npm - molstar - Versions diffs - 2.3.5 → 2.3.9 - Mend

molstar 2.3.5 → 2.3.9

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (1658) hide show

package/lib/commonjs/mol-repr/structure/visual/util/bond.d.ts CHANGED Viewed

@@ -12,15 +12,15 @@ import { Loci } from '../../../../mol-model/loci';
 import { Interval } from '../../../../mol-data/int';
 import { StructureGroup } from './common';
 export declare const BondParams: {
-    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
-    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    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;
     aromaticBonds: PD.BooleanParam;
     multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
 };
 export declare const DefaultBondProps: PD.Values<{
-    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
-    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    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;
     aromaticBonds: PD.BooleanParam;
     multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
@@ -28,14 +28,17 @@ export declare const DefaultBondProps: PD.Values<{
 export declare type BondProps = typeof DefaultBondProps;
 export declare const BondCylinderParams: {
     adjustCylinderLength: PD.BooleanParam;
-    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
-    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    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;
     aromaticBonds: PD.BooleanParam;
     multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
+    aromaticScale: PD.Numeric;
+    aromaticSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
     dashScale: PD.Numeric;
     dashCap: PD.BooleanParam;
@@ -44,14 +47,17 @@ export declare const BondCylinderParams: {
 };
 export declare const DefaultBondCylinderProps: PD.Values<{
     adjustCylinderLength: PD.BooleanParam;
-    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
-    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    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;
     aromaticBonds: PD.BooleanParam;
     multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
+    aromaticScale: PD.Numeric;
+    aromaticSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
     dashScale: PD.Numeric;
     dashCap: PD.BooleanParam;
@@ -60,23 +66,25 @@ export declare const DefaultBondCylinderProps: PD.Values<{
 }>;
 export declare type BondCylinderProps = typeof DefaultBondCylinderProps;
 export declare const BondLineParams: {
-    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
-    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    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;
     aromaticBonds: PD.BooleanParam;
     multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
 };
 export declare const DefaultBondLineProps: PD.Values<{
-    includeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
-    excludeTypes: PD.MultiSelect<"covalent" | "computed" | "aromatic" | "metal-coordination" | "hydrogen-bond" | "disulfide">;
+    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;
     aromaticBonds: PD.BooleanParam;
     multipleBonds: PD.Select<"off" | "symmetric" | "offset">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
 }>;
 export declare type BondLineProps = typeof DefaultBondLineProps;
@@ -87,11 +95,11 @@ export declare namespace BondIterator {
     function fromGroup(structureGroup: StructureGroup): LocationIterator;
     function fromStructure(structure: Structure): LocationIterator;
 }
-export declare function getIntraBondLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): Bond.Loci | {
+export declare function getIntraBondLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): {
     kind: "empty-loci";
-};
+} | Bond.Loci;
 export declare function eachIntraBond(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean, isMarking: boolean): boolean;
-export declare function getInterBondLoci(pickingId: PickingId, structure: Structure, id: number): Bond.Loci | {
+export declare function getInterBondLoci(pickingId: PickingId, structure: Structure, id: number): {
     kind: "empty-loci";
-};
+} | Bond.Loci;
 export declare function eachInterBond(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean, isMarking: boolean): boolean;

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

@@ -24,7 +24,7 @@ exports.BondParams = {
     multipleBonds: param_definition_1.ParamDefinition.Select('symmetric', param_definition_1.ParamDefinition.arrayToOptions(['off', 'symmetric', 'offset'])),
 };
 exports.DefaultBondProps = param_definition_1.ParamDefinition.getDefaultValues(exports.BondParams);
-exports.BondCylinderParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, link_1.LinkCylinderParams), exports.BondParams), { adjustCylinderLength: param_definition_1.ParamDefinition.Boolean(true, { description: 'Shorten cylinders to reduce overlap with spheres.' }) });
+exports.BondCylinderParams = (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({}, link_1.LinkCylinderParams), exports.BondParams), { adjustCylinderLength: param_definition_1.ParamDefinition.Boolean(false, { description: 'Shorten cylinders to reduce overlap with spheres. Useful for for transparent bonds. Not working well with aromatic bonds.' }) });
 exports.DefaultBondCylinderProps = param_definition_1.ParamDefinition.getDefaultValues(exports.BondCylinderParams);
 exports.BondLineParams = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, link_1.LinkLineParams), exports.BondParams);
 exports.DefaultBondLineProps = param_definition_1.ParamDefinition.getDefaultValues(exports.BondLineParams);

