molstar 3.26.0 → 3.28.0

package/lib/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/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;

package/lib/mol-repr/structure/visual/bond-inter-unit-cylinder.d.ts

@@ -16,6 +16,7 @@ export declare const InterUnitBondCylinderParams: {
     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;
@@ -34,6 +35,7 @@ export declare const InterUnitBondCylinderParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -67,6 +69,7 @@ export declare function InterUnitBondCylinderVisual(materialId: number, structur
     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;
@@ -85,6 +88,7 @@ export declare function InterUnitBondCylinderVisual(materialId: number, structur
     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/visual/bond-inter-unit-cylinder.js

@@ -186,6 +186,7 @@ export function InterUnitBondCylinderImpostorVisual(materialId) {
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
                 newProps.linkCap !== currentProps.linkCap ||
                 newProps.aromaticScale !== currentProps.aromaticScale ||
                 newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
@@ -224,6 +225,7 @@ export function InterUnitBondCylinderMeshVisual(materialId) {
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
                 newProps.linkCap !== currentProps.linkCap ||
                 newProps.aromaticScale !== currentProps.aromaticScale ||
                 newProps.aromaticSpacing !== currentProps.aromaticSpacing ||

package/lib/mol-repr/structure/visual/bond-inter-unit-line.d.ts

@@ -10,6 +10,7 @@ export declare const InterUnitBondLineParams: {
     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;

package/lib/mol-repr/structure/visual/bond-inter-unit-line.js

@@ -122,6 +122,7 @@ export function InterUnitBondLineVisual(materialId) {
                 newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
                 newProps.dashCount !== currentProps.dashCount ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
                 !arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
                 !arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
                 newProps.multipleBonds !== currentProps.multipleBonds);

package/lib/mol-repr/structure/visual/bond-intra-unit-cylinder.d.ts

@@ -17,6 +17,7 @@ export declare const IntraUnitBondCylinderParams: {
     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;
@@ -35,6 +36,7 @@ export declare const IntraUnitBondCylinderParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -68,6 +70,7 @@ export declare function IntraUnitBondCylinderVisual(materialId: number, structur
     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;
@@ -86,6 +89,7 @@ export declare function IntraUnitBondCylinderVisual(materialId: number, structur
     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/visual/bond-intra-unit-cylinder.js

@@ -207,6 +207,7 @@ export function IntraUnitBondCylinderImpostorVisual(materialId) {
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
                 newProps.linkCap !== currentProps.linkCap ||
                 newProps.aromaticScale !== currentProps.aromaticScale ||
                 newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
@@ -250,6 +251,7 @@ export function IntraUnitBondCylinderMeshVisual(materialId) {
                 newProps.linkScale !== currentProps.linkScale ||
                 newProps.linkSpacing !== currentProps.linkSpacing ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
                 newProps.linkCap !== currentProps.linkCap ||
                 newProps.aromaticScale !== currentProps.aromaticScale ||
                 newProps.aromaticSpacing !== currentProps.aromaticSpacing ||

package/lib/mol-repr/structure/visual/bond-intra-unit-line.d.ts

@@ -10,6 +10,7 @@ export declare const IntraUnitBondLineParams: {
     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;

package/lib/mol-repr/structure/visual/bond-intra-unit-line.js

@@ -144,6 +144,7 @@ export function IntraUnitBondLineVisual(materialId) {
                 newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
                 newProps.dashCount !== currentProps.dashCount ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
                 !arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
                 !arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
                 newProps.aromaticBonds !== currentProps.aromaticBonds ||

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

@@ -12,6 +12,7 @@ import { Lines } from '../../../mol-geo/geometry/lines/lines';
 export declare const ElementCrossParams: {
     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/visual/element-cross.js

