molstar 3.26.0 → 3.28.0

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

@@ -2,6 +2,7 @@
  * Copyright (c) 2018-2022 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>
  */
 import { Unit, Structure, ElementIndex, StructureElement, ResidueIndex } from '../../../../mol-model/structure';
 import { TransformData } from '../../../../mol-geo/geometry/transform-data';
@@ -52,11 +53,13 @@ export declare function ensureReasonableResolution<T>(box: Box3D, props: {
 export declare function getConformation(unit: Unit): import("../../../../mol-model/structure/model/properties/atomic").AtomicConformation | import("../../../../mol-model/structure/model/properties/coarse").CoarseSphereConformation | import("../../../../mol-model/structure/model/properties/coarse").CoarseGaussianConformation;
 export declare const CommonSurfaceParams: {
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     includeParent: PD.BooleanParam;
 };
 export declare const DefaultCommonSurfaceProps: PD.Values<{
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     includeParent: PD.BooleanParam;
 }>;
@@ -83,6 +86,6 @@ export declare function getStructureConformationAndRadius(structure: Structure,
     boundary: import("../../../../mol-math/geometry/boundary").Boundary;
     radius: (index: number) => number;
 };
-export declare function isHydrogen(unit: Unit, element: ElementIndex): boolean;
+export declare function isHydrogen(structure: Structure, unit: Unit, element: ElementIndex, variant: 'all' | 'non-polar'): boolean;
 export declare function isH(atomicNumber: ArrayLike<number>, element: ElementIndex): boolean;
 export declare function isTrace(unit: Unit, element: ElementIndex): boolean;