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

	@@ -1 +1 @@
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package/lib/commonjs/mol-repr/structure/visual/util/color.d.ts CHANGED Viewed

@@ -10,10 +10,10 @@ import { Texture } from '../../../../mol-gl/webgl/texture';
 import { Theme } from '../../../../mol-theme/theme';
 import { ParamDefinition as PD } from '../../../../mol-util/param-definition';
 export declare const ColorSmoothingParams: {
-    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
+    smoothColors: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<unknown>, "auto"> | PD.NamedParams<PD.Normalize<{
         resolutionFactor: number;
         sampleStride: number;
-    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
+    }>, "on">>;
 };
 export declare type ColorSmoothingParams = typeof ColorSmoothingParams;
 export declare function getColorSmoothingProps(props: PD.Values<ColorSmoothingParams>, theme: Theme, resolution?: number): {

package/lib/commonjs/mol-repr/structure/visual/util/element.d.ts CHANGED Viewed

@@ -29,13 +29,13 @@ export declare type ElementSphereImpostorProps = {
 } & ElementProps;
 export declare function createElementSphereImpostor(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: ElementSphereImpostorProps, spheres?: Spheres): Spheres;
 export declare function eachElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean): boolean;
-export declare function getElementLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): StructureElement.Loci | {
+export declare function getElementLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): {
     kind: "empty-loci";
-};
+} | StructureElement.Loci;
 export declare function eachSerialElement(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean): boolean;
-export declare function getSerialElementLoci(pickingId: PickingId, structure: Structure, id: number): StructureElement.Loci | {
+export declare function getSerialElementLoci(pickingId: PickingId, structure: Structure, id: number): {
     kind: "empty-loci";
-};
+} | StructureElement.Loci;
 export declare namespace ElementIterator {
     function fromGroup(structureGroup: StructureGroup): LocationIterator;
     function fromStructure(structure: Structure): LocationIterator;

package/lib/commonjs/mol-repr/structure/visual/util/link.d.ts CHANGED Viewed

@@ -13,6 +13,9 @@ export declare const LinkCylinderParams: {
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
+    aromaticScale: PD.Numeric;
+    aromaticSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
     dashScale: PD.Numeric;
     dashCap: PD.BooleanParam;
@@ -23,6 +26,9 @@ export declare const DefaultLinkCylinderProps: PD.Values<{
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
     linkCap: PD.BooleanParam;
+    aromaticScale: PD.Numeric;
+    aromaticSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
     dashScale: PD.Numeric;
     dashCap: PD.BooleanParam;
@@ -33,11 +39,13 @@ export declare type LinkCylinderProps = typeof DefaultLinkCylinderProps;
 export declare const LinkLineParams: {
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
 };
 export declare const DefaultLinkLineProps: PD.Values<{
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
 }>;
 export declare type LinkLineProps = typeof DefaultLinkLineProps;

