molstar 3.0.0-dev.0 → 3.0.0-dev.10

package/lib/commonjs/mol-repr/structure/representation/ball-and-stick.d.ts

@@ -14,6 +14,7 @@ export declare const BallAndStickParams: {
     sizeFactor: PD.Numeric;
     sizeAspectRatio: PD.Numeric;
     visuals: PD.MultiSelect<"element-sphere" | "intra-bond" | "inter-bond">;
+    bumpFrequency: PD.Numeric;
     tryUseImpostor: PD.BooleanParam;
     adjustCylinderLength: PD.BooleanParam;
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
@@ -35,11 +36,23 @@ export declare const BallAndStickParams: {
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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;
@@ -53,6 +66,7 @@ export declare function getBallAndStickParams(ctx: ThemeRegistryContext, structu
     sizeFactor: PD.Numeric;
     sizeAspectRatio: PD.Numeric;
     visuals: PD.MultiSelect<"element-sphere" | "intra-bond" | "inter-bond">;
+    bumpFrequency: PD.Numeric;
     tryUseImpostor: PD.BooleanParam;
     adjustCylinderLength: PD.BooleanParam;
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
@@ -74,11 +88,23 @@ export declare function getBallAndStickParams(ctx: ThemeRegistryContext, structu
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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;
@@ -93,6 +119,7 @@ export declare const BallAndStickRepresentationProvider: StructureRepresentation
     sizeFactor: PD.Numeric;
     sizeAspectRatio: PD.Numeric;
     visuals: PD.MultiSelect<"element-sphere" | "intra-bond" | "inter-bond">;
+    bumpFrequency: PD.Numeric;
     tryUseImpostor: PD.BooleanParam;
     adjustCylinderLength: PD.BooleanParam;
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
@@ -114,11 +141,23 @@ export declare const BallAndStickRepresentationProvider: StructureRepresentation
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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/commonjs/mol-repr/structure/representation/ball-and-stick.js

@@ -16,12 +16,13 @@ var complex_representation_1 = require("../complex-representation");
 var representation_1 = require("../representation");
 var representation_2 = require("../../../mol-repr/representation");
 var params_1 = require("../params");
+var base_1 = require("../../../mol-geo/geometry/base");
 var BallAndStickVisuals = {
     'element-sphere': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Element sphere', ctx, getParams, element_sphere_1.ElementSphereVisual); },
     'intra-bond': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Intra-unit bond cylinder', ctx, getParams, bond_intra_unit_cylinder_1.IntraUnitBondCylinderVisual); },
     'inter-bond': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Inter-unit bond cylinder', ctx, getParams, bond_inter_unit_cylinder_1.InterUnitBondCylinderVisual); },
 };
-exports.BallAndStickParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, element_sphere_1.ElementSphereParams), { traceOnly: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) }), bond_intra_unit_cylinder_1.IntraUnitBondCylinderParams), bond_inter_unit_cylinder_1.InterUnitBondCylinderParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(0.15, { min: 0.01, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(2 / 3, { min: 0.01, max: 3, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['element-sphere', 'intra-bond', 'inter-bond'], param_definition_1.ParamDefinition.objectToOptions(BallAndStickVisuals)) });
+exports.BallAndStickParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, element_sphere_1.ElementSphereParams), { traceOnly: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) }), bond_intra_unit_cylinder_1.IntraUnitBondCylinderParams), bond_inter_unit_cylinder_1.InterUnitBondCylinderParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(0.15, { min: 0.01, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(2 / 3, { min: 0.01, max: 3, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['element-sphere', 'intra-bond', 'inter-bond'], param_definition_1.ParamDefinition.objectToOptions(BallAndStickVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
 function getBallAndStickParams(ctx, structure) {
     return param_definition_1.ParamDefinition.clone(exports.BallAndStickParams);
 }

