molstar 4.2.0 → 4.4.0

package/lib/commonjs/mol-math/geometry/molecular-surface.js

@@ -8,7 +8,8 @@
  * ported from NGL (https://github.com/arose/ngl), licensed under MIT
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.calcMolecularSurface = exports.DefaultMolecularSurfaceCalculationProps = exports.MolecularSurfaceCalculationParams = void 0;
+exports.DefaultMolecularSurfaceCalculationProps = exports.MolecularSurfaceCalculationParams = void 0;
+exports.calcMolecularSurface = calcMolecularSurface;
 const linear_algebra_1 = require("../../mol-math/linear-algebra");
 const param_definition_1 = require("../../mol-util/param-definition");
 const int_1 = require("../../mol-data/int");
@@ -311,4 +312,3 @@ async function calcMolecularSurface(ctx, position, boundary, maxRadius, box, pro
     // console.log({ field, idField, transform, updateChunk })
     return { field, idField, transform, resolution, maxRadius };
 }
-exports.calcMolecularSurface = calcMolecularSurface;

package/lib/commonjs/mol-math/geometry/polygon.js

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.pointInPolygon = void 0;
+exports.pointInPolygon = pointInPolygon;
 /** raycast along x-axis and apply even-odd rule */
 function pointInPolygon(point, polygon, count) {
     const [x, y] = point;
@@ -19,4 +19,3 @@ function pointInPolygon(point, polygon, count) {
     }
     return inside;
 }
-exports.pointInPolygon = pointInPolygon;

package/lib/commonjs/mol-math/geometry/primitives/axes3d.js

@@ -5,12 +5,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Axes3D = void 0;
+exports.Axes3D = Axes3D;
 const linear_algebra_1 = require("../../linear-algebra");
 function Axes3D() {
     return Axes3D.empty();
 }
-exports.Axes3D = Axes3D;
 (function (Axes3D) {
     function create(origin, dirA, dirB, dirC) { return { origin, dirA, dirB, dirC }; }
     Axes3D.create = create;

package/lib/commonjs/mol-math/geometry/primitives/box3d.js

@@ -6,14 +6,13 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Box3D = void 0;
+exports.Box3D = Box3D;
 const int_1 = require("../../../mol-data/int");
 const sphere3d_1 = require("./sphere3d");
 const vec3_1 = require("../../linear-algebra/3d/vec3");
 function Box3D() {
     return Box3D.zero();
 }
-exports.Box3D = Box3D;
 (function (Box3D) {
     function create(min, max) { return { min, max }; }
     Box3D.create = create;

package/lib/commonjs/mol-math/geometry/primitives/frustum3d.js

@@ -8,13 +8,12 @@
  * copyright (c) 2010-2022 three.js authors. MIT License
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Frustum3D = void 0;
+exports.Frustum3D = Frustum3D;
 const vec3_1 = require("../../linear-algebra/3d/vec3");
 const plane3d_1 = require("./plane3d");
 function Frustum3D() {
     return Frustum3D.create((0, plane3d_1.Plane3D)(), (0, plane3d_1.Plane3D)(), (0, plane3d_1.Plane3D)(), (0, plane3d_1.Plane3D)(), (0, plane3d_1.Plane3D)(), (0, plane3d_1.Plane3D)());
 }
-exports.Frustum3D = Frustum3D;
 (function (Frustum3D) {
     ;
     function create(right, left, bottom, top, far, near) {

package/lib/commonjs/mol-math/geometry/primitives/plane3d.js

@@ -8,12 +8,11 @@
  * copyright (c) 2010-2022 three.js authors. MIT License
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Plane3D = void 0;
+exports.Plane3D = Plane3D;
 const vec3_1 = require("../../linear-algebra/3d/vec3");
 function Plane3D() {
     return Plane3D.create(vec3_1.Vec3.create(1, 0, 0), 0);
 }
-exports.Plane3D = Plane3D;
 (function (Plane3D) {
     function create(normal, constant) { return { normal, constant }; }
     Plane3D.create = create;

package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Sphere3D = void 0;
+exports.Sphere3D = Sphere3D;
 const linear_algebra_1 = require("../../linear-algebra");
 const int_1 = require("../../../mol-data/int");
 const axes3d_1 = require("./axes3d");
@@ -14,7 +14,6 @@ const principal_axes_1 = require("../../linear-algebra/matrix/principal-axes");
 function Sphere3D() {
     return Sphere3D.zero();
 }
-exports.Sphere3D = Sphere3D;
 (function (Sphere3D) {
     function hasExtrema(sphere) {
         return sphere.extrema !== undefined;