@@ -18,7 +18,7 @@ var v3scaleAndAdd = Vec3.scaleAndAdd;
 var v3unitX = Vec3.unitX;
 var v3unitY = Vec3.unitY;
 var v3unitZ = Vec3.unitZ;
-export var ElementCrossParams = __assign(__assign({}, UnitsLinesParams), { lineSizeAttenuation: PD.Boolean(false), ignoreHydrogens: PD.Boolean(false), traceOnly: PD.Boolean(false), crosses: PD.Select('lone', PD.arrayToOptions(['lone', 'all'])), crossSize: PD.Numeric(0.35, { min: 0, max: 2, step: 0.01 }) });
+export var ElementCrossParams = __assign(__assign({}, UnitsLinesParams), { lineSizeAttenuation: PD.Boolean(false), ignoreHydrogens: PD.Boolean(false), ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'])), traceOnly: PD.Boolean(false), crosses: PD.Select('lone', PD.arrayToOptions(['lone', 'all'])), crossSize: PD.Numeric(0.35, { min: 0, max: 2, step: 0.01 }) });
 export function createElementCross(ctx, unit, structure, theme, props, lines) {
     var child = structure.child;
     if (child && !child.unitMap.get(unit.id))
@@ -63,6 +63,7 @@ export function ElementCrossVisual(materialId) {
         eachLocation: eachElement,
         setUpdateState: function (state, newProps, currentProps) {
             state.createGeometry = (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
                 newProps.traceOnly !== currentProps.traceOnly ||
                 newProps.crosses !== currentProps.crosses ||
                 newProps.crossSize !== currentProps.crossSize);

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

@@ -12,6 +12,7 @@ import { Points } from '../../../mol-geo/geometry/points/points';
 export declare const ElementPointParams: {
     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/mol-repr/structure/visual/element-point.js

@@ -13,7 +13,7 @@ import { ElementIterator, getElementLoci, eachElement, makeElementIgnoreTest } f
 import { Sphere3D } from '../../../mol-math/geometry';
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 var v3add = Vec3.add;
-export var ElementPointParams = __assign(__assign({}, UnitsPointsParams), { pointSizeAttenuation: PD.Boolean(false), ignoreHydrogens: PD.Boolean(false), traceOnly: PD.Boolean(false) });
+export var ElementPointParams = __assign(__assign({}, UnitsPointsParams), { pointSizeAttenuation: PD.Boolean(false), ignoreHydrogens: PD.Boolean(false), ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'])), traceOnly: PD.Boolean(false) });
 // TODO size
 export function createElementPoint(ctx, unit, structure, theme, props, points) {
     // TODO sizeFactor
@@ -71,6 +71,7 @@ export function ElementPointVisual(materialId) {
         eachLocation: eachElement,
         setUpdateState: function (state, newProps, currentProps) {
             state.createGeometry = (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
                 newProps.traceOnly !== currentProps.traceOnly);
         }
     }, materialId);

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

@@ -12,6 +12,7 @@ export declare const ElementSphereParams: {
     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">;
@@ -20,6 +21,7 @@ export declare const ElementSphereParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -48,6 +50,7 @@ export declare function ElementSphereVisual(materialId: number, structure: Struc
     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">;
@@ -56,6 +59,7 @@ export declare function ElementSphereVisual(materialId: number, structure: Struc
     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/visual/element-sphere.js

@@ -9,7 +9,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { UnitsMeshParams, UnitsSpheresParams, UnitsSpheresVisual, UnitsMeshVisual } from '../units-visual';
 import { createElementSphereImpostor, ElementIterator, getElementLoci, eachElement, createElementSphereMesh } from './util/element';
 import { BaseGeometry } from '../../../mol-geo/geometry/base';
-export var ElementSphereParams = __assign(__assign(__assign({}, UnitsMeshParams), UnitsSpheresParams), { sizeFactor: PD.Numeric(1, { min: 0, max: 10, step: 0.1 }), detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo), ignoreHydrogens: PD.Boolean(false), traceOnly: PD.Boolean(false), tryUseImpostor: PD.Boolean(true) });
+export var ElementSphereParams = __assign(__assign(__assign({}, UnitsMeshParams), UnitsSpheresParams), { sizeFactor: PD.Numeric(1, { min: 0, max: 10, step: 0.1 }), detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo), ignoreHydrogens: PD.Boolean(false), ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'])), traceOnly: PD.Boolean(false), tryUseImpostor: PD.Boolean(true) });
 export function ElementSphereVisual(materialId, structure, props, webgl) {
     return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
         ? ElementSphereImpostorVisual(materialId)
@@ -24,6 +24,7 @@ export function ElementSphereImpostorVisual(materialId) {
         eachLocation: eachElement,
         setUpdateState: function (state, newProps, currentProps) {
             state.createGeometry = (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
                 newProps.traceOnly !== currentProps.traceOnly);
         },
         mustRecreate: function (structureGroup, props, webgl) {
@@ -42,6 +43,7 @@ export function ElementSphereMeshVisual(materialId) {
             state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
                 newProps.detail !== currentProps.detail ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
                 newProps.traceOnly !== currentProps.traceOnly);
         },
         mustRecreate: function (structureGroup, props, webgl) {