package/lib/commonjs/mol-repr/structure/representation/carbohydrate.d.ts

@@ -10,6 +10,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { StructureRepresentation, StructureRepresentationProvider } from '../representation';
 export declare const CarbohydrateParams: {
     visuals: PD.MultiSelect<"carbohydrate-symbol" | "carbohydrate-link" | "carbohydrate-terminal-link">;
+    bumpFrequency: PD.Numeric;
     terminalLinkSizeFactor: PD.Numeric;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
@@ -29,11 +30,23 @@ export declare const CarbohydrateParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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;
+        }>[];
     }>>;
     linkSizeFactor: PD.Numeric;
     detail: PD.Numeric;
@@ -42,6 +55,7 @@ export declare const CarbohydrateParams: {
 export declare type CarbohydrateParams = typeof CarbohydrateParams;
 export declare function getCarbohydrateParams(ctx: ThemeRegistryContext, structure: Structure): {
     visuals: PD.MultiSelect<"carbohydrate-symbol" | "carbohydrate-link" | "carbohydrate-terminal-link">;
+    bumpFrequency: PD.Numeric;
     terminalLinkSizeFactor: PD.Numeric;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
@@ -61,11 +75,23 @@ export declare function getCarbohydrateParams(ctx: ThemeRegistryContext, structu
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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;
+        }>[];
     }>>;
     linkSizeFactor: PD.Numeric;
     detail: PD.Numeric;
@@ -75,6 +101,7 @@ export declare type CarbohydrateRepresentation = StructureRepresentation<Carbohy
 export declare function CarbohydrateRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, CarbohydrateParams>): CarbohydrateRepresentation;
 export declare const CarbohydrateRepresentationProvider: StructureRepresentationProvider<{
     visuals: PD.MultiSelect<"carbohydrate-symbol" | "carbohydrate-link" | "carbohydrate-terminal-link">;
+    bumpFrequency: PD.Numeric;
     terminalLinkSizeFactor: PD.Numeric;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
@@ -94,11 +121,23 @@ export declare const CarbohydrateRepresentationProvider: StructureRepresentation
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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;
+        }>[];
     }>>;
     linkSizeFactor: PD.Numeric;
     detail: PD.Numeric;

package/lib/commonjs/mol-repr/structure/representation/carbohydrate.js

@@ -7,6 +7,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.CarbohydrateRepresentationProvider = exports.CarbohydrateRepresentation = exports.getCarbohydrateParams = exports.CarbohydrateParams = void 0;
 var tslib_1 = require("tslib");
+var base_1 = require("../../../mol-geo/geometry/base");
 var structure_1 = require("../../../mol-model/structure");
 var representation_1 = require("../../../mol-repr/representation");
 var param_definition_1 = require("../../../mol-util/param-definition");
@@ -20,7 +21,7 @@ var CarbohydrateVisuals = {
     'carbohydrate-link': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Carbohydrate link cylinder', ctx, getParams, carbohydrate_link_cylinder_1.CarbohydrateLinkVisual); },
     'carbohydrate-terminal-link': function (ctx, getParams) { return (0, complex_representation_1.ComplexRepresentation)('Carbohydrate terminal link cylinder', ctx, getParams, carbohydrate_terminal_link_cylinder_1.CarbohydrateTerminalLinkVisual); },
 };
-exports.CarbohydrateParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, carbohydrate_symbol_mesh_1.CarbohydrateSymbolParams), carbohydrate_link_cylinder_1.CarbohydrateLinkParams), carbohydrate_terminal_link_cylinder_1.CarbohydrateTerminalLinkParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['carbohydrate-symbol', 'carbohydrate-link', 'carbohydrate-terminal-link'], param_definition_1.ParamDefinition.objectToOptions(CarbohydrateVisuals)) });
+exports.CarbohydrateParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, carbohydrate_symbol_mesh_1.CarbohydrateSymbolParams), carbohydrate_link_cylinder_1.CarbohydrateLinkParams), carbohydrate_terminal_link_cylinder_1.CarbohydrateTerminalLinkParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['carbohydrate-symbol', 'carbohydrate-link', 'carbohydrate-terminal-link'], param_definition_1.ParamDefinition.objectToOptions(CarbohydrateVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
 function getCarbohydrateParams(ctx, structure) {
     return param_definition_1.ParamDefinition.clone(exports.CarbohydrateParams);
 }

