molstar 2.3.3 → 2.3.8

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

@@ -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();
@@ -91,12 +95,13 @@ export 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;
@@ -108,28 +113,54 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
             cylinderProps.topCap = cylinderProps.bottomCap = dashCap;
             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;
                 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);
-                if (linkStyle === 6 /* MirroredAromatic */) {
-                    v3setMagnitude(vShift, vShift, absOffset * aromaticOffsetFactor * 2);
+                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);
+                    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;
+                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);
+                addCylinder(builderState, va, vb, 0.5, cylinderProps);
+                if (order === 3) {
+                    v3setMagnitude(vShift, vShift, multipleOffset * 2);
                     v3add(va, va, vShift);
                     v3add(vb, vb, vShift);
-                    addFixedCountDashedCylinder(builderState, va, vb, 0.5, 3, cylinderProps);
+                    addCylinder(builderState, va, vb, 0.5, cylinderProps);
                 }
             }
             else {
@@ -140,7 +171,7 @@ export function createLinkCylinderMesh(ctx, linkBuilder, props, mesh) {
                 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);
@@ -160,7 +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();
@@ -170,9 +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 = 4.5;
     for (var edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
         if (ignore && ignore(edgeIndex))
             continue;
@@ -189,37 +219,50 @@ export 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);
@@ -236,7 +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();
@@ -246,9 +289,10 @@ 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;
     for (var edgeIndex = 0, _eI = linkCount; edgeIndex < _eI; ++edgeIndex) {
         if (ignore && ignore(edgeIndex))
             continue;
@@ -263,14 +307,14 @@ export 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);
@@ -278,22 +322,31 @@ export 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/mol-repr/structure/visual/util/link.js.map

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

@@ -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

@@ -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

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

@@ -0,0 +1 @@
+{"version":3,"file":"orientation.js","sourceRoot":"","sources":["../../../../../src/mol-repr/structure/visual/util/orientation.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,SAAS,EAAE,gBAAgB,EAAE,MAAM,iCAAiC,CAAC;AAEpF,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE,MAAM,0BAA0B,CAAC;AAChE,OAAO,EAAE,SAAS,EAAQ,MAAM,4BAA4B,CAAC;AAE7D,OAAO,EAAE,gBAAgB,EAAE,MAAM,4CAA4C,CAAC;AAI9E,MAAM,UAAU,gBAAgB,CAAC,IAAU;IACvC,IAAI,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,qBAAwB;QAAE,OAAO,KAAK,CAAC;IACrE,IAAI,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC,MAAM,sBAAyB;QAAE,OAAO,KAAK,CAAC;IACtE,IAAI,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC;QAAE,OAAO,IAAI,CAAC;IACrC,IAAI,IAAI,CAAC,QAAQ,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,KAAK,CAAC;IAC7C,IAAI,CAAC,KAAK,CAAC,eAAe,CAAC,OAAO,CAAC,OAAO,CAAC,YAAY,CAAC;IACxD,IAAM,EAAE,GAAG,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC;IAC/C,IAAM,EAAE,GAAG,IAAI,CAAC,KAAK,CAAC,eAAe,CAAC,OAAO,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE,CAAC,CAAC;IACvE,IAAI,EAAE,gBAAqB;QAAE,OAAO,KAAK,CAAC;IAC1C,IAAI,EAAE,kBAAuB;QAAE,OAAO,KAAK,CAAC;IAC5C,OAAO,IAAI,CAAC;AAChB,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,cAA8B;IAC/C,IAAA,KAAK,GAAgB,cAAc,MAA9B,EAAE,SAAS,GAAK,cAAc,UAAnB,CAAoB;IAC5C,IAAM,UAAU,GAAG,CAAC,CAAC;IACrB,IAAM,aAAa,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC;IACzC,IAAM,QAAQ,GAAG,gBAAgB,CAAC,QAAQ,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;IAC7D,IAAM,WAAW,GAAG,UAAC,UAAkB,EAAE,aAAqB;QAC1D,IAAM,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC;QACxC,QAAQ,CAAC,IAAI,GAAG,IAAI,CAAC;QACrB,QAAQ,CAAC,OAAO,GAAG,IAAI,CAAC,QAAQ,CAAC,UAAU,CAAC,CAAC;QAC7C,OAAO,QAAQ,CAAC;IACpB,CAAC,CAAC;IACF,OAAO,gBAAgB,CAAC,UAAU,EAAE,aAAa,EAAE,CAAC,EAAE,WAAW,CAAC,CAAC;AACvE,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,SAAoB,EAAE,cAA8B,EAAE,EAAU;IAChF,IAAA,QAAQ,GAAiB,SAAS,SAA1B,EAAE,UAAU,GAAK,SAAS,WAAd,CAAe;IAC3C,IAAI,EAAE,KAAK,QAAQ,EAAE;QACT,IAAA,SAAS,GAAY,cAAc,UAA1B,EAAE,KAAK,GAAK,cAAc,MAAnB,CAAoB;QAC5C,IAAM,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;QACrC,IAAM,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,QAAQ,CAAC,MAAM,CAA0B,CAAC;QACtF,OAAO,gBAAgB,CAAC,IAAI,CAAC,SAAS,EAAE,CAAC,EAAE,IAAI,MAAA,EAAE,OAAO,SAAA,EAAE,CAAC,CAAC,CAAC;KAChE;IACD,OAAO,SAAS,CAAC;AACrB,CAAC;AAED,MAAM,UAAU,QAAQ,CAAC,IAAU,EAAE,cAA8B,EAAE,KAAsC;IACvG,IAAI,OAAO,GAAG,KAAK,CAAC;IACpB,IAAI,CAAC,gBAAgB,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC;QAAE,OAAO,KAAK,CAAC;IAC1C,IAAA,SAAS,GAAY,cAAc,UAA1B,EAAE,KAAK,GAAK,cAAc,MAAnB,CAAoB;IAC5C,IAAI,CAAC,SAAS,CAAC,aAAa,CAAC,IAAI,CAAC,SAAS,EAAE,SAAS,CAAC;QAAE,OAAO,KAAK,CAAC;IACtE,IAAM,YAAY,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,CAAC;IAC3C,KAAgB,UAAa,EAAb,KAAA,IAAI,CAAC,QAAQ,EAAb,cAAa,EAAb,IAAa,EAAE;QAA1B,IAAM,CAAC,SAAA;QACR,IAAM,OAAO,GAAG,KAAK,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAClD,IAAI,OAAO,KAAK,SAAS,EAAE;YACvB,IAAI,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,YAAY,EAAE;gBAC7C,IAAI,KAAK,CAAC,QAAQ,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC;oBAAE,OAAO,GAAG,IAAI,CAAC;aAC5D;SACJ;KACJ;IACD,OAAO,OAAO,CAAC;AACnB,CAAC"}