package/lib/commonjs/mol-repr/structure/visual/util/link.js CHANGED Viewed

@@ -20,6 +20,9 @@ exports.LinkCylinderParams = {
     linkScale: param_definition_1.ParamDefinition.Numeric(0.45, { min: 0, max: 1, step: 0.01 }),
     linkSpacing: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 2, step: 0.01 }),
     linkCap: param_definition_1.ParamDefinition.Boolean(false),
+    aromaticScale: param_definition_1.ParamDefinition.Numeric(0.3, { min: 0, max: 1, step: 0.01 }),
+    aromaticSpacing: param_definition_1.ParamDefinition.Numeric(1.5, { min: 0, max: 3, step: 0.01 }),
+    aromaticDashCount: param_definition_1.ParamDefinition.Numeric(2, { min: 2, max: 6, step: 2 }),
     dashCount: param_definition_1.ParamDefinition.Numeric(4, { min: 2, max: 10, step: 2 }),
     dashScale: param_definition_1.ParamDefinition.Numeric(0.8, { min: 0, max: 2, step: 0.1 }),
     dashCap: param_definition_1.ParamDefinition.Boolean(true),
@@ -30,6 +33,7 @@ exports.DefaultLinkCylinderProps = param_definition_1.ParamDefinition.getDefault
 exports.LinkLineParams = {
     linkScale: param_definition_1.ParamDefinition.Numeric(0.5, { min: 0, max: 1, step: 0.1 }),
     linkSpacing: param_definition_1.ParamDefinition.Numeric(0.1, { min: 0, max: 2, step: 0.01 }),
+    aromaticDashCount: param_definition_1.ParamDefinition.Numeric(2, { min: 2, max: 6, step: 2 }),
     dashCount: param_definition_1.ParamDefinition.Numeric(4, { min: 2, max: 10, step: 2 }),
 };
 exports.DefaultLinkLineProps = param_definition_1.ParamDefinition.getDefaultValues(exports.LinkLineParams);
@@ -76,7 +80,7 @@ function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
     var linkCount = linkBuilder.linkCount, referencePosition = linkBuilder.referencePosition, position = linkBuilder.position, style = linkBuilder.style, radius = linkBuilder.radius, ignore = linkBuilder.ignore, stub = linkBuilder.stub;
     if (!linkCount)
         return mesh_1.Mesh.createEmpty(mesh);
-    var linkScale = props.linkScale, linkSpacing = props.linkSpacing, radialSegments = props.radialSegments, linkCap = props.linkCap, dashCount = props.dashCount, dashScale = props.dashScale, dashCap = props.dashCap, stubCap = props.stubCap;
+    var linkScale = props.linkScale, linkSpacing = props.linkSpacing, radialSegments = props.radialSegments, linkCap = props.linkCap, aromaticScale = props.aromaticScale, aromaticSpacing = props.aromaticSpacing, aromaticDashCount = props.aromaticDashCount, dashCount = props.dashCount, dashScale = props.dashScale, dashCap = props.dashCap, stubCap = props.stubCap;
     var vertexCountEstimate = radialSegments * 2 * linkCount * 2;
     var builderState = mesh_builder_1.MeshBuilder.createState(vertexCountEstimate, vertexCountEstimate / 4, mesh);
     var va = (0, linear_algebra_1.Vec3)();
@@ -101,8 +105,7 @@ function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
         var linkStub = stubCap && (stub ? stub(edgeIndex) : false);
         var _a = dirFlag ? [linkStub, linkCap] : [linkCap, linkStub], topCap = _a[0], bottomCap = _a[1];
         builderState.currentGroup = edgeIndex;
-        var aromaticOffsetFactor = 5.5;
-        var multipleOffsetFactor = 4;
+        var aromaticSegmentCount = aromaticDashCount + 1;
         if (linkStyle === 0 /* Solid */) {
             cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
             cylinderProps.topCap = topCap;
@@ -115,8 +118,8 @@ function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
             (0, cylinder_1.addFixedCountDashedCylinder)(builderState, va, vb, 0.5, segmentCount, cylinderProps);
         }
         else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ || linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ || linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
-            var order = linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ ? 2 :
-                linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ ? 3 : 1.5;
+            var order = (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */) ? 2 :
+                (linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */) ? 3 : 1.5;
             var multiRadius = linkRadius * (linkScale / (0.5 * order));
             var absOffset = (linkRadius - multiRadius) * linkSpacing;
             calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
@@ -125,21 +128,26 @@ function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
             if (linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
                 cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
                 (0, cylinder_1.addCylinder)(builderState, va, vb, 0.5, cylinderProps);
-                cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius * linkScale;
