molstar 3.26.0 → 3.28.0

package/lib/commonjs/mol-plugin-ui/sequence.d.ts

@@ -6,7 +6,25 @@
  */
 /// <reference types="react" />
 import { PluginUIComponent } from './base';
-import { Structure } from '../mol-model/structure';
+import { Structure, StructureElement } from '../mol-model/structure';
+import { SequenceWrapper } from './sequence/wrapper';
+import { State } from '../mol-state';
+import { StructureSelectionManager } from '../mol-plugin-state/manager/structure/selection';
+export declare function opKey(l: StructureElement.Location): string;
+export declare function splitModelEntityId(modelEntityId: string): (string | number)[];
+export declare function getSequenceWrapper(state: {
+    structure: Structure;
+    modelEntityId: string;
+    chainGroupId: number;
+    operatorKey: string;
+}, structureSelection: StructureSelectionManager): SequenceWrapper.Any | string;
+export declare function getModelEntityOptions(structure: Structure, polymersOnly?: boolean): [string, string][];
+export declare function getChainOptions(structure: Structure, modelEntityId: string): [number, string][];
+export declare function getOperatorOptions(structure: Structure, modelEntityId: string, chainGroupId: number): [string, string][];
+export declare function getStructureOptions(state: State): {
+    options: [string, string][];
+    all: Structure[];
+};
 export type SequenceViewMode = 'single' | 'polymers' | 'all';
 type SequenceViewState = {
     structureOptions: {

package/lib/commonjs/mol-plugin-ui/sequence.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.SequenceView = void 0;
+exports.SequenceView = exports.getStructureOptions = exports.getOperatorOptions = exports.getChainOptions = exports.getModelEntityOptions = exports.getSequenceWrapper = exports.splitModelEntityId = exports.opKey = void 0;
 var tslib_1 = require("tslib");
 var jsx_runtime_1 = require("react/jsx-runtime");
 /**
@@ -36,10 +36,12 @@ function opKey(l) {
     var spgrOp = structure_1.StructureProperties.unit.spgrOp(l);
     return "".concat(ids.sort().join(','), "|").concat(ncs, "|").concat(hkl, "|").concat(spgrOp);
 }
+exports.opKey = opKey;
 function splitModelEntityId(modelEntityId) {
     var _a = modelEntityId.split('|'), modelIdx = _a[0], entityId = _a[1];
     return [parseInt(modelIdx), entityId];
 }
+exports.splitModelEntityId = splitModelEntityId;
 function getSequenceWrapper(state, structureSelection) {
     var structure = state.structure, modelEntityId = state.modelEntityId, chainGroupId = state.chainGroupId, operatorKey = state.operatorKey;
     var l = structure_1.StructureElement.Location.create(structure);
@@ -99,6 +101,7 @@ function getSequenceWrapper(state, structureSelection) {
         return 'No sequence available';
     }
 }
+exports.getSequenceWrapper = getSequenceWrapper;
 function getModelEntityOptions(structure, polymersOnly) {
     if (polymersOnly === void 0) { polymersOnly = false; }
     var options = [];
@@ -134,6 +137,7 @@ function getModelEntityOptions(structure, polymersOnly) {
         options.push(['', 'No entities']);
     return options;
 }
+exports.getModelEntityOptions = getModelEntityOptions;
 function getChainOptions(structure, modelEntityId) {
     var options = [];
     var l = structure_1.StructureElement.Location.create(structure);
@@ -162,6 +166,7 @@ function getChainOptions(structure, modelEntityId) {
         options.push([-1, 'No chains']);
     return options;
 }
+exports.getChainOptions = getChainOptions;
 function getOperatorOptions(structure, modelEntityId, chainGroupId) {
     var options = [];
     var l = structure_1.StructureElement.Location.create(structure);
@@ -190,6 +195,7 @@ function getOperatorOptions(structure, modelEntityId, chainGroupId) {
         options.push(['', 'No operators']);
     return options;
 }
+exports.getOperatorOptions = getOperatorOptions;
 function getStructureOptions(state) {
     var _a;
     var options = [];
@@ -206,6 +212,7 @@ function getStructureOptions(state) {
         options.push(['', 'No structure']);
     return { options: options, all: all };
 }
+exports.getStructureOptions = getStructureOptions;
 var SequenceViewModeParam = param_definition_1.ParamDefinition.Select('single', [['single', 'Chain'], ['polymers', 'Polymers'], ['all', 'Everything']]);
 var SequenceView = /** @class */ (function (_super) {
     tslib_1.__extends(SequenceView, _super);

