizeTheme: SizeTheme<any>, props: GaussianDensityProps): Task<import("../../../../mol-math/geometry/gaussian-density").GaussianDensityData>;
+export declare function computeStructureGaussianDensityTexture(structure: Structure, sizeTheme: SizeTheme<any>, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture): Task<import("../../../../mol-math/geometry/gaussian-density").GaussianDensityTextureData>;
+export declare function computeStructureGaussianDensityTexture2d(structure: Structure, sizeTheme: SizeTheme<any>, powerOfTwo: boolean, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture): Task<import("../../../../mol-math/geometry/gaussian-density").GaussianDensityTextureData>;

package/lib/commonjs/mol-repr/structure/visual/util/gaussian.js

@@ -22,11 +22,11 @@ function getTextureMaxCells(webgl, structure) {
 }
 exports.getTextureMaxCells = getTextureMaxCells;
 //
-function computeUnitGaussianDensity(structure, unit, props) {
+function computeUnitGaussianDensity(structure, unit, sizeTheme, props) {
     var _this = this;
     var box = unit.lookup3d.boundary.box;
     var p = (0, common_1.ensureReasonableResolution)(box, props);
-    var _a = (0, common_1.getUnitConformationAndRadius)(structure, unit, p), position = _a.position, radius = _a.radius;
+    var _a = (0, common_1.getUnitConformationAndRadius)(structure, unit, sizeTheme, p), position = _a.position, radius = _a.radius;
     return mol_task_1.Task.create('Gaussian Density', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
         return (0, tslib_1.__generator)(this, function (_a) {
             switch (_a.label) {
@@ -37,11 +37,11 @@ function computeUnitGaussianDensity(structure, unit, props) {
     }); });
 }
 exports.computeUnitGaussianDensity = computeUnitGaussianDensity;
-function computeUnitGaussianDensityTexture(structure, unit, props, webgl, texture) {
+function computeUnitGaussianDensityTexture(structure, unit, sizeTheme, props, webgl, texture) {
     var _this = this;
     var box = unit.lookup3d.boundary.box;
     var p = (0, common_1.ensureReasonableResolution)(box, props, getTextureMaxCells(webgl, structure));
-    var _a = (0, common_1.getUnitConformationAndRadius)(structure, unit, p), position = _a.position, radius = _a.radius;
+    var _a = (0, common_1.getUnitConformationAndRadius)(structure, unit, sizeTheme, p), position = _a.position, radius = _a.radius;
     return mol_task_1.Task.create('Gaussian Density', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
         return (0, tslib_1.__generator)(this, function (_a) {
             return [2 /*return*/, (0, gpu_1.GaussianDensityTexture)(webgl, position, box, radius, p, texture)];
@@ -49,11 +49,11 @@ function computeUnitGaussianDensityTexture(structure, unit, props, webgl, textur
     }); });
 }
 exports.computeUnitGaussianDensityTexture = computeUnitGaussianDensityTexture;
-function computeUnitGaussianDensityTexture2d(structure, unit, powerOfTwo, props, webgl, texture) {
+function computeUnitGaussianDensityTexture2d(structure, unit, sizeTheme, powerOfTwo, props, webgl, texture) {
     var _this = this;
     var box = unit.lookup3d.boundary.box;
     var p = (0, common_1.ensureReasonableResolution)(box, props, getTextureMaxCells(webgl, structure));
-    var _a = (0, common_1.getUnitConformationAndRadius)(structure, unit, p), position = _a.position, radius = _a.radius;
+    var _a = (0, common_1.getUnitConformationAndRadius)(structure, unit, sizeTheme, p), position = _a.position, radius = _a.radius;
     return mol_task_1.Task.create('Gaussian Density', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
         return (0, tslib_1.__generator)(this, function (_a) {
             return [2 /*return*/, (0, gpu_1.GaussianDensityTexture2d)(webgl, position, box, radius, powerOfTwo, p, texture)];
@@ -62,11 +62,11 @@ function computeUnitGaussianDensityTexture2d(structure, unit, powerOfTwo, props,
 }
 exports.computeUnitGaussianDensityTexture2d = computeUnitGaussianDensityTexture2d;
 //
-function computeStructureGaussianDensity(structure, props) {
+function computeStructureGaussianDensity(structure, sizeTheme, props) {
     var _this = this;
     var box = structure.lookup3d.boundary.box;
     var p = (0, common_1.ensureReasonableResolution)(box, props);
-    var _a = (0, common_1.getStructureConformationAndRadius)(structure, props.ignoreHydrogens, props.traceOnly), position = _a.position, radius = _a.radius;
+    var _a = (0, common_1.getStructureConformationAndRadius)(structure, sizeTheme, props.ignoreHydrogens, props.traceOnly), position = _a.position, radius = _a.radius;
     return mol_task_1.Task.create('Gaussian Density', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
         return (0, tslib_1.__generator)(this, function (_a) {
             switch (_a.label) {
@@ -77,11 +77,11 @@ function computeStructureGaussianDensity(structure, props) {
     }); });
 }
 exports.computeStructureGaussianDensity = computeStructureGaussianDensity;
-function computeStructureGaussianDensityTexture(structure, props, webgl, texture) {
+function computeStructureGaussianDensityTexture(structure, sizeTheme, props, webgl, texture) {
     var _this = this;
     var box = structure.lookup3d.boundary.box;
     var p = (0, common_1.ensureReasonableResolution)(box, props, getTextureMaxCells(webgl));
-    var _a = (0, common_1.getStructureConformationAndRadius)(structure, props.ignoreHydrogens, props.traceOnly), position = _a.position, radius = _a.radius;
+    var _a = (0, common_1.getStructureConformationAndRadius)(structure, sizeTheme, props.ignoreHydrogens, props.traceOnly), position = _a.position, radius = _a.radius;
     return mol_task_1.Task.create('Gaussian Density', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
         return (0, tslib_1.__generator)(this, function (_a) {
             return [2 /*return*/, (0, gpu_1.GaussianDensityTexture)(webgl, position, box, radius, p, texture)];
@@ -89,11 +89,11 @@ function computeStructureGaussianDensityTexture(structure, props, webgl, texture
     }); });
 }
 exports.computeStructureGaussianDensityTexture = computeStructureGaussianDensityTexture;
-function computeStructureGaussianDensityTexture2d(structure, powerOfTwo, props, webgl, texture) {
+function computeStructureGaussianDensityTexture2d(structure, sizeTheme, powerOfTwo, props, webgl, texture) {
     var _this = this;
     var box = structure.lookup3d.boundary.box;
     var p = (0, common_1.ensureReasonableResolution)(box, props, getTextureMaxCells(webgl));
-    var _a = (0, common_1.getStructureConformationAndRadius)(structure, props.ignoreHydrogens, props.traceOnly), position = _a.position, radius = _a.radius;
+    var _a = (0, common_1.getStructureConformationAndRadius)(structure, sizeTheme, props.ignoreHydrogens, props.traceOnly), position = _a.position, radius = _a.radius;
     return mol_task_1.Task.create('Gaussian Density', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
         return (0, tslib_1.__generator)(this, function (_a) {
             return [2 /*return*/, (0, gpu_1.GaussianDensityTexture2d)(webgl, position, box, radius, powerOfTwo, p, texture)];

