molstar 3.26.0 → 3.28.0

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

@@ -190,6 +190,7 @@ 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 ||
@@ -229,6 +230,7 @@ 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/commonjs/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/commonjs/mol-repr/structure/visual/bond-inter-unit-line.js

@@ -125,6 +125,7 @@ function InterUnitBondLineVisual(materialId) {
                 newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
                 newProps.dashCount !== currentProps.dashCount ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
                 !(0, mol_util_1.arrayEqual)(newProps.includeTypes, currentProps.includeTypes) ||
                 !(0, mol_util_1.arrayEqual)(newProps.excludeTypes, currentProps.excludeTypes) ||
                 newProps.multipleBonds !== currentProps.multipleBonds);

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

@@ -211,6 +211,7 @@ 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 ||
@@ -255,6 +256,7 @@ 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/commonjs/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/commonjs/mol-repr/structure/visual/bond-intra-unit-line.js

@@ -147,6 +147,7 @@ function IntraUnitBondLineVisual(materialId) {
                 newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
                 newProps.dashCount !== currentProps.dashCount ||
                 newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
                 !(0, mol_util_1.arrayEqual)(newProps.includeTypes, currentProps.includeTypes) ||
                 !(0, mol_util_1.arrayEqual)(newProps.excludeTypes, currentProps.excludeTypes) ||
                 newProps.aromaticBonds !== currentProps.aromaticBonds ||

package/lib/commonjs/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/commonjs/mol-repr/structure/visual/element-cross.js

@@ -21,7 +21,7 @@ var v3scaleAndAdd = linear_algebra_1.Vec3.scaleAndAdd;
 var v3unitX = linear_algebra_1.Vec3.unitX;
 var v3unitY = linear_algebra_1.Vec3.unitY;
 var v3unitZ = linear_algebra_1.Vec3.unitZ;
-exports.ElementCrossParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsLinesParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), traceOnly: param_definition_1.ParamDefinition.Boolean(false), crosses: param_definition_1.ParamDefinition.Select('lone', param_definition_1.ParamDefinition.arrayToOptions(['lone', 'all'])), crossSize: param_definition_1.ParamDefinition.Numeric(0.35, { min: 0, max: 2, step: 0.01 }) });
+exports.ElementCrossParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsLinesParams), { lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogensVariant: param_definition_1.ParamDefinition.Select('all', param_definition_1.ParamDefinition.arrayToOptions(['all', 'non-polar'])), traceOnly: param_definition_1.ParamDefinition.Boolean(false), crosses: param_definition_1.ParamDefinition.Select('lone', param_definition_1.ParamDefinition.arrayToOptions(['lone', 'all'])), crossSize: param_definition_1.ParamDefinition.Numeric(0.35, { min: 0, max: 2, step: 0.01 }) });
 function createElementCross(ctx, unit, structure, theme, props, lines) {
     var child = structure.child;
     if (child && !child.unitMap.get(unit.id))
@@ -67,6 +67,7 @@ function ElementCrossVisual(materialId) {
         eachLocation: element_1.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/commonjs/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/commonjs/mol-repr/structure/visual/element-point.js

@@ -16,7 +16,7 @@ var element_1 = require("./util/element");
 var geometry_1 = require("../../../mol-math/geometry");
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 var v3add = linear_algebra_1.Vec3.add;
-exports.ElementPointParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsPointsParams), { pointSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), traceOnly: param_definition_1.ParamDefinition.Boolean(false) });
+exports.ElementPointParams = tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsPointsParams), { pointSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogensVariant: param_definition_1.ParamDefinition.Select('all', param_definition_1.ParamDefinition.arrayToOptions(['all', 'non-polar'])), traceOnly: param_definition_1.ParamDefinition.Boolean(false) });
 // TODO size
 function createElementPoint(ctx, unit, structure, theme, props, points) {
     // TODO sizeFactor
@@ -75,6 +75,7 @@ function ElementPointVisual(materialId) {
         eachLocation: element_1.eachElement,
         setUpdateState: function (state, newProps, currentProps) {
             state.createGeometry = (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
+                newProps.ignoreHydrogensVariant !== currentProps.ignoreHydrogensVariant ||
                 newProps.traceOnly !== currentProps.traceOnly);
         }
     }, materialId);

package/lib/commonjs/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/commonjs/mol-repr/structure/visual/element-sphere.js

