molstar 2.3.3 → 2.3.8

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

@@ -21,9 +21,10 @@ exports.BondParams = {
     excludeTypes: param_definition_1.ParamDefinition.MultiSelect([], param_definition_1.ParamDefinition.objectToOptions(types_1.BondType.Names)),
     ignoreHydrogens: param_definition_1.ParamDefinition.Boolean(false),
     aromaticBonds: param_definition_1.ParamDefinition.Boolean(false, { description: 'Display aromatic bonds with dashes' }),
+    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

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

@@ -29,7 +29,7 @@ export declare const UnitKindInfo: {
     gaussians: {};
 };
 export declare type UnitKind = keyof typeof UnitKindInfo;
-export declare const UnitKindOptions: ["spheres" | "atomic" | "gaussians", string][];
+export declare const UnitKindOptions: ["spheres" | "gaussians" | "atomic", string][];
 export declare function includesUnitKind(unitKinds: UnitKind[], unit: Unit): boolean;
 export declare function getVolumeSliceInfo(box: Box3D, resolution: number, maxCells?: number): {
     area: number;
@@ -48,7 +48,7 @@ export declare function ensureReasonableResolution<T>(box: Box3D, props: {
 } & T & {
     resolution: number;
 };
-export declare function getConformation(unit: Unit): import("../../../../mol-model/structure/model/properties/coarse").CoarseSphereConformation | import("../../../../mol-model/structure/model/properties/coarse").CoarseGaussianConformation | import("../../../../mol-model/structure/model/properties/atomic").AtomicConformation;
+export declare function getConformation(unit: Unit): import("../../../../mol-model/structure/model/properties/atomic").AtomicConformation | import("../../../../mol-model/structure/model/properties/coarse").CoarseSphereConformation | import("../../../../mol-model/structure/model/properties/coarse").CoarseGaussianConformation;
 export declare const CommonSurfaceParams: {
     ignoreHydrogens: PD.BooleanParam;
     traceOnly: PD.BooleanParam;

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

@@ -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): {
+export declare function getElementLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): StructureElement.Loci | {
     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): {
+export declare function getSerialElementLoci(pickingId: PickingId, structure: Structure, id: number): StructureElement.Loci | {
     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

@@ -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;
@@ -56,10 +64,12 @@ export declare const enum LinkStyle {
     Solid = 0,
     Dashed = 1,
     Double = 2,
-    Triple = 3,
-    Disk = 4,
-    Aromatic = 5,
-    MirroredAromatic = 6
+    OffsetDouble = 3,
+    Triple = 4,
+    OffsetTriple = 5,
+    Disk = 6,
+    Aromatic = 7,
+    MirroredAromatic = 8
 }
 /**
  * Each edge is included twice to allow for coloring/picking