+                var aromaticOffset = linkRadius + aromaticScale * linkRadius + aromaticScale * linkRadius * aromaticSpacing;
+                v3setMagnitude(tmpV12, v3sub(tmpV12, vb, va), linkRadius * 0.5);
+                v3add(va, va, tmpV12);
+                v3sub(vb, vb, tmpV12);
+                cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius * aromaticScale;
                 cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
-                v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor);
+                v3setMagnitude(vShift, vShift, aromaticOffset);
                 v3sub(va, va, vShift);
                 v3sub(vb, vb, vShift);
-                (0, cylinder_1.addFixedCountDashedCylinder)(builderState, va, vb, 0.5, 3, cylinderProps);
+                (0, cylinder_1.addFixedCountDashedCylinder)(builderState, va, vb, 0.5, aromaticSegmentCount, cylinderProps);
                 if (linkStyle === 8 /* MirroredAromatic */) {
-                    v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
+                    v3setMagnitude(vShift, vShift, aromaticOffset * 2);
                     v3add(va, va, vShift);
                     v3add(vb, vb, vShift);
-                    (0, cylinder_1.addFixedCountDashedCylinder)(builderState, va, vb, 0.5, 3, cylinderProps);
+                    (0, cylinder_1.addFixedCountDashedCylinder)(builderState, va, vb, 0.5, aromaticSegmentCount, cylinderProps);
                 }
             }
             else if (linkStyle === 3 /* OffsetDouble */ || linkStyle === 5 /* OffsetTriple */) {
-                v3setMagnitude(vShift, vShift, absOffset);
+                var multipleOffset = linkRadius + multiRadius + linkScale * linkRadius * linkSpacing;
+                v3setMagnitude(vShift, vShift, multipleOffset);
                 cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
                 (0, cylinder_1.addCylinder)(builderState, va, vb, 0.5, cylinderProps);
                 v3scale(tmpV12, tmpV12, linkSpacing * linkScale * 0.2);
@@ -148,12 +156,12 @@ function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
                 cylinderProps.radiusTop = cylinderProps.radiusBottom = multiRadius;
                 cylinderProps.topCap = dirFlag ? linkStub : dashCap;
                 cylinderProps.bottomCap = dirFlag ? dashCap : linkStub;
-                v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor);
+                v3setMagnitude(vShift, vShift, multipleOffset);
                 v3sub(va, va, vShift);
                 v3sub(vb, vb, vShift);
                 (0, cylinder_1.addCylinder)(builderState, va, vb, 0.5, cylinderProps);
                 if (order === 3) {
-                    v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor * 2);
+                    v3setMagnitude(vShift, vShift, multipleOffset * 2);
                     v3add(va, va, vShift);
                     v3add(vb, vb, vShift);
                     (0, cylinder_1.addCylinder)(builderState, va, vb, 0.5, cylinderProps);
@@ -188,7 +196,7 @@ function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders) {
     var linkCount = linkBuilder.linkCount, referencePosition = linkBuilder.referencePosition, position = linkBuilder.position, style = linkBuilder.style, radius = linkBuilder.radius, ignore = linkBuilder.ignore, stub = linkBuilder.stub;
     if (!linkCount)
         return cylinders_1.Cylinders.createEmpty(cylinders);
-    var linkScale = props.linkScale, linkSpacing = props.linkSpacing, linkCap = props.linkCap, dashCount = props.dashCount, dashScale = props.dashScale, dashCap = props.dashCap, stubCap = props.stubCap;
+    var linkScale = props.linkScale, linkSpacing = props.linkSpacing, linkCap = props.linkCap, aromaticScale = props.aromaticScale, aromaticSpacing = props.aromaticSpacing, aromaticDashCount = props.aromaticDashCount, dashCount = props.dashCount, dashScale = props.dashScale, dashCap = props.dashCap, stubCap = props.stubCap;
     var cylindersCountEstimate = linkCount * 2;
     var builder = cylinders_builder_1.CylindersBuilder.create(cylindersCountEstimate, cylindersCountEstimate / 4, cylinders);
     var va = (0, linear_algebra_1.Vec3)();
@@ -198,10 +206,8 @@ function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders) {
     // automatically adjust length for evenly spaced dashed cylinders
     var segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
     var lengthScale = 0.5 - (0.5 / 2 / segmentCount);
-    var aromaticSegmentCount = 3;
+    var aromaticSegmentCount = aromaticDashCount + 1;
     var aromaticLengthScale = 0.5 - (0.5 / 2 / aromaticSegmentCount);
-    var aromaticOffsetFactor = 5.5;
-    var multipleOffsetFactor = 4;
     for (var edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
         if (ignore && ignore(edgeIndex))