@@ -12,7 +12,7 @@ var param_definition_1 = require("../../../mol-util/param-definition");
 var units_visual_1 = require("../units-visual");
 var element_1 = require("./util/element");
 var base_1 = require("../../../mol-geo/geometry/base");
-exports.ElementSphereParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsSpheresParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), traceOnly: param_definition_1.ParamDefinition.Boolean(false), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true) });
+exports.ElementSphereParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsSpheresParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogensVariant: param_definition_1.ParamDefinition.Select('all', param_definition_1.ParamDefinition.arrayToOptions(['all', 'non-polar'])), traceOnly: param_definition_1.ParamDefinition.Boolean(false), tryUseImpostor: param_definition_1.ParamDefinition.Boolean(true) });
 function ElementSphereVisual(materialId, structure, props, webgl) {
     return props.tryUseImpostor && webgl && webgl.extensions.fragDepth
         ? ElementSphereImpostorVisual(materialId)
@@ -28,6 +28,7 @@ function ElementSphereImpostorVisual(materialId) {
         eachLocation: element_1.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) {
@@ -47,6 +48,7 @@ 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/commonjs/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/commonjs/mol-repr/structure/visual/gaussian-density-volume.js

@@ -42,7 +42,7 @@ function createGaussianDensityVolume(ctx, structure, theme, props, directVolume)
         });
     });
 }
-exports.GaussianDensityVolumeParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexDirectVolumeParams), gaussian_1.GaussianDensityParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
+exports.GaussianDensityVolumeParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexDirectVolumeParams), gaussian_1.GaussianDensityParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogensVariant: param_definition_1.ParamDefinition.Select('all', param_definition_1.ParamDefinition.arrayToOptions(['all', 'non-polar'])), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
 function GaussianDensityVolumeVisual(materialId) {
     return (0, complex_visual_1.ComplexDirectVolumeVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.GaussianDensityVolumeParams),
@@ -59,6 +59,8 @@ 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)
@@ -101,7 +103,7 @@ function createUnitsGaussianDensityVolume(ctx, unit, structure, theme, props, di
         });
     });
 }
-exports.UnitsGaussianDensityVolumeParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsDirectVolumeParams), gaussian_1.GaussianDensityParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
+exports.UnitsGaussianDensityVolumeParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsDirectVolumeParams), gaussian_1.GaussianDensityParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogensVariant: param_definition_1.ParamDefinition.Select('all', param_definition_1.ParamDefinition.arrayToOptions(['all', 'non-polar'])), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
 function UnitsGaussianDensityVolumeVisual(materialId) {
     return (0, units_visual_1.UnitsDirectVolumeVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.UnitsGaussianDensityVolumeParams),
@@ -118,6 +120,8 @@ 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/commonjs/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/commonjs/mol-repr/structure/visual/gaussian-surface-mesh.js