package/lib/commonjs/mol-math/geometry/spacegroup/cell.js

@@ -5,12 +5,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Cell = void 0;
+exports.Cell = Cell;
 const linear_algebra_1 = require("../../linear-algebra");
 function Cell() {
     return Cell.empty();
 }
-exports.Cell = Cell;
 (function (Cell) {
     function create(size, anglesInRadians) {
         return { size, anglesInRadians };

package/lib/commonjs/mol-math/geometry/spacegroup/tables.js

@@ -6,7 +6,10 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getSpacegroupIndex = exports.SpacegroupNumber = exports.SpacegroupName = exports.getSpacegroupNumberFromIndex = exports.getSpacegroupIndexFromNumber = exports.SpacegroupNameToIndexMap = exports.GroupData = exports.OperatorData = exports.TransformData = void 0;
+exports.SpacegroupNumber = exports.SpacegroupName = exports.SpacegroupNameToIndexMap = exports.GroupData = exports.OperatorData = exports.TransformData = void 0;
+exports.getSpacegroupIndexFromNumber = getSpacegroupIndexFromNumber;
+exports.getSpacegroupNumberFromIndex = getSpacegroupNumberFromIndex;
+exports.getSpacegroupIndex = getSpacegroupIndex;
 exports.TransformData = [
     [1.0, 0.0, 0.0, 0.0],
     [0.0, 1.0, 0.0, 0.0],
@@ -1403,7 +1406,6 @@ function getSpacegroupIndexFromNumber(num) {
         ++offset;
     return num - 1 + offset;
 }
-exports.getSpacegroupIndexFromNumber = getSpacegroupIndexFromNumber;
 function getSpacegroupNumberFromIndex(idx) {
     if (idx < 146)
         return idx + 1;
@@ -1499,7 +1501,6 @@ function getSpacegroupNumberFromIndex(idx) {
         return 1197;
     throw new Error(`unknown spacegroup index '${idx}'`);
 }
-exports.getSpacegroupNumberFromIndex = getSpacegroupNumberFromIndex;
 /** Maps spacegroup index to Hermann-Mauguin spacegroup name */
 exports.SpacegroupName = (function () {
     const names = Object.create(null);
@@ -1526,4 +1527,3 @@ function getSpacegroupIndex(nameOrNumber) {
         return -1;
     return index;
 }
-exports.getSpacegroupIndex = getSpacegroupIndex;

package/lib/commonjs/mol-math/histogram.js

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.calculateHistogram = void 0;
+exports.calculateHistogram = calculateHistogram;
 const array_1 = require("../mol-util/array");
 function calculateHistogram(data, binCount, options) {
     if (!options) {
@@ -16,7 +16,6 @@ function calculateHistogram(data, binCount, options) {
         return _calcHistogram(data, binCount, options.min, options.max);
     }
 }
-exports.calculateHistogram = calculateHistogram;
 function _calcHistogram(data, binCount, min, max) {
     let binWidth = (max - min) / binCount;
     if (binWidth === 0)