package/lib/commonjs/mol-repr/structure/representation/cartoon.d.ts

@@ -11,6 +11,7 @@ import { StructureRepresentation, StructureRepresentationProvider } from '../rep
 export declare const CartoonParams: {
     sizeFactor: PD.Numeric;
     visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
+    bumpFrequency: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
@@ -18,11 +19,23 @@ export declare const CartoonParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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;
+        }>[];
     }>>;
     radialSegments: PD.Numeric;
     detail: PD.Numeric;
@@ -36,6 +49,7 @@ export declare type CartoonParams = typeof CartoonParams;
 export declare function getCartoonParams(ctx: ThemeRegistryContext, structure: Structure): {
     sizeFactor: PD.Numeric;
     visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
+    bumpFrequency: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
@@ -43,11 +57,23 @@ export declare function getCartoonParams(ctx: ThemeRegistryContext, structure: S
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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;
+        }>[];
     }>>;
     radialSegments: PD.Numeric;
     detail: PD.Numeric;
@@ -62,6 +88,7 @@ export declare function CartoonRepresentation(ctx: RepresentationContext, getPar
 export declare const CartoonRepresentationProvider: StructureRepresentationProvider<{
     sizeFactor: PD.Numeric;
     visuals: PD.MultiSelect<"polymer-trace" | "polymer-gap" | "nucleotide-block" | "nucleotide-ring" | "direction-wedge">;
+    bumpFrequency: PD.Numeric;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
@@ -69,11 +96,23 @@ export declare const CartoonRepresentationProvider: StructureRepresentationProvi
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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;
+        }>[];
     }>>;
     radialSegments: PD.Numeric;
     detail: PD.Numeric;

package/lib/commonjs/mol-repr/structure/representation/cartoon.js

@@ -19,6 +19,7 @@ var polymer_gap_cylinder_1 = require("../visual/polymer-gap-cylinder");
 var polymer_trace_mesh_1 = require("../visual/polymer-trace-mesh");
 var secondary_structure_1 = require("../../../mol-model-props/computed/secondary-structure");
 var helix_orientation_1 = require("../../../mol-model-props/computed/helix-orientation");
+var base_1 = require("../../../mol-geo/geometry/base");
 var CartoonVisuals = {
     'polymer-trace': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer trace mesh', ctx, getParams, polymer_trace_mesh_1.PolymerTraceVisual); },
     'polymer-gap': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer gap cylinder', ctx, getParams, polymer_gap_cylinder_1.PolymerGapVisual); },
@@ -26,7 +27,7 @@ var CartoonVisuals = {
     'nucleotide-ring': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Nucleotide ring mesh', ctx, getParams, nucleotide_ring_mesh_1.NucleotideRingVisual); },
     'direction-wedge': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Polymer direction wedge', ctx, getParams, polymer_direction_wedge_1.PolymerDirectionVisual); }
 };
-exports.CartoonParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_trace_mesh_1.PolymerTraceParams), polymer_gap_cylinder_1.PolymerGapParams), nucleotide_block_mesh_1.NucleotideBlockParams), nucleotide_ring_mesh_1.NucleotideRingParams), polymer_direction_wedge_1.PolymerDirectionParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-block'], param_definition_1.ParamDefinition.objectToOptions(CartoonVisuals)) });
+exports.CartoonParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, polymer_trace_mesh_1.PolymerTraceParams), polymer_gap_cylinder_1.PolymerGapParams), nucleotide_block_mesh_1.NucleotideBlockParams), nucleotide_ring_mesh_1.NucleotideRingParams), polymer_direction_wedge_1.PolymerDirectionParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }), visuals: param_definition_1.ParamDefinition.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-block'], param_definition_1.ParamDefinition.objectToOptions(CartoonVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
 function getCartoonParams(ctx, structure) {
     var params = param_definition_1.ParamDefinition.clone(exports.CartoonParams);
     var hasNucleotides = false;

package/lib/commonjs/mol-repr/structure/representation/ellipsoid.d.ts

@@ -16,6 +16,7 @@ export declare const EllipsoidParams: {
     sizeAspectRatio: PD.Numeric;
     linkCap: PD.BooleanParam;
     visuals: PD.MultiSelect<"intra-bond" | "inter-bond" | "ellipsoid-mesh">;
+    bumpFrequency: PD.Numeric;
     tryUseImpostor: PD.BooleanParam;
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
@@ -35,11 +36,23 @@ export declare const EllipsoidParams: {
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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;
@@ -54,6 +67,7 @@ export declare function getEllipsoidParams(ctx: ThemeRegistryContext, structure:
     sizeAspectRatio: PD.Numeric;
     linkCap: PD.BooleanParam;
     visuals: PD.MultiSelect<"intra-bond" | "inter-bond" | "ellipsoid-mesh">;
+    bumpFrequency: PD.Numeric;
     tryUseImpostor: PD.BooleanParam;
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
@@ -73,11 +87,23 @@ export declare function getEllipsoidParams(ctx: ThemeRegistryContext, structure:
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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;
@@ -93,6 +119,7 @@ export declare const EllipsoidRepresentationProvider: StructureRepresentationPro
     sizeAspectRatio: PD.Numeric;
     linkCap: PD.BooleanParam;
     visuals: PD.MultiSelect<"intra-bond" | "inter-bond" | "ellipsoid-mesh">;
+    bumpFrequency: PD.Numeric;
     tryUseImpostor: PD.BooleanParam;
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
@@ -112,11 +139,23 @@ export declare const EllipsoidRepresentationProvider: StructureRepresentationPro
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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/commonjs/mol-repr/structure/representation/ellipsoid.js

