npm - molstar - Versions diffs - 2.3.3 → 2.3.8 - Mend

molstar 2.3.3 → 2.3.8

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Files changed (1829) hide show

package/lib/mol-repr/structure/visual/orientation-axes-mesh.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"orientation-axes-mesh.js","sourceRoot":"","sources":["../../../../src/mol-repr/structure/visual/orientation-axes-mesh.ts"],"names":[],"mappings":"AAAA;;;;GAIG;;AAEH,OAAO,EAAE,eAAe,IAAI,EAAE,EAAE,MAAM,oCAAoC,CAAC;AAC3E,OAAO,EAAE,eAAe,EAAe,eAAe,EAAE,MAAM,iBAAiB,CAAC;AAKhF,OAAO,EAAE,IAAI,EAAE,MAAM,qCAAqC,CAAC;AAC3D,OAAO,EAAE,WAAW,EAAE,MAAM,6CAA6C,CAAC;AAC1E,OAAO,EAAE,OAAO,EAAE,MAAM,6CAA6C,CAAC;AACtE,OAAO,EAAE,QAAQ,EAAE,MAAM,4BAA4B,CAAC;AACtD,OAAO,EAAE,YAAY,EAAE,MAAM,gCAAgC,CAAC;AAC9D,OAAO,EAAE,QAAQ,EAAE,WAAW,EAAE,gBAAgB,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAE3F,MAAM,CAAC,IAAM,yBAAyB,yBAC/B,eAAe,KAClB,UAAU,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC,EACxD,SAAS,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC,EACxD,cAAc,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,YAAY,CAAC,sBAAsB,CAAC,EACjG,MAAM,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,YAAY,CAAC,sBAAsB,CAAC,GAC1F,CAAC;AAGF,MAAM,UAAU,yBAAyB,CAAC,UAAkB;IACxD,OAAO,eAAe,CAA4B;QAC9C,YAAY,EAAE,EAAE,CAAC,gBAAgB,CAAC,yBAAyB,CAAC;QAC5D,cAAc,EAAE,yBAAyB;QACzC,sBAAsB,EAAE,YAAY;QACpC,OAAO,EAAE,WAAW;QACpB,YAAY,EAAE,QAAQ;QACtB,cAAc,EAAE,UAAC,KAAwB,EAAE,QAA8C,EAAE,YAAkD;YACzI,KAAK,CAAC,cAAc,GAAG,CACnB,QAAQ,CAAC,UAAU,KAAK,YAAY,CAAC,UAAU;gBAC/C,QAAQ,CAAC,MAAM,KAAK,YAAY,CAAC,MAAM,CAC1C,CAAC;QACN,CAAC;KACJ,EAAE,UAAU,CAAC,CAAC;AACnB,CAAC;AAWD,MAAM,UAAU,yBAAyB,CAAC,GAAkB,EAAE,IAAU,EAAE,SAAoB,EAAE,KAAY,EAAE,KAA+B,EAAE,IAAW;IACtJ,IAAI,CAAC,gBAAgB,CAAC,IAAI,CAAC;QAAE,OAAO,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC;IAEnD,IAAA,MAAM,GAA4C,KAAK,OAAjD,EAAE,UAAU,GAAgC,KAAK,WAArC,EAAE,cAAc,GAAgB,KAAK,eAArB,EAAE,SAAS,GAAK,KAAK,UAAV,CAAW;IAEhE,IAAM,WAAW,GAAG,GAAG,CAAC;IACxB,IAAM,YAAY,GAAG,WAAW,CAAC,WAAW,CAAC,WAAW,EAAE,WAAW,GAAG,CAAC,EAAE,IAAI,CAAC,CAAC;IACjF,IAAM,IAAI,GAAG,IAAI,CAAC,aAAa,CAAC,WAAW,CAAC;IAE5C,YAAY,CAAC,YAAY,GAAG,CAAC,CAAC;IAC9B,OAAO,CAAC,YAAY,EAAE,IAAI,EAAE,SAAS,EAAE,MAAM,EAAE,cAAc,CAAC,CAAC;IAE/D,IAAM,CAAC,GAAG,WAAW,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC;IAE5C,IAAM,MAAM,GAAG,QAAQ,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC;IACvF,CAAC,CAAC,iBAAiB,CAAC,MAAM,CAAC,CAAC;IAE5B,OAAO,CAAC,CAAC;AACb,CAAC"}

package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh copy.d.ts ADDED Viewed