package/lib/commonjs/mol-math/interpolate.js

@@ -5,32 +5,37 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.almostIdentity = exports.smootheststep = exports.smootherstep = exports.smoothstep = exports.quadraticBezier = exports.spline = exports.lerp = exports.damp = exports.saturate = exports.pclamp = exports.clamp = exports.normalize = void 0;
+exports.normalize = normalize;
+exports.clamp = clamp;
+exports.pclamp = pclamp;
+exports.saturate = saturate;
+exports.damp = damp;
+exports.lerp = lerp;
+exports.spline = spline;
+exports.quadraticBezier = quadraticBezier;
+exports.smoothstep = smoothstep;
+exports.smootherstep = smootherstep;
+exports.smootheststep = smootheststep;
+exports.almostIdentity = almostIdentity;
 function normalize(value, min, max) {
     return (value - min) / (max - min);
 }
-exports.normalize = normalize;
 function clamp(value, min, max) {
     return Math.max(min, Math.min(max, value));
 }
-exports.clamp = clamp;
 function pclamp(value) {
     return clamp(value, 0, 100);
 }
-exports.pclamp = pclamp;
 function saturate(value) {
     return clamp(value, 0, 1);
 }
-exports.saturate = saturate;
 function damp(value, dampingFactor) {
     const dampedValue = value * dampingFactor;
     return Math.abs(dampedValue) < 0.1 ? 0 : dampedValue;
 }
-exports.damp = damp;
 function lerp(start, stop, alpha) {
     return start + (stop - start) * alpha;
 }
-exports.lerp = lerp;
 /** Catmul-Rom spline */
 function spline(p0, p1, p2, p3, t, tension) {
     const v0 = (p2 - p0) * tension;
@@ -39,27 +44,22 @@ function spline(p0, p1, p2, p3, t, tension) {
     const t3 = t * t2;
     return (2 * p1 - 2 * p2 + v0 + v1) * t3 + (-3 * p1 + 3 * p2 - 2 * v0 - v1) * t2 + v0 * t + p1;
 }
-exports.spline = spline;
 function quadraticBezier(p0, p1, p2, t) {
     const k = 1 - t;
     return (k * k * p0) + (2 * k * t * p1) + (t * t * p2);
 }
-exports.quadraticBezier = quadraticBezier;
 function smoothstep(min, max, x) {
     x = saturate(normalize(x, min, max));
     return x * x * (3 - 2 * x);
 }
-exports.smoothstep = smoothstep;
 function smootherstep(min, max, x) {
     x = saturate(normalize(x, min, max));
     return x * x * x * (x * (x * 6 - 15) + 10);
 }
-exports.smootherstep = smootherstep;
 function smootheststep(min, max, x) {
     x = saturate(normalize(x, min, max));
     return -20 * Math.pow(x, 7) + 70 * Math.pow(x, 6) - 84 * Math.pow(x, 5) + 35 * Math.pow(x, 4);
 }
-exports.smootheststep = smootheststep;
 function almostIdentity(value, start, stop) {
     if (value > start)
         return value;
@@ -68,4 +68,3 @@ function almostIdentity(value, start, stop) {
     const t = value / start;
     return (a * t + b) * t * t + stop;
 }
-exports.almostIdentity = almostIdentity;

package/lib/commonjs/mol-math/linear-algebra/3d/common.js

@@ -6,7 +6,8 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.equalEps = exports.EPSILON = void 0;
+exports.EPSILON = void 0;
+exports.equalEps = equalEps;
 /*
  * This code has been modified from https://github.com/toji/gl-matrix/,
  * copyright (c) 2015, Brandon Jones, Colin MacKenzie IV.
@@ -22,4 +23,3 @@ exports.EPSILON = 0.000001;
 function equalEps(a, b, eps) {
     return Math.abs(a - b) <= eps;
 }
-exports.equalEps = equalEps;

package/lib/commonjs/mol-math/linear-algebra/3d/euler.js

@@ -8,14 +8,13 @@
  * copyright (c) 2010-2023 three.js authors. MIT License
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Euler = void 0;
+exports.Euler = Euler;
 const mat4_1 = require("./mat4");
 const type_helpers_1 = require("../../../mol-util/type-helpers");
 const interpolate_1 = require("../../interpolate");
 function Euler() {
     return Euler.zero();
 }
-exports.Euler = Euler;
 (function (Euler) {
     function zero() {
         // force double backing array by 0.1.

package/lib/commonjs/mol-math/linear-algebra/3d/mat3.js

@@ -6,14 +6,13 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Mat3 = void 0;
+exports.Mat3 = Mat3;
 const common_1 = require("./common");
 const mat4_1 = require("./mat4");
 const vec3_1 = require("./vec3");
 function Mat3() {
     return Mat3.zero();
 }
-exports.Mat3 = Mat3;
 (function (Mat3) {
     function zero() {
         // force double backing array by 0.1.

package/lib/commonjs/mol-math/linear-algebra/3d/mat4.js

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Mat4 = void 0;
+exports.Mat4 = Mat4;
 /*
  * This code has been modified from https://github.com/toji/gl-matrix/,
  * copyright (c) 2015, Brandon Jones, Colin MacKenzie IV.
@@ -24,7 +24,6 @@ const misc_1 = require("../../misc");
 function Mat4() {
     return Mat4.zero();
 }
-exports.Mat4 = Mat4;
 /**
  * Stores a 4x4 matrix in a column major (j * 4 + i indexing) format.
  */

