npm - molstar - Versions diffs - 2.3.5 → 2.3.9 - Mend

molstar 2.3.5 → 2.3.9

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (1658) hide show

package/lib/mol-data/int/impl/ordered-set.d.ts CHANGED Viewed

@@ -31,9 +31,9 @@ export declare function findPredecessorIndex(set: OrderedSetImpl, x: number): nu
 export declare function findPredecessorIndexInInterval(set: OrderedSetImpl, x: number, bounds: I): number;
 export declare function findRange(set: OrderedSetImpl, min: number, max: number): I<number>;
 export declare function intersectionSize(a: OrderedSetImpl, b: OrderedSetImpl): number;
-export declare function union(a: OrderedSetImpl, b: OrderedSetImpl): S<number> | I<number>;
-export declare function intersect(a: OrderedSetImpl, b: OrderedSetImpl): S<number> | I<number>;
-export declare function subtract(a: OrderedSetImpl, b: OrderedSetImpl): S<number> | I<number>;
+export declare function union(a: OrderedSetImpl, b: OrderedSetImpl): I<number> | S<number>;
+export declare function intersect(a: OrderedSetImpl, b: OrderedSetImpl): I<number> | S<number>;
+export declare function subtract(a: OrderedSetImpl, b: OrderedSetImpl): I<number> | S<number>;
 export declare function forEach(set: OrderedSetImpl, f: (value: number, i: number, ctx: any) => void, ctx: any): any;
 export declare function forEachSegment(set: OrderedSetImpl, segment: (v: number) => number, f: (value: number, segIndex: number, ctx: any) => void, ctx: any): any;
 export declare function indexedIntersect(idxA: OrderedSetImpl, a: S, b: S): OrderedSetImpl;

package/lib/mol-data/int/impl/sorted-array.js CHANGED Viewed

@@ -36,8 +36,8 @@ export function hashCode(xs) {
 export function toString(xs) {
     var s = xs.length;
     if (s > 5)
-        return "[" + xs[0] + ", " + xs[1] + ", ..., " + xs[s - 1] + "], length " + s;
-    return "[" + xs.join(', ') + "]";
+        return "[".concat(xs[0], ", ").concat(xs[1], ", ..., ").concat(xs[s - 1], "], length ").concat(s);
+    return "[".concat(xs.join(', '), "]");
 }
 /** Returns the index of `x` in `set` or -1 if not found. */
 export function indexOf(xs, v) {

package/lib/mol-data/int/impl/sorted-array.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/mol-data/int/tuple.js CHANGED Viewed

@@ -75,7 +75,7 @@ var IntTuple;
     IntTuple.hashCode = hashCode;
     function toString(t) {
         _float64[0] = t;
-        return "(" + _int32[0] + ", " + _int32[1] + ")";
+        return "(".concat(_int32[0], ", ").concat(_int32[1], ")");
     }
     IntTuple.toString = toString;
 })(IntTuple || (IntTuple = {}));

