molstar 2.3.3 → 2.3.8

package/lib/commonjs/mol-repr/structure/visual/label-text.js

@@ -60,7 +60,7 @@ function createChainText(ctx, structure, theme, props, text) {
         linear_algebra_1.Vec3.transformMat4(tmpVec, center, unit.conformation.operator.matrix);
         var authId = auth_asym_id(l);
         var labelId = label_asym_id(l);
-        var text_1 = authId === labelId ? labelId : labelId + " [" + authId + "]";
+        var text_1 = authId === labelId ? labelId : "".concat(labelId, " [").concat(authId, "]");
         builder.add(text_1, tmpVec[0], tmpVec[1], tmpVec[2], radius, chainScale, cumulativeUnitElementCount[i]);
     }
     return builder.getText();
@@ -103,7 +103,7 @@ function createResidueText(ctx, structure, theme, props, text) {
             var _a = boundaryHelper.getSphere(), center = _a.center, radius = _a.radius;
             var authSeqId = auth_seq_id(l);
             var compId = label_comp_id(l);
-            var text_2 = compId + " " + authSeqId;
+            var text_2 = "".concat(compId, " ").concat(authSeqId);
             builder.add(text_2, center[0], center[1], center[2], radius, residueScale, groupOffset + start);
         }
     }
@@ -129,7 +129,7 @@ function createElementText(ctx, structure, theme, props, text) {
             pos(l.element, tmpVec);
             var atomId = label_atom_id(l);
             var altId = label_alt_id(l);
-            var text_3 = altId ? atomId + "%" + altId : atomId;
+            var text_3 = altId ? "".concat(atomId, "%").concat(altId) : atomId;
             builder.add(text_3, tmpVec[0], tmpVec[1], tmpVec[2], sizeTheme.size(l), elementScale, groupOffset + j);
         }
     }

package/lib/commonjs/mol-repr/structure/visual/label-text.js.map

@@ -1 +1 @@
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package/lib/commonjs/mol-repr/structure/visual/molecular-surface-mesh.d.ts

@@ -16,14 +16,14 @@ export declare const MolecularSurfaceMeshParams: {
     probeRadius: PD.Numeric;
     resolution: PD.Numeric;
     probePositions: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type MolecularSurfaceMeshParams = typeof MolecularSurfaceMeshParams;
 export declare type MolecularSurfaceMeshProps = PD.Values<MolecularSurfaceMeshParams>;

package/lib/commonjs/mol-repr/structure/visual/molecular-surface-wireframe.d.ts

@@ -13,10 +13,10 @@ export declare const MolecularSurfaceWireframeParams: {
     probeRadius: PD.Numeric;
     resolution: PD.Numeric;
     probePositions: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     lineSizeAttenuation: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type MolecularSurfaceWireframeParams = typeof MolecularSurfaceWireframeParams;
 export declare function MolecularSurfaceWireframeVisual(materialId: number): UnitsVisual<MolecularSurfaceWireframeParams>;

package/lib/commonjs/mol-repr/structure/visual/nucleotide-block-mesh.d.ts

@@ -17,7 +17,7 @@ export declare type NucleotideBlockMeshProps = typeof DefaultNucleotideBlockMesh
 export declare const NucleotideBlockParams: {
     sizeFactor: PD.Numeric;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -25,7 +25,7 @@ export declare const NucleotideBlockParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type NucleotideBlockParams = typeof NucleotideBlockParams;
 export declare function NucleotideBlockVisual(materialId: number): UnitsVisual<NucleotideBlockParams>;

package/lib/commonjs/mol-repr/structure/visual/nucleotide-ring-mesh.d.ts

@@ -20,7 +20,7 @@ export declare const NucleotideRingParams: {
     sizeFactor: PD.Numeric;
     radialSegments: PD.Numeric;
     detail: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -28,7 +28,7 @@ export declare const NucleotideRingParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type NucleotideRingParams = typeof NucleotideRingParams;
 export declare function NucleotideRingVisual(materialId: number): UnitsVisual<NucleotideRingParams>;

package/lib/commonjs/mol-repr/structure/visual/orientation-ellipsoid-mesh.d.ts

@@ -12,7 +12,7 @@ import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
 export declare const OrientationEllipsoidMeshParams: {
     sizeFactor: PD.Numeric;
     detail: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -20,7 +20,7 @@ export declare const OrientationEllipsoidMeshParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type OrientationEllipsoidMeshParams = typeof OrientationEllipsoidMeshParams;
 export declare function OrientationEllipsoidMeshVisual(materialId: number): UnitsVisual<OrientationEllipsoidMeshParams>;

