molstar 2.3.9 → 3.0.0-dev.10

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

@@ -44,76 +44,157 @@ interface UnitsVisualGeometryBuilder<P extends StructureParams, G extends Geomet
 }
 export declare function UnitsVisual<G extends Geometry, P extends StructureParams & Geometry.Params<G>>(builder: UnitsVisualGeometryBuilder<P, G>, materialId: number): UnitsVisual<P>;
 export declare const UnitsMeshParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsMeshParams = typeof UnitsMeshParams;
 export interface UnitsMeshVisualBuilder<P extends UnitsMeshParams> extends UnitsVisualBuilder<P, Mesh> {
 }
 export declare function UnitsMeshVisual<P extends UnitsMeshParams>(builder: UnitsMeshVisualBuilder<P>, materialId: number): UnitsVisual<P>;
 export declare const UnitsSpheresParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsSpheresParams = typeof UnitsSpheresParams;
 export interface UnitsSpheresVisualBuilder<P extends UnitsSpheresParams> extends UnitsVisualBuilder<P, Spheres> {
 }
 export declare function UnitsSpheresVisual<P extends UnitsSpheresParams>(builder: UnitsSpheresVisualBuilder<P>, materialId: number): UnitsVisual<P>;
 export declare const UnitsCylindersParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     sizeAspectRatio: PD.Numeric;
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsCylindersParams = typeof UnitsCylindersParams;
 export interface UnitsCylindersVisualBuilder<P extends UnitsCylindersParams> extends UnitsVisualBuilder<P, Cylinders> {
 }
 export declare function UnitsCylindersVisual<P extends UnitsCylindersParams>(builder: UnitsCylindersVisualBuilder<P>, materialId: number): UnitsVisual<P>;
 export declare const UnitsPointsParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     pointSizeAttenuation: PD.BooleanParam;
-    pointStyle: PD.Select<"square" | "circle" | "fuzzy">;
+    pointStyle: PD.Select<"circle" | "square" | "fuzzy">;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsPointsParams = typeof UnitsPointsParams;
 export interface UnitsPointVisualBuilder<P extends UnitsPointsParams> extends UnitsVisualBuilder<P, Points> {
 }
 export declare function UnitsPointsVisual<P extends UnitsPointsParams>(builder: UnitsPointVisualBuilder<P>, materialId: number): UnitsVisual<P>;
 export declare const UnitsLinesParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     lineSizeAttenuation: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsLinesParams = typeof UnitsLinesParams;
 export interface UnitsLinesVisualBuilder<P extends UnitsLinesParams> extends UnitsVisualBuilder<P, Lines> {
 }
 export declare function UnitsLinesVisual<P extends UnitsLinesParams>(builder: UnitsLinesVisualBuilder<P>, materialId: number): UnitsVisual<P>;
 export declare const UnitsTextParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     borderWidth: PD.Numeric;
@@ -128,62 +209,91 @@ export declare const UnitsTextParams: {
     tether: PD.BooleanParam;
     tetherLength: PD.Numeric;
     tetherBaseWidth: PD.Numeric;
-    attachment: PD.Select<"middle-center" | "bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-right" | "top-left" | "top-center" | "top-right">;
+    attachment: PD.Select<"bottom-left" | "bottom-center" | "bottom-right" | "middle-left" | "middle-center" | "middle-right" | "top-left" | "top-center" | "top-right">;
     fontFamily: PD.Select<import("../../mol-geo/geometry/text/font-atlas").FontFamily>;
     fontQuality: PD.Select<number>;
     fontStyle: PD.Select<import("../../mol-geo/geometry/text/font-atlas").FontStyle>;
     fontVariant: PD.Select<import("../../mol-geo/geometry/text/font-atlas").FontVariant>;
     fontWeight: PD.Select<import("../../mol-geo/geometry/text/font-atlas").FontWeight>;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsTextParams = typeof UnitsTextParams;
 export interface UnitsTextVisualBuilder<P extends UnitsTextParams> extends UnitsVisualBuilder<P, Text> {
 }
 export declare function UnitsTextVisual<P extends UnitsTextParams>(builder: UnitsTextVisualBuilder<P>, materialId: number): UnitsVisual<P>;
 export declare const UnitsDirectVolumeParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
-    doubleSided: PD.BooleanParam;
-    flipSided: PD.BooleanParam;
-    flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
-    renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
-        controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
-        list: {
-            kind: "interpolate" | "set";
-            colors: import("../../mol-util/color/color").ColorListEntry[];
-        };
-    }>, "volume"> | PD.NamedParams<PD.Normalize<{
-        isoValue: Readonly<{
-            kind: "absolute";
-            absoluteValue: number;
-        }> | Readonly<{
-            kind: "relative";
-            relativeValue: number;
-        }>;
-        singleLayer: boolean;
-    }>, "isosurface">>;
+    controlPoints: PD.LineGraph;
     stepsPerCell: PD.Numeric;
     jumpLength: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsDirectVolumeParams = typeof UnitsDirectVolumeParams;
 export interface UnitsDirectVolumeVisualBuilder<P extends UnitsDirectVolumeParams> extends UnitsVisualBuilder<P, DirectVolume> {
 }
 export declare function UnitsDirectVolumeVisual<P extends UnitsDirectVolumeParams>(builder: UnitsDirectVolumeVisualBuilder<P>, materialId: number): UnitsVisual<P>;
 export declare const UnitsTextureMeshParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type UnitsTextureMeshParams = typeof UnitsTextureMeshParams;
 export interface UnitsTextureMeshVisualBuilder<P extends UnitsTextureMeshParams> extends UnitsVisualBuilder<P, TextureMesh> {