@@ -0,0 +1,31 @@
+/**
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { UnitsVisual } from '../../../mol-repr/structure/units-visual';
+import { VisualContext } from '../../../mol-repr/visual';
+import { Unit, Structure } from '../../../mol-model/structure';
+import { Theme } from '../../../mol-theme/theme';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+export declare const OrientationEllipsoidMeshParams: {
+    sizeFactor: PD.Numeric;
+    detail: PD.Numeric;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
+    includeParent: PD.BooleanParam;
+    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">;
+};
+export declare type OrientationEllipsoidMeshParams = typeof OrientationEllipsoidMeshParams;
+export declare function OrientationEllipsoidMeshVisual(materialId: number): UnitsVisual<OrientationEllipsoidMeshParams>;
+export interface OrientationEllipsoidMeshProps {
+    detail: number;
+    sizeFactor: number;
+}
+export declare function createOrientationEllipsoidMesh(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: OrientationEllipsoidMeshProps, mesh?: Mesh): Mesh;

package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh copy.js ADDED Viewed

@@ -0,0 +1,48 @@
+/**
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+import { __assign } from "tslib";
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { UnitsMeshParams, UnitsMeshVisual } from '../../../mol-repr/structure/units-visual';
+import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from '../../../mol-geo/geometry/mesh/mesh-builder';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { addEllipsoid } from '../../../mol-geo/geometry/mesh/builder/ellipsoid';
+import { Axes3D, Sphere3D } from '../../../mol-math/geometry';
+import { BaseGeometry } from '../../../mol-geo/geometry/base';
+import { eachUnit, getUnitLoci, isUnitApplicable, UnitIterator } from './util/orientation';
+export var OrientationEllipsoidMeshParams = __assign(__assign({}, UnitsMeshParams), { sizeFactor: PD.Numeric(1, { min: 0, max: 2, step: 0.1 }), detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo) });
+export function OrientationEllipsoidMeshVisual(materialId) {
+    return UnitsMeshVisual({
+        defaultProps: PD.getDefaultValues(OrientationEllipsoidMeshParams),
+        createGeometry: createOrientationEllipsoidMesh,
+        createLocationIterator: UnitIterator,
+        getLoci: getUnitLoci,
+        eachLocation: eachUnit,
+        setUpdateState: function (state, newProps, currentProps) {
+            state.createGeometry = (newProps.sizeFactor !== currentProps.sizeFactor ||
+                newProps.detail !== currentProps.detail);
+        }
+    }, materialId);
+}
+export function createOrientationEllipsoidMesh(ctx, unit, structure, theme, props, mesh) {
+    if (!isUnitApplicable(unit))
+        return Mesh.createEmpty(mesh);
+    var detail = props.detail, sizeFactor = props.sizeFactor;
+    var vertexCount = 256;
+    var builderState = MeshBuilder.createState(vertexCount, vertexCount / 2, mesh);
+    var axes = unit.principalAxes.boxAxes;
+    var origin = axes.origin, dirA = axes.dirA, dirB = axes.dirB;
+    var size = Axes3D.size(Vec3(), axes);
+    Vec3.scale(size, size, sizeFactor / 2);
+    var radiusScale = Vec3.create(size[2], size[1], size[0]);
+    builderState.currentGroup = 0;
+    addEllipsoid(builderState, origin, dirA, dirB, radiusScale, detail + 1);
+    var m = MeshBuilder.getMesh(builderState);
+    var sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, 1 * props.sizeFactor);
+    m.setBoundingSphere(sphere);
+    return m;
+}
+//# sourceMappingURL=orientation-ellipsoid-mesh%20copy.js.map