package/lib/commonjs/mol-repr/structure/visual/util/molecular-surface.d.ts

@@ -8,5 +8,6 @@ import { Task } from '../../../../mol-task';
 import { CommonSurfaceProps } from './common';
 import { DensityData } from '../../../../mol-math/geometry';
 import { MolecularSurfaceCalculationProps } from '../../../../mol-math/geometry/molecular-surface';
+import { SizeTheme } from '../../../../mol-theme/size';
 export declare type MolecularSurfaceProps = MolecularSurfaceCalculationProps & CommonSurfaceProps;
-export declare function computeUnitMolecularSurface(structure: Structure, unit: Unit, props: MolecularSurfaceProps): Task<DensityData>;
+export declare function computeUnitMolecularSurface(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, props: MolecularSurfaceProps): Task<DensityData>;

package/lib/commonjs/mol-repr/structure/visual/util/molecular-surface.js

@@ -11,9 +11,9 @@ var mol_task_1 = require("../../../../mol-task");
 var common_1 = require("./common");
 var molecular_surface_1 = require("../../../../mol-math/geometry/molecular-surface");
 var int_1 = require("../../../../mol-data/int");
-function getPositionDataAndMaxRadius(structure, unit, props) {
+function getPositionDataAndMaxRadius(structure, unit, sizeTheme, props) {
     var probeRadius = props.probeRadius;
-    var _a = (0, common_1.getUnitConformationAndRadius)(structure, unit, props), position = _a.position, boundary = _a.boundary, radius = _a.radius;
+    var _a = (0, common_1.getUnitConformationAndRadius)(structure, unit, sizeTheme, props), position = _a.position, boundary = _a.boundary, radius = _a.radius;
     var indices = position.indices;
     var n = int_1.OrderedSet.size(indices);
     var radii = new Float32Array(int_1.OrderedSet.end(indices));
@@ -27,11 +27,11 @@ function getPositionDataAndMaxRadius(structure, unit, props) {
     }
     return { position: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, position), { radius: radii }), boundary: boundary, maxRadius: maxRadius };
 }
-function computeUnitMolecularSurface(structure, unit, props) {
+function computeUnitMolecularSurface(structure, unit, sizeTheme, props) {
     var _this = this;
     var box = unit.lookup3d.boundary.box;
     var p = (0, common_1.ensureReasonableResolution)(box, props);
-    var _a = getPositionDataAndMaxRadius(structure, unit, p), position = _a.position, boundary = _a.boundary, maxRadius = _a.maxRadius;
+    var _a = getPositionDataAndMaxRadius(structure, unit, sizeTheme, p), position = _a.position, boundary = _a.boundary, maxRadius = _a.maxRadius;
     return mol_task_1.Task.create('Molecular Surface', function (ctx) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
         return (0, tslib_1.__generator)(this, function (_a) {
             switch (_a.label) {

package/lib/commonjs/mol-repr/visual.js

@@ -46,7 +46,7 @@ var Visual;
     function mark(renderObject, loci, action, lociApply, previous) {
         if (!renderObject || (0, loci_1.isEmptyLoci)(loci))
             return false;
-        var _a = renderObject.values, tMarker = _a.tMarker, dMarkerType = _a.dMarkerType, uMarker = _a.uMarker, markerAverage = _a.markerAverage, markerStatus = _a.markerStatus, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
+        var _a = renderObject.values, tMarker = _a.tMarker, uMarker = _a.uMarker, markerAverage = _a.markerAverage, markerStatus = _a.markerStatus, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
         var count = uGroupCount.ref.value * instanceCount.ref.value;
         var array = tMarker.ref.value.array;
         var currentStatus = markerStatus.ref.value;
@@ -103,7 +103,6 @@ var Visual;
             mol_util_1.ValueCell.updateIfChanged(uMarker, status);
             if (status === -1)
                 mol_util_1.ValueCell.update(tMarker, tMarker.ref.value);
-            mol_util_1.ValueCell.updateIfChanged(dMarkerType, status === -1 ? 'groupInstance' : 'uniform');
             mol_util_1.ValueCell.updateIfChanged(markerAverage, average);
             mol_util_1.ValueCell.updateIfChanged(markerStatus, status);
         }
@@ -113,7 +112,7 @@ var Visual;
     function setOverpaint(renderObject, overpaint, lociApply, clear, smoothing) {
         if (!renderObject)
             return;
-        var _a = renderObject.values, tOverpaint = _a.tOverpaint, dOverpaintType = _a.dOverpaintType, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
+        var _a = renderObject.values, tOverpaint = _a.tOverpaint, dOverpaintType = _a.dOverpaintType, dOverpaint = _a.dOverpaint, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