package/lib/mol-data/int/tuple.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"tuple.js","sourceRoot":"","sources":["../../../src/mol-data/int/tuple.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,KAAK,EAAE,MAAM,SAAS,CAAC;AAQhC,IAAU,QAAQ,CAwEjB;AAxED,WAAU,QAAQ;IACD,aAAI,GAAa,CAAQ,CAAC;IAEjC,IAAA,KAA6C,CAAC;QAChD,IAAM,IAAI,GAAG,IAAI,WAAW,CAAC,CAAC,CAAC,CAAC;QAChC,IAAM,MAAM,GAAG,IAAI,WAAW,CAAC,CAAC,CAAC,CAAC;QAClC,OAAO;YACH,MAAM,EAAE,IAAI,UAAU,CAAC,IAAI,CAAC;YAC5B,QAAQ,EAAE,IAAI,YAAY,CAAC,IAAI,CAAC;YAChC,QAAQ,EAAE,IAAI,UAAU,CAAC,MAAM,CAAC;YAChC,UAAU,EAAE,IAAI,YAAY,CAAC,MAAM,CAAC;SACvC,CAAC;IACN,CAAC,EAAE,CAAC,EATI,MAAM,YAAA,EAAE,QAAQ,cAAA,EAAE,QAAQ,cAAA,EAAE,UAAU,gBAS1C,CAAC;IAEL,SAAgB,EAAE,CAAC,CAAM;QACrB,OAAO,OAAO,CAAC,KAAK,QAAQ,CAAC;IACjC,CAAC;IAFe,WAAE,KAEjB,CAAA;IAED,SAAgB,MAAM,CAAC,GAAW,EAAE,GAAW;QAC3C,MAAM,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC;QAChB,MAAM,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC;QAChB,OAAO,QAAQ,CAAC,CAAC,CAAQ,CAAC;IAC9B,CAAC;IAJe,eAAM,SAIrB,CAAA;IAED,gBAAgB;IAChB,SAAgB,IAAI,CAAC,CAAW;QAC5B,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAQ,CAAC;QACvB,OAAO,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC;IACjC,CAAC;IAHe,aAAI,OAGnB,CAAA;IAED,SAAgB,GAAG,CAAC,CAAW;QAC3B,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAQ,CAAC;QACvB,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC;IACrB,CAAC;IAHe,YAAG,MAGlB,CAAA;IAED,SAAgB,GAAG,CAAC,CAAW;QAC3B,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAQ,CAAC;QACvB,OAAO,MAAM,CAAC,CAAC,CAAC,CAAC;IACrB,CAAC;IAHe,YAAG,MAGlB,CAAA;IAED,kEAAkE;IAClE,SAAgB,QAAQ,CAAC,CAAW,EAAE,CAAW;QAC7C,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAQ,CAAC;QACvB,UAAU,CAAC,CAAC,CAAC,GAAG,CAAQ,CAAC;QACzB,OAAO,MAAM,CAAC,CAAC,CAAC,KAAK,QAAQ,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC;IAClE,CAAC;IAJe,iBAAQ,WAIvB,CAAA;IAED,SAAgB,OAAO,CAAC,CAAW,EAAE,CAAW;QAC5C,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAQ,CAAC;QACvB,UAAU,CAAC,CAAC,CAAC,GAAG,CAAQ,CAAC;QACzB,IAAM,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC;QAClC,IAAI,CAAC,KAAK,CAAC;YAAE,OAAO,CAAC,CAAC;QACtB,OAAO,MAAM,CAAC,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC;IACnC,CAAC;IANe,gBAAO,UAMtB,CAAA;IAED,SAAgB,cAAc,CAAC,EAAuB,EAAE,CAAS,EAAE,CAAS;QACxE,QAAQ,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,CAAQ,CAAC;QAC3B,UAAU,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,CAAQ,CAAC;QAC7B,IAAM,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC;QAClC,IAAI,CAAC,KAAK,CAAC;YAAE,OAAO,CAAC,CAAC;QACtB,OAAO,MAAM,CAAC,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAC;IACnC,CAAC;IANe,uBAAc,iBAM7B,CAAA;IAED,SAAgB,QAAQ,CAAC,CAAW;QAChC,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAQ,CAAC;QACvB,OAAO,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC;IACvC,CAAC;IAHe,iBAAQ,WAGvB,CAAA;IAED,SAAgB,QAAQ,CAAC,CAAW;QAChC,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAQ,CAAC;QACvB,OAAO,WAAI,MAAM,CAAC,CAAC,CAAC,eAAK,MAAM,CAAC,CAAC,CAAC,MAAG,CAAC;IAC1C,CAAC;IAHe,iBAAQ,WAGvB,CAAA;AACL,CAAC,EAxES,QAAQ,KAAR,QAAQ,QAwEjB;AAED,OAAO,EAAE,QAAQ,EAAE,CAAC"}

package/lib/mol-data/util/_spec/interval-iterator.spec.js CHANGED Viewed

@@ -7,7 +7,7 @@ import { Interval, SortedArray } from '../../int';
 import { IntervalIterator } from '../interval-iterator';
 describe('interval', function () {
     function testIterator(name, interval, set, expectedValues) {
-        it("iterator, " + name, function () {
+        it("iterator, ".concat(name), function () {
             var intervalIt = new IntervalIterator(interval, set);
             var index = expectedValues.index, start = expectedValues.start, end = expectedValues.end;
             var i = 0;