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

@@ -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)();
@@ -95,12 +99,13 @@ function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
             continue;
         position(va, vb, edgeIndex);
         v3sub(tmpV12, vb, va);
+        var dirFlag = v3dot(tmpV12, up) > 0;
         var linkRadius = radius(edgeIndex);
         var linkStyle = style ? style(edgeIndex) : 0 /* Solid */;
         var linkStub = stubCap && (stub ? stub(edgeIndex) : false);
-        var _a = (v3dot(tmpV12, up) > 0) ? [linkStub, linkCap] : [linkCap, linkStub], topCap = _a[0], bottomCap = _a[1];
+        var _a = dirFlag ? [linkStub, linkCap] : [linkCap, linkStub], topCap = _a[0], bottomCap = _a[1];
         builderState.currentGroup = edgeIndex;
-        var aromaticOffsetFactor = 4.5;
+        var aromaticSegmentCount = aromaticDashCount + 1;
         if (linkStyle === 0 /* Solid */) {
             cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
             cylinderProps.topCap = topCap;
@@ -112,28 +117,54 @@ function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
             cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
             (0, cylinder_1.addFixedCountDashedCylinder)(builderState, va, vb, 0.5, segmentCount, cylinderProps);
         }
-        else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* Triple */ || linkStyle === 5 /* Aromatic */ || linkStyle === 6 /* MirroredAromatic */) {
-            var order = linkStyle === 2 /* Double */ ? 2 :
-                linkStyle === 3 /* Triple */ ? 3 : 1.5;
+        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 multiRadius = linkRadius * (linkScale / (0.5 * order));
             var absOffset = (linkRadius - multiRadius) * linkSpacing;
             calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
             cylinderProps.topCap = topCap;
             cylinderProps.bottomCap = bottomCap;
-            if (linkStyle === 5 /* Aromatic */ || linkStyle === 6 /* MirroredAromatic */) {
+            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);
-                if (linkStyle === 6 /* MirroredAromatic */) {
-                    v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
+                (0, cylinder_1.addFixedCountDashedCylinder)(builderState, va, vb, 0.5, aromaticSegmentCount, cylinderProps);
+                if (linkStyle === 8 /* MirroredAromatic */) {
+                    v3setMagnitude(vShift, vShift, aromaticOffset * 2);
+                    v3add(va, va, vShift);
+                    v3add(vb, vb, vShift);
+                    (0, cylinder_1.addFixedCountDashedCylinder)(builderState, va, vb, 0.5, aromaticSegmentCount, cylinderProps);
+                }
+            }
+            else if (linkStyle === 3 /* OffsetDouble */ || linkStyle === 5 /* OffsetTriple */) {
+                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);
+                v3add(va, va, tmpV12);
+                v3sub(vb, vb, tmpV12);
+                cylinderProps.radiusTop = cylinderProps.radiusBottom = multiRadius;
+                cylinderProps.topCap = dirFlag ? linkStub : dashCap;
+                cylinderProps.bottomCap = dirFlag ? dashCap : linkStub;
+                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, multipleOffset * 2);
                     v3add(va, va, vShift);
                     v3add(vb, vb, vShift);
-                    (0, cylinder_1.addFixedCountDashedCylinder)(builderState, va, vb, 0.5, 3, cylinderProps);
+                    (0, cylinder_1.addCylinder)(builderState, va, vb, 0.5, cylinderProps);
                 }
             }
             else {
@@ -144,7 +175,7 @@ function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
                 (0, cylinder_1.addDoubleCylinder)(builderState, va, vb, 0.5, vShift, cylinderProps);
             }
         }
-        else if (linkStyle === 4 /* Disk */) {
+        else if (linkStyle === 6 /* Disk */) {
             v3scale(tmpV12, tmpV12, 0.475);
             v3add(va, va, tmpV12);
             v3sub(vb, vb, tmpV12);
@@ -165,7 +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)();
@@ -175,9 +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 = 4.5;
     for (var edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
         if (ignore && ignore(edgeIndex))
             continue;
@@ -194,37 +224,50 @@ function createLinkCylinderImpostors(ctx, linkBuilder, props, cylinders) {
             v3sub(vb, vb, tmpV12);
             builder.addFixedCountDashes(va, vb, segmentCount, dashScale, dashCap, dashCap, edgeIndex);
         }
-        else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* Triple */ || linkStyle === 5 /* Aromatic */ || linkStyle === 6 /* MirroredAromatic */) {
-            var order = linkStyle === 2 /* Double */ ? 2 :
-                linkStyle === 3 /* Triple */ ? 3 : 1.5;
+        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 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 === 5 /* Aromatic */ || linkStyle === 6 /* MirroredAromatic */) {
+            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);
-                if (linkStyle === 6 /* MirroredAromatic */) {
-                    v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
+                builder.addFixedCountDashes(va, vb, aromaticSegmentCount, aromaticScale, dashCap, dashCap, edgeIndex);
+                if (linkStyle === 8 /* MirroredAromatic */) {
+                    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 */) {
+                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);
+                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);
+                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, dashCap, linkStub, edgeIndex);
+            }
             else {
                 v3setMagnitude(vShift, vShift, absOffset);
                 if (order === 3)
-                    builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], multiScale, linkCap, false, edgeIndex);
+                    builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], multiScale, linkCap, linkStub, edgeIndex);
                 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);
                 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);
             }
         }
-        else if (linkStyle === 4 /* Disk */) {
+        else if (linkStyle === 6 /* Disk */) {
             v3scale(tmpV12, v3sub(tmpV12, vb, va), 0.475);
             v3add(va, va, tmpV12);
             v3sub(vb, vb, tmpV12);
@@ -242,7 +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)();
@@ -252,9 +295,10 @@ 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;
     for (var edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
         if (ignore && ignore(edgeIndex))
             continue;
@@ -269,14 +313,14 @@ function createLinkLines(ctx, linkBuilder, props, lines) {
             v3sub(vb, vb, tmpV12);
             builder.addFixedCountDashes(va, vb, segmentCount, edgeIndex);
         }
-        else if (linkStyle === 2 /* Double */ || linkStyle === 3 /* Triple */ || linkStyle === 5 /* Aromatic */ || linkStyle === 6 /* MirroredAromatic */) {
-            var order = linkStyle === 2 /* Double */ ? 2 :
-                linkStyle === 3 /* Triple */ ? 3 : 1.5;
+        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 multiRadius = 1 * (linkScale / (0.5 * order));
             var absOffset = (1 - multiRadius) * linkSpacing;
             v3scale(vm, v3add(vm, va, vb), 0.5);
             calculateShiftDir(vShift, va, vb, referencePosition ? referencePosition(edgeIndex) : null);
-            if (linkStyle === 5 /* Aromatic */ || linkStyle === 6 /* MirroredAromatic */) {
+            if (linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
                 builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
                 v3scale(tmpV12, v3sub(tmpV12, vb, va), aromaticLengthScale);
                 v3sub(vb, vb, tmpV12);
@@ -284,22 +328,31 @@ function createLinkLines(ctx, linkBuilder, props, lines) {
                 v3sub(va, va, vShift);
                 v3sub(vb, vb, vShift);
                 builder.addFixedCountDashes(va, vb, aromaticSegmentCount, edgeIndex);
-                if (linkStyle === 6 /* MirroredAromatic */) {
+                if (linkStyle === 8 /* MirroredAromatic */) {
                     v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
                     v3add(va, va, vShift);
                     v3add(vb, vb, vShift);
                     builder.addFixedCountDashes(va, vb, aromaticSegmentCount, edgeIndex);
                 }
             }
+            else if (linkStyle === 3 /* OffsetDouble */ || linkStyle === 5 /* OffsetTriple */) {
+                v3setMagnitude(vShift, vShift, absOffset * multipleOffsetFactor);
+                builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
+                v3scale(tmpV12, v3sub(tmpV12, va, vb), linkSpacing * linkScale);
+                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], edgeIndex);
+                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], edgeIndex);
+            }
             else {
-                v3setMagnitude(vShift, vShift, absOffset);
+                v3setMagnitude(vShift, vShift, absOffset * 1.5);
                 if (order === 3)
                     builder.add(va[0], va[1], va[2], vm[0], vm[1], vm[2], edgeIndex);
                 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], edgeIndex);
                 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], edgeIndex);
             }
         }
-        else if (linkStyle === 4 /* Disk */) {
+        else if (linkStyle === 6 /* Disk */) {
             v3scale(tmpV12, v3sub(tmpV12, vb, va), 0.475);
             v3add(va, va, tmpV12);
             v3sub(vb, vb, tmpV12);