@@ -15,12 +15,13 @@ var anisotropic_1 = require("../../../mol-model-formats/structure/property/aniso
 var bond_intra_unit_cylinder_1 = require("../visual/bond-intra-unit-cylinder");
 var bond_inter_unit_cylinder_1 = require("../visual/bond-inter-unit-cylinder");
 var params_1 = require("../params");
+var base_1 = require("../../../mol-geo/geometry/base");
 var EllipsoidVisuals = {
     'ellipsoid-mesh': function (ctx, getParams) { return (0, representation_2.UnitsRepresentation)('Ellipsoid Mesh', ctx, getParams, ellipsoid_mesh_1.EllipsoidMeshVisual); },
     'intra-bond': function (ctx, getParams) { return (0, representation_2.UnitsRepresentation)('Intra-unit bond cylinder', ctx, getParams, bond_intra_unit_cylinder_1.IntraUnitBondCylinderVisual); },
     'inter-bond': function (ctx, getParams) { return (0, representation_2.ComplexRepresentation)('Inter-unit bond cylinder', ctx, getParams, bond_inter_unit_cylinder_1.InterUnitBondCylinderVisual); },
 };
-exports.EllipsoidParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, ellipsoid_mesh_1.EllipsoidMeshParams), bond_intra_unit_cylinder_1.IntraUnitBondCylinderParams), bond_inter_unit_cylinder_1.InterUnitBondCylinderParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false), adjustCylinderLength: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0.01, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(0.1, { min: 0.01, max: 3, step: 0.01 }), linkCap: param_definition_1.ParamDefinition.Boolean(true), visuals: param_definition_1.ParamDefinition.MultiSelect(['ellipsoid-mesh', 'intra-bond', 'inter-bond'], param_definition_1.ParamDefinition.objectToOptions(EllipsoidVisuals)) });
+exports.EllipsoidParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, ellipsoid_mesh_1.EllipsoidMeshParams), bond_intra_unit_cylinder_1.IntraUnitBondCylinderParams), bond_inter_unit_cylinder_1.InterUnitBondCylinderParams), { includeParent: param_definition_1.ParamDefinition.Boolean(false), adjustCylinderLength: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }), unitKinds: (0, params_1.getUnitKindsParam)(['atomic']), sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0.01, max: 10, step: 0.01 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(0.1, { min: 0.01, max: 3, step: 0.01 }), linkCap: param_definition_1.ParamDefinition.Boolean(true), visuals: param_definition_1.ParamDefinition.MultiSelect(['ellipsoid-mesh', 'intra-bond', 'inter-bond'], param_definition_1.ParamDefinition.objectToOptions(EllipsoidVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
 function getEllipsoidParams(ctx, structure) {
     return param_definition_1.ParamDefinition.clone(exports.EllipsoidParams);
 }