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

@@ -8,6 +8,7 @@ import { ComplexVisual } from '../complex-visual';
 import { UnitsVisual } from '../units-visual';
 export declare const GaussianDensityVolumeParams: {
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     traceOnly: PD.BooleanParam;
     resolution: PD.Numeric;
@@ -42,6 +43,7 @@ export type GaussianDensityVolumeParams = typeof GaussianDensityVolumeParams;
 export declare function GaussianDensityVolumeVisual(materialId: number): ComplexVisual<GaussianDensityVolumeParams>;
 export declare const UnitsGaussianDensityVolumeParams: {
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     includeParent: PD.BooleanParam;
     traceOnly: PD.BooleanParam;
     resolution: PD.Numeric;

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

@@ -39,7 +39,7 @@ function createGaussianDensityVolume(ctx, structure, theme, props, directVolume)
         });
     });
 }
-export var GaussianDensityVolumeParams = __assign(__assign(__assign({}, ComplexDirectVolumeParams), GaussianDensityParams), { ignoreHydrogens: PD.Boolean(false), includeParent: PD.Boolean(false, { isHidden: true }) });
+export var GaussianDensityVolumeParams = __assign(__assign(__assign({}, ComplexDirectVolumeParams), GaussianDensityParams), { ignoreHydrogens: PD.Boolean(false), ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'])), includeParent: PD.Boolean(false, { isHidden: true }) });
 export function GaussianDensityVolumeVisual(materialId) {
     return ComplexDirectVolumeVisual({
         defaultProps: PD.getDefaultValues(GaussianDensityVolumeParams),
@@ -56,6 +56,8 @@ export function GaussianDensityVolumeVisual(materialId) {
                 state.createGeometry = true;
             if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
                 state.createGeometry = true;
+            if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
+                state.createGeometry = true;
             if (newProps.traceOnly !== currentProps.traceOnly)
                 state.createGeometry = true;
             if (newProps.includeParent !== currentProps.includeParent)
@@ -97,7 +99,7 @@ function createUnitsGaussianDensityVolume(ctx, unit, structure, theme, props, di
         });
     });
 }
-export var UnitsGaussianDensityVolumeParams = __assign(__assign(__assign({}, UnitsDirectVolumeParams), GaussianDensityParams), { ignoreHydrogens: PD.Boolean(false), includeParent: PD.Boolean(false, { isHidden: true }) });
+export var UnitsGaussianDensityVolumeParams = __assign(__assign(__assign({}, UnitsDirectVolumeParams), GaussianDensityParams), { ignoreHydrogens: PD.Boolean(false), ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'])), includeParent: PD.Boolean(false, { isHidden: true }) });
 export function UnitsGaussianDensityVolumeVisual(materialId) {
     return UnitsDirectVolumeVisual({
         defaultProps: PD.getDefaultValues(UnitsGaussianDensityVolumeParams),
@@ -114,6 +116,8 @@ export function UnitsGaussianDensityVolumeVisual(materialId) {
                 state.createGeometry = true;
             if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
                 state.createGeometry = true;
+            if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
+                state.createGeometry = true;
             if (newProps.traceOnly !== currentProps.traceOnly)
                 state.createGeometry = true;
             if (newProps.includeParent !== currentProps.includeParent)

