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

@@ -12,30 +12,33 @@ 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">;
+    multipleBonds: PD.Select<"off" | "offset" | "symmetric">;
 };
 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">;
+    multipleBonds: PD.Select<"off" | "offset" | "symmetric">;
 }>;
 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">;
+    multipleBonds: PD.Select<"off" | "offset" | "symmetric">;
     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">;
+    multipleBonds: PD.Select<"off" | "offset" | "symmetric">;
     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">;
+    multipleBonds: PD.Select<"off" | "offset" | "symmetric">;
     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">;
+    multipleBonds: PD.Select<"off" | "offset" | "symmetric">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
 }>;
 export declare type BondLineProps = typeof DefaultBondLineProps;

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

@@ -21,7 +21,7 @@ export var BondParams = {
     multipleBonds: PD.Select('symmetric', PD.arrayToOptions(['off', 'symmetric', 'offset'])),
 };
 export var DefaultBondProps = PD.getDefaultValues(BondParams);
-export var BondCylinderParams = __assign(__assign(__assign({}, LinkCylinderParams), BondParams), { adjustCylinderLength: PD.Boolean(true, { description: 'Shorten cylinders to reduce overlap with spheres.' }) });
+export var BondCylinderParams = __assign(__assign(__assign({}, LinkCylinderParams), BondParams), { adjustCylinderLength: PD.Boolean(false, { description: 'Shorten cylinders to reduce overlap with spheres. Useful for for transparent bonds. Not working well with aromatic bonds.' }) });
 export var DefaultBondCylinderProps = PD.getDefaultValues(BondCylinderParams);
 export var BondLineParams = __assign(__assign({}, LinkLineParams), BondParams);
 export var DefaultBondLineProps = PD.getDefaultValues(BondLineParams);

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

	@@ -1 +1 @@
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package/lib/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<{
         resolutionFactor: number;
         sampleStride: number;
-    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "off">>;
+    }>, "on"> | PD.NamedParams<PD.Normalize<unknown>, "auto">>;
 };
 export declare type ColorSmoothingParams = typeof ColorSmoothingParams;
 export declare function getColorSmoothingProps(props: PD.Values<ColorSmoothingParams>, theme: Theme, resolution?: number): {

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

@@ -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/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/mol-repr/structure/visual/util/link.js CHANGED Viewed

@@ -17,6 +17,9 @@ export var LinkCylinderParams = {
     linkScale: PD.Numeric(0.45, { min: 0, max: 1, step: 0.01 }),
     linkSpacing: PD.Numeric(1, { min: 0, max: 2, step: 0.01 }),
     linkCap: PD.Boolean(false),
+    aromaticScale: PD.Numeric(0.3, { min: 0, max: 1, step: 0.01 }),
+    aromaticSpacing: PD.Numeric(1.5, { min: 0, max: 3, step: 0.01 }),
+    aromaticDashCount: PD.Numeric(2, { min: 2, max: 6, step: 2 }),
     dashCount: PD.Numeric(4, { min: 2, max: 10, step: 2 }),
     dashScale: PD.Numeric(0.8, { min: 0, max: 2, step: 0.1 }),
     dashCap: PD.Boolean(true),
@@ -27,6 +30,7 @@ export var DefaultLinkCylinderProps = PD.getDefaultValues(LinkCylinderParams);
 export var LinkLineParams = {
     linkScale: PD.Numeric(0.5, { min: 0, max: 1, step: 0.1 }),
     linkSpacing: PD.Numeric(0.1, { min: 0, max: 2, step: 0.01 }),
+    aromaticDashCount: PD.Numeric(2, { min: 2, max: 6, step: 2 }),
     dashCount: PD.Numeric(4, { min: 2, max: 10, step: 2 }),
 };
 export var DefaultLinkLineProps = PD.getDefaultValues(LinkLineParams);
@@ -72,7 +76,7 @@ export 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.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 = MeshBuilder.createState(vertexCountEstimate, vertexCountEstimate / 4, mesh);
     var va = Vec3();
@@ -97,8 +101,7 @@ export 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;
@@ -111,8 +114,8 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
             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);
@@ -121,21 +124,26 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
             if (linkStyle === 7 /* Aromatic */ || linkStyle === 8 /* MirroredAromatic */) {
                 cylinderProps.radiusTop = cylinderProps.radiusBottom = linkRadius;
                 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);
-                addFixedCountDashedCylinder(builderState, va, vb, 0.5, 3, cylinderProps);
+                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);
-                    addFixedCountDashedCylinder(builderState, va, vb, 0.5, 3, cylinderProps);
+                    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;
                 addCylinder(builderState, va, vb, 0.5, cylinderProps);
                 v3scale(tmpV12, tmpV12, linkSpacing * linkScale * 0.2);
@@ -144,12 +152,12 @@ export 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);
                 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);
                     addCylinder(builderState, va, vb, 0.5, cylinderProps);
@@ -183,7 +191,7 @@ export 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.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 = CylindersBuilder.create(cylindersCountEstimate, cylindersCountEstimate / 4, cylinders);
     var va = Vec3();
@@ -193,10 +201,8 @@ export 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;
@@ -214,31 +220,35 @@ export 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);
@@ -269,7 +279,7 @@ export 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.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 = LinesBuilder.create(linesCountEstimate, linesCountEstimate / 4, lines);
     var va = Vec3();
@@ -279,7 +289,7 @@ export 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/mol-repr/structure/visual/util/link.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-repr/structure/visual/util/orientation.d.ts ADDED Viewed