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

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

@@ -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): {
+export declare function getPolymerGapElementLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): Bond.Loci | {
     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

@@ -26,10 +26,10 @@ export declare const DirectVolumeParams: {
     quality: {
         isEssential: boolean;
         type: "select";
-        options: readonly (readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string] | readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string, string | undefined])[];
+        options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
         cycle?: boolean | undefined;
         isOptional?: boolean | undefined;
-        defaultValue: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+        defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
         label?: string | undefined;
         description?: string | undefined;
         legend?: import("../../mol-util/legend").Legend | undefined;
@@ -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: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{
@@ -76,10 +76,10 @@ export declare function getDirectVolumeParams(ctx: ThemeRegistryContext, volume:
     quality: {
         isEssential: boolean;
         type: "select";
-        options: readonly (readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string] | readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string, string | undefined])[];
+        options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
         cycle?: boolean | undefined;
         isOptional?: boolean | undefined;
-        defaultValue: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+        defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
         label?: string | undefined;
         description?: string | undefined;
         legend?: import("../../mol-util/legend").Legend | undefined;
@@ -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: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{
@@ -128,10 +128,10 @@ export declare const DirectVolumeRepresentationProvider: VolumeRepresentationPro
     quality: {
         isEssential: boolean;
         type: "select";
-        options: readonly (readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string] | readonly ["custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest", string, string | undefined])[];
+        options: readonly (readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string] | readonly ["auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest", string, string | undefined])[];
         cycle?: boolean | undefined;
         isOptional?: boolean | undefined;
-        defaultValue: "custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest";
+        defaultValue: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
         label?: string | undefined;
         description?: string | undefined;
         legend?: import("../../mol-util/legend").Legend | undefined;
@@ -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: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{