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

@@ -10,6 +10,7 @@ import { ComplexVisual } from '../complex-visual';
 import { WebGLContext } from '../../../mol-gl/webgl/context';
 export declare const GaussianSurfaceMeshParams: {
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     tryUseGpu: PD.BooleanParam;
     includeParent: PD.BooleanParam;
     smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
@@ -51,6 +52,7 @@ export declare const GaussianSurfaceMeshParams: {
 export type GaussianSurfaceMeshParams = typeof GaussianSurfaceMeshParams;
 export declare const StructureGaussianSurfaceMeshParams: {
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     tryUseGpu: PD.BooleanParam;
     includeParent: PD.BooleanParam;
     smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
@@ -92,6 +94,7 @@ export declare const StructureGaussianSurfaceMeshParams: {
 export type StructureGaussianSurfaceMeshParams = typeof StructureGaussianSurfaceMeshParams;
 export declare function GaussianSurfaceVisual(materialId: number, structure: Structure, props: PD.Values<GaussianSurfaceMeshParams>, webgl?: WebGLContext): UnitsVisual<{
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     tryUseGpu: PD.BooleanParam;
     includeParent: PD.BooleanParam;
     smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
@@ -132,6 +135,7 @@ export declare function GaussianSurfaceVisual(materialId: number, structure: Str
 }>;
 export declare function StructureGaussianSurfaceVisual(materialId: number, structure: Structure, props: PD.Values<StructureGaussianSurfaceMeshParams>, webgl?: WebGLContext): ComplexVisual<{
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     tryUseGpu: PD.BooleanParam;
     includeParent: PD.BooleanParam;
     smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{

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

@@ -21,7 +21,7 @@ import { ColorSmoothingParams, getColorSmoothingProps } from '../../../mol-geo/g
 import { Vec3 } from '../../../mol-math/linear-algebra';
 import { isTimingMode } from '../../../mol-util/debug';
 import { ValueCell } from '../../../mol-util/value-cell';
-var SharedParams = __assign(__assign(__assign({}, GaussianDensityParams), ColorSmoothingParams), { ignoreHydrogens: PD.Boolean(false), tryUseGpu: PD.Boolean(true), includeParent: PD.Boolean(false, { isHidden: true }) });
+var SharedParams = __assign(__assign(__assign({}, GaussianDensityParams), ColorSmoothingParams), { ignoreHydrogens: PD.Boolean(false), ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'])), tryUseGpu: PD.Boolean(true), includeParent: PD.Boolean(false, { isHidden: true }) });
 export var GaussianSurfaceMeshParams = __assign(__assign(__assign({}, UnitsMeshParams), UnitsTextureMeshParams), SharedParams);
 export var StructureGaussianSurfaceMeshParams = __assign(__assign(__assign({}, ComplexMeshParams), ComplexTextureMeshParams), SharedParams);
 function gpuSupport(webgl) {
@@ -101,6 +101,8 @@ export function GaussianSurfaceMeshVisual(materialId) {
                 state.createGeometry = true;
             if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
                 state.createGeometry = true;
+            if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
+                state.createGeometry = true;
             if (newProps.traceOnly !== currentProps.traceOnly)
                 state.createGeometry = true;
             if (newProps.includeParent !== currentProps.includeParent)
@@ -183,6 +185,8 @@ export function StructureGaussianSurfaceMeshVisual(materialId) {
                 state.createGeometry = true;
             if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
                 state.createGeometry = true;
+            if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
+                state.createGeometry = true;
             if (newProps.traceOnly !== currentProps.traceOnly)
                 state.createGeometry = true;
             if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
@@ -267,6 +271,8 @@ export function GaussianSurfaceTextureMeshVisual(materialId) {
                 state.createGeometry = true;
             if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
                 state.createGeometry = true;
+            if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
+                state.createGeometry = true;
             if (newProps.traceOnly !== currentProps.traceOnly)
                 state.createGeometry = true;
             if (newProps.includeParent !== currentProps.includeParent)
@@ -356,6 +362,8 @@ export function StructureGaussianSurfaceTextureMeshVisual(materialId) {
                 state.createGeometry = true;
             if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
                 state.createGeometry = true;
+            if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
+                state.createGeometry = true;
             if (newProps.traceOnly !== currentProps.traceOnly)
                 state.createGeometry = true;
             if (newProps.includeParent !== currentProps.includeParent)

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

@@ -9,6 +9,7 @@ export declare const GaussianWireframeParams: {
     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/visual/gaussian-surface-wireframe.js