package/lib/mol-data/util/_spec/interval-iterator.spec.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"interval-iterator.spec.js","sourceRoot":"","sources":["../../../../src/mol-data/util/_spec/interval-iterator.spec.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,QAAQ,EAAc,WAAW,EAAE,MAAM,WAAW,CAAC;AAC9D,OAAO,EAAE,gBAAgB,EAAE,MAAM,sBAAsB,CAAC;AAExD,QAAQ,CAAC,UAAU,EAAE;IACjB,SAAS,YAAY,CAAC,IAAY,EAAE,QAAkB,EAAE,GAAe,EAAE,cAAkE;QACvI,EAAE,CAAC,~~eAAa~~,~~IAAM~~,EAAE;YACpB,IAAM,UAAU,GAAG,IAAI,gBAAgB,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC;YAC/C,IAAA,KAAK,GAAiB,cAAc,MAA/B,EAAE,KAAK,GAAU,cAAc,MAAxB,EAAE,GAAG,GAAK,cAAc,IAAnB,CAAoB;YAE7C,IAAI,CAAC,GAAG,CAAC,CAAC;YACV,OAAO,UAAU,CAAC,OAAO,EAAE;gBACvB,IAAM,OAAO,GAAG,UAAU,CAAC,IAAI,EAAE,CAAC;gBAClC,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC;gBACrC,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC;gBACrC,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;gBACjC,EAAE,CAAC,CAAC;aACP;YACD,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QACjC,CAAC,CAAC,CAAC;IACP,CAAC;IAED,YAAY,CAAC,OAAO,EAChB,QAAQ,CAAC,OAAO,CAAC,CAAC,EAAE,CAAC,CAAC,EACtB,WAAW,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,EACvC,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAChD,CAAC;AACN,CAAC,CAAC,CAAC"}
1	+ {"version":3,"file":"interval-iterator.spec.js","sourceRoot":"","sources":["../../../../src/mol-data/util/_spec/interval-iterator.spec.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,QAAQ,EAAc,WAAW,EAAE,MAAM,WAAW,CAAC;AAC9D,OAAO,EAAE,gBAAgB,EAAE,MAAM,sBAAsB,CAAC;AAExD,QAAQ,CAAC,UAAU,EAAE;IACjB,SAAS,YAAY,CAAC,IAAY,EAAE,QAAkB,EAAE,GAAe,EAAE,cAAkE;QACvI,EAAE,CAAC,oBAAa,IAAI,CAAE,EAAE;YACpB,IAAM,UAAU,GAAG,IAAI,gBAAgB,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC;YAC/C,IAAA,KAAK,GAAiB,cAAc,MAA/B,EAAE,KAAK,GAAU,cAAc,MAAxB,EAAE,GAAG,GAAK,cAAc,IAAnB,CAAoB;YAE7C,IAAI,CAAC,GAAG,CAAC,CAAC;YACV,OAAO,UAAU,CAAC,OAAO,EAAE;gBACvB,IAAM,OAAO,GAAG,UAAU,CAAC,IAAI,EAAE,CAAC;gBAClC,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC;gBACrC,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC;gBACrC,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;gBACjC,EAAE,CAAC,CAAC;aACP;YACD,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QACjC,CAAC,CAAC,CAAC;IACP,CAAC;IAED,YAAY,CAAC,OAAO,EAChB,QAAQ,CAAC,OAAO,CAAC,CAAC,EAAE,CAAC,CAAC,EACtB,WAAW,CAAC,aAAa,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,EACvC,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAChD,CAAC;AACN,CAAC,CAAC,CAAC"}

package/lib/mol-geo/geometry/image/image.d.ts CHANGED Viewed

@@ -16,7 +16,7 @@ export declare const InterpolationTypes: {
     bspline: string;
 };
 export declare type InterpolationTypes = keyof typeof InterpolationTypes;
-export declare const InterpolationTypeNames: ("bspline" | "nearest" | "catmulrom" | "mitchell")[];
+export declare const InterpolationTypeNames: ("nearest" | "catmulrom" | "mitchell" | "bspline")[];
 export { Image };
 interface Image {
     readonly kind: 'image';
@@ -31,7 +31,7 @@ declare namespace Image {
     function create(imageTexture: TextureImage<Uint8Array>, corners: Float32Array, groupTexture: TextureImage<Uint8Array>, image?: Image): Image;
     function createEmpty(image?: Image): Image;
     const Params: {
-        interpolation: PD.Select<"bspline" | "nearest" | "catmulrom" | "mitchell">;
+        interpolation: PD.Select<"nearest" | "catmulrom" | "mitchell" | "bspline">;
         alpha: PD.Numeric;
         quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
     };