@@ -24,7 +24,7 @@ var base_1 = require("../../../mol-geo/geometry/base");
 var linear_algebra_1 = require("../../../mol-math/linear-algebra");
 var debug_1 = require("../../../mol-util/debug");
 var value_cell_1 = require("../../../mol-util/value-cell");
-var SharedParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, gaussian_1.GaussianDensityParams), base_1.ColorSmoothingParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), tryUseGpu: param_definition_1.ParamDefinition.Boolean(true), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
+var SharedParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, gaussian_1.GaussianDensityParams), base_1.ColorSmoothingParams), { ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogensVariant: param_definition_1.ParamDefinition.Select('all', param_definition_1.ParamDefinition.arrayToOptions(['all', 'non-polar'])), tryUseGpu: param_definition_1.ParamDefinition.Boolean(true), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
 exports.GaussianSurfaceMeshParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsMeshParams), units_visual_1.UnitsTextureMeshParams), SharedParams);
 exports.StructureGaussianSurfaceMeshParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, complex_visual_1.ComplexMeshParams), complex_visual_1.ComplexTextureMeshParams), SharedParams);
 function gpuSupport(webgl) {
@@ -106,6 +106,8 @@ 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)
@@ -189,6 +191,8 @@ 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) {
@@ -274,6 +278,8 @@ 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)
@@ -364,6 +370,8 @@ 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/commonjs/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/commonjs/mol-repr/structure/visual/gaussian-surface-wireframe.js

@@ -40,7 +40,7 @@ function createGaussianWireframe(ctx, unit, structure, theme, props, lines) {
         });
     });
 }
-exports.GaussianWireframeParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsLinesParams), gaussian_1.GaussianDensityParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(3, { min: 0, max: 10, step: 0.1 }), lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
+exports.GaussianWireframeParams = tslib_1.__assign(tslib_1.__assign(tslib_1.__assign({}, units_visual_1.UnitsLinesParams), gaussian_1.GaussianDensityParams), { sizeFactor: param_definition_1.ParamDefinition.Numeric(3, { min: 0, max: 10, step: 0.1 }), lineSizeAttenuation: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false), ignoreHydrogensVariant: param_definition_1.ParamDefinition.Select('all', param_definition_1.ParamDefinition.arrayToOptions(['all', 'non-polar'])), includeParent: param_definition_1.ParamDefinition.Boolean(false, { isHidden: true }) });
 function GaussianWireframeVisual(materialId) {
     return (0, units_visual_1.UnitsLinesVisual)({
         defaultProps: param_definition_1.ParamDefinition.getDefaultValues(exports.GaussianWireframeParams),
@@ -57,6 +57,8 @@ 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/commonjs/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/commonjs/mol-repr/structure/visual/molecular-surface-mesh.js

@@ -74,6 +74,8 @@ 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)
@@ -156,6 +158,8 @@ 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/commonjs/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/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.js

@@ -58,6 +58,8 @@ 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/commonjs/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/commonjs/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/commonjs/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;