package/lib/commonjs/mol-math/linear-algebra/3d/minimize-rmsd.js

@@ -55,7 +55,8 @@ function computeN(state) {
     const cA = state.centerA;
     const cB = state.centerB;
     let sizeSq = 0.0;
-    for (let i = 0, _l = state.a.x.length; i < _l; i++) {
+    const L = Math.min(state.a.x.length, state.b.x.length);
+    for (let i = 0; i < L; i++) {
         const aX = xsA[i] - cA[0], aY = ysA[i] - cA[1], aZ = zsA[i] - cA[2];
         const bX = xsB[i] - cB[0], bY = ysB[i] - cB[1], bZ = zsB[i] - cB[2];
         sizeSq += aX * aX + aY * aY + aZ * aZ + bX * bX + bY * bY + bZ * bZ;

package/lib/commonjs/mol-math/linear-algebra/3d/quat.js

@@ -6,14 +6,13 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Quat = void 0;
+exports.Quat = Quat;
 const vec3_1 = require("./vec3");
 const common_1 = require("./common");
 const type_helpers_1 = require("../../../mol-util/type-helpers");
 function Quat() {
     return Quat.zero();
 }
-exports.Quat = Quat;
 (function (Quat) {
     function zero() {
         // force double backing array by 0.1.

package/lib/commonjs/mol-math/linear-algebra/3d/vec2.js

@@ -5,11 +5,10 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Vec2 = void 0;
+exports.Vec2 = Vec2;
 function Vec2() {
     return Vec2.zero();
 }
-exports.Vec2 = Vec2;
 (function (Vec2) {
     function zero() {
         // force double backing array by 0.1.

package/lib/commonjs/mol-math/linear-algebra/3d/vec3.js

@@ -6,7 +6,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Vec3 = void 0;
+exports.Vec3 = Vec3;
 /*
  * This code has been modified from https://github.com/toji/gl-matrix/,
  * copyright (c) 2015, Brandon Jones, Colin MacKenzie IV.
@@ -25,7 +25,6 @@ const _isFinite = isFinite;
 function Vec3() {
     return Vec3.zero();
 }
-exports.Vec3 = Vec3;
 (function (Vec3) {
     function zero() {
         const out = [0.1, 0.0, 0.0]; // ensure backing array of type double

package/lib/commonjs/mol-math/linear-algebra/3d/vec4.js

@@ -6,12 +6,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Vec4 = void 0;
+exports.Vec4 = Vec4;
 const common_1 = require("./common");
 function Vec4() {
     return Vec4.zero();
 }
-exports.Vec4 = Vec4;
 (function (Vec4) {
     function zero() {
         // force double backing array by 0.1.

package/lib/commonjs/mol-math/linear-algebra/matrix/svd.js

@@ -5,7 +5,10 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.svd = exports.JacobiSVDImpl = exports.hypot = exports.swap = void 0;
+exports.swap = swap;
+exports.hypot = hypot;
+exports.JacobiSVDImpl = JacobiSVDImpl;
+exports.svd = svd;
 const matrix_1 = require("./matrix");
 // svd method adapted from http://inspirit.github.io/jsfeat/ MIT Eugene Zatepyakin
 function swap(A, i0, i1, t) {
@@ -13,7 +16,6 @@ function swap(A, i0, i1, t) {
     A[i0] = A[i1];
     A[i1] = t;
 }
-exports.swap = swap;
 function hypot(a, b) {
     a = Math.abs(a);
     b = Math.abs(b);
@@ -27,7 +29,6 @@ function hypot(a, b) {
     }
     return 0.0;
 }
-exports.hypot = hypot;
 const EPSILON = 0.0000001192092896;
 const FLT_MIN = 1E-37;
 function JacobiSVDImpl(At, astep, _W, Vt, vstep, m, n, n1) {
@@ -227,7 +228,6 @@ function JacobiSVDImpl(At, astep, _W, Vt, vstep, m, n, n1) {
         }
     }
 }
-exports.JacobiSVDImpl = JacobiSVDImpl;
 function svd(A, W, U, V) {
     let at = 0;
     let i = 0;
@@ -277,4 +277,3 @@ function svd(A, W, U, V) {
             matrix_1.Matrix.transpose(V, amt);
     }
 }
-exports.svd = svd;