package/lib/mol-geo/geometry/mesh/builder/sheet.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>

package/lib/mol-geo/geometry/mesh/builder/sheet.js CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -33,7 +33,7 @@ var v3cross = Vec3.cross;
 var v3set = Vec3.set;
 var caAdd3 = ChunkedArray.add3;
 var caAdd = ChunkedArray.add;
-function addCap(offset, state, controlPoints, normalVectors, binormalVectors, width, leftHeight, rightHeight) {
+function addCap(offset, state, controlPoints, normalVectors, binormalVectors, width, leftHeight, rightHeight, flip) {
     var vertices = state.vertices, normals = state.normals, indices = state.indices;
     var vertexCount = vertices.elementCount;
     v3fromArray(tA, normalVectors, offset);
@@ -61,11 +61,20 @@ function addCap(offset, state, controlPoints, normalVectors, binormalVectors, wi
         caAdd3(vertices, p4[0], p4[1], p4[2]);
         v3copy(verticalVector, verticalLeftVector);
     }
-    for (var i = 0; i < 4; ++i) {
-        caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
+    if (flip) {
+        for (var i = 0; i < 4; ++i) {
+            caAdd3(normals, -normalVector[0], -normalVector[1], -normalVector[2]);
+        }
+        caAdd3(indices, vertexCount, vertexCount + 1, vertexCount + 2);
+        caAdd3(indices, vertexCount + 2, vertexCount + 3, vertexCount);
+    }
+    else {
+        for (var i = 0; i < 4; ++i) {
+            caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
+        }
+        caAdd3(indices, vertexCount + 2, vertexCount + 1, vertexCount);
+        caAdd3(indices, vertexCount, vertexCount + 3, vertexCount + 2);
     }
-    caAdd3(indices, vertexCount + 2, vertexCount + 1, vertexCount);
-    caAdd3(indices, vertexCount, vertexCount + 3, vertexCount + 2);
 }
 /** set arrowHeight = 0 for no arrow */
 export function addSheet(state, controlPoints, normalVectors, binormalVectors, linearSegments, widthValues, heightValues, arrowHeight, startCap, endCap) {
@@ -152,19 +161,18 @@ export function addSheet(state, controlPoints, normalVectors, binormalVectors, l
         var width = widthValues[0];
         var height = heightValues[0];
         var h = arrowHeight === 0 ? height : arrowHeight;
-        addCap(0, state, controlPoints, normalVectors, binormalVectors, width, h, h);
+        addCap(0, state, controlPoints, normalVectors, binormalVectors, width, h, h, false);
     }
     else if (arrowHeight > 0) {
         var width = widthValues[0];
         var height = heightValues[0];
-        addCap(0, state, controlPoints, normalVectors, binormalVectors, width, arrowHeight, -height);
-        addCap(0, state, controlPoints, normalVectors, binormalVectors, width, -arrowHeight, height);
+        addCap(0, state, controlPoints, normalVectors, binormalVectors, width, arrowHeight, -height, false);
+        addCap(0, state, controlPoints, normalVectors, binormalVectors, width, -arrowHeight, height, false);
     }
     if (endCap && arrowHeight === 0) {
         var width = widthValues[linearSegments];
         var height = heightValues[linearSegments];
-        // use negative height to flip the direction the cap's triangles are facing
-        addCap(linearSegments * 3, state, controlPoints, normalVectors, binormalVectors, width, -height, -height);
+        addCap(linearSegments * 3, state, controlPoints, normalVectors, binormalVectors, width, height, height, true);
     }
     var addedVertexCount = (linearSegments + 1) * 8 +
         (startCap ? 4 : (arrowHeight > 0 ? 8 : 0)) +

package/lib/mol-geo/geometry/mesh/builder/sheet.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/mol-geo/geometry/mesh/builder/tube.d.ts CHANGED Viewed