package/lib/mol-repr/structure/visual/orientation-ellipsoid-mesh copy.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"orientation-ellipsoid-mesh copy.js","sourceRoot":"","sources":["../../../../src/mol-repr/structure/visual/orientation-ellipsoid-mesh copy.ts"],"names":[],"mappings":"AAAA;;;;GAIG;;AAEH,OAAO,EAAE,eAAe,IAAI,EAAE,EAAE,MAAM,oCAAoC,CAAC;AAC3E,OAAO,EAAE,eAAe,EAAe,eAAe,EAAE,MAAM,0CAA0C,CAAC;AAKzG,OAAO,EAAE,IAAI,EAAE,MAAM,qCAAqC,CAAC;AAC3D,OAAO,EAAE,WAAW,EAAE,MAAM,6CAA6C,CAAC;AAC1E,OAAO,EAAE,IAAI,EAAE,MAAM,kCAAkC,CAAC;AACxD,OAAO,EAAE,YAAY,EAAE,MAAM,kDAAkD,CAAC;AAChF,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,4BAA4B,CAAC;AAC9D,OAAO,EAAE,YAAY,EAAE,MAAM,gCAAgC,CAAC;AAC9D,OAAO,EAAE,QAAQ,EAAE,WAAW,EAAE,gBAAgB,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAE3F,MAAM,CAAC,IAAM,8BAA8B,yBACpC,eAAe,KAClB,UAAU,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC,EACxD,MAAM,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,YAAY,CAAC,sBAAsB,CAAC,GAC1F,CAAC;AAGF,MAAM,UAAU,8BAA8B,CAAC,UAAkB;IAC7D,OAAO,eAAe,CAAiC;QACnD,YAAY,EAAE,EAAE,CAAC,gBAAgB,CAAC,8BAA8B,CAAC;QACjE,cAAc,EAAE,8BAA8B;QAC9C,sBAAsB,EAAE,YAAY;QACpC,OAAO,EAAE,WAAW;QACpB,YAAY,EAAE,QAAQ;QACtB,cAAc,EAAE,UAAC,KAAwB,EAAE,QAAmD,EAAE,YAAuD;YACnJ,KAAK,CAAC,cAAc,GAAG,CACnB,QAAQ,CAAC,UAAU,KAAK,YAAY,CAAC,UAAU;gBAC/C,QAAQ,CAAC,MAAM,KAAK,YAAY,CAAC,MAAM,CAC1C,CAAC;QACN,CAAC;KACJ,EAAE,UAAU,CAAC,CAAC;AACnB,CAAC;AASD,MAAM,UAAU,8BAA8B,CAAC,GAAkB,EAAE,IAAU,EAAE,SAAoB,EAAE,KAAY,EAAE,KAAoC,EAAE,IAAW;IAChK,IAAI,CAAC,gBAAgB,CAAC,IAAI,CAAC;QAAE,OAAO,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC;IAEnD,IAAA,MAAM,GAAiB,KAAK,OAAtB,EAAE,UAAU,GAAK,KAAK,WAAV,CAAW;IAErC,IAAM,WAAW,GAAG,GAAG,CAAC;IACxB,IAAM,YAAY,GAAG,WAAW,CAAC,WAAW,CAAC,WAAW,EAAE,WAAW,GAAG,CAAC,EAAE,IAAI,CAAC,CAAC;IACjF,IAAM,IAAI,GAAG,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC;IAChC,IAAA,MAAM,GAAiB,IAAI,OAArB,EAAE,IAAI,GAAW,IAAI,KAAf,EAAE,IAAI,GAAK,IAAI,KAAT,CAAU;IAEpC,IAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,EAAE,EAAE,IAAI,CAAC,CAAC;IACvC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,IAAI,EAAE,UAAU,GAAG,CAAC,CAAC,CAAC;IACvC,IAAM,WAAW,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;IAE3D,YAAY,CAAC,YAAY,GAAG,CAAC,CAAC;IAC9B,YAAY,CAAC,YAAY,EAAE,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,WAAW,EAAE,MAAM,GAAG,CAAC,CAAC,CAAC;IAExE,IAAM,CAAC,GAAG,WAAW,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC;IAE5C,IAAM,MAAM,GAAG,QAAQ,CAAC,MAAM,CAAC,QAAQ,EAAE,EAAE,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC;IACvF,CAAC,CAAC,iBAAiB,CAAC,MAAM,CAAC,CAAC;IAE5B,OAAO,CAAC,CAAC;AACb,CAAC"}

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

@@ -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;

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

@@ -11,7 +11,7 @@ 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;
@@ -27,7 +27,7 @@ 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;

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

@@ -11,7 +11,7 @@ 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;
@@ -26,7 +26,7 @@ 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;