package/lib/commonjs/mol-repr/structure/units-visual.js

@@ -53,6 +53,7 @@ function UnitsVisual(builder, materialId) {
     var currentTheme;
     var currentStructureGroup;
     var geometry;
+    var geometryVersion = -1;
     var locationIt;
     var positionIt;
     function prepareUpdate(theme, props, structureGroup) {
@@ -184,8 +185,10 @@ function UnitsVisual(builder, materialId) {
         currentProps = newProps;
         currentTheme = newTheme;
         currentStructureGroup = newStructureGroup;
-        if (newGeometry)
+        if (newGeometry) {
             geometry = newGeometry;
+            geometryVersion += 1;
+        }
     }
     function _createGeometry(ctx, unit, structure, theme, props, geometry) {
         return (0, common_1.includesUnitKind)(props.unitKinds, unit)
@@ -219,6 +222,7 @@ function UnitsVisual(builder, materialId) {
     return {
         get groupCount() { return locationIt ? locationIt.count : 0; },
         get renderObject() { return locationIt && locationIt.count ? renderObject : undefined; },
+        get geometryVersion() { return geometryVersion; },
         createOrUpdate: function (ctx, theme, props, structureGroup) {
             prepareUpdate(theme, props, structureGroup || currentStructureGroup);
             if (updateState.createGeometry) {
@@ -269,11 +273,17 @@ function UnitsVisual(builder, materialId) {
         setTransform: function (matrix, instanceMatrices) {
             visual_1.Visual.setTransform(renderObject, matrix, instanceMatrices);
         },
-        setOverpaint: function (overpaint) {
-            visual_1.Visual.setOverpaint(renderObject, overpaint, lociApply, true);
+        setOverpaint: function (overpaint, webgl) {
+            var smoothing = { geometry: geometry, props: currentProps, webgl: webgl };
+            visual_1.Visual.setOverpaint(renderObject, overpaint, lociApply, true, smoothing);
+        },
+        setTransparency: function (transparency, webgl) {
+            var smoothing = { geometry: geometry, props: currentProps, webgl: webgl };
+            visual_1.Visual.setTransparency(renderObject, transparency, lociApply, true, smoothing);
         },
-        setTransparency: function (transparency) {
-            visual_1.Visual.setTransparency(renderObject, transparency, lociApply, true);
+        setSubstance: function (substance, webgl) {
+            var smoothing = { geometry: geometry, props: currentProps, webgl: webgl };
+            visual_1.Visual.setSubstance(renderObject, substance, lociApply, true, smoothing);
         },
         setClipping: function (clipping) {
             visual_1.Visual.setClipping(renderObject, clipping, lociApply, true);

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

@@ -17,7 +17,7 @@ export declare const InterUnitBondCylinderParams: {
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
-    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
+    multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
@@ -29,12 +29,29 @@ export declare const InterUnitBondCylinderParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 };
@@ -49,7 +66,7 @@ export declare function InterUnitBondCylinderVisual(materialId: number, structur
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
-    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
+    multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
@@ -61,12 +78,29 @@ export declare function InterUnitBondCylinderVisual(materialId: number, structur
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 }>;

