molstar 3.26.0 → 3.28.0

package/lib/mol-plugin-ui/skin/colors/blue.scss

@@ -1,24 +1,24 @@
-$default-background:         #2D3E50;
-$font-color:                 #EDF1F2; 
-$hover-font-color:           #3B9AD9;
-$entity-current-font-color:  #FFFFFF;
-$msp-btn-remove-background:      #BF3A31;
-$msp-btn-remove-hover-font-color:#ffffff;
-$msp-btn-commit-on-font-color:   #ffffff; 
-$entity-badge-font-color:    #ccd4e0;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: rgba(0,0,0,0.75);
-
-@function color-lower-contrast($color, $amount) {
-    @return darken($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return lighten($color, $amount);
+$default-background:         #2D3E50;
+$font-color:                 #EDF1F2; 
+$hover-font-color:           #3B9AD9;
+$entity-current-font-color:  #FFFFFF;
+$msp-btn-remove-background:      #BF3A31;
+$msp-btn-remove-hover-font-color:#ffffff;
+$msp-btn-commit-on-font-color:   #ffffff; 
+$entity-badge-font-color:    #ccd4e0;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: rgba(0,0,0,0.75);
+
+@function color-lower-contrast($color, $amount) {
+    @return darken($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return lighten($color, $amount);
 }

package/lib/mol-plugin-ui/skin/colors/dark.scss

@@ -1,24 +1,24 @@
-$default-background:         #111318;
-$font-color:                 #ccd4e0;
-$hover-font-color:           #51A2FB;
-$entity-current-font-color:  #68BEFD;
-$msp-btn-remove-background:      #DE0A28;
-$msp-btn-remove-hover-font-color:#F2F4F7;
-$msp-btn-commit-on-font-color:   #68BEFD;
-$entity-badge-font-color:    #ccd4e0;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: rgba(0,0,0,0.75);
-
-@function color-lower-contrast($color, $amount) {
-    @return darken($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return lighten($color, $amount);
+$default-background:         #111318;
+$font-color:                 #ccd4e0;
+$hover-font-color:           #51A2FB;
+$entity-current-font-color:  #68BEFD;
+$msp-btn-remove-background:      #DE0A28;
+$msp-btn-remove-hover-font-color:#F2F4F7;
+$msp-btn-commit-on-font-color:   #68BEFD;
+$entity-badge-font-color:    #ccd4e0;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: rgba(0,0,0,0.75);
+
+@function color-lower-contrast($color, $amount) {
+    @return darken($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return lighten($color, $amount);
 }

package/lib/mol-plugin-ui/skin/colors/light.scss

@@ -1,30 +1,30 @@
-// this is complement of the dark theme
-
-@function compl($color) {
-    @return rgb(255 - red($color), 255 - green($color), 255 - blue($color));
-}
-
-$default-background:         compl(#111318);
-$font-color:                 compl(#ccd4e0);
-$hover-font-color:           compl(#51A2FB);
-$entity-current-font-color:  compl(#68BEFD);
-$msp-btn-commit-on-font-color:   compl(#68BEFD);
-$entity-badge-font-color:    lighten(#ccd4e0,10%);
-$msp-btn-remove-background:      #DE0A28;
-$msp-btn-remove-hover-font-color:#F2F4F7;
-
-// used in LOG
-$log-message:          #0CCA5D;
-$log-info:             #5E3673;
-$log-warning:          #FCC937;
-$log-error:            #FD354B;
-
-$logo-background: compl(#111318);
-
-@function color-lower-contrast($color, $amount) {
-    @return lighten($color, $amount);
-}
-
-@function color-increase-contrast($color, $amount) {
-    @return darken($color, $amount);
+// this is complement of the dark theme
+
+@function compl($color) {
+    @return rgb(255 - red($color), 255 - green($color), 255 - blue($color));
+}
+
+$default-background:         compl(#111318);
+$font-color:                 compl(#ccd4e0);
+$hover-font-color:           compl(#51A2FB);
+$entity-current-font-color:  compl(#68BEFD);
+$msp-btn-commit-on-font-color:   compl(#68BEFD);
+$entity-badge-font-color:    lighten(#ccd4e0,10%);
+$msp-btn-remove-background:      #DE0A28;
+$msp-btn-remove-hover-font-color:#F2F4F7;
+
+// used in LOG
+$log-message:          #0CCA5D;
+$log-info:             #5E3673;
+$log-warning:          #FCC937;
+$log-error:            #FD354B;
+
+$logo-background: compl(#111318);
+
+@function color-lower-contrast($color, $amount) {
+    @return lighten($color, $amount);
+}
+
+@function color-increase-contrast($color, $amount) {
+    @return darken($color, $amount);
 }

package/lib/mol-plugin-ui/skin/dark.scss

@@ -1,2 +1,2 @@
-@import 'colors/dark';
+@import 'colors/dark';
 @import 'base/base';

package/lib/mol-plugin-ui/skin/light.scss

@@ -1,2 +1,2 @@
-@import 'colors/light';
+@import 'colors/light';
 @import 'base/base';

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

@@ -13,7 +13,7 @@ var ApplyActionControl = /** @class */ (function (_super) {
     __extends(ApplyActionControl, _super);
     function ApplyActionControl() {
         var _this = _super !== null && _super.apply(this, arguments) || this;
-        _this._getInfo = memoizeLatest(function (t, v) { return StateTransformParameters.infoFromAction(_this.plugin, _this.props.state, _this.props.action, _this.props.nodeRef); });
+        _this._getInfo = memoizeLatest(function (t, v, collapsed) { return 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;
     }
@@ -24,7 +24,7 @@ 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/mol-plugin-ui/structure/quick-styles.js

@@ -76,7 +76,7 @@ var QuickStyles = /** @class */ (function (_super) {
                                 postprocessing: {
                                     outline: {
                                         name: 'on',
-                                        params: { scale: 1, color: Color(0x000000), threshold: 0.25 }
+                                        params: { scale: 1, color: Color(0x000000), threshold: 0.25, includeTransparent: true }
                                     },
                                     occlusion: {
                                         name: 'on',
@@ -104,7 +104,7 @@ var QuickStyles = /** @class */ (function (_super) {
                                 name: 'on',
                                 params: pp.outline.name === 'on'
                                     ? pp.outline.params
-                                    : { scale: 1, color: Color(0x000000), threshold: 0.33 }
+                                    : { scale: 1, color: Color(0x000000), threshold: 0.33, includeTransparent: true }
                             },
                             occlusion: {
                                 name: 'on',

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

@@ -297,10 +297,11 @@ 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/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/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/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/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/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/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/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/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/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/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/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;