package/lib/commonjs/mol-math/misc.js

@@ -5,21 +5,24 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.spiral2d = exports.arcLength = exports.absMax = exports.isPowerOfTwo = exports.radToDeg = exports.degToRad = exports.PiDiv180 = exports.halfPI = void 0;
+exports.PiDiv180 = exports.halfPI = void 0;
+exports.degToRad = degToRad;
+exports.radToDeg = radToDeg;
+exports.isPowerOfTwo = isPowerOfTwo;
+exports.absMax = absMax;
+exports.arcLength = arcLength;
+exports.spiral2d = spiral2d;
 exports.halfPI = Math.PI / 2;
 exports.PiDiv180 = Math.PI / 180;
 function degToRad(deg) {
     return deg * exports.PiDiv180; // deg * Math.PI / 180
 }
-exports.degToRad = degToRad;
 function radToDeg(rad) {
     return rad / exports.PiDiv180; // rad * 180 / Math.PI
 }
-exports.radToDeg = radToDeg;
 function isPowerOfTwo(x) {
     return (x !== 0) && (x & (x - 1)) === 0;
 }
-exports.isPowerOfTwo = isPowerOfTwo;
 /** return the value that has the largest absolute value */
 function absMax(...values) {
     let max = 0;
@@ -34,12 +37,10 @@ function absMax(...values) {
     }
     return max;
 }
-exports.absMax = absMax;
 /** Length of an arc with angle in radians */
 function arcLength(angle, radius) {
     return angle * radius;
 }
-exports.arcLength = arcLength;
 /** Create an outward spiral of given `radius` on a 2d grid */
 function spiral2d(radius) {
     let x = 0;
@@ -60,4 +61,3 @@ function spiral2d(radius) {
     }
     return out;
 }
-exports.spiral2d = spiral2d;

package/lib/commonjs/mol-model/custom-property.js

@@ -6,12 +6,12 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.CustomProperties = exports.CustomPropertyDescriptor = void 0;
+exports.CustomProperties = void 0;
+exports.CustomPropertyDescriptor = CustomPropertyDescriptor;
 const mol_util_1 = require("../mol-util");
 function CustomPropertyDescriptor(desc) {
     return desc;
 }
-exports.CustomPropertyDescriptor = CustomPropertyDescriptor;
 (function (CustomPropertyDescriptor) {
     function getUUID(prop) {
         if (!prop.__key) {

package/lib/commonjs/mol-model/location.js

@@ -5,18 +5,18 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isDataLocation = exports.DataLocation = exports.isNullLocation = exports.NullLocation = void 0;
+exports.NullLocation = void 0;
+exports.isNullLocation = isNullLocation;
+exports.DataLocation = DataLocation;
+exports.isDataLocation = isDataLocation;
 /** A null value Location */
 exports.NullLocation = { kind: 'null-location' };
 function isNullLocation(x) {
     return !!x && x.kind === 'null-location';
 }
-exports.isNullLocation = isNullLocation;
 function DataLocation(tag, data, element) {
     return { kind: 'data-location', tag, data, element };
 }
-exports.DataLocation = DataLocation;
 function isDataLocation(x) {
     return !!x && x.kind === 'data-location';
 }
-exports.isDataLocation = isDataLocation;

package/lib/commonjs/mol-model/loci.d.ts

@@ -103,7 +103,7 @@ declare namespace Loci {
     export type Granularity = keyof typeof Granularity;
     export const GranularityOptions: ["element" | "operator" | "residue" | "entity" | "chain" | "model" | "structure" | "elementInstances" | "residueInstances" | "chainInstances", string][];
     /** Exclude `Instances` granularity kinds */
-    export function simpleGranularity(granularity: Granularity): "element" | "operator" | "residue" | "entity" | "chain" | "model" | "structure" | "elementInstances" | "residueInstances" | "chainInstances";
+    export function simpleGranularity(granularity: Granularity): Granularity;
     export function applyGranularity(loci: Loci, granularity: Granularity): Loci;
     /**
      * Converts structure related loci to StructureElement.Loci and applies