             continue;
@@ -219,31 +225,35 @@ function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders) {
             builder.addFixedCountDashes(va, vb, segmentCount, dashScale, dashCap, dashCap, edgeIndex);
         }
         else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ || linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ || linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
-            var order = linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */ ? 2 :
-                linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */ ? 3 : 1.5;
+            var order = (linkStyle === 2 /* Double */ || linkStyle === 3 /* OffsetDouble */) ? 2 :
+                (linkStyle === 4 /* Triple */ || linkStyle === 5 /* OffsetTriple */) ? 3 : 1.5;
             var multiScale = linkScale / (0.5 * order);
             var absOffset = (linkRadius - multiScale * linkRadius) * linkSpacing;
             v3scale(vm, v3add(vm, va, vb), 0.5);
             calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
             if (linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
                 builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
+                var aromaticOffset = linkRadius + aromaticScale * linkRadius + aromaticScale * linkRadius * aromaticSpacing;
                 v3scale(tmpV12, v3sub(tmpV12, vb, va), aromaticLengthScale);
                 v3sub(vb, vb, tmpV12);
-                v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor);
+                v3setMagnitude(tmpV12, v3sub(tmpV12, vb, va), linkRadius * 0.5);
+                v3add(va, va, tmpV12);
+                v3setMagnitude(vShift, vShift, aromaticOffset);
                 v3sub(va, va, vShift);
                 v3sub(vb, vb, vShift);
-                builder.addFixedCountDashes(va, vb, aromaticSegmentCount, linkScale, dashCap, dashCap, edgeIndex);
+                builder.addFixedCountDashes(va, vb, aromaticSegmentCount, aromaticScale, dashCap, dashCap, edgeIndex);
                 if (linkStyle === 8 /* MirroredAromatic */) {
-                    v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
+                    v3setMagnitude(vShift, vShift, aromaticOffset * 2);
                     v3add(va, va, vShift);
                     v3add(vb, vb, vShift);
-                    builder.addFixedCountDashes(va, vb, aromaticSegmentCount, linkScale, dashCap, dashCap, edgeIndex);
+                    builder.addFixedCountDashes(va, vb, aromaticSegmentCount, aromaticScale, dashCap, dashCap, edgeIndex);
                 }
             }
             else if (linkStyle === 3 /* OffsetDouble */ || linkStyle === 5 /* OffsetTriple */) {
-                v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor);
+                var multipleOffset = linkRadius + multiScale * linkRadius + linkScale * linkRadius * linkSpacing;
+                v3setMagnitude(vShift, vShift, multipleOffset);
                 builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], 1, linkCap, linkStub, edgeIndex);
-                v3scale(tmpV12, v3sub(tmpV12, va, vb), linkSpacing * linkScale * 0.2);
+                v3setMagnitude(tmpV12, v3sub(tmpV12, va, vb), linkRadius / 1.5);
                 v3sub(va, va, tmpV12);
                 if (order === 3)
                     builder.add(va[0] + vShift[0], va[1] + vShift[1], va[2] + vShift[2], vm[0] + vShift[0], vm[1] + vShift[1], vm[2] + vShift[2], multiScale, linkCap, linkStub, edgeIndex);
@@ -275,7 +285,7 @@ function createLinkLines(ctx, linkBuilder, props, lines) {
     var linkCount = linkBuilder.linkCount, referencePosition = linkBuilder.referencePosition, position = linkBuilder.position, style = linkBuilder.style, ignore = linkBuilder.ignore;
     if (!linkCount)
         return lines_1.Lines.createEmpty(lines);
-    var linkScale = props.linkScale, linkSpacing = props.linkSpacing, dashCount = props.dashCount;
+    var linkScale = props.linkScale, linkSpacing = props.linkSpacing, aromaticDashCount = props.aromaticDashCount, dashCount = props.dashCount;
     var linesCountEstimate = linkCount * 2;
     var builder = lines_builder_1.LinesBuilder.create(linesCountEstimate, linesCountEstimate / 4, lines);
     var va = (0, linear_algebra_1.Vec3)();
@@ -285,7 +295,7 @@ function createLinkLines(ctx, linkBuilder, props, lines) {
     // automatically adjust length for evenly spaced dashed lines
     var segmentCount = dashCount % 2 === 1 ? dashCount : dashCount + 1;
     var lengthScale = 0.5 - (0.5 / 2 / segmentCount);
-    var aromaticSegmentCount = 3;
+    var aromaticSegmentCount = aromaticDashCount + 1;
     var aromaticLengthScale = 0.5 - (0.5 / 2 / aromaticSegmentCount);
     var aromaticOffsetFactor = 4.5;
     var multipleOffsetFactor = 3;