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

@@ -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;

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

@@ -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;

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

@@ -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;

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

@@ -22,8 +22,9 @@ import { Sphere3D } from '../../../mol-math/geometry';
 export var PolymerTraceMeshParams = {
     sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
     aspectRatio: PD.Numeric(5, { min: 0.1, max: 10, step: 0.1 }),
-    arrowFactor: PD.Numeric(1.5, { min: 0, max: 3, step: 0.1 }),
-    tubularHelices: PD.Boolean(false),
+    arrowFactor: PD.Numeric(1.5, { min: 0, max: 3, step: 0.1 }, { description: 'Size factor for sheet arrows' }),
+    tubularHelices: PD.Boolean(false, { description: 'Draw alpha helices as tubes' }),
+    helixProfile: PD.Select('elliptical', PD.arrayToOptions(['elliptical', 'rounded', 'square']), { description: 'Protein and nucleic helix trace profile' }),
     detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
     linearSegments: PD.Numeric(8, { min: 1, max: 48, step: 1 }, BaseGeometry.CustomQualityParamInfo),
     radialSegments: PD.Numeric(16, { min: 2, max: 56, step: 2 }, BaseGeometry.CustomQualityParamInfo)
@@ -31,11 +32,10 @@ export var PolymerTraceMeshParams = {
 export var DefaultPolymerTraceMeshProps = PD.getDefaultValues(PolymerTraceMeshParams);
 var tmpV1 = Vec3();
 function createPolymerTraceMesh(ctx, unit, structure, theme, props, mesh) {
-    var _a, _b, _c;
     var polymerElementCount = unit.polymerElements.length;
     if (!polymerElementCount)
         return 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 = MeshBuilder.createState(vertexCount, vertexCount / 10, mesh);
     var isCoarse = Unit.isCoarse(unit);
@@ -118,9 +118,6 @@ 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;
@@ -128,22 +125,31 @@ function createPolymerTraceMesh(ctx, unit, structure, theme, props, mesh) {
                 h2 = w2;
             }
             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;
-                    addRibbon(builderState, curvePoints, binormalVectors, normalVectors, segmentCount, heightValues, widthValues, 0);
+                    addRibbon(builderState, curvePoints, normals, binormals, segmentCount, heightValues, widthValues, 0);
                 }
                 else {
-                    addRibbon(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0);
+                    addRibbon(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0);
                 }
             }
             else if (radialSegments === 4) {
-                addSheet(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0, startCap, endCap);
+                addSheet(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0, startCap, endCap);
+            }
+            else if (h1 === w1) {
+                addTube(builderState, curvePoints, normals, binormals, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, 'elliptical');
+            }
+            else if (helixProfile === 'square') {
+                addSheet(builderState, curvePoints, normals, binormals, segmentCount, widthValues, heightValues, 0, startCap, endCap);
             }
             else {
-                addTube(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap);
+                addTube(builderState, curvePoints, normals, binormals, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, helixProfile);
             }
         }
         ++i;
@@ -168,7 +174,8 @@ export 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 = SecondaryStructureProvider.get(newStructureGroup.structure).version;
             if (state.info.secondaryStructureHash !== secondaryStructureHash) {
                 state.createGeometry = true;

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

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

@@ -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;

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

@@ -79,7 +79,7 @@ function createPolymerTubeMesh(ctx, unit, structure, theme, props, mesh) {
             addSheet(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, widthValues, heightValues, 0, startCap, endCap);
         }
         else {
-            addTube(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap);
+            addTube(builderState, curvePoints, normalVectors, binormalVectors, segmentCount, radialSegments, widthValues, heightValues, startCap, endCap, 'elliptical');
         }
         ++i;
     }

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

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

@@ -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<"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" | "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" | "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" | "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;
@@ -41,13 +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" | "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;
@@ -56,21 +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" | "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" | "offset" | "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;

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

@@ -18,9 +18,10 @@ export var BondParams = {
     excludeTypes: PD.MultiSelect([], PD.objectToOptions(BondType.Names)),
     ignoreHydrogens: PD.Boolean(false),
     aromaticBonds: PD.Boolean(false, { description: 'Display aromatic bonds with dashes' }),
+    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 @@
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>, "off"> | 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">>;
+    }>, "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;