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

@@ -3,6 +3,7 @@
  * Copyright (c) 2018-2022 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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.isTrace = exports.isH = exports.isHydrogen = exports.getStructureConformationAndRadius = exports.getUnitConformationAndRadius = exports.DefaultCommonSurfaceProps = exports.CommonSurfaceParams = exports.getConformation = exports.ensureReasonableResolution = exports.getVolumeSliceInfo = exports.includesUnitKind = exports.UnitKindOptions = exports.UnitKindInfo = exports.createUnitsTransform = exports.getAltResidueLociFromId = exports.getAltResidueLoci = exports.getResidueLoci = void 0;
@@ -17,6 +18,7 @@ var array_1 = require("../../../../mol-util/array");
 var param_definition_1 = require("../../../../mol-util/param-definition");
 var boundary_1 = require("../../../../mol-math/geometry/boundary");
 var geometry_1 = require("../../../../mol-math/geometry");
+var functional_group_1 = require("../../../../mol-model-props/computed/chemistry/functional-group");
 /** Return a Loci for the elements of a whole residue the elementIndex belongs to. */
 function getResidueLoci(structure, unit, elementIndex) {
     var elements = unit.elements, model = unit.model;
@@ -136,6 +138,7 @@ function getConformation(unit) {
 exports.getConformation = getConformation;
 exports.CommonSurfaceParams = {
     ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false, { description: 'Whether or not to include hydrogen atoms in the surface calculation.' }),
+    ignoreHydrogensVariant: param_definition_1.ParamDefinition.Select('all', param_definition_1.ParamDefinition.arrayToOptions(['all', 'non-polar'])),
     traceOnly: param_definition_1.ParamDefinition.Boolean(false, { description: 'Whether or not to only use trace atoms in the surface calculation.' }),
     includeParent: param_definition_1.ParamDefinition.Boolean(false, { description: 'Include elements of the parent structure in surface calculation to get a surface patch of the current structure.' }),
 };
@@ -160,7 +163,7 @@ function filterUnitId(id, elements, indices) {
     }
 }
 function getUnitConformationAndRadius(structure, unit, sizeTheme, props) {
-    var ignoreHydrogens = props.ignoreHydrogens, traceOnly = props.traceOnly, includeParent = props.includeParent;
+    var ignoreHydrogens = props.ignoreHydrogens, ignoreHydrogensVariant = props.ignoreHydrogensVariant, traceOnly = props.traceOnly, includeParent = props.includeParent;
     var rootUnit = includeParent ? structure.root.unitMap.get(unit.id) : unit;
     var differentRoot = includeParent && rootUnit !== unit;
     var _a = getConformation(rootUnit), x = _a.x, y = _a.y, z = _a.z;
@@ -175,7 +178,7 @@ function getUnitConformationAndRadius(structure, unit, sizeTheme, props) {
         var _id = [];
         for (var i = 0, il = elements.length; i < il; ++i) {
             var eI = elements[i];
-            if (ignoreHydrogens && isHydrogen(rootUnit, eI))
+            if (ignoreHydrogens && isHydrogen(structure, rootUnit, eI, ignoreHydrogensVariant))
                 continue;
             if (traceOnly && !isTrace(rootUnit, eI))
                 continue;
@@ -205,7 +208,7 @@ function getUnitConformationAndRadius(structure, unit, sizeTheme, props) {
 }
 exports.getUnitConformationAndRadius = getUnitConformationAndRadius;
 function getStructureConformationAndRadius(structure, sizeTheme, props) {
-    var ignoreHydrogens = props.ignoreHydrogens, traceOnly = props.traceOnly, includeParent = props.includeParent;
+    var ignoreHydrogens = props.ignoreHydrogens, ignoreHydrogensVariant = props.ignoreHydrogensVariant, traceOnly = props.traceOnly, includeParent = props.includeParent;
     var differentRoot = includeParent && !!structure.parent;
     var l = structure_1.StructureElement.Location.create(structure.root);
     var _a = structure.boundary.sphere, center = _a.center, sphereRadius = _a.radius;
@@ -233,7 +236,7 @@ function getStructureConformationAndRadius(structure, sizeTheme, props) {
             l.unit = unit;
             for (var j = 0, jl = elements.length; j < jl; ++j) {
                 var eI = elements[j];
-                if (ignoreHydrogens && isHydrogen(unit, eI))
+                if (ignoreHydrogens && isHydrogen(structure, unit, eI, ignoreHydrogensVariant))
                     continue;
                 if (traceOnly && !isTrace(unit, eI))
                     continue;
@@ -296,10 +299,11 @@ function getStructureConformationAndRadius(structure, sizeTheme, props) {
 }
 exports.getStructureConformationAndRadius = getStructureConformationAndRadius;
 var _H = atomic_1.AtomicNumbers['H'];
-function isHydrogen(unit, element) {
+function isHydrogen(structure, unit, element, variant) {
     if (structure_1.Unit.isCoarse(unit))
         return false;
-    return unit.model.atomicHierarchy.derived.atom.atomicNumber[element] === _H;
+    return (unit.model.atomicHierarchy.derived.atom.atomicNumber[element] === _H &&
+        (variant === 'all' || !(0, functional_group_1.hasPolarNeighbour)(structure, unit, int_1.SortedArray.indexOf(unit.elements, element))));
 }
 exports.isHydrogen = isHydrogen;
 function isH(atomicNumber, element) {

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

@@ -16,6 +16,7 @@ import { Spheres } from '../../../../mol-geo/geometry/spheres/spheres';
 import { StructureGroup } from './common';
 type ElementProps = {
     ignoreHydrogens: boolean;
+    ignoreHydrogensVariant: 'all' | 'non-polar';
     traceOnly: boolean;
 };
 export type ElementSphereMeshProps = {

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

@@ -23,8 +23,7 @@ var geometry_1 = require("../../../../mol-math/geometry");
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 var v3add = linear_algebra_1.Vec3.add;
 function makeElementIgnoreTest(structure, unit, props) {
-    var ignoreHydrogens = props.ignoreHydrogens, traceOnly = props.traceOnly;
-    var atomicNumber = unit.model.atomicHierarchy.derived.atom.atomicNumber;
+    var ignoreHydrogens = props.ignoreHydrogens, ignoreHydrogensVariant = props.ignoreHydrogensVariant, traceOnly = props.traceOnly;
     var isCoarse = structure_1.Unit.isCoarse(unit);
     var child = structure.child;
     var childUnit = child === null || child === void 0 ? void 0 : child.unitMap.get(unit.id);
@@ -34,7 +33,7 @@ function makeElementIgnoreTest(structure, unit, props) {
         return;
     return function (element) {
         return ((!!childUnit && !int_1.SortedArray.has(childUnit.elements, element)) ||
-            (!isCoarse && ignoreHydrogens && (0, common_1.isH)(atomicNumber, element)) ||
+            (!isCoarse && ignoreHydrogens && (0, common_1.isHydrogen)(structure, unit, element, ignoreHydrogensVariant)) ||
             (traceOnly && !(0, common_1.isTrace)(unit, element)));
     };
 }