package/lib/commonjs/mol-repr/structure/visual/util/bond.js

@@ -3,6 +3,7 @@
  * 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>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.eachInterBond = exports.getInterBondLoci = exports.eachIntraBond = exports.getIntraBondLoci = exports.BondIterator = exports.makeInterBondIgnoreTest = exports.makeIntraBondIgnoreTest = exports.ignoreBondType = exports.DefaultBondLineProps = exports.BondLineParams = exports.DefaultBondCylinderProps = exports.BondCylinderParams = exports.DefaultBondProps = exports.BondParams = void 0;
@@ -20,6 +21,7 @@ exports.BondParams = {
     includeTypes: param_definition_1.ParamDefinition.MultiSelect((0, type_helpers_1.ObjectKeys)(types_1.BondType.Names), param_definition_1.ParamDefinition.objectToOptions(types_1.BondType.Names)),
     excludeTypes: param_definition_1.ParamDefinition.MultiSelect([], param_definition_1.ParamDefinition.objectToOptions(types_1.BondType.Names)),
     ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false),
+    ignoreHydrogensVariant: param_definition_1.ParamDefinition.Select('all', param_definition_1.ParamDefinition.arrayToOptions(['all', 'non-polar'])),
     aromaticBonds: param_definition_1.ParamDefinition.Boolean(true, { description: 'Display aromatic bonds with dashes' }),
     multipleBonds: param_definition_1.ParamDefinition.Select('symmetric', param_definition_1.ParamDefinition.arrayToOptions(['off', 'symmetric', 'offset'])),
 };
@@ -34,11 +36,10 @@ function ignoreBondType(include, exclude, f) {
 exports.ignoreBondType = ignoreBondType;
 function makeIntraBondIgnoreTest(structure, unit, props) {
     var elements = unit.elements;
-    var atomicNumber = unit.model.atomicHierarchy.derived.atom.atomicNumber;
     var bonds = unit.bonds;
     var a = bonds.a, b = bonds.b, edgeProps = bonds.edgeProps;
     var _flags = edgeProps.flags;
-    var ignoreHydrogens = props.ignoreHydrogens, includeTypes = props.includeTypes, excludeTypes = props.excludeTypes;
+    var ignoreHydrogens = props.ignoreHydrogens, ignoreHydrogensVariant = props.ignoreHydrogensVariant, includeTypes = props.includeTypes, excludeTypes = props.excludeTypes;
     var include = types_1.BondType.fromNames(includeTypes);
     var exclude = types_1.BondType.fromNames(excludeTypes);
     var allBondTypes = types_1.BondType.isAll(include) && 0 /* BondType.Flag.None */ === exclude;
@@ -49,16 +50,26 @@ function makeIntraBondIgnoreTest(structure, unit, props) {
     if (allBondTypes && !ignoreHydrogens && !child)
         return;
     return function (edgeIndex) {
-        return ((!!childUnit && !int_1.SortedArray.has(childUnit.elements, elements[a[edgeIndex]])) ||
-            (ignoreHydrogens && ((0, common_1.isH)(atomicNumber, elements[a[edgeIndex]]) || (0, common_1.isH)(atomicNumber, elements[b[edgeIndex]]))) ||
-            (!allBondTypes && ignoreBondType(include, exclude, _flags[edgeIndex])));
+        var aI = a[edgeIndex];
+        var bI = b[edgeIndex];
+        if ((!!childUnit && !int_1.SortedArray.has(childUnit.elements, elements[aI]))) {
+            return true;
+        }
+        if (!allBondTypes && ignoreBondType(include, exclude, _flags[edgeIndex])) {
+            return true;
+        }
+        if (!ignoreHydrogens)
+            return false;
+        if ((0, common_1.isHydrogen)(structure, unit, elements[aI], ignoreHydrogensVariant) || (0, common_1.isHydrogen)(structure, unit, elements[bI], ignoreHydrogensVariant))
+            return true;
+        return false;
     };
 }
 exports.makeIntraBondIgnoreTest = makeIntraBondIgnoreTest;
 function makeInterBondIgnoreTest(structure, props) {
     var bonds = structure.interUnitBonds;
     var edges = bonds.edges;
-    var ignoreHydrogens = props.ignoreHydrogens, includeTypes = props.includeTypes, excludeTypes = props.excludeTypes;
+    var ignoreHydrogens = props.ignoreHydrogens, ignoreHydrogensVariant = props.ignoreHydrogensVariant, includeTypes = props.includeTypes, excludeTypes = props.excludeTypes;
     var include = types_1.BondType.fromNames(includeTypes);
     var exclude = types_1.BondType.fromNames(excludeTypes);
     var allBondTypes = types_1.BondType.isAll(include) && 0 /* BondType.Flag.None */ === exclude;
@@ -80,7 +91,7 @@ function makeInterBondIgnoreTest(structure, props) {
             var b = edges[edgeIndex];
             var uA = structure.unitMap.get(b.unitA);
             var uB = structure.unitMap.get(b.unitB);
-            if ((0, common_1.isHydrogen)(uA, uA.elements[b.indexA]) || (0, common_1.isHydrogen)(uB, uB.elements[b.indexB]))
+            if ((0, common_1.isHydrogen)(structure, uA, uA.elements[b.indexA], ignoreHydrogensVariant) || (0, common_1.isHydrogen)(structure, uB, uB.elements[b.indexB], ignoreHydrogensVariant))
                 return true;
         }
         if (!allBondTypes) {