package/lib/commonjs/mol-plugin-ui/state/apply-action.d.ts

@@ -24,6 +24,7 @@ declare namespace ApplyActionControl {
         error?: string;
         busy: boolean;
         isInitial: boolean;
+        isCollapsed?: boolean;
     }
 }
 declare class ApplyActionControl extends TransformControlBase<ApplyActionControl.Props, ApplyActionControl.ComponentState> {
@@ -46,15 +47,6 @@ declare class ApplyActionControl extends TransformControlBase<ApplyActionControl
         a: import("../../mol-state/object").StateObject<any, import("../../mol-state/object").StateObject.Type<any>> | undefined;
     };
     private _getInfo;
-    state: {
-        plugin: import("../context").PluginUIContext;
-        ref: string;
-        version: string;
-        error: undefined;
-        isInitial: boolean;
-        params: any;
-        busy: boolean;
-        isCollapsed: boolean | undefined;
-    };
+    state: ApplyActionControl.ComponentState;
     static getDerivedStateFromProps(props: ApplyActionControl.Props, state: ApplyActionControl.ComponentState): Partial<ApplyActionControl.ComponentState> | null;
 }

package/lib/commonjs/mol-plugin-ui/state/apply-action.js

@@ -15,7 +15,7 @@ var ApplyActionControl = /** @class */ (function (_super) {
     tslib_1.__extends(ApplyActionControl, _super);
     function ApplyActionControl() {
         var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this._getInfo = (0, memoize_1.memoizeLatest)(function (t, v) { return common_1.StateTransformParameters.infoFromAction(_this.plugin, _this.props.state, _this.props.action, _this.props.nodeRef); });
+        _this._getInfo = (0, memoize_1.memoizeLatest)(function (t, v, collapsed) { return common_1.StateTransformParameters.infoFromAction(_this.plugin, _this.props.state, _this.props.action, _this.props.nodeRef); });
         _this.state = { plugin: _this.plugin, ref: _this.props.nodeRef, version: _this.props.state.transforms.get(_this.props.nodeRef).version, error: void 0, isInitial: true, params: _this.getInfo().initialValues, busy: false, isCollapsed: _this.props.initiallyCollapsed };
         return _this;
     }
@@ -26,7 +26,7 @@ var ApplyActionControl = /** @class */ (function (_super) {
             ref: this.props.nodeRef
         });
     };
-    ApplyActionControl.prototype.getInfo = function () { return this._getInfo(this.props.nodeRef, this.props.state.transforms.get(this.props.nodeRef).version); };
+    ApplyActionControl.prototype.getInfo = function () { var _a; return this._getInfo(this.props.nodeRef, this.props.state.transforms.get(this.props.nodeRef).version, (_a = this.state) === null || _a === void 0 ? void 0 : _a.isCollapsed); };
     ApplyActionControl.prototype.getTransformerId = function () { return this.props.state.transforms.get(this.props.nodeRef).transformer.id; };
     ApplyActionControl.prototype.getHeader = function () { return this.props.hideHeader ? 'none' : this.props.action.definition.display; };
     ApplyActionControl.prototype.canApply = function () { return !this.state.error && !this.state.busy; };

