molstar 3.0.0-dev.6 → 3.0.0

package/lib/mol-repr/structure/visual/gaussian-density-volume.js

@@ -15,7 +15,7 @@ import { UnitsDirectVolumeParams, UnitsDirectVolumeVisual } from '../units-visua
 import { getStructureExtraRadius, getUnitExtraRadius } from './util/common';
 function createGaussianDensityVolume(ctx, structure, theme, props, directVolume) {
     return __awaiter(this, void 0, void 0, function () {
-        var runtime, webgl, oldTexture, densityTextureData, transform, texture, bbox, gridDim, stats, unitToCartn, cellDim, vol, sphere;
+        var runtime, webgl, oldTexture, densityTextureData, transform, texture, bbox, gridDim, stats, unitToCartn, cellDim, axisOrder, vol, sphere;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -24,14 +24,15 @@ function createGaussianDensityVolume(ctx, structure, theme, props, directVolume)
                         throw new Error('GaussianDensityVolume requires `webgl` and `blendMinMax` extension');
                     }
                     oldTexture = directVolume ? directVolume.gridTexture.ref.value : undefined;
-                    return [4 /*yield*/, computeStructureGaussianDensityTexture(structure, props, webgl, oldTexture).runInContext(runtime)];
+                    return [4 /*yield*/, computeStructureGaussianDensityTexture(structure, theme.size, props, webgl, oldTexture).runInContext(runtime)];
                 case 1:
                     densityTextureData = _a.sent();
                     transform = densityTextureData.transform, texture = densityTextureData.texture, bbox = densityTextureData.bbox, gridDim = densityTextureData.gridDim;
                     stats = { min: 0, max: 1, mean: 0.04, sigma: 0.01 };
                     unitToCartn = Mat4.mul(Mat4(), transform, Mat4.fromScaling(Mat4(), gridDim));
                     cellDim = Mat4.getScaling(Vec3(), transform);
-                    vol = DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, directVolume);
+                    axisOrder = Vec3.create(0, 1, 2);
+                    vol = DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, axisOrder, directVolume);
                     sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
                     vol.setBoundingSphere(sphere);
                     return [2 /*return*/, vol];
@@ -69,7 +70,7 @@ export function GaussianDensityVolumeVisual(materialId) {
 //
 function createUnitsGaussianDensityVolume(ctx, unit, structure, theme, props, directVolume) {
     return __awaiter(this, void 0, void 0, function () {
-        var runtime, webgl, oldTexture, densityTextureData, transform, texture, bbox, gridDim, stats, unitToCartn, cellDim, vol, sphere;
+        var runtime, webgl, oldTexture, densityTextureData, transform, texture, bbox, gridDim, stats, unitToCartn, cellDim, axisOrder, vol, sphere;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -81,14 +82,15 @@ function createUnitsGaussianDensityVolume(ctx, unit, structure, theme, props, di
                         throw new Error('GaussianDensityVolume requires `webgl`');
                     }
                     oldTexture = directVolume ? directVolume.gridTexture.ref.value : undefined;
-                    return [4 /*yield*/, computeUnitGaussianDensityTexture(structure, unit, props, webgl, oldTexture).runInContext(runtime)];
+                    return [4 /*yield*/, computeUnitGaussianDensityTexture(structure, unit, theme.size, props, webgl, oldTexture).runInContext(runtime)];
                 case 1:
                     densityTextureData = _a.sent();
                     transform = densityTextureData.transform, texture = densityTextureData.texture, bbox = densityTextureData.bbox, gridDim = densityTextureData.gridDim;
                     stats = { min: 0, max: 1, mean: 0.04, sigma: 0.01 };
                     unitToCartn = Mat4.mul(Mat4(), transform, Mat4.fromScaling(Mat4(), gridDim));
                     cellDim = Mat4.getScaling(Vec3(), transform);
-                    vol = DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, directVolume);
+                    axisOrder = Vec3.create(0, 1, 2);
+                    vol = DirectVolume.create(bbox, gridDim, transform, unitToCartn, cellDim, texture, stats, true, axisOrder, directVolume);
                     sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getUnitExtraRadius(unit));
                     vol.setBoundingSphere(sphere);
                     return [2 /*return*/, vol];