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

@@ -11,16 +11,31 @@ export declare const InterUnitBondLineParams: {
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
-    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
+    multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     sizeFactor: PD.Numeric;
     lineSizeAttenuation: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type InterUnitBondLineParams = typeof InterUnitBondLineParams;
 export declare function InterUnitBondLineVisual(materialId: number): ComplexVisual<InterUnitBondLineParams>;

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

@@ -18,7 +18,7 @@ export declare const IntraUnitBondCylinderParams: {
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
-    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
+    multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
@@ -30,12 +30,29 @@ export declare const IntraUnitBondCylinderParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 };
@@ -50,7 +67,7 @@ export declare function IntraUnitBondCylinderVisual(materialId: number, structur
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
-    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
+    multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
@@ -62,12 +79,29 @@ export declare function IntraUnitBondCylinderVisual(materialId: number, structur
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 }>;

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

@@ -74,13 +74,13 @@ function getIntraUnitBondCylinderBuilderProps(unit, structure, theme, props) {
                 _a = [bI, aI], aI = _a[0], bI = _a[1];
             if (offset[aI + 1] - offset[aI] === 1)
                 _b = [bI, aI], aI = _b[0], bI = _b[1];
-            var aR = elementRingIndices.get(aI);
+            var aR = elementAromaticRingIndices.get(aI) || elementRingIndices.get(aI);
             var maxSize = 0;
             for (var i = offset[aI], il = offset[aI + 1]; i < il; ++i) {
                 var _bI = b[i];
                 if (_bI !== bI && _bI !== aI) {
                     if (aR) {
-                        var _bR = elementRingIndices.get(_bI);
+                        var _bR = elementAromaticRingIndices.get(_bI) || elementRingIndices.get(_bI);
                         if (!_bR)
                             continue;
                         var size = (0, array_1.arrayIntersectionSize)(aR, _bR);

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

@@ -11,16 +11,31 @@ export declare const IntraUnitBondLineParams: {
     excludeTypes: PD.MultiSelect<"covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic" | "computed">;
     ignoreHydrogens: PD.BooleanParam;
     aromaticBonds: PD.BooleanParam;
-    multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
+    multipleBonds: PD.Select<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     sizeFactor: PD.Numeric;
     lineSizeAttenuation: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type IntraUnitBondLineParams = typeof IntraUnitBondLineParams;
 export declare function IntraUnitBondLineVisual(materialId: number): UnitsVisual<IntraUnitBondLineParams>;

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

@@ -53,13 +53,13 @@ function createIntraUnitBondLines(ctx, unit, structure, theme, props, lines) {
                 _a = [bI, aI], aI = _a[0], bI = _a[1];
             if (offset[aI + 1] - offset[aI] === 1)
                 _b = [bI, aI], aI = _b[0], bI = _b[1];
-            var aR = elementRingIndices.get(aI);
+            var aR = elementAromaticRingIndices.get(aI) || elementRingIndices.get(aI);
             var maxSize = 0;
             for (var i = offset[aI], il = offset[aI + 1]; i < il; ++i) {
                 var _bI = b[i];
                 if (_bI !== bI && _bI !== aI) {
                     if (aR) {
-                        var _bR = elementRingIndices.get(_bI);
+                        var _bR = elementAromaticRingIndices.get(_bI) || elementRingIndices.get(_bI);
                         if (!_bR)
                             continue;
                         var size = (0, array_1.arrayIntersectionSize)(aR, _bR);

package/lib/commonjs/mol-repr/structure/visual/carbohydrate-link-cylinder.d.ts

@@ -18,15 +18,32 @@ export declare const CarbohydrateLinkParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
+    material: PD.Group<PD.Normalize<{
+        metalness: number;
+        roughness: number;
+        bumpiness: number;
+    }>>;
+    clip: PD.Group<PD.Normalize<{
+        variant: import("../../../mol-util/clip").Clip.Variant;
+        objects: PD.Normalize<{
+            type: any;
+            invert: any;
+            position: any;
+            rotation: any;
+            scale: any;
+        }>[];
+    }>>;
 };
 export declare type CarbohydrateLinkParams = typeof CarbohydrateLinkParams;
 export declare function CarbohydrateLinkVisual(materialId: number): ComplexVisual<CarbohydrateLinkParams>;