         var count = uGroupCount.ref.value * instanceCount.ref.value;
         // ensure texture has right size
         (0, overpaint_data_1.createOverpaint)(overpaint.layers.length ? count : 0, renderObject.values);
@@ -137,6 +136,7 @@ var Visual;
         }
         mol_util_1.ValueCell.update(tOverpaint, tOverpaint.ref.value);
         mol_util_1.ValueCell.updateIfChanged(dOverpaintType, 'groupInstance');
+        mol_util_1.ValueCell.updateIfChanged(dOverpaint, overpaint.layers.length > 0);
         if (overpaint.layers.length === 0)
             return;
         if (smoothing && (0, base_1.hasColorSmoothingProp)(smoothing.props)) {
@@ -163,7 +163,7 @@ var Visual;
     function setTransparency(renderObject, transparency, lociApply, clear, smoothing) {
         if (!renderObject)
             return;
-        var _a = renderObject.values, tTransparency = _a.tTransparency, dTransparencyType = _a.dTransparencyType, transparencyAverage = _a.transparencyAverage, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
+        var _a = renderObject.values, tTransparency = _a.tTransparency, dTransparencyType = _a.dTransparencyType, transparencyAverage = _a.transparencyAverage, dTransparency = _a.dTransparency, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
         var count = uGroupCount.ref.value * instanceCount.ref.value;
         // ensure texture has right size and variant
         (0, transparency_data_1.createTransparency)(transparency.layers.length ? count : 0, renderObject.values);
@@ -186,6 +186,7 @@ var Visual;
         mol_util_1.ValueCell.update(tTransparency, tTransparency.ref.value);
         mol_util_1.ValueCell.updateIfChanged(transparencyAverage, (0, transparency_data_1.getTransparencyAverage)(array, count));
         mol_util_1.ValueCell.updateIfChanged(dTransparencyType, 'groupInstance');
+        mol_util_1.ValueCell.updateIfChanged(dTransparency, transparency.layers.length > 0);
         if (transparency.layers.length === 0)
             return;
         if (smoothing && (0, base_1.hasColorSmoothingProp)(smoothing.props)) {
@@ -212,7 +213,7 @@ var Visual;
     function setSubstance(renderObject, substance, lociApply, clear, smoothing) {
         if (!renderObject)
             return;
-        var _a = renderObject.values, tSubstance = _a.tSubstance, dSubstanceType = _a.dSubstanceType, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
+        var _a = renderObject.values, tSubstance = _a.tSubstance, dSubstanceType = _a.dSubstanceType, dSubstance = _a.dSubstance, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
         var count = uGroupCount.ref.value * instanceCount.ref.value;
         // ensure texture has right size
         (0, substance_data_1.createSubstance)(substance.layers.length ? count : 0, renderObject.values);
@@ -236,6 +237,7 @@ var Visual;
         }
         mol_util_1.ValueCell.update(tSubstance, tSubstance.ref.value);
         mol_util_1.ValueCell.updateIfChanged(dSubstanceType, 'groupInstance');
+        mol_util_1.ValueCell.updateIfChanged(dSubstance, substance.layers.length > 0);
         if (substance.layers.length === 0)
             return;
         if (smoothing && (0, base_1.hasColorSmoothingProp)(smoothing.props)) {
@@ -262,10 +264,11 @@ var Visual;
     function setClipping(renderObject, clipping, lociApply, clear) {
         if (!renderObject)
             return;
-        var _a = renderObject.values, tClipping = _a.tClipping, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
+        var _a = renderObject.values, tClipping = _a.tClipping, dClipping = _a.dClipping, uGroupCount = _a.uGroupCount, instanceCount = _a.instanceCount;
         var count = uGroupCount.ref.value * instanceCount.ref.value;
+        var layers = clipping.layers;
         // ensure texture has right size
-        (0, clipping_data_1.createClipping)(clipping.layers.length ? count : 0, renderObject.values);
+        (0, clipping_data_1.createClipping)(layers.length ? count : 0, renderObject.values);
         var array = tClipping.ref.value.array;
         // clear if requested
         if (clear)
@@ -283,6 +286,7 @@ var Visual;
             _loop_4(i, il);
         }
         mol_util_1.ValueCell.update(tClipping, tClipping.ref.value);
+        mol_util_1.ValueCell.updateIfChanged(dClipping, clipping.layers.length > 0);
     }
     Visual.setClipping = setClipping;
     function setTransform(renderObject, transform, instanceTransforms) {