package/lib/mol-repr/structure/visual/gaussian-surface-mesh.d.ts

@@ -35,6 +35,16 @@ export declare const GaussianSurfaceMeshParams: {
         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 GaussianSurfaceMeshParams = typeof GaussianSurfaceMeshParams;
 export declare const StructureGaussianSurfaceMeshParams: {
@@ -64,6 +74,16 @@ export declare const StructureGaussianSurfaceMeshParams: {
         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 StructureGaussianSurfaceMeshParams = typeof StructureGaussianSurfaceMeshParams;
 export declare function GaussianSurfaceVisual(materialId: number, structure: Structure, props: PD.Values<GaussianSurfaceMeshParams>, webgl?: WebGLContext): UnitsVisual<{
@@ -93,6 +113,16 @@ export declare function GaussianSurfaceVisual(materialId: number, structure: Str
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }>;
 export declare function StructureGaussianSurfaceVisual(materialId: number, structure: Structure, props: PD.Values<StructureGaussianSurfaceMeshParams>, webgl?: WebGLContext): ComplexVisual<{
     ignoreHydrogens: PD.BooleanParam;
@@ -121,6 +151,16 @@ export declare function StructureGaussianSurfaceVisual(materialId: number, struc
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 }>;
 export declare function GaussianSurfaceMeshVisual(materialId: number): UnitsVisual<GaussianSurfaceMeshParams>;
 export declare function StructureGaussianSurfaceMeshVisual(materialId: number): ComplexVisual<StructureGaussianSurfaceMeshParams>;