package/lib/commonjs/mol-plugin-ui/structure/quick-styles.js

@@ -79,7 +79,7 @@ var QuickStyles = /** @class */ (function (_super) {
                                 postprocessing: {
                                     outline: {
                                         name: 'on',
-                                        params: { scale: 1, color: (0, color_1.Color)(0x000000), threshold: 0.25 }
+                                        params: { scale: 1, color: (0, color_1.Color)(0x000000), threshold: 0.25, includeTransparent: true }
                                     },
                                     occlusion: {
                                         name: 'on',
@@ -107,7 +107,7 @@ var QuickStyles = /** @class */ (function (_super) {
                                 name: 'on',
                                 params: pp.outline.name === 'on'
                                     ? pp.outline.params
-                                    : { scale: 1, color: (0, color_1.Color)(0x000000), threshold: 0.33 }
+                                    : { scale: 1, color: (0, color_1.Color)(0x000000), threshold: 0.33, includeTransparent: true }
                             },
                             occlusion: {
                                 name: 'on',

package/lib/commonjs/mol-plugin-ui/structure/superposition.d.ts

@@ -37,7 +37,7 @@ type SuperpositionControlsState = {
     canUseDb?: boolean;
     options: StructureSuperpositionOptions;
 };
-interface LociEntry {
+export interface LociEntry {
     loci: StructureElement.Loci;
     label: string;
     cell: StateObjectCell<PluginStateObject.Molecule.Structure>;

package/lib/commonjs/mol-plugin-ui/structure/volume.d.ts

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

package/lib/commonjs/mol-plugin-ui/structure/volume.js

@@ -300,10 +300,11 @@ var VolumeRepresentationControls = /** @class */ (function (_super) {
         _this.focus = function () {
             var _a;
             var repr = _this.props.representation;
-            var objects = (_a = _this.props.representation.cell.obj) === null || _a === void 0 ? void 0 : _a.data.repr.renderObjects;
+            var lociList = (_a = repr.cell.obj) === null || _a === void 0 ? void 0 : _a.data.repr.getAllLoci();
             if (repr.cell.state.isHidden)
                 _this.plugin.managers.volume.hierarchy.toggleVisibility([_this.props.representation], 'show');
-            _this.plugin.managers.camera.focusRenderObjects(objects, { extraRadius: 1 });
+            if (lociList)
+                _this.plugin.managers.camera.focusLoci(lociList, { extraRadius: 1 });
         };
         return _this;
     }

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

@@ -82,6 +82,7 @@ export declare const ComplexCylindersParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

package/lib/commonjs/mol-repr/structure/params.d.ts

@@ -47,6 +47,7 @@ export declare const StructureSpheresParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -76,6 +77,7 @@ export declare const StructureCylindersParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;