@@ -1,8 +1,8 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 import { MeshBuilder } from '../mesh-builder';
-export declare function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<number>, normalVectors: ArrayLike<number>, binormalVectors: ArrayLike<number>, linearSegments: number, radialSegments: number, widthValues: ArrayLike<number>, heightValues: ArrayLike<number>, startCap: boolean, endCap: boolean): void;
+export declare function addTube(state: MeshBuilder.State, controlPoints: ArrayLike<number>, normalVectors: ArrayLike<number>, binormalVectors: ArrayLike<number>, linearSegments: number, radialSegments: number, widthValues: ArrayLike<number>, heightValues: ArrayLike<number>, startCap: boolean, endCap: boolean, crossSection: 'elliptical' | 'rounded'): void;

package/lib/mol-geo/geometry/mesh/builder/tube.js CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -24,9 +24,10 @@ function add3AndScale2(out, a, b, c, sa, sb) {
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 var v3fromArray = Vec3.fromArray;
 var v3normalize = Vec3.normalize;
-var v3negate = Vec3.negate;
-var v3copy = Vec3.copy;
+var v3scaleAndAdd = Vec3.scaleAndAdd;
 var v3cross = Vec3.cross;
+var v3dot = Vec3.dot;
+var v3unitX = Vec3.unitX;
 var caAdd3 = ChunkedArray.add3;
 var CosSinCache = new Map();
 function getCosSin(radialSegments) {
@@ -42,10 +43,12 @@ function getCosSin(radialSegments) {
     }
     return CosSinCache.get(radialSegments);
 }
-export function addTube(state, controlPoints, normalVectors, binormalVectors, linearSegments, radialSegments, widthValues, heightValues, startCap, endCap) {
+export function addTube(state, controlPoints, normalVectors, binormalVectors, linearSegments, radialSegments, widthValues, heightValues, startCap, endCap, crossSection) {
     var currentGroup = state.currentGroup, vertices = state.vertices, normals = state.normals, indices = state.indices, groups = state.groups;
     var vertexCount = vertices.elementCount;
     var _a = getCosSin(radialSegments), cos = _a.cos, sin = _a.sin;
+    var q1 = radialSegments / 4;
+    var q3 = q1 * 3;
     for (var i = 0; i <= linearSegments; ++i) {
         var i3 = i * 3;
         v3fromArray(u, normalVectors, i3);
@@ -53,15 +56,18 @@ export function addTube(state, controlPoints, normalVectors, binormalVectors, li
         v3fromArray(controlPoint, controlPoints, i3);
         var width = widthValues[i];
         var height = heightValues[i];
+        var rounded = crossSection === 'rounded' && height > width;
         for (var j = 0; j < radialSegments; ++j) {
-            add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[j], width * sin[j]);
-            if (radialSegments === 2) {
-                v3copy(normalVector, v);
-                v3normalize(normalVector, normalVector);
-                if (j !== 0 || i % 2 === 0)
-                    v3negate(normalVector, normalVector);
+            if (rounded) {
+                add3AndScale2(surfacePoint, u, v, controlPoint, width * cos[j], width * sin[j]);
+                var h = v3dot(v, v3unitX) < 0
+                    ? (j < q1 || j >= q3) ? height - width : -height + width
+                    : (j >= q1 && j < q3) ? -height + width : height - width;
+                v3scaleAndAdd(surfacePoint, surfacePoint, u, h);
+                add2AndScale2(normalVector, u, v, cos[j], sin[j]);
             }
             else {
+                add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[j], width * sin[j]);
                 add2AndScale2(normalVector, u, v, width * cos[j], height * sin[j]);
             }
             v3normalize(normalVector, normalVector);
@@ -69,10 +75,28 @@ export function addTube(state, controlPoints, normalVectors, binormalVectors, li
             caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
         }
     }
+    var radialSegmentsHalf = Math.round(radialSegments / 2);
     for (var i = 0; i < linearSegments; ++i) {
-        for (var j = 0; j < radialSegments; ++j) {
-            caAdd3(indices, vertexCount + i * radialSegments + (j + 1) % radialSegments, vertexCount + (i + 1) * radialSegments + (j + 1) % radialSegments, vertexCount + i * radialSegments + j);
-            caAdd3(indices, vertexCount + (i + 1) * radialSegments + (j + 1) % radialSegments, vertexCount + (i + 1) * radialSegments + j, vertexCount + i * radialSegments + j);
+        // the triangles are arranged such that opposing triangles of the sheet align
+        // which prevents triangle intersection within tight curves