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

@@ -11,6 +11,7 @@ import { WebGLContext } from '../../../../mol-gl/webgl/context';
 import { SizeTheme } from '../../../../mol-theme/size';
 export declare const GaussianDensityParams: {
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     includeParent: PD.BooleanParam;
     resolution: PD.Numeric;
@@ -19,6 +20,7 @@ export declare const GaussianDensityParams: {
 };
 export declare const DefaultGaussianDensityProps: PD.Values<{
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     includeParent: PD.BooleanParam;
     resolution: PD.Numeric;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -17,11 +17,11 @@ import { Loci } from '../../mol-model/loci';
 import { PickingId } from '../../mol-geo/geometry/picking';
 export declare function createDirectVolume2d(ctx: RuntimeContext, webgl: WebGLContext, volume: Volume, directVolume?: DirectVolume): DirectVolume;
 export declare function createDirectVolume3d(ctx: RuntimeContext, webgl: WebGLContext, volume: Volume, directVolume?: DirectVolume): DirectVolume;
-export declare function createDirectVolume(ctx: VisualContext, volume: Volume, theme: Theme, props: PD.Values<DirectVolumeParams>, directVolume?: DirectVolume): Promise<DirectVolume>;
-export declare function getDirectVolumeLoci(pickingId: PickingId, volume: Volume, props: DirectVolumeProps, id: number): Volume.Cell.Loci | {
+export declare function createDirectVolume(ctx: VisualContext, volume: Volume, key: number, theme: Theme, props: PD.Values<DirectVolumeParams>, directVolume?: DirectVolume): Promise<DirectVolume>;
+export declare function getDirectVolumeLoci(pickingId: PickingId, volume: Volume, key: number, props: DirectVolumeProps, id: number): Volume.Cell.Loci | {
     kind: "empty-loci";
 };
-export declare function eachDirectVolume(loci: Loci, volume: Volume, props: DirectVolumeProps, apply: (interval: Interval) => boolean): boolean;
+export declare function eachDirectVolume(loci: Loci, volume: Volume, key: number, props: DirectVolumeProps, apply: (interval: Interval) => boolean): boolean;
 export declare const DirectVolumeParams: {
     quality: {
         isEssential: boolean;

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -73,7 +73,7 @@ function createDirectVolume3d(ctx, webgl, volume, directVolume) {
 }
 exports.createDirectVolume3d = createDirectVolume3d;
 //
-function createDirectVolume(ctx, volume, theme, props, directVolume) {
+function createDirectVolume(ctx, volume, key, theme, props, directVolume) {
     return tslib_1.__awaiter(this, void 0, void 0, function () {
         var runtime, webgl;
         return tslib_1.__generator(this, function (_a) {
@@ -90,7 +90,7 @@ exports.createDirectVolume = createDirectVolume;
 function getLoci(volume, props) {
     return volume_1.Volume.Loci(volume);
 }
-function getDirectVolumeLoci(pickingId, volume, props, id) {
+function getDirectVolumeLoci(pickingId, volume, key, props, id) {
     var objectId = pickingId.objectId, groupId = pickingId.groupId;
     if (id === objectId) {
         return volume_1.Volume.Cell.Loci(volume, int_1.Interval.ofSingleton(groupId));
@@ -98,14 +98,16 @@ function getDirectVolumeLoci(pickingId, volume, props, id) {
     return loci_1.EmptyLoci;
 }
 exports.getDirectVolumeLoci = getDirectVolumeLoci;
-function eachDirectVolume(loci, volume, props, apply) {
+function eachDirectVolume(loci, volume, key, props, apply) {
     return (0, util_1.eachVolumeLoci)(loci, volume, undefined, apply);
 }
 exports.eachDirectVolume = eachDirectVolume;
 //
 exports.DirectVolumeParams = tslib_1.__assign(tslib_1.__assign({}, direct_volume_1.DirectVolume.Params), { quality: tslib_1.__assign(tslib_1.__assign({}, direct_volume_1.DirectVolume.Params.quality), { isEssential: false }) });
 function getDirectVolumeParams(ctx, volume) {
-    return param_definition_1.ParamDefinition.clone(exports.DirectVolumeParams);
+    var params = param_definition_1.ParamDefinition.clone(exports.DirectVolumeParams);
+    params.controlPoints.getVolume = function () { return volume; };
+    return params;
 }
 exports.getDirectVolumeParams = getDirectVolumeParams;
 function DirectVolumeVisual(materialId) {
@@ -137,5 +139,5 @@ exports.DirectVolumeRepresentationProvider = (0, representation_1.VolumeRepresen
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.DirectVolumeParams),
     defaultColorTheme: { name: 'volume-value' },
     defaultSizeTheme: { name: 'uniform' },
-    isApplicable: function (volume) { return !volume_1.Volume.isEmpty(volume); }
+    isApplicable: function (volume) { return !volume_1.Volume.isEmpty(volume) && !volume_1.Volume.Segmentation.get(volume); }
 });