package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-cylinder.d.ts

@@ -11,14 +11,14 @@ export declare const PolymerBackboneCylinderParams: {
     sizeFactor: PD.Numeric;
     radialSegments: PD.Numeric;
     tryUseImpostor: PD.BooleanParam;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     sizeAspectRatio: PD.Numeric;
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 };
@@ -27,14 +27,14 @@ export declare function PolymerBackboneCylinderVisual(materialId: number, struct
     sizeFactor: PD.Numeric;
     radialSegments: PD.Numeric;
     tryUseImpostor: PD.BooleanParam;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     sizeAspectRatio: PD.Numeric;
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 }>;

package/lib/commonjs/mol-repr/structure/visual/polymer-backbone-sphere.d.ts

@@ -11,13 +11,13 @@ export declare const PolymerBackboneSphereParams: {
     sizeFactor: PD.Numeric;
     detail: PD.Numeric;
     tryUseImpostor: PD.BooleanParam;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 };
@@ -26,13 +26,13 @@ export declare function PolymerBackboneSphereVisual(materialId: number, structur
     sizeFactor: PD.Numeric;
     detail: PD.Numeric;
     tryUseImpostor: PD.BooleanParam;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
 }>;

package/lib/commonjs/mol-repr/structure/visual/polymer-direction-wedge.d.ts

@@ -14,7 +14,7 @@ export declare const DefaultPolymerDirectionWedgeProps: PD.Values<{
 export declare type PolymerDirectionWedgeProps = typeof DefaultPolymerDirectionWedgeProps;
 export declare const PolymerDirectionParams: {
     sizeFactor: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -22,7 +22,7 @@ export declare const PolymerDirectionParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type PolymerDirectionParams = typeof PolymerDirectionParams;
 export declare function PolymerDirectionVisual(materialId: number): UnitsVisual<PolymerDirectionParams>;

package/lib/commonjs/mol-repr/structure/visual/polymer-gap-cylinder.d.ts

@@ -17,7 +17,7 @@ export declare type PolymerGapCylinderProps = typeof DefaultPolymerGapCylinderPr
 export declare const PolymerGapParams: {
     sizeFactor: PD.Numeric;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -25,7 +25,7 @@ export declare const PolymerGapParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type PolymerGapParams = typeof PolymerGapParams;
 export declare function PolymerGapVisual(materialId: number): UnitsVisual<PolymerGapParams>;

package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.d.ts

@@ -10,6 +10,7 @@ export declare const PolymerTraceMeshParams: {
     aspectRatio: PD.Numeric;
     arrowFactor: PD.Numeric;
     tubularHelices: PD.BooleanParam;
+    helixProfile: PD.Select<"square" | "elliptical" | "rounded">;
     detail: PD.Numeric;
     linearSegments: PD.Numeric;
     radialSegments: PD.Numeric;
@@ -19,6 +20,7 @@ export declare const DefaultPolymerTraceMeshProps: PD.Values<{
     aspectRatio: PD.Numeric;
     arrowFactor: PD.Numeric;
     tubularHelices: PD.BooleanParam;
+    helixProfile: PD.Select<"square" | "elliptical" | "rounded">;
     detail: PD.Numeric;
     linearSegments: PD.Numeric;
     radialSegments: PD.Numeric;
@@ -29,10 +31,11 @@ export declare const PolymerTraceParams: {
     aspectRatio: PD.Numeric;
     arrowFactor: PD.Numeric;
     tubularHelices: PD.BooleanParam;
+    helixProfile: PD.Select<"square" | "elliptical" | "rounded">;
     detail: PD.Numeric;
     linearSegments: PD.Numeric;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -40,7 +43,7 @@ export declare const PolymerTraceParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type PolymerTraceParams = typeof PolymerTraceParams;
 export declare function PolymerTraceVisual(materialId: number): UnitsVisual<PolymerTraceParams>;