@@ -0,0 +1,17 @@
+/**
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { Unit, StructureElement } from '../../../../mol-model/structure';
+import { PickingId } from '../../../../mol-geo/geometry/picking';
+import { Interval } from '../../../../mol-data/int';
+import { Loci } from '../../../../mol-model/loci';
+import { LocationIterator } from '../../../../mol-geo/util/location-iterator';
+import { StructureGroup } from './common';
+export declare function isUnitApplicable(unit: Unit): boolean;
+export declare function UnitIterator(structureGroup: StructureGroup): LocationIterator;
+export declare function getUnitLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): StructureElement.Loci | {
+    kind: "empty-loci";
+};
+export declare function eachUnit(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean): boolean;

package/lib/mol-repr/structure/visual/util/orientation.js ADDED Viewed

@@ -0,0 +1,71 @@
+/**
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { Unit, Structure, StructureElement } from '../../../../mol-model/structure';
+import { OrderedSet, Interval } from '../../../../mol-data/int';
+import { EmptyLoci } from '../../../../mol-model/loci';
+import { LocationIterator } from '../../../../mol-geo/util/location-iterator';
+export function isUnitApplicable(unit) {
+    if (Unit.Traits.is(unit.traits, 1 /* MultiChain */))
+        return false;
+    if (Unit.Traits.is(unit.traits, 2 /* Partitioned */))
+        return false;
+    if (Unit.isCoarse(unit))
+        return true;
+    if (unit.elements.length === 0)
+        return false;
+    unit.model.atomicHierarchy.derived.residue.moleculeType;
+    var rI = unit.residueIndex[unit.elements[0]];
+    var mt = unit.model.atomicHierarchy.derived.residue.moleculeType[rI];
+    if (mt === 3 /* Ion */)
+        return false;
+    if (mt === 2 /* Water */)
+        return false;
+    return true;
+}
+export function UnitIterator(structureGroup) {
+    var group = structureGroup.group, structure = structureGroup.structure;
+    var groupCount = 1;
+    var instanceCount = group.units.length;
+    var location = StructureElement.Location.create(structure);
+    var getLocation = function (groupIndex, instanceIndex) {
+        var unit = group.units[instanceIndex];
+        location.unit = unit;
+        location.element = unit.elements[groupIndex];
+        return location;
+    };
+    return LocationIterator(groupCount, instanceCount, 1, getLocation);
+}
+export function getUnitLoci(pickingId, structureGroup, id) {
+    var objectId = pickingId.objectId, instanceId = pickingId.instanceId;
+    if (id === objectId) {
+        var structure = structureGroup.structure, group = structureGroup.group;
+        var unit = group.units[instanceId];
+        var indices = OrderedSet.ofBounds(0, unit.elements.length);
+        return StructureElement.Loci(structure, [{ unit: unit, indices: indices }]);
+    }
+    return EmptyLoci;
+}
+export function eachUnit(loci, structureGroup, apply) {
+    var changed = false;
+    if (!StructureElement.Loci.is(loci))
+        return false;
+    var structure = structureGroup.structure, group = structureGroup.group;
+    if (!Structure.areEquivalent(loci.structure, structure))
+        return false;
+    var elementCount = group.elements.length;
+    for (var _i = 0, _a = loci.elements; _i < _a.length; _i++) {
+        var e = _a[_i];
+        var unitIdx = group.unitIndexMap.get(e.unit.id);
+        if (unitIdx !== undefined) {
+            if (OrderedSet.size(e.indices) === elementCount) {
+                if (apply(Interval.ofSingleton(unitIdx)))
+                    changed = true;
+            }
+        }
+    }
+    return changed;
+}
+//# sourceMappingURL=orientation.js.map