package/lib/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/mol-repr/volume/direct-volume.d.ts

@@ -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<{
@@ -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<{
@@ -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<{

package/lib/mol-repr/volume/registry.d.ts

@@ -149,7 +149,7 @@ export declare namespace VolumeRepresentationRegistry {
             renderMode: import("../../mol-util/param-definition").ParamDefinition.Mapped<import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.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"> | import("../../mol-util/param-definition").ParamDefinition.NamedParams<import("../../mol-util/param-definition").ParamDefinition.Normalize<{

package/lib/mol-repr/volume/registry.js

@@ -15,7 +15,7 @@ var VolumeRepresentationRegistry = /** @class */ (function (_super) {
         var _this = _super.call(this) || this;
         objectForEach(VolumeRepresentationRegistry.BuiltIn, function (p, k) {
             if (p.name !== k)
-                throw new Error("Fix BuiltInVolumeRepresentations to have matching names. " + p.name + " " + k);
+                throw new Error("Fix BuiltInVolumeRepresentations to have matching names. ".concat(p.name, " ").concat(k));
             _this.add(p);
         });
         return _this;

package/lib/mol-repr/volume/registry.js.map

@@ -1 +1 @@
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+{"version":3,"file":"registry.js","sourceRoot":"","sources":["../../../src/mol-repr/volume/registry.ts"],"names":[],"mappings":"AAAA;;;;GAIG;;AAEH,OAAO,EAAE,sBAAsB,EAA0C,MAAM,mBAAmB,CAAC;AAEnG,OAAO,EAAE,gCAAgC,EAAE,MAAM,cAAc,CAAC;AAChE,OAAO,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;AACtD,OAAO,EAAE,2BAA2B,EAAE,MAAM,SAAS,CAAC;AACtD,OAAO,EAAE,kCAAkC,EAAE,MAAM,iBAAiB,CAAC;AAErE;IAAkD,gDAAoD;IAClG;QAAA,YACI,iBAAO,SAKV;QAJG,aAAa,CAAC,4BAA4B,CAAC,OAAO,EAAE,UAAC,CAAC,EAAE,CAAC;YACrD,IAAI,CAAC,CAAC,IAAI,KAAK,CAAC;gBAAE,MAAM,IAAI,KAAK,CAAC,mEAA4D,CAAC,CAAC,IAAI,cAAI,CAAC,CAAE,CAAC,CAAC;YAC7G,KAAI,CAAC,GAAG,CAAC,CAAQ,CAAC,CAAC;QACvB,CAAC,CAAC,CAAC;;IACP,CAAC;IACL,mCAAC;AAAD,CAAC,AARD,CAAkD,sBAAsB,GAQvE;;AAED,WAAiB,4BAA4B;IAC5B,oCAAO,GAAG;QACnB,YAAY,EAAE,gCAAgC;QAC9C,OAAO,EAAE,2BAA2B;QACpC,eAAe,EAAE,kCAAkC;KACtD,CAAC;AAKN,CAAC,EAVgB,4BAA4B,KAA5B,4BAA4B,QAU5C"}

package/lib/mol-script/language/builder.d.ts

@@ -10,7 +10,6 @@ export declare namespace MolScriptBuilder {
         '@header': string;
         type: {
             '@header': string;
-            /** atom macromolecular property set */
             bool: MSymbol<import("./symbol").Arguments<import("./symbol").Arguments.PropTypes<{
                 0: import("./symbol").Argument<import("./type").Type.AnyValue>;
             }>>, import("./type").Type.OneOf<boolean>>;