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

@@ -41,7 +41,7 @@ export declare const VolumeIsosurfaceParams: {
 };
 export type VolumeIsosurfaceParams = typeof VolumeIsosurfaceParams;
 export type VolumeIsosurfaceProps = PD.Values<VolumeIsosurfaceParams>;
-export declare function IsosurfaceVisual(materialId: number, volume: Volume, props: PD.Values<IsosurfaceMeshParams>, webgl?: WebGLContext): VolumeVisual<{
+export declare function IsosurfaceVisual(materialId: number, volume: Volume, key: number, props: PD.Values<IsosurfaceMeshParams>, webgl?: WebGLContext): VolumeVisual<{
     quality: {
         isEssential: boolean;
         type: "select";
@@ -114,8 +114,8 @@ export declare function IsosurfaceVisual(materialId: number, volume: Volume, pro
     }>>;
     instanceGranularity: PD.BooleanParam;
 }>;
-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>;
+export declare function eachIsosurface(loci: Loci, volume: Volume, key: number, props: VolumeIsosurfaceProps, apply: (interval: Interval) => boolean): boolean;
+export declare function createVolumeIsosurfaceMesh(ctx: VisualContext, volume: Volume, key: number, theme: Theme, props: VolumeIsosurfaceProps, mesh?: Mesh): Promise<Mesh>;
 export declare const IsosurfaceMeshParams: {
     quality: {
         isEssential: boolean;
@@ -192,7 +192,7 @@ export declare const IsosurfaceMeshParams: {
 export type IsosurfaceMeshParams = typeof IsosurfaceMeshParams;
 export declare function IsosurfaceMeshVisual(materialId: number): VolumeVisual<IsosurfaceMeshParams>;
 export declare function IsosurfaceTextureMeshVisual(materialId: number): VolumeVisual<IsosurfaceMeshParams>;
-export declare function createVolumeIsosurfaceWireframe(ctx: VisualContext, volume: Volume, theme: Theme, props: VolumeIsosurfaceProps, lines?: Lines): Promise<Lines>;
+export declare function createVolumeIsosurfaceWireframe(ctx: VisualContext, volume: Volume, key: number, theme: Theme, props: VolumeIsosurfaceProps, lines?: Lines): Promise<Lines>;
 export declare const IsosurfaceWireframeParams: {
     quality: {
         isEssential: boolean;