package/lib/commonjs/mol-repr/volume/direct-volume.d.ts

@@ -46,27 +46,9 @@ export declare const DirectVolumeParams: {
             legend?: import("../../mol-util/legend").Legend | undefined;
         }) | undefined;
     };
-    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;
@@ -75,6 +57,16 @@ export declare const DirectVolumeParams: {
         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 DirectVolumeParams = typeof DirectVolumeParams;
 export declare function getDirectVolumeParams(ctx: ThemeRegistryContext, volume: Volume): {
@@ -101,27 +93,9 @@ export declare function getDirectVolumeParams(ctx: ThemeRegistryContext, volume:
             legend?: import("../../mol-util/legend").Legend | undefined;
         }) | undefined;
     };
-    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;
@@ -130,6 +104,16 @@ export declare function getDirectVolumeParams(ctx: ThemeRegistryContext, volume:
         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 DirectVolumeProps = PD.Values<DirectVolumeParams>;
 export declare function DirectVolumeVisual(materialId: number): VolumeVisual<DirectVolumeParams>;
@@ -158,27 +142,9 @@ export declare const DirectVolumeRepresentationProvider: VolumeRepresentationPro
             legend?: import("../../mol-util/legend").Legend | undefined;
         }) | undefined;
     };
-    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;
@@ -187,4 +153,14 @@ export declare const DirectVolumeRepresentationProvider: VolumeRepresentationPro
         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;
+        }>[];
+    }>>;
 }, "direct-volume">;