package/lib/commonjs/mol-repr/structure/visual/util/link.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/commonjs/mol-repr/structure/visual/util/polymer.d.ts CHANGED Viewed

@@ -34,7 +34,7 @@ export declare function eachAtomicUnitTracedElement(offset: number, groupSize: n
 /** Mark a polymer element (e.g. part of a cartoon trace) */
 export declare function eachPolymerElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean): boolean;
 /** Return a Loci for both directions of the polymer gap element. */
-export declare function getPolymerGapElementLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): Bond.Loci | {
+export declare function getPolymerGapElementLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): {
     kind: "empty-loci";
-};
+} | Bond.Loci;
 export declare function eachPolymerGapElement(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean): boolean;

package/lib/commonjs/mol-repr/volume/direct-volume.d.ts CHANGED Viewed

@@ -18,9 +18,9 @@ import { PickingId } from '../../mol-geo/geometry/picking';
 export declare function createDirectVolume2d(ctx: RuntimeContext, webgl: WebGLContext, volume: Volume, directVolume?: DirectVolume): DirectVolume;
 export declare function createDirectVolume3d(ctx: RuntimeContext, webgl: WebGLContext, volume: Volume, directVolume?: DirectVolume): DirectVolume;
 export declare function createDirectVolume(ctx: VisualContext, volume: Volume, theme: Theme, props: PD.Values<DirectVolumeParams>, directVolume?: DirectVolume): Promise<DirectVolume>;
-export declare function getDirectVolumeLoci(pickingId: PickingId, volume: Volume, props: DirectVolumeProps, id: number): {
+export declare function getDirectVolumeLoci(pickingId: PickingId, volume: Volume, props: DirectVolumeProps, id: number): Volume.Cell.Loci | {
     kind: "empty-loci";
-} | Volume.Cell.Loci;
+};
 export declare function eachDirectVolume(loci: Loci, volume: Volume, props: DirectVolumeProps, apply: (interval: Interval) => boolean): boolean;
 export declare const DirectVolumeParams: {
     quality: {
@@ -54,7 +54,7 @@ export declare const DirectVolumeParams: {
     renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
         controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
         list: {
-            kind: "set" | "interpolate";
+            kind: "interpolate" | "set";
             colors: import("../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{
@@ -104,7 +104,7 @@ export declare function getDirectVolumeParams(ctx: ThemeRegistryContext, volume:
     renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
         controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
         list: {
-            kind: "set" | "interpolate";
+            kind: "interpolate" | "set";
             colors: import("../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{
@@ -156,7 +156,7 @@ export declare const DirectVolumeRepresentationProvider: VolumeRepresentationPro
     renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
         controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
         list: {
-            kind: "set" | "interpolate";
+            kind: "interpolate" | "set";
             colors: import("../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{

package/lib/commonjs/mol-repr/volume/isosurface.d.ts CHANGED Viewed

@@ -208,7 +208,7 @@ export declare const IsosurfaceWireframeParams: {
 export declare type IsosurfaceWireframeParams = typeof IsosurfaceWireframeParams;
 export declare function IsosurfaceWireframeVisual(materialId: number): VolumeVisual<IsosurfaceWireframeParams>;
 export declare const IsosurfaceParams: {
-    visuals: PD.MultiSelect<"wireframe" | "solid">;
+    visuals: PD.MultiSelect<"solid" | "wireframe">;
     quality: {
         isEssential: boolean;
         type: "select";
@@ -266,7 +266,7 @@ export declare const IsosurfaceParams: {
 };
 export declare type IsosurfaceParams = typeof IsosurfaceParams;
 export declare function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: Volume): {
-    visuals: PD.MultiSelect<"wireframe" | "solid">;
+    visuals: PD.MultiSelect<"solid" | "wireframe">;
     quality: {
         isEssential: boolean;
         type: "select";
@@ -325,7 +325,7 @@ export declare function getIsosurfaceParams(ctx: ThemeRegistryContext, volume: V
 export declare type IsosurfaceRepresentation = VolumeRepresentation<IsosurfaceParams>;
 export declare function IsosurfaceRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, IsosurfaceParams>): IsosurfaceRepresentation;
 export declare const IsosurfaceRepresentationProvider: VolumeRepresentationProvider<{
-    visuals: PD.MultiSelect<"wireframe" | "solid">;
+    visuals: PD.MultiSelect<"solid" | "wireframe">;
     quality: {
         isEssential: boolean;
         type: "select";