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

@@ -44,7 +44,7 @@ function suitableForGpu(volume, webgl) {
     var powerOfTwoSize = (0, util_1.getVolumeTexture2dLayout)(gridDim, Padding).powerOfTwoSize;
     return powerOfTwoSize <= webgl.maxTextureSize / 2;
 }
-function IsosurfaceVisual(materialId, volume, props, webgl) {
+function IsosurfaceVisual(materialId, volume, key, props, webgl) {
     if (props.tryUseGpu && webgl && gpuSupport(webgl) && suitableForGpu(volume, webgl)) {
         return IsosurfaceTextureMeshVisual(materialId);
     }
@@ -54,7 +54,7 @@ exports.IsosurfaceVisual = IsosurfaceVisual;
 function getLoci(volume, props) {
     return volume_1.Volume.Isosurface.Loci(volume, props.isoValue);
 }
-function getIsosurfaceLoci(pickingId, volume, props, id) {
+function getIsosurfaceLoci(pickingId, volume, key, props, id) {
     var objectId = pickingId.objectId, groupId = pickingId.groupId;
     if (id === objectId) {
         var granularity = volume_1.Volume.PickingGranularity.get(volume);
@@ -70,12 +70,12 @@ function getIsosurfaceLoci(pickingId, volume, props, id) {
     }
     return loci_1.EmptyLoci;
 }
-function eachIsosurface(loci, volume, props, apply) {
-    return (0, util_1.eachVolumeLoci)(loci, volume, props.isoValue, apply);
+function eachIsosurface(loci, volume, key, props, apply) {
+    return (0, util_1.eachVolumeLoci)(loci, volume, { isoValue: props.isoValue }, apply);
 }
 exports.eachIsosurface = eachIsosurface;
 //
-function createVolumeIsosurfaceMesh(ctx, volume, theme, props, mesh) {
+function createVolumeIsosurfaceMesh(ctx, volume, key, theme, props, mesh) {
     return tslib_1.__awaiter(this, void 0, void 0, function () {
         var ids, surface, transform;
         return tslib_1.__generator(this, function (_a) {
@@ -101,7 +101,7 @@ function createVolumeIsosurfaceMesh(ctx, volume, theme, props, mesh) {
                     else {
                         value_cell_1.ValueCell.updateIfChanged(surface.varyingGroup, true);
                     }
-                    surface.setBoundingSphere(volume_1.Volume.getBoundingSphere(volume));
+                    surface.setBoundingSphere(volume_1.Volume.Isosurface.getBoundingSphere(volume, props.isoValue));
                     return [2 /*return*/, surface];
             }
         });
@@ -121,8 +121,8 @@ function IsosurfaceMeshVisual(materialId) {
                 state.createGeometry = true;
         },
         geometryUtils: mesh_1.Mesh.Utils,
-        mustRecreate: function (volume, props, webgl) {
-            return props.tryUseGpu && !!webgl && suitableForGpu(volume, webgl);
+        mustRecreate: function (volumekey, props, webgl) {
+            return props.tryUseGpu && !!webgl && suitableForGpu(volumekey.volume, webgl);
         }
     }, materialId);
 }
@@ -164,9 +164,9 @@ var VolumeIsosurfaceTexture;
     }
     VolumeIsosurfaceTexture.get = get;
 })(VolumeIsosurfaceTexture || (VolumeIsosurfaceTexture = {}));
-function createVolumeIsosurfaceTextureMesh(ctx, volume, theme, props, textureMesh) {
+function createVolumeIsosurfaceTextureMesh(ctx, volume, key, theme, props, textureMesh) {
     return tslib_1.__awaiter(this, void 0, void 0, function () {
-        var _a, max, min, diff, value, isoLevel, _b, texture, gridDimension, gridTexDim, gridTexScale, transform, axisOrder, buffer, gv, groupCount, surface;
+        var _a, max, min, diff, value, isoLevel, _b, texture, gridDimension, gridTexDim, gridTexScale, transform, axisOrder, buffer, gv, groupCount, boundingSphere, surface;
         return tslib_1.__generator(this, function (_c) {
             if (!ctx.webgl)
                 throw new Error('webgl context required to create volume isosurface texture-mesh');
@@ -182,7 +182,8 @@ function createVolumeIsosurfaceTextureMesh(ctx, volume, theme, props, textureMes
             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, axisOrder, true, 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);
             groupCount = volume.grid.cells.data.length;
-            surface = texture_mesh_1.TextureMesh.create(gv.vertexCount, groupCount, gv.vertexTexture, gv.groupTexture, gv.normalTexture, volume_1.Volume.getBoundingSphere(volume), textureMesh);
+            boundingSphere = volume_1.Volume.getBoundingSphere(volume);
+            surface = texture_mesh_1.TextureMesh.create(gv.vertexCount, groupCount, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
             surface.meta.webgl = ctx.webgl;
             return [2 /*return*/, surface];
         });
@@ -200,8 +201,8 @@ function IsosurfaceTextureMeshVisual(materialId) {
                 state.createGeometry = true;
         },
         geometryUtils: texture_mesh_1.TextureMesh.Utils,
-        mustRecreate: function (volume, props, webgl) {
-            return !props.tryUseGpu || !webgl || !suitableForGpu(volume, webgl);
+        mustRecreate: function (volumeKey, props, webgl) {
+            return !props.tryUseGpu || !webgl || !suitableForGpu(volumeKey.volume, webgl);
         },
         dispose: function (geometry) {
             geometry.vertexTexture.ref.value.destroy();
@@ -213,7 +214,7 @@ function IsosurfaceTextureMeshVisual(materialId) {
 }
 exports.IsosurfaceTextureMeshVisual = IsosurfaceTextureMeshVisual;
 //
-function createVolumeIsosurfaceWireframe(ctx, volume, theme, props, lines) {
+function createVolumeIsosurfaceWireframe(ctx, volume, key, theme, props, lines) {
     return tslib_1.__awaiter(this, void 0, void 0, function () {
         var ids, wireframe, transform;
         return tslib_1.__generator(this, function (_a) {
@@ -230,7 +231,7 @@ function createVolumeIsosurfaceWireframe(ctx, volume, theme, props, lines) {
                     wireframe = _a.sent();
                     transform = volume_1.Grid.getGridToCartesianTransform(volume.grid);
                     lines_1.Lines.transform(wireframe, transform);
-                    wireframe.setBoundingSphere(volume_1.Volume.getBoundingSphere(volume));
+                    wireframe.setBoundingSphere(volume_1.Volume.Isosurface.getBoundingSphere(volume, props.isoValue));
                     return [2 /*return*/, wireframe];
             }
         });
@@ -278,5 +279,5 @@ exports.IsosurfaceRepresentationProvider = (0, representation_1.VolumeRepresenta
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.IsosurfaceParams),
     defaultColorTheme: { name: 'uniform' },
     defaultSizeTheme: { name: 'uniform' },
-    isApplicable: function (volume) { return !volume_1.Volume.isEmpty(volume); }
+    isApplicable: function (volume) { return !volume_1.Volume.isEmpty(volume) && !volume_1.Volume.Segmentation.get(volume); }
 });