package/lib/commonjs/mol-repr/volume/direct-volume.js

@@ -38,7 +38,8 @@ function createDirectVolume2d(ctx, webgl, volume, directVolume) {
     var texture = directVolume ? directVolume.gridTexture.ref.value : webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
     texture.load(textureImage);
     var _b = getUnitToCartn(volume.grid), unitToCartn = _b.unitToCartn, cellDim = _b.cellDim;
-    return direct_volume_1.DirectVolume.create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, volume.grid.stats, false, directVolume);
+    var axisOrder = volume.grid.cells.space.axisOrderSlowToFast;
+    return direct_volume_1.DirectVolume.create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, volume.grid.stats, false, axisOrder, directVolume);
 }
 exports.createDirectVolume2d = createDirectVolume2d;
 // 3d volume texture
@@ -67,7 +68,8 @@ function createDirectVolume3d(ctx, webgl, volume, directVolume) {
     var texture = directVolume ? directVolume.gridTexture.ref.value : webgl.resources.texture('volume-uint8', 'rgba', 'ubyte', 'linear');
     texture.load(textureVolume);
     var _a = getUnitToCartn(volume.grid), unitToCartn = _a.unitToCartn, cellDim = _a.cellDim;
-    return direct_volume_1.DirectVolume.create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, volume.grid.stats, false, directVolume);
+    var axisOrder = volume.grid.cells.space.axisOrderSlowToFast;
+    return direct_volume_1.DirectVolume.create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, volume.grid.stats, false, axisOrder, directVolume);
 }
 exports.createDirectVolume3d = createDirectVolume3d;
 //
@@ -86,9 +88,7 @@ function createDirectVolume(ctx, volume, theme, props, directVolume) {
 }
 exports.createDirectVolume = createDirectVolume;
 function getLoci(volume, props) {
-    return props.renderMode.name === 'isosurface'
-        ? volume_1.Volume.Isosurface.Loci(volume, props.renderMode.params.isoValue)
-        : volume_1.Volume.Loci(volume);
+    return volume_1.Volume.Loci(volume);
 }
 function getDirectVolumeLoci(pickingId, volume, props, id) {
     var objectId = pickingId.objectId, groupId = pickingId.groupId;
@@ -99,17 +99,13 @@ function getDirectVolumeLoci(pickingId, volume, props, id) {
 }
 exports.getDirectVolumeLoci = getDirectVolumeLoci;
 function eachDirectVolume(loci, volume, props, apply) {
-    var isoValue = props.renderMode.name === 'isosurface'
-        ? props.renderMode.params.isoValue : undefined;
-    return (0, util_1.eachVolumeLoci)(loci, volume, isoValue, apply);
+    return (0, util_1.eachVolumeLoci)(loci, volume, undefined, apply);
 }
 exports.eachDirectVolume = eachDirectVolume;
 //
 exports.DirectVolumeParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, direct_volume_1.DirectVolume.Params), { quality: (0, tslib_1.__assign)((0, tslib_1.__assign)({}, direct_volume_1.DirectVolume.Params.quality), { isEssential: false }) });
 function getDirectVolumeParams(ctx, volume) {
-    var p = param_definition_1.ParamDefinition.clone(exports.DirectVolumeParams);
-    p.renderMode = direct_volume_1.DirectVolume.createRenderModeParam(volume.grid.stats);
-    return p;
+    return param_definition_1.ParamDefinition.clone(exports.DirectVolumeParams);
 }
 exports.getDirectVolumeParams = getDirectVolumeParams;
 function DirectVolumeVisual(materialId) {
@@ -139,7 +135,7 @@ exports.DirectVolumeRepresentationProvider = (0, representation_1.VolumeRepresen
     factory: DirectVolumeRepresentation,
     getParams: getDirectVolumeParams,
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.DirectVolumeParams),
-    defaultColorTheme: { name: 'uniform' },
+    defaultColorTheme: { name: 'volume-value' },
     defaultSizeTheme: { name: 'uniform' },
     isApplicable: function (volume) { return !volume_1.Volume.isEmpty(volume); }
 });