package/lib/commonjs/mol-model/loci.js

@@ -5,7 +5,13 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.Loci = exports.DataLoci = exports.isDataLociEmpty = exports.areDataLociEqual = exports.isDataLoci = exports.isEmptyLoci = exports.EmptyLoci = exports.isEveryLoci = exports.EveryLoci = void 0;
+exports.Loci = exports.EmptyLoci = exports.EveryLoci = void 0;
+exports.isEveryLoci = isEveryLoci;
+exports.isEmptyLoci = isEmptyLoci;
+exports.isDataLoci = isDataLoci;
+exports.areDataLociEqual = areDataLociEqual;
+exports.isDataLociEmpty = isDataLociEmpty;
+exports.DataLoci = DataLoci;
 const structure_1 = require("./structure");
 const bonds_1 = require("./structure/structure/unit/bonds");
 const shape_1 = require("./shape");
@@ -22,17 +28,14 @@ exports.EveryLoci = { kind: 'every-loci' };
 function isEveryLoci(x) {
     return !!x && x.kind === 'every-loci';
 }
-exports.isEveryLoci = isEveryLoci;
 /** A Loci that is empty */
 exports.EmptyLoci = { kind: 'empty-loci' };
 function isEmptyLoci(x) {
     return !!x && x.kind === 'empty-loci';
 }
-exports.isEmptyLoci = isEmptyLoci;
 function isDataLoci(x) {
     return !!x && x.kind === 'data-loci';
 }
-exports.isDataLoci = isDataLoci;
 function areDataLociEqual(a, b) {
     // use shallowEqual to allow simple data objects that are contructed on-the-fly
     if (!(0, mol_util_1.shallowEqual)(a.data, b.data) || a.tag !== b.tag)
@@ -45,15 +48,12 @@ function areDataLociEqual(a, b) {
     }
     return true;
 }
-exports.areDataLociEqual = areDataLociEqual;
 function isDataLociEmpty(loci) {
     return loci.elements.length === 0 ? true : false;
 }
-exports.isDataLociEmpty = isDataLociEmpty;
 function DataLoci(tag, data, elements, getBoundingSphere, getLabel) {
     return { kind: 'data-loci', tag, data, elements, getBoundingSphere, getLabel };
 }
-exports.DataLoci = DataLoci;
 var Loci;
 (function (Loci) {
     const boundaryHelper = new boundary_helper_1.BoundaryHelper('98');

package/lib/commonjs/mol-model/sequence/alignment/alignment.d.ts

@@ -3,10 +3,11 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
+import { SubstitutionMatrix } from './substitution-matrix';
 declare const DefaultAlignmentOptions: {
     gapPenalty: number;
     gapExtensionPenalty: number;
-    substMatrix: "default" | "blosum62" | "blosum62x";
+    substMatrix: SubstitutionMatrix | "default";
 };
 export type AlignmentOptions = typeof DefaultAlignmentOptions;
 export declare function align(seqA: ArrayLike<string>, seqB: ArrayLike<string>, options?: Partial<AlignmentOptions>): {

package/lib/commonjs/mol-model/sequence/alignment/alignment.js

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.align = void 0;
+exports.align = align;
 const substitution_matrix_1 = require("./substitution-matrix");
 const DefaultAlignmentOptions = {
     gapPenalty: -11,
@@ -18,7 +18,6 @@ function align(seqA, seqB, options = {}) {
     alignment.calculate();
     return alignment.trace();
 }
-exports.align = align;
 class Alignment {
     constructor(seqA, seqB, options) {
         this.seqA = seqA;

package/lib/commonjs/mol-model/sequence/alignment/sequence.js

@@ -5,7 +5,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getSequence = exports.entityKey = exports.AlignSequences = void 0;
+exports.AlignSequences = void 0;
+exports.entityKey = entityKey;
+exports.getSequence = getSequence;
 const structure_1 = require("../../structure/structure");
 const alignment_1 = require("./alignment");
 const int_1 = require("../../../mol-data/int");
@@ -90,8 +92,6 @@ function entityKey(unit) {
             return unit.model.coarseHierarchy.gaussians.entityKey[unit.elements[0]];
     }
 }
-exports.entityKey = entityKey;
 function getSequence(unit) {
     return unit.model.sequence.byEntityKey[entityKey(unit)].sequence;
 }
-exports.getSequence = getSequence;

package/lib/commonjs/mol-model/sequence/constants.js

@@ -5,7 +5,9 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getDnaOneLetterCode = exports.getRnaOneLetterCode = exports.getProteinOneLetterCode = void 0;
+exports.getProteinOneLetterCode = getProteinOneLetterCode;
+exports.getRnaOneLetterCode = getRnaOneLetterCode;
+exports.getDnaOneLetterCode = getDnaOneLetterCode;
 // from NGL
 const ProteinOneLetterCodes = {
     'HIS': 'H',
@@ -59,14 +61,11 @@ function getProteinOneLetterCode(residueName) {
     const code = ProteinOneLetterCodes[residueName];
     return code || 'X';
 }
-exports.getProteinOneLetterCode = getProteinOneLetterCode;
 function getRnaOneLetterCode(residueName) {
     const code = RnaOneLetterCodes[residueName];
     return code || 'X';
 }
-exports.getRnaOneLetterCode = getRnaOneLetterCode;
 function getDnaOneLetterCode(residueName) {
     const code = DnaOneLetterCodes[residueName];
     return code || 'X';
 }
-exports.getDnaOneLetterCode = getDnaOneLetterCode;