package/lib/mol-repr/structure/visual/gaussian-surface-mesh.js

@@ -18,6 +18,7 @@ import { getUnitExtraRadius, getStructureExtraRadius, getVolumeSliceInfo } from
 import { applyMeshColorSmoothing } from '../../../mol-geo/geometry/mesh/color-smoothing';
 import { applyTextureMeshColorSmoothing } from '../../../mol-geo/geometry/texture-mesh/color-smoothing';
 import { ColorSmoothingParams, getColorSmoothingProps } from '../../../mol-geo/geometry/base';
+import { Vec3 } from '../../../mol-math/linear-algebra';
 var SharedParams = __assign(__assign(__assign({}, GaussianDensityParams), ColorSmoothingParams), { ignoreHydrogens: PD.Boolean(false), tryUseGpu: PD.Boolean(true), includeParent: PD.Boolean(false, { isHidden: true }) });
 export var GaussianSurfaceMeshParams = __assign(__assign(__assign({}, UnitsMeshParams), UnitsTextureMeshParams), SharedParams);
 export var StructureGaussianSurfaceMeshParams = __assign(__assign(__assign({}, ComplexMeshParams), ComplexTextureMeshParams), SharedParams);
@@ -55,7 +56,7 @@ function createGaussianSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
             switch (_b.label) {
                 case 0:
                     smoothness = props.smoothness;
-                    return [4 /*yield*/, computeUnitGaussianDensity(structure, unit, props).runInContext(ctx.runtime)];
+                    return [4 /*yield*/, computeUnitGaussianDensity(structure, unit, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
                     _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, radiusFactor = _a.radiusFactor, resolution = _a.resolution;
                     params = {
@@ -132,7 +133,7 @@ function createStructureGaussianSurfaceMesh(ctx, structure, theme, props, mesh)
             switch (_b.label) {
                 case 0:
                     smoothness = props.smoothness;
-                    return [4 /*yield*/, computeStructureGaussianDensity(structure, props).runInContext(ctx.runtime)];
+                    return [4 /*yield*/, computeStructureGaussianDensity(structure, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
                     _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, radiusFactor = _a.radiusFactor, resolution = _a.resolution;
                     params = {
@@ -203,7 +204,7 @@ export function StructureGaussianSurfaceMeshVisual(materialId) {
 var GaussianSurfaceName = 'gaussian-surface';
 function createGaussianSurfaceTextureMesh(ctx, unit, structure, theme, props, textureMesh) {
     return __awaiter(this, void 0, void 0, function () {
-        var _a, namedTextures, resources, _b, colorBufferFloat, textureFloat, colorBufferHalfFloat, textureHalfFloat, densityTextureData, isoLevel, buffer, gv, boundingSphere, surface;
+        var _a, namedTextures, resources, _b, colorBufferFloat, textureFloat, colorBufferHalfFloat, textureHalfFloat, densityTextureData, isoLevel, axisOrder, buffer, gv, boundingSphere, surface;
         return __generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
@@ -217,12 +218,13 @@ function createGaussianSurfaceTextureMesh(ctx, unit, structure, theme, props, te
                                 ? resources.texture('image-float32', 'rgba', 'float', 'linear')
                                 : resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
                     }
-                    return [4 /*yield*/, computeUnitGaussianDensityTexture2d(structure, unit, true, props, ctx.webgl, namedTextures[GaussianSurfaceName]).runInContext(ctx.runtime)];
+                    return [4 /*yield*/, computeUnitGaussianDensityTexture2d(structure, unit, theme.size, true, props, ctx.webgl, namedTextures[GaussianSurfaceName]).runInContext(ctx.runtime)];
                 case 1:
                     densityTextureData = _c.sent();
                     isoLevel = Math.exp(-props.smoothness) / densityTextureData.radiusFactor;
+                    axisOrder = Vec3.create(0, 1, 2);
                     buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
-                    gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, 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);
+                    gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, 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);
                     boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
                     surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
                     surface.meta.resolution = densityTextureData.resolution;
@@ -285,7 +287,7 @@ export function GaussianSurfaceTextureMeshVisual(materialId) {
 //
 function createStructureGaussianSurfaceTextureMesh(ctx, structure, theme, props, textureMesh) {
     return __awaiter(this, void 0, void 0, function () {
-        var _a, namedTextures, resources, _b, colorBufferFloat, textureFloat, colorBufferHalfFloat, textureHalfFloat, densityTextureData, isoLevel, buffer, gv, boundingSphere, surface;
+        var _a, namedTextures, resources, _b, colorBufferFloat, textureFloat, colorBufferHalfFloat, textureHalfFloat, densityTextureData, isoLevel, axisOrder, buffer, gv, boundingSphere, surface;
         return __generator(this, function (_c) {
             switch (_c.label) {
                 case 0:
@@ -299,12 +301,13 @@ function createStructureGaussianSurfaceTextureMesh(ctx, structure, theme, props,
                                 ? resources.texture('image-float32', 'rgba', 'float', 'linear')
                                 : resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
                     }
-                    return [4 /*yield*/, computeStructureGaussianDensityTexture2d(structure, true, props, ctx.webgl, namedTextures[GaussianSurfaceName]).runInContext(ctx.runtime)];
+                    return [4 /*yield*/, computeStructureGaussianDensityTexture2d(structure, theme.size, true, props, ctx.webgl, namedTextures[GaussianSurfaceName]).runInContext(ctx.runtime)];
                 case 1:
                     densityTextureData = _c.sent();
                     isoLevel = Math.exp(-props.smoothness) / densityTextureData.radiusFactor;
+                    axisOrder = Vec3.create(0, 1, 2);
                     buffer = textureMesh === null || textureMesh === void 0 ? void 0 : textureMesh.doubleBuffer.get();
-                    gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, 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);
+                    gv = extractIsosurface(ctx.webgl, densityTextureData.texture, densityTextureData.gridDim, densityTextureData.gridTexDim, densityTextureData.gridTexScale, densityTextureData.transform, isoLevel, false, true, 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);
                     boundingSphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, props.radiusOffset + getStructureExtraRadius(structure));
                     surface = TextureMesh.create(gv.vertexCount, 1, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
                     surface.meta.resolution = densityTextureData.resolution;

package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.d.ts

@@ -22,6 +22,16 @@ export declare const GaussianWireframeParams: {
         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 GaussianWireframeParams = typeof GaussianWireframeParams;
 export declare function GaussianWireframeVisual(materialId: number): UnitsVisual<GaussianWireframeParams>;

package/lib/mol-repr/structure/visual/gaussian-surface-wireframe.js

@@ -19,7 +19,7 @@ function createGaussianWireframe(ctx, unit, structure, theme, props, lines) {
             switch (_b.label) {
                 case 0:
                     smoothness = props.smoothness;
-                    return [4 /*yield*/, computeUnitGaussianDensity(structure, unit, props).runInContext(ctx.runtime)];
+                    return [4 /*yield*/, computeUnitGaussianDensity(structure, unit, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
                     _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField;
                     params = {

package/lib/mol-repr/structure/visual/label-text.d.ts

@@ -39,6 +39,16 @@ export declare const LabelTextParams: {
         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 LabelTextParams = typeof LabelTextParams;
 export declare type LabelTextProps = PD.Values<LabelTextParams>;