package/lib/commonjs/mol-repr/volume/isosurface.d.ts

@@ -101,6 +101,16 @@ export declare function IsosurfaceVisual(materialId: number, volume: Volume, pro
         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 function eachIsosurface(loci: Loci, volume: Volume, props: VolumeIsosurfaceProps, apply: (interval: Interval) => boolean): boolean;
 export declare function createVolumeIsosurfaceMesh(ctx: VisualContext, volume: Volume, theme: Theme, props: VolumeIsosurfaceProps, mesh?: Mesh): Promise<Mesh>;
@@ -164,6 +174,16 @@ export declare const IsosurfaceMeshParams: {
         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 IsosurfaceMeshParams = typeof IsosurfaceMeshParams;
 export declare function IsosurfaceMeshVisual(materialId: number): VolumeVisual<IsosurfaceMeshParams>;
@@ -223,6 +243,16 @@ export declare const IsosurfaceWireframeParams: {
         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 IsosurfaceWireframeParams = typeof IsosurfaceWireframeParams;
 export declare function IsosurfaceWireframeVisual(materialId: number): VolumeVisual<IsosurfaceWireframeParams>;
@@ -282,6 +312,16 @@ export declare const IsosurfaceParams: {
         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;
+        }>[];
+    }>>;
     tryUseGpu: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -347,6 +387,16 @@ export declare function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: V
         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;
+        }>[];
+    }>>;
     tryUseGpu: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -413,6 +463,16 @@ export declare const IsosurfaceRepresentationProvider: VolumeRepresentationProvi
         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;
+        }>[];
+    }>>;
     tryUseGpu: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;

package/lib/commonjs/mol-repr/volume/isosurface.js

@@ -34,6 +34,11 @@ function gpuSupport(webgl) {
 }
 var Padding = 1;
 function suitableForGpu(volume, webgl) {
+    // small volumes are about as fast or faster on CPU vs integrated GPU
+    if (volume.grid.cells.data.length < Math.pow(10, 3))
+        return false;
+    // the GPU is much more memory contraint, especially true for integrated GPUs,
+    // fallback to CPU for large volumes
     var gridDim = volume.grid.cells.space.dimensions;
     var powerOfTwoSize = (0, util_1.getVolumeTexture2dLayout)(gridDim, Padding).powerOfTwoSize;
     return powerOfTwoSize <= webgl.maxTextureSize / 2;
@@ -147,17 +152,21 @@ var VolumeIsosurfaceTexture;
 })(VolumeIsosurfaceTexture || (VolumeIsosurfaceTexture = {}));
 function createVolumeIsosurfaceTextureMesh(ctx, volume, theme, props, textureMesh) {
     return (0, tslib_1.__awaiter)(this, void 0, void 0, function () {
-        var _a, max, min, diff, value, isoLevel, _b, texture, gridDimension, gridTexDim, gridTexScale, transform, buffer, gv, surface;
+        var _a, max, min, diff, value, isoLevel, _b, texture, gridDimension, gridTexDim, gridTexScale, transform, axisOrder, buffer, gv, surface;
         return (0, tslib_1.__generator)(this, function (_c) {
             if (!ctx.webgl)
                 throw new Error('webgl context required to create volume isosurface texture-mesh');
+            if (volume.grid.cells.data.length <= 1) {
+                return [2 /*return*/, texture_mesh_1.TextureMesh.createEmpty(textureMesh)];
+            }
             _a = volume.grid.stats, max = _a.max, min = _a.min;
             diff = max - min;
             value = volume_1.Volume.IsoValue.toAbsolute(props.isoValue, volume.grid.stats).absoluteValue;
             isoLevel = ((value - min) / diff);
             _b = VolumeIsosurfaceTexture.get(volume, ctx.webgl), texture = _b.texture, gridDimension = _b.gridDimension, gridTexDim = _b.gridTexDim, gridTexScale = _b.gridTexScale, transform = _b.transform;
+            axisOrder = volume.grid.cells.space.axisOrderSlowToFast;
             buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
-            gv = (0, isosurface_1.extractIsosurface)(ctx.webgl, texture, gridDimension, gridTexDim, gridTexScale, transform, isoLevel, value < 0, false, buffer === null || buffer === void 0 ? void 0 : buffer.vertex, buffer === null || buffer === void 0 ? void 0 : buffer.group, buffer === null || buffer === void 0 ? void 0 : buffer.normal);
+            gv = (0, isosurface_1.extractIsosurface)(ctx.webgl, texture, gridDimension, gridTexDim, gridTexScale, transform, isoLevel, value < 0, false, axisOrder, buffer === null || buffer === void 0 ? void 0 : buffer.vertex, buffer === null || buffer === void 0 ? void 0 : buffer.group, buffer === null || buffer === void 0 ? void 0 : buffer.normal);
             surface = texture_mesh_1.TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, volume_1.Volume.getBoundingSphere(volume), textureMesh);
             return [2 /*return*/, surface];
         });