+        for (var j = 0; j < radialSegmentsHalf; ++j) {
+            caAdd3(indices, vertexCount + i * radialSegments + (j + 1) % radialSegments, // a
+            vertexCount + (i + 1) * radialSegments + (j + 1) % radialSegments, // c
+            vertexCount + i * radialSegments + j // b
+            );
+            caAdd3(indices, vertexCount + (i + 1) * radialSegments + (j + 1) % radialSegments, // c
+            vertexCount + (i + 1) * radialSegments + j, // d
+            vertexCount + i * radialSegments + j // b
+            );
+        }
+        for (var j = radialSegmentsHalf; j < radialSegments; ++j) {
+            caAdd3(indices, vertexCount + i * radialSegments + (j + 1) % radialSegments, // a
+            vertexCount + (i + 1) * radialSegments + j, // d
+            vertexCount + i * radialSegments + j // b
+            );
+            caAdd3(indices, vertexCount + (i + 1) * radialSegments + (j + 1) % radialSegments, // c
+            vertexCount + (i + 1) * radialSegments + j, // d
+            vertexCount + i * radialSegments + (j + 1) % radialSegments);
         }
     }
     if (startCap) {
@@ -86,9 +110,18 @@ export function addTube(state, controlPoints, normalVectors, binormalVectors, li
         caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
         var width = widthValues[0];
         var height = heightValues[0];
+        var rounded = crossSection === 'rounded' && height > width;
+        if (rounded)
+            height -= width;
         vertexCount = vertices.elementCount;
         for (var i = 0; i < radialSegments; ++i) {
-            add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[i], width * sin[i]);
+            if (rounded) {
+                add3AndScale2(surfacePoint, u, v, controlPoint, width * cos[i], width * sin[i]);
+                v3scaleAndAdd(surfacePoint, surfacePoint, u, (i < q1 || i >= q3) ? height : -height);
+            }
+            else {
+                add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[i], width * sin[i]);
+            }
             caAdd3(vertices, surfacePoint[0], surfacePoint[1], surfacePoint[2]);
             caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
             caAdd3(indices, vertexCount + (i + 1) % radialSegments, vertexCount + i, centerVertex);
@@ -105,9 +138,18 @@ export function addTube(state, controlPoints, normalVectors, binormalVectors, li
         caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
         var width = widthValues[linearSegments];
         var height = heightValues[linearSegments];
+        var rounded = crossSection === 'rounded' && height > width;
+        if (rounded)
+            height -= width;
         vertexCount = vertices.elementCount;
         for (var i = 0; i < radialSegments; ++i) {
-            add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[i], width * sin[i]);
+            if (rounded) {
+                add3AndScale2(surfacePoint, u, v, controlPoint, width * cos[i], width * sin[i]);
+                v3scaleAndAdd(surfacePoint, surfacePoint, u, (i < q1 || i >= q3) ? height : -height);
+            }
+            else {
+                add3AndScale2(surfacePoint, u, v, controlPoint, height * cos[i], width * sin[i]);
+            }
             caAdd3(vertices, surfacePoint[0], surfacePoint[1], surfacePoint[2]);
             caAdd3(normals, normalVector[0], normalVector[1], normalVector[2]);
             caAdd3(indices, vertexCount + i, vertexCount + (i + 1) % radialSegments, centerVertex);

package/lib/mol-geo/geometry/mesh/builder/tube.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/lib/mol-geo/geometry/mesh/color-smoothing.d.ts CHANGED Viewed

@@ -27,7 +27,7 @@ export declare function calcMeshColorSmoothing(input: ColorSmoothingInput, resol
     gridTexDim: Vec2;
     gridDim: Vec3;
     gridTransform: Vec4;
-    type: "volume" | "volumeInstance";
+    type: "volumeInstance" | "volume";
     texDim?: undefined;
 } | {
     kind: "vertex";

package/lib/mol-geo/geometry/mesh/mesh.js CHANGED Viewed

@@ -108,7 +108,7 @@ export var Mesh;
         if (fractionDigits === void 0) { fractionDigits = 3; }
         var v = mesh.vertexBuffer.ref.value;
         var map = new Map();
-        var hash = function (v, d) { return v[0].toFixed(d) + "|" + v[1].toFixed(d) + "|" + v[2].toFixed(d); };
+        var hash = function (v, d) { return "".concat(v[0].toFixed(d), "|").concat(v[1].toFixed(d), "|").concat(v[2].toFixed(d)); };
         var duplicates = 0;
         var a = Vec3();
         for (var i = 0, il = mesh.vertexCount; i < il; ++i) {