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -199,6 +199,59 @@ export declare namespace VolumeRepresentationRegistry {
             }>>;
             instanceGranularity: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
         }, "direct-volume">;
+        segment: import("./representation").VolumeRepresentationProvider<{
+            visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"segment">;
+            bumpFrequency: import("../../mol-util/param-definition").ParamDefinition.Numeric;
+            quality: {
+                isEssential: boolean;
+                type: "select";
+                options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
+                cycle?: boolean | undefined;
+                isOptional?: boolean | undefined;
+                defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
+                label?: string | undefined;
+                description?: string | undefined;
+                legend?: import("../../mol-util/legend").Legend | undefined;
+                fieldLabels?: {
+                    [name: string]: string;
+                } | undefined;
+                isHidden?: boolean | undefined;
+                shortLabel?: boolean | undefined;
+                twoColumns?: boolean | undefined;
+                category?: string | undefined;
+                hideIf?: ((currentGroup: any) => boolean) | undefined;
+                help?: ((value: any) => {
+                    description?: string | undefined;
+                    legend?: import("../../mol-util/legend").Legend | undefined;
+                }) | undefined;
+            };
+            tryUseGpu: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            segments: import("../../mol-util/param-definition").ParamDefinition.Converted<number[], string[]>;
+            doubleSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            flipSided: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            flatShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            ignoreLight: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            xrayShaded: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            transparentBackfaces: import("../../mol-util/param-definition").ParamDefinition.Select<string>;
+            bumpAmplitude: import("../../mol-util/param-definition").ParamDefinition.Numeric;
+            alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
+            material: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+                metalness: number;
+                roughness: number;
+                bumpiness: number;
+            }>>;
+            clip: import("../../mol-util/param-definition").ParamDefinition.Group<import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+                variant: import("../../mol-util/clip").Clip.Variant;
+                objects: import("../../mol-util/param-definition").ParamDefinition.Normalize<{
+                    type: any;
+                    invert: any;
+                    position: any;
+                    rotation: any;
+                    scale: any;
+                }>[];
+            }>>;
+            instanceGranularity: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+        }, "segment">;
     };
     type _BuiltIn = typeof BuiltIn;
     export type BuiltIn = keyof _BuiltIn;