package/lib/mol-repr/structure/visual/label-text.js

@@ -12,7 +12,6 @@ import { ComplexTextVisual, ComplexTextParams } from '../complex-visual';
 import { ElementIterator, getSerialElementLoci, eachSerialElement } from './util/element';
 import { ColorNames } from '../../../mol-util/color/names';
 import { Vec3 } from '../../../mol-math/linear-algebra';
-import { PhysicalSizeTheme } from '../../../mol-theme/size/physical';
 import { BoundaryHelper } from '../../../mol-math/geometry/boundary-helper';
 export var LabelTextParams = __assign(__assign({}, ComplexTextParams), { background: PD.Boolean(false), backgroundMargin: PD.Numeric(0, { min: 0, max: 1, step: 0.01 }), backgroundColor: PD.Color(ColorNames.black), backgroundOpacity: PD.Numeric(0.5, { min: 0, max: 1, step: 0.01 }), borderWidth: PD.Numeric(0.25, { min: 0, max: 0.5, step: 0.01 }), level: PD.Select('residue', [['chain', 'Chain'], ['residue', 'Residue'], ['element', 'Element']], { isEssential: true }), chainScale: PD.Numeric(10, { min: 0, max: 20, step: 0.1 }), residueScale: PD.Numeric(1, { min: 0, max: 20, step: 0.1 }), elementScale: PD.Numeric(0.5, { min: 0, max: 20, step: 0.1 }) });
 export function LabelTextVisual(materialId) {
@@ -110,7 +109,7 @@ function createElementText(ctx, structure, theme, props, text) {
     var units = structure.units, serialMapping = structure.serialMapping;
     var _a = StructureProperties.atom, label_atom_id = _a.label_atom_id, label_alt_id = _a.label_alt_id;
     var cumulativeUnitElementCount = serialMapping.cumulativeUnitElementCount;
-    var sizeTheme = PhysicalSizeTheme({}, { scale: 1 });
+    var sizeTheme = theme.size;
     var count = structure.elementCount;
     var elementScale = props.elementScale;
     var builder = TextBuilder.create(props, count, count / 2, text);

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

@@ -31,6 +31,16 @@ export declare const MolecularSurfaceMeshParams: {
         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 MolecularSurfaceMeshParams = typeof MolecularSurfaceMeshParams;
 export declare type MolecularSurfaceMeshProps = PD.Values<MolecularSurfaceMeshParams>;

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

@@ -22,7 +22,7 @@ function createMolecularSurfaceMesh(ctx, unit, structure, theme, props, mesh) {
         var _a, transform, field, idField, resolution, params, surface, iterations, sphere;
         return __generator(this, function (_b) {
             switch (_b.label) {
-                case 0: return [4 /*yield*/, computeUnitMolecularSurface(structure, unit, props).runInContext(ctx.runtime)];
+                case 0: return [4 /*yield*/, computeUnitMolecularSurface(structure, unit, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
                     _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField, resolution = _a.resolution;
                     params = {

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

@@ -22,6 +22,16 @@ export declare const MolecularSurfaceWireframeParams: {
         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 MolecularSurfaceWireframeParams = typeof MolecularSurfaceWireframeParams;
 export declare function MolecularSurfaceWireframeVisual(materialId: number): UnitsVisual<MolecularSurfaceWireframeParams>;

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

@@ -20,7 +20,7 @@ function createMolecularSurfaceWireframe(ctx, unit, structure, theme, props, lin
         var _a, transform, field, idField, params, wireframe, sphere;
         return __generator(this, function (_b) {
             switch (_b.label) {
-                case 0: return [4 /*yield*/, computeUnitMolecularSurface(structure, unit, props).runInContext(ctx.runtime)];
+                case 0: return [4 /*yield*/, computeUnitMolecularSurface(structure, unit, theme.size, props).runInContext(ctx.runtime)];
                 case 1:
                     _a = _b.sent(), transform = _a.transform, field = _a.field, idField = _a.idField;
                     params = {

package/lib/mol-repr/structure/visual/nucleotide-block-mesh.d.ts

@@ -33,6 +33,16 @@ export declare const NucleotideBlockParams: {
         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 NucleotideBlockParams = typeof NucleotideBlockParams;
 export declare function NucleotideBlockVisual(materialId: number): UnitsVisual<NucleotideBlockParams>;