package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.d.ts

@@ -10,6 +10,7 @@ import { ThemeRegistryContext } from '../../../mol-theme/theme';
 import { Structure } from '../../../mol-model/structure';
 export declare const GaussianSurfaceParams: {
     visuals: PD.MultiSelect<"gaussian-surface-mesh" | "structure-gaussian-surface-mesh" | "gaussian-surface-wireframe">;
+    bumpFrequency: PD.Numeric;
     sizeFactor: PD.Numeric;
     lineSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
@@ -21,9 +22,20 @@ export declare const GaussianSurfaceParams: {
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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;
     smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
@@ -35,10 +47,12 @@ export declare const GaussianSurfaceParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
 };
 export declare type GaussianSurfaceParams = typeof GaussianSurfaceParams;
 export declare function getGaussianSurfaceParams(ctx: ThemeRegistryContext, structure: Structure): {
     visuals: PD.MultiSelect<"gaussian-surface-mesh" | "structure-gaussian-surface-mesh" | "gaussian-surface-wireframe">;
+    bumpFrequency: PD.Numeric;
     sizeFactor: PD.Numeric;
     lineSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
@@ -50,9 +64,20 @@ export declare function getGaussianSurfaceParams(ctx: ThemeRegistryContext, stru
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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;
     smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
@@ -64,11 +89,13 @@ export declare function getGaussianSurfaceParams(ctx: ThemeRegistryContext, stru
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
 };
 export declare type GaussianSurfaceRepresentation = StructureRepresentation<GaussianSurfaceParams>;
 export declare function GaussianSurfaceRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, GaussianSurfaceParams>): GaussianSurfaceRepresentation;
 export declare const GaussianSurfaceRepresentationProvider: StructureRepresentationProvider<{
     visuals: PD.MultiSelect<"gaussian-surface-mesh" | "structure-gaussian-surface-mesh" | "gaussian-surface-wireframe">;
+    bumpFrequency: PD.Numeric;
     sizeFactor: PD.Numeric;
     lineSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
@@ -80,9 +107,20 @@ export declare const GaussianSurfaceRepresentationProvider: StructureRepresentat
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
-    material: PD.Converted<import("../../../mol-util/material").Material, PD.Normalize<{
+    material: PD.Group<PD.Normalize<{
         metalness: number;
         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;
     smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
@@ -94,4 +132,5 @@ export declare const GaussianSurfaceRepresentationProvider: StructureRepresentat
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpAmplitude: PD.Numeric;
 }, "gaussian-surface">;

package/lib/commonjs/mol-repr/structure/representation/gaussian-surface.js

@@ -13,12 +13,13 @@ var gaussian_surface_wireframe_1 = require("../visual/gaussian-surface-wireframe
 var param_definition_1 = require("../../../mol-util/param-definition");
 var representation_1 = require("../representation");
 var representation_2 = require("../../../mol-repr/representation");
+var base_1 = require("../../../mol-geo/geometry/base");
 var GaussianSurfaceVisuals = {
     'gaussian-surface-mesh': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Gaussian surface mesh', ctx, getParams, gaussian_surface_mesh_1.GaussianSurfaceVisual); },
     'structure-gaussian-surface-mesh': function (ctx, getParams) { return (0, representation_1.ComplexRepresentation)('Structure-Gaussian surface mesh', ctx, getParams, gaussian_surface_mesh_1.StructureGaussianSurfaceVisual); },
     'gaussian-surface-wireframe': function (ctx, getParams) { return (0, units_representation_1.UnitsRepresentation)('Gaussian surface wireframe', ctx, getParams, gaussian_surface_wireframe_1.GaussianWireframeVisual); },
 };
-exports.GaussianSurfaceParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, gaussian_surface_mesh_1.GaussianSurfaceMeshParams), gaussian_surface_wireframe_1.GaussianWireframeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['gaussian-surface-mesh'], param_definition_1.ParamDefinition.objectToOptions(GaussianSurfaceVisuals)) });
+exports.GaussianSurfaceParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, gaussian_surface_mesh_1.GaussianSurfaceMeshParams), gaussian_surface_wireframe_1.GaussianWireframeParams), { visuals: param_definition_1.ParamDefinition.MultiSelect(['gaussian-surface-mesh'], param_definition_1.ParamDefinition.objectToOptions(GaussianSurfaceVisuals)), bumpFrequency: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
 function getGaussianSurfaceParams(ctx, structure) {
     return param_definition_1.ParamDefinition.clone(exports.GaussianSurfaceParams);
 }
@@ -35,7 +36,7 @@ exports.GaussianSurfaceRepresentationProvider = (0, representation_1.StructureRe
     getParams: getGaussianSurfaceParams,
     defaultValues: param_definition_1.ParamDefinition.getDefaultValues(exports.GaussianSurfaceParams),
     defaultColorTheme: { name: 'chain-id' },
-    defaultSizeTheme: { name: 'uniform' },
+    defaultSizeTheme: { name: 'physical' },
     isApplicable: function (structure) { return structure.elementCount > 0; }
 });
 //# sourceMappingURL=gaussian-surface.js.map