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

@@ -84,6 +84,7 @@ export declare namespace StructureRepresentationRegistry {
             }>>;
             instanceGranularity: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             tryUseImpostor: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            solidInterior: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             detail: import("../../mol-util/param-definition").ParamDefinition.Numeric;
         }, "backbone">;
         'ball-and-stick': import("./representation").StructureRepresentationProvider<{
@@ -98,6 +99,7 @@ export declare namespace StructureRepresentationRegistry {
             includeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
             excludeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
             ignoreHydrogens: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            ignoreHydrogensVariant: import("../../mol-util/param-definition").ParamDefinition.Select<"all" | "non-polar">;
             aromaticBonds: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             multipleBonds: import("../../mol-util/param-definition").ParamDefinition.Select<"offset" | "off" | "symmetric">;
             linkScale: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -115,6 +117,7 @@ export declare namespace StructureRepresentationRegistry {
             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>;
+            solidInterior: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             bumpAmplitude: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             quality: import("../../mol-util/param-definition").ParamDefinition.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -198,6 +201,7 @@ export declare namespace StructureRepresentationRegistry {
             includeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
             excludeTypes: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
             ignoreHydrogens: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            ignoreHydrogensVariant: import("../../mol-util/param-definition").ParamDefinition.Select<"all" | "non-polar">;
             aromaticBonds: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             multipleBonds: import("../../mol-util/param-definition").ParamDefinition.Select<"offset" | "off" | "symmetric">;
             linkScale: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -214,6 +218,7 @@ export declare namespace StructureRepresentationRegistry {
             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>;
+            solidInterior: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             bumpAmplitude: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             quality: import("../../mol-util/param-definition").ParamDefinition.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -243,6 +248,7 @@ export declare namespace StructureRepresentationRegistry {
             sizeFactor: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             lineSizeAttenuation: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             ignoreHydrogens: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            ignoreHydrogensVariant: import("../../mol-util/param-definition").ParamDefinition.Select<"all" | "non-polar">;
             includeParent: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             traceOnly: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             resolution: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -283,6 +289,7 @@ export declare namespace StructureRepresentationRegistry {
         'gaussian-volume': import("./representation").StructureRepresentationProvider<{
             visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"gaussian-volume" | "units-gaussian-volume">;
             ignoreHydrogens: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            ignoreHydrogensVariant: import("../../mol-util/param-definition").ParamDefinition.Select<"all" | "non-polar">;
             includeParent: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             traceOnly: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             resolution: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -367,6 +374,7 @@ export declare namespace StructureRepresentationRegistry {
             visuals: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"intra-bond" | "inter-bond" | "element-point" | "element-cross">;
             lineSizeAttenuation: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             ignoreHydrogens: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            ignoreHydrogensVariant: import("../../mol-util/param-definition").ParamDefinition.Select<"all" | "non-polar">;
             traceOnly: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             crosses: import("../../mol-util/param-definition").ParamDefinition.Select<"all" | "lone">;
             crossSize: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -403,6 +411,7 @@ export declare namespace StructureRepresentationRegistry {
             bumpFrequency: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             sizeFactor: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             ignoreHydrogens: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            ignoreHydrogensVariant: import("../../mol-util/param-definition").ParamDefinition.Select<"all" | "non-polar">;
             traceOnly: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             includeParent: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             probeRadius: import("../../mol-util/param-definition").ParamDefinition.Numeric;
@@ -476,6 +485,7 @@ export declare namespace StructureRepresentationRegistry {
         point: import("./representation").StructureRepresentationProvider<{
             pointSizeAttenuation: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             ignoreHydrogens: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            ignoreHydrogensVariant: import("../../mol-util/param-definition").ParamDefinition.Select<"all" | "non-polar">;
             traceOnly: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             unitKinds: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"spheres" | "gaussians" | "atomic">;
             includeParent: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
@@ -540,6 +550,7 @@ export declare namespace StructureRepresentationRegistry {
             sizeFactor: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             detail: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             ignoreHydrogens: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
+            ignoreHydrogensVariant: import("../../mol-util/param-definition").ParamDefinition.Select<"all" | "non-polar">;
             traceOnly: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             tryUseImpostor: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             unitKinds: import("../../mol-util/param-definition").ParamDefinition.MultiSelect<"spheres" | "gaussians" | "atomic">;
@@ -548,6 +559,7 @@ export declare namespace StructureRepresentationRegistry {
             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>;
+            solidInterior: import("../../mol-util/param-definition").ParamDefinition.BooleanParam;
             bumpAmplitude: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             alpha: import("../../mol-util/param-definition").ParamDefinition.Numeric;
             quality: import("../../mol-util/param-definition").ParamDefinition.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;