package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.js

@@ -25,8 +25,9 @@ var geometry_1 = require("../../../mol-math/geometry");
 exports.PolymerTraceMeshParams = {
     sizeFactor: param_definition_1.ParamDefinition.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
     aspectRatio: param_definition_1.ParamDefinition.Numeric(5, { min: 0.1, max: 10, step: 0.1 }),
-    arrowFactor: param_definition_1.ParamDefinition.Numeric(1.5, { min: 0, max: 3, step: 0.1 }),
-    tubularHelices: param_definition_1.ParamDefinition.Boolean(false),
+    arrowFactor: param_definition_1.ParamDefinition.Numeric(1.5, { min: 0, max: 3, step: 0.1 }, { description: 'Size factor for sheet arrows' }),
+    tubularHelices: param_definition_1.ParamDefinition.Boolean(false, { description: 'Draw alpha helices as tubes' }),
+    helixProfile: param_definition_1.ParamDefinition.Select('elliptical', param_definition_1.ParamDefinition.arrayToOptions(['elliptical', 'rounded', 'square']), { description: 'Protein and nucleic helix trace profile' }),
     detail: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 3, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo),
     linearSegments: param_definition_1.ParamDefinition.Numeric(8, { min: 1, max: 48, step: 1 }, base_1.BaseGeometry.CustomQualityParamInfo),
     radialSegments: param_definition_1.ParamDefinition.Numeric(16, { min: 2, max: 56, step: 2 }, base_1.BaseGeometry.CustomQualityParamInfo)
@@ -34,11 +35,10 @@ exports.PolymerTraceMeshParams = {
 exports.DefaultPolymerTraceMeshProps = param_definition_1.ParamDefinition.getDefaultValues(exports.PolymerTraceMeshParams);
 var tmpV1 = (0, linear_algebra_1.Vec3)();
 function createPolymerTraceMesh(ctx, unit, structure, theme, props, mesh) {
-    var _a, _b, _c;
     var polymerElementCount = unit.polymerElements.length;
     if (!polymerElementCount)
         return mesh_1.Mesh.createEmpty(mesh);
-    var sizeFactor = props.sizeFactor, detail = props.detail, linearSegments = props.linearSegments, radialSegments = props.radialSegments, aspectRatio = props.aspectRatio, arrowFactor = props.arrowFactor, tubularHelices = props.tubularHelices;
+    var sizeFactor = props.sizeFactor, detail = props.detail, linearSegments = props.linearSegments, radialSegments = props.radialSegments, aspectRatio = props.aspectRatio, arrowFactor = props.arrowFactor, tubularHelices = props.tubularHelices, helixProfile = props.helixProfile;
     var vertexCount = linearSegments * radialSegments * polymerElementCount + (radialSegments + 1) * polymerElementCount * 2;
     var builderState = mesh_builder_1.MeshBuilder.createState(vertexCount, vertexCount / 10, mesh);
     var isCoarse = structure_1.Unit.isCoarse(unit);
@@ -121,9 +121,6 @@ function createPolymerTraceMesh(ctx, unit, structure, theme, props, mesh) {
                 h0 = w0 * aspectRatio;
                 h1 = w1 * aspectRatio;
                 h2 = w2 * aspectRatio;
-                _a = [h0, w0], w0 = _a[0], h0 = _a[1];
-                _b = [h1, w1], w1 = _b[0], h1 = _b[1];
-                _c = [h2, w2], w2 = _c[0], h2 = _c[1];
             }
             else {
                 h0 = w0;
@@ -131,22 +128,31 @@ function createPolymerTraceMesh(ctx, unit, structure, theme, props, mesh) {
                 h2 = w2;
             }
             (0, polymer_1.interpolateSizes)(state, w0, w1, w2, h0, h1, h2, shift);
+            var _a = isNucleicType && !v.isCoarseBackbone ? [binormalVectors, normalVectors] : [normalVectors, binormalVectors], normals = _a[0], binormals = _a[1];
+            if (isNucleicType && !v.isCoarseBackbone) {
+                // TODO: find a cleaner way to swap normal and binormal for nucleic types
+                for (var i_1 = 0, il = normals.length; i_1 < il; i_1++)
+                    normals[i_1] *= -1;
+            }
             if (radialSegments === 2) {
                 if (isNucleicType && !v.isCoarseBackbone) {
-                    // TODO find a cleaner way to swap normal and binormal for nucleic types
-                    for (var i_1 = 0, il = binormalVectors.length; i_1 < il; i_1++)
-                        binormalVectors[i_1] *= -1;
-                    (0, ribbon_1.addRibbon)(builderState, curvePoints, binormalVectors, normalVectors, segmentCount, heightValues, widthValues, 0);
+                    (0, ribbon_1.addRibbon)(builderState, curvePoints, normals, binormals, segmentCount, heightValues, widthValues, 0);
                 }
                 else {
-                    (0, ribbon_1.addRibbon)(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0);
+                    (0, ribbon_1.addRibbon)(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0);
                 }
             }
             else if (radialSegments === 4) {
-                (0, sheet_1.addSheet)(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0, startCap, endCap);
+                (0, sheet_1.addSheet)(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0, startCap, endCap);
+            }
+            else if (h1 === w1) {
+                (0, tube_1.addTube)(builderState, curvePoints, normals, binormals, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, 'elliptical');
+            }
+            else if (helixProfile === 'square') {
+                (0, sheet_1.addSheet)(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0, startCap, endCap);
             }
             else {
-                (0, tube_1.addTube)(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap);
+                (0, tube_1.addTube)(builderState, curvePoints, normals, binormals, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, helixProfile);
             }
         }
         ++i;
@@ -171,7 +177,8 @@ function PolymerTraceVisual(materialId) {
                 newProps.linearSegments !== currentProps.linearSegments ||
                 newProps.radialSegments !== currentProps.radialSegments ||
                 newProps.aspectRatio !== currentProps.aspectRatio ||
-                newProps.arrowFactor !== currentProps.arrowFactor);
+                newProps.arrowFactor !== currentProps.arrowFactor ||
+                newProps.helixProfile !== currentProps.helixProfile);
             var secondaryStructureHash = secondary_structure_1.SecondaryStructureProvider.get(newStructureGroup.structure).version;
             if (state.info.secondaryStructureHash !== secondaryStructureHash) {
                 state.createGeometry = true;