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

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -12,6 +12,7 @@ var isosurface_1 = require("./isosurface");
 var object_1 = require("../../mol-util/object");
 var slice_1 = require("./slice");
 var direct_volume_1 = require("./direct-volume");
+var segment_1 = require("./segment");
 var VolumeRepresentationRegistry = /** @class */ (function (_super) {
     tslib_1.__extends(VolumeRepresentationRegistry, _super);
     function VolumeRepresentationRegistry() {
@@ -31,6 +32,7 @@ exports.VolumeRepresentationRegistry = VolumeRepresentationRegistry;
         'isosurface': isosurface_1.IsosurfaceRepresentationProvider,
         'slice': slice_1.SliceRepresentationProvider,
         'direct-volume': direct_volume_1.DirectVolumeRepresentationProvider,
+        'segment': segment_1.SegmentRepresentationProvider,
     };
 })(VolumeRepresentationRegistry = exports.VolumeRepresentationRegistry || (exports.VolumeRepresentationRegistry = {}));
 exports.VolumeRepresentationRegistry = VolumeRepresentationRegistry;

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

@@ -15,16 +15,20 @@ import { Interval } from '../../mol-data/int';
 import { VisualUpdateState } from '../util';
 import { Representation, RepresentationProvider, RepresentationContext, RepresentationParamsGetter } from '../representation';
 import { WebGLContext } from '../../mol-gl/webgl/context';
-export interface VolumeVisual<P extends VolumeParams> extends Visual<Volume, P> {
+export type VolumeKey = {
+    volume: Volume;
+    key: number;
+};
+export interface VolumeVisual<P extends VolumeParams> extends Visual<VolumeKey, P> {
 }
 interface VolumeVisualBuilder<P extends VolumeParams, G extends Geometry> {
     defaultProps: PD.Values<P>;
-    createGeometry(ctx: VisualContext, volume: Volume, theme: Theme, props: PD.Values<P>, geometry?: G): Promise<G> | G;
-    createLocationIterator(volume: Volume): LocationIterator;
-    getLoci(pickingId: PickingId, volume: Volume, props: PD.Values<P>, id: number): Loci;
-    eachLocation(loci: Loci, volume: Volume, props: PD.Values<P>, apply: (interval: Interval) => boolean): boolean;
+    createGeometry(ctx: VisualContext, volume: Volume, key: number, theme: Theme, props: PD.Values<P>, geometry?: G): Promise<G> | G;
+    createLocationIterator(volume: Volume, key: number): LocationIterator;
+    getLoci(pickingId: PickingId, volume: Volume, key: number, props: PD.Values<P>, id: number): Loci;
+    eachLocation(loci: Loci, volume: Volume, key: number, props: PD.Values<P>, apply: (interval: Interval) => boolean): boolean;
     setUpdateState(state: VisualUpdateState, volume: Volume, newProps: PD.Values<P>, currentProps: PD.Values<P>, newTheme: Theme, currentTheme: Theme): void;
-    mustRecreate?: (volume: Volume, props: PD.Values<P>) => boolean;
+    mustRecreate?: (volumeKey: VolumeKey, props: PD.Values<P>) => boolean;
     dispose?: (geometry: G) => void;
 }
 interface VolumeVisualGeometryBuilder<P extends VolumeParams, G extends Geometry> extends VolumeVisualBuilder<P, G> {
@@ -56,5 +60,5 @@ export declare const VolumeParams: {
     instanceGranularity: PD.BooleanParam;
 };
 export type VolumeParams = typeof VolumeParams;
-export declare function VolumeRepresentation<P extends VolumeParams>(label: string, ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, P>, visualCtor: (materialId: number, volume: Volume, props: PD.Values<P>, webgl?: WebGLContext) => VolumeVisual<P>, getLoci: (volume: Volume, props: PD.Values<P>) => Loci): VolumeRepresentation<P>;
+export declare function VolumeRepresentation<P extends VolumeParams>(label: string, ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, P>, visualCtor: (materialId: number, volume: Volume, key: number, props: PD.Values<P>, webgl?: WebGLContext) => VolumeVisual<P>, getLoci: (volume: Volume, props: PD.Values<P>) => Loci, getKeys?: (props: PD.Values<P>) => ArrayLike<number>): VolumeRepresentation<P>;
 export {};