package/lib/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts

@@ -36,6 +36,16 @@ export declare const NucleotideRingParams: {
         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 NucleotideRingParams = typeof NucleotideRingParams;
 export declare function NucleotideRingVisual(materialId: number): UnitsVisual<NucleotideRingParams>;

package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts

@@ -28,6 +28,16 @@ export declare const OrientationEllipsoidMeshParams: {
         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 OrientationEllipsoidMeshParams = typeof OrientationEllipsoidMeshParams;
 export declare function OrientationEllipsoidMeshVisual(materialId: number): UnitsVisual<OrientationEllipsoidMeshParams>;

package/lib/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts

@@ -26,6 +26,16 @@ export declare const PolymerBackboneCylinderParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 };
@@ -49,6 +59,16 @@ export declare function PolymerBackboneCylinderVisual(materialId: number, struct
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 }>;

package/lib/mol-repr/structure/visual/polymer-backbone-sphere.d.ts

@@ -25,6 +25,16 @@ export declare const PolymerBackboneSphereParams: {
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 };
@@ -47,6 +57,16 @@ export declare function PolymerBackboneSphereVisual(materialId: number, structur
         roughness: number;
         bumpiness: number;
     }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 }>;

package/lib/mol-repr/structure/visual/polymer-direction-wedge.d.ts

@@ -30,6 +30,16 @@ export declare const PolymerDirectionParams: {
         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 PolymerDirectionParams = typeof PolymerDirectionParams;
 export declare function PolymerDirectionVisual(materialId: number): UnitsVisual<PolymerDirectionParams>;

package/lib/mol-repr/structure/visual/polymer-gap-cylinder.d.ts

@@ -33,6 +33,16 @@ export declare const PolymerGapParams: {
         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 PolymerGapParams = typeof PolymerGapParams;
 export declare function PolymerGapVisual(materialId: number): UnitsVisual<PolymerGapParams>;

package/lib/mol-repr/structure/visual/polymer-trace-mesh.d.ts

@@ -51,6 +51,16 @@ export declare const PolymerTraceParams: {
         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 PolymerTraceParams = typeof PolymerTraceParams;
 export declare function PolymerTraceVisual(materialId: number): UnitsVisual<PolymerTraceParams>;

package/lib/mol-repr/structure/visual/polymer-tube-mesh.d.ts

@@ -39,6 +39,16 @@ export declare const PolymerTubeParams: {
         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 PolymerTubeParams = typeof PolymerTubeParams;
 export declare function PolymerTubeVisual(materialId: number): UnitsVisual<PolymerTubeParams>;

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

@@ -9,7 +9,6 @@ import { Mat4, Vec3 } from '../../../../mol-math/linear-algebra';
 import { createTransform } from '../../../../mol-geo/geometry/transform-data';
 import { OrderedSet, SortedArray } from '../../../../mol-data/int';
 import { EmptyLoci } from '../../../../mol-model/loci';
-import { PhysicalSizeTheme } from '../../../../mol-theme/size/physical';
 import { AtomicNumbers } from '../../../../mol-model/structure/model/properties/atomic';
 import { fillSerial } from '../../../../mol-util/array';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
@@ -149,7 +148,7 @@ function filterId(id, elements, indices) {
         }
     }
 }
-export function getUnitConformationAndRadius(structure, unit, props) {
+export 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;
@@ -186,16 +185,14 @@ export function getUnitConformationAndRadius(structure, unit, props) {
     var position = { indices: indices, x: x, y: y, z: z, id: id };
     var boundary = unit === rootUnit ? unit.boundary : getBoundary(position);
     var l = StructureElement.Location.create(structure, rootUnit);
-    var sizeTheme = PhysicalSizeTheme({}, { scale: 1 });
     var radius = function (index) {
         l.element = index;
         return sizeTheme.size(l);
     };
     return { position: position, boundary: boundary, radius: radius };
 }
-export function getStructureConformationAndRadius(structure, ignoreHydrogens, traceOnly) {
+export function getStructureConformationAndRadius(structure, sizeTheme, ignoreHydrogens, traceOnly) {
     var l = StructureElement.Location.create(structure);
-    var sizeTheme = PhysicalSizeTheme({}, { scale: 1 });
     var xs;
     var ys;
     var zs;

package/lib/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>;