package/lib/commonjs/mol-repr/structure/visual/polymer-trace-mesh.js.map

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

@@ -23,7 +23,7 @@ export declare const PolymerTubeParams: {
     detail: PD.Numeric;
     linearSegments: PD.Numeric;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -31,7 +31,7 @@ export declare const PolymerTubeParams: {
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type PolymerTubeParams = typeof PolymerTubeParams;
 export declare function PolymerTubeVisual(materialId: number): UnitsVisual<PolymerTubeParams>;

package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.js

@@ -82,7 +82,7 @@ function createPolymerTubeMesh(ctx, unit, structure, theme, props, mesh) {
             (0, sheet_1.addSheet)(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0, startCap, endCap);
         }
         else {
-            (0, tube_1.addTube)(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap);
+            (0, tube_1.addTube)(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, 'elliptical');
         }
         ++i;
     }

package/lib/commonjs/mol-repr/structure/visual/polymer-tube-mesh.js.map

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

@@ -12,27 +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<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    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<"offset" | "off" | "symmetric">;
 };
 export declare const DefaultBondProps: PD.Values<{
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    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<"offset" | "off" | "symmetric">;
 }>;
 export declare type BondProps = typeof DefaultBondProps;
 export declare const BondCylinderParams: {
     adjustCylinderLength: PD.BooleanParam;
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    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<"offset" | "off" | "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;
@@ -41,13 +47,17 @@ export declare const BondCylinderParams: {
 };
 export declare const DefaultBondCylinderProps: PD.Values<{
     adjustCylinderLength: PD.BooleanParam;
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    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<"offset" | "off" | "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;
@@ -56,21 +66,25 @@ export declare const DefaultBondCylinderProps: PD.Values<{
 }>;
 export declare type BondCylinderProps = typeof DefaultBondCylinderProps;
 export declare const BondLineParams: {
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    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<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
 };
 export declare const DefaultBondLineProps: PD.Values<{
-    includeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
-    excludeTypes: PD.MultiSelect<"computed" | "covalent" | "metal-coordination" | "hydrogen-bond" | "disulfide" | "aromatic">;
+    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<"offset" | "off" | "symmetric">;
     linkScale: PD.Numeric;
     linkSpacing: PD.Numeric;
+    aromaticDashCount: PD.Numeric;
     dashCount: PD.Numeric;
 }>;
 export declare type BondLineProps = typeof DefaultBondLineProps;
@@ -81,11 +95,11 @@ export declare namespace BondIterator {
     function fromGroup(structureGroup: StructureGroup): LocationIterator;
     function fromStructure(structure: Structure): LocationIterator;
 }
-export declare function getIntraBondLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): {
+export declare function getIntraBondLoci(pickingId: PickingId, structureGroup: StructureGroup, id: number): Bond.Loci | {
     kind: "empty-loci";
-} | Bond.Loci;
+};
 export declare function eachIntraBond(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean, isMarking: boolean): boolean;
-export declare function getInterBondLoci(pickingId: PickingId, structure: Structure, id: number): {
+export declare function getInterBondLoci(pickingId: PickingId, structure: Structure, id: number): Bond.Loci | {
     kind: "empty-loci";
-} | Bond.Loci;
+};
 export declare function eachInterBond(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean, isMarking: boolean): boolean;