@@ -37,7 +37,7 @@ function createGaussianWireframe(ctx, unit, structure, theme, props, lines) {
         });
     });
 }
-export var GaussianWireframeParams = __assign(__assign(__assign({}, UnitsLinesParams), GaussianDensityParams), { sizeFactor: PD.Numeric(3, { min: 0, max: 10, step: 0.1 }), lineSizeAttenuation: PD.Boolean(false), ignoreHydrogens: PD.Boolean(false), includeParent: PD.Boolean(false, { isHidden: true }) });
+export var GaussianWireframeParams = __assign(__assign(__assign({}, UnitsLinesParams), GaussianDensityParams), { sizeFactor: PD.Numeric(3, { min: 0, max: 10, step: 0.1 }), lineSizeAttenuation: PD.Boolean(false), ignoreHydrogens: PD.Boolean(false), ignoreHydrogensVariant: PD.Select('all', PD.arrayToOptions(['all', 'non-polar'])), includeParent: PD.Boolean(false, { isHidden: true }) });
 export function GaussianWireframeVisual(materialId) {
     return UnitsLinesVisual({
         defaultProps: PD.getDefaultValues(GaussianWireframeParams),
@@ -54,6 +54,8 @@ export function GaussianWireframeVisual(materialId) {
                 state.createGeometry = true;
             if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
                 state.createGeometry = true;
+            if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
+                state.createGeometry = true;
             if (newProps.traceOnly !== currentProps.traceOnly)
                 state.createGeometry = true;
             if (newProps.includeParent !== currentProps.includeParent)

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

@@ -12,6 +12,7 @@ export declare const MolecularSurfaceMeshParams: {
         sampleStride: number;
     }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
     ignoreHydrogens: PD.BooleanParam;
+    ignoreHydrogensVariant: PD.Select<"all" | "non-polar">;
     traceOnly: PD.BooleanParam;
     includeParent: PD.BooleanParam;
     probeRadius: PD.Numeric;

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

@@ -71,6 +71,8 @@ export function MolecularSurfaceMeshVisual(materialId) {
                 state.createGeometry = true;
             if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
                 state.createGeometry = true;
+            if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
+                state.createGeometry = true;
             if (newProps.traceOnly !== currentProps.traceOnly)
                 state.createGeometry = true;
             if (newProps.includeParent !== currentProps.includeParent)
@@ -152,6 +154,8 @@ export function StructureMolecularSurfaceMeshVisual(materialId) {
                 state.createGeometry = true;
             if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
                 state.createGeometry = true;
+            if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
+                state.createGeometry = true;
             if (newProps.traceOnly !== currentProps.traceOnly)
                 state.createGeometry = true;
             if (newProps.includeParent !== currentProps.includeParent)

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

@@ -8,6 +8,7 @@ import { UnitsVisual } from '../units-visual';
 export declare const MolecularSurfaceWireframeParams: {
     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/visual/molecular-surface-wireframe.js

@@ -55,6 +55,8 @@ export function MolecularSurfaceWireframeVisual(materialId) {
                 state.createGeometry = true;
             if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens)
                 state.createGeometry = true;
+            if (newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant)
+                state.createGeometry = true;
             if (newProps.includeParent !== currentProps.includeParent)
                 state.createGeometry = true;
         }

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

@@ -18,6 +18,7 @@ export declare const PolymerBackboneCylinderParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -53,6 +54,7 @@ export declare function PolymerBackboneCylinderVisual(materialId: number, struct
     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/visual/polymer-backbone-sphere.d.ts

@@ -17,6 +17,7 @@ export declare const PolymerBackboneSphereParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     transparentBackfaces: PD.Select<string>;
+    solidInterior: PD.BooleanParam;
     bumpFrequency: PD.Numeric;
     bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
@@ -51,6 +52,7 @@ export declare function PolymerBackboneSphereVisual(materialId: number, structur
     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/visual/util/bond.d.ts

@@ -2,6 +2,7 @@
  * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { BondType } from '../../../../mol-model/structure/model/types';
 import { Unit, Structure, Bond } from '../../../../mol-model/structure';
@@ -15,6 +16,7 @@ export declare const BondParams: {
     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">;
 };
@@ -22,6 +24,7 @@ export declare const DefaultBondProps: PD.Values<{
     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">;
 }>;
@@ -31,6 +34,7 @@ export declare const BondCylinderParams: {
     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;
@@ -50,6 +54,7 @@ export declare const DefaultBondCylinderProps: PD.Values<{
     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;
@@ -69,6 +74,7 @@ export declare const BondLineParams: {
     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;
@@ -80,6 +86,7 @@ export declare const DefaultBondLineProps: PD.Values<{
     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;