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

@@ -42,6 +42,7 @@ export declare const BackboneParams: {
     }>>;
     instanceGranularity: PD.BooleanParam;
     tryUseImpostor: PD.BooleanParam;
+    solidInterior: PD.BooleanParam;
     detail: PD.Numeric;
 };
 export type BackboneParams = typeof BackboneParams;
@@ -79,6 +80,7 @@ export declare function getBackboneParams(ctx: ThemeRegistryContext, structure:
     }>>;
     instanceGranularity: PD.BooleanParam;
     tryUseImpostor: PD.BooleanParam;
+    solidInterior: PD.BooleanParam;
     detail: PD.Numeric;
 };
 export type BackboneRepresentation = StructureRepresentation<BackboneParams>;
@@ -117,5 +119,6 @@ export declare const BackboneRepresentationProvider: StructureRepresentationProv
     }>>;
     instanceGranularity: PD.BooleanParam;
     tryUseImpostor: PD.BooleanParam;
+    solidInterior: PD.BooleanParam;
     detail: PD.Numeric;
 }, "backbone">;

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

@@ -20,6 +20,7 @@ export declare const BallAndStickParams: {
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     aromaticBonds: PD.BooleanParam;
     multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
@@ -37,6 +38,7 @@ export declare const BallAndStickParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -74,6 +76,7 @@ export declare function getBallAndStickParams(ctx: ThemeRegistryContext, structu
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     aromaticBonds: PD.BooleanParam;
     multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
@@ -91,6 +94,7 @@ export declare function getBallAndStickParams(ctx: ThemeRegistryContext, structu
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -129,6 +133,7 @@ export declare const BallAndStickRepresentationProvider: StructureRepresentation
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     aromaticBonds: PD.BooleanParam;
     multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
@@ -146,6 +151,7 @@ export declare const BallAndStickRepresentationProvider: StructureRepresentation
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;

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

@@ -21,6 +21,7 @@ export declare const EllipsoidParams: {
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     aromaticBonds: PD.BooleanParam;
     multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
@@ -37,6 +38,7 @@ export declare const EllipsoidParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -74,6 +76,7 @@ export declare function getEllipsoidParams(ctx: ThemeRegistryContext, structure:
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     aromaticBonds: PD.BooleanParam;
     multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
@@ -90,6 +93,7 @@ export declare function getEllipsoidParams(ctx: ThemeRegistryContext, structure:
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -128,6 +132,7 @@ export declare const EllipsoidRepresentationProvider: StructureRepresentationPro
     includeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     aromaticBonds: PD.BooleanParam;
     multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
@@ -144,6 +149,7 @@ export declare const EllipsoidRepresentationProvider: StructureRepresentationPro
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;

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

@@ -14,6 +14,7 @@ export declare const GaussianSurfaceParams: {
     sizeFactor: PD.Numeric;
     lineSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     traceOnly: PD.BooleanParam;
     resolution: PD.Numeric;
@@ -58,6 +59,7 @@ export declare function getGaussianSurfaceParams(ctx: ThemeRegistryContext, stru
     sizeFactor: PD.Numeric;
     lineSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     traceOnly: PD.BooleanParam;
     resolution: PD.Numeric;
@@ -103,6 +105,7 @@ export declare const GaussianSurfaceRepresentationProvider: StructureRepresentat
     sizeFactor: PD.Numeric;
     lineSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     traceOnly: PD.BooleanParam;
     resolution: PD.Numeric;

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

@@ -11,6 +11,7 @@ import { Structure } from '../../../mol-model/structure';
 export declare const GaussianVolumeParams: {
     visuals: PD.MultiSelect<"gaussian-volume" | "units-gaussian-volume">;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     traceOnly: PD.BooleanParam;
     resolution: PD.Numeric;
@@ -45,6 +46,7 @@ export type GaussianVolumeParams = typeof GaussianVolumeParams;
 export declare function getGaussianVolumeParams(ctx: ThemeRegistryContext, structure: Structure): {
     visuals: PD.MultiSelect<"gaussian-volume" | "units-gaussian-volume">;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     traceOnly: PD.BooleanParam;
     resolution: PD.Numeric;
@@ -80,6 +82,7 @@ export declare function GaussianVolumeRepresentation(ctx: RepresentationContext,
 export declare const GaussianVolumeRepresentationProvider: StructureRepresentationProvider<{
     visuals: PD.MultiSelect<"gaussian-volume" | "units-gaussian-volume">;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     traceOnly: PD.BooleanParam;
     resolution: PD.Numeric;

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

@@ -16,6 +16,7 @@ export declare const LineParams: {
     visuals: PD.MultiSelect<"intra-bond" | "inter-bond" | "element-point" | "element-cross">;
     lineSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     crosses: PD.Select<"all" | "lone">;
     crossSize: PD.Numeric;
@@ -56,6 +57,7 @@ export declare function getLineParams(ctx: ThemeRegistryContext, structure: Stru
     visuals: PD.MultiSelect<"intra-bond" | "inter-bond" | "element-point" | "element-cross">;
     lineSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     crosses: PD.Select<"all" | "lone">;
     crossSize: PD.Numeric;
@@ -97,6 +99,7 @@ export declare const LineRepresentationProvider: StructureRepresentationProvider
     visuals: PD.MultiSelect<"intra-bond" | "inter-bond" | "element-point" | "element-cross">;
     lineSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     crosses: PD.Select<"all" | "lone">;
     crossSize: PD.Numeric;

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

@@ -13,6 +13,7 @@ export declare const MolecularSurfaceParams: {
     bumpFrequency: PD.Numeric;
     sizeFactor: PD.Numeric;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     includeParent: PD.BooleanParam;
     probeRadius: PD.Numeric;
@@ -56,6 +57,7 @@ export declare function getMolecularSurfaceParams(ctx: ThemeRegistryContext, str
     bumpFrequency: PD.Numeric;
     sizeFactor: PD.Numeric;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     includeParent: PD.BooleanParam;
     probeRadius: PD.Numeric;
@@ -100,6 +102,7 @@ export declare const MolecularSurfaceRepresentationProvider: StructureRepresenta
     bumpFrequency: PD.Numeric;
     sizeFactor: PD.Numeric;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     includeParent: PD.BooleanParam;
     probeRadius: PD.Numeric;

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

@@ -11,6 +11,7 @@ import { Structure } from '../../../mol-model/structure';
 export declare const PointParams: {
     pointSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
@@ -39,6 +40,7 @@ export type PointParams = typeof PointParams;
 export declare function getPointParams(ctx: ThemeRegistryContext, structure: Structure): {
     pointSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
@@ -68,6 +70,7 @@ export declare function PointRepresentation(ctx: RepresentationContext, getParam
 export declare const PointRepresentationProvider: StructureRepresentationProvider<{
     pointSizeAttenuation: PD.BooleanParam;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;

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

@@ -13,6 +13,7 @@ export declare const SpacefillParams: {
     sizeFactor: PD.Numeric;
     detail: PD.Numeric;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     tryUseImpostor: PD.BooleanParam;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
@@ -21,6 +22,7 @@ export declare const SpacefillParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -49,6 +51,7 @@ export declare function getSpacefillParams(ctx: ThemeRegistryContext, structure:
     sizeFactor: PD.Numeric;
     detail: PD.Numeric;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     tryUseImpostor: PD.BooleanParam;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
@@ -57,6 +60,7 @@ export declare function getSpacefillParams(ctx: ThemeRegistryContext, structure:
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
@@ -86,6 +90,7 @@ export declare const SpacefillRepresentationProvider: StructureRepresentationPro
     sizeFactor: PD.Numeric;
     detail: PD.Numeric;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     tryUseImpostor: PD.BooleanParam;
     unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
@@ -94,6 +99,7 @@ export declare const SpacefillRepresentationProvider: StructureRepresentationPro
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;

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

@@ -85,6 +85,7 @@ export declare const UnitsSpheresParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -119,6 +120,7 @@